index.json

[{"authors":["admin"],"categories":null,"content":"I am an Assistant Professor in the Department of Biomedical Informatics, University of Colorado Anschutz. I am affiliated with 4 graduate programs at CU Anschutz, Computational Bioscience, Human Medical Genetics and Genomics, Microbiology, and the umbrella Biomedical Sciences.\nMy research group develops computational approaches that can leverage large-scale genomic data to gain testable insights into infectious disease biology, focusing on microbial genotypes, phenotypes, and diseases. I also teach fundamentals of data analysis, visualization, and reproducible research, especially programming in non-traditional settings. As part of this effort, I founded R-Ladies East Lansing, Women+ Data Science, AsiaR, and R-Ladies Aurora, four organizations that promote leadership and technical networking opportunities in data science via meetups \u0026amp; webinars (featured in the CU newsletter).\n","date":1769904e3,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1769904e3,"objectID":"2525497d367e79493fd32b198b28f040","permalink":"/authors/admin/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/admin/","section":"authors","summary":"I am an Assistant Professor in the Department of Biomedical Informatics, University of Colorado Anschutz. I am affiliated with 4 graduate programs at CU Anschutz, Computational Bioscience, Human Medical Genetics and Genomics, Microbiology, and the umbrella Biomedical Sciences.\nMy research group develops computational approaches that can leverage large-scale genomic data to gain testable insights into infectious disease biology, focusing on microbial genotypes, phenotypes, and diseases. I also teach fundamentals of data analysis, visualization, and reproducible research, especially programming in non-traditional settings.","tags":null,"title":"Janani Ravi","type":"authors"},{"authors":["admin"],"categories":null,"content":"Accomplishments Fellowships 2023, 2026 NIH NLM Computational Bioscience T15 Postdoctoral Fellowship Awards $2024 First place for talk, University of Colorado Annual Orthopedic Research Symposium \u0026amp; D’Ambrosia Diversity Lectureship $2024 First place for short talks, ISMB, Evolution and Comparative Genomics track $2024 First place for postdoc talks, Rocky Mountain Branch, ASM 2024 ISMB registration award Presentations Talks 2026-03 Bioinformatics Symposium, CU Anschutz. Aurora, CO 2025-05 DBMI Bytes to Bedside Seminar Series, Aurora, CO 2025-02 Pacific Northwest National Laboratory. DOE BRAVE symposium. Richland, WA $2024-10 University of Colorado Annual Orthopedic Research Symposium \u0026amp; D’Ambrosia Diversity Lectureship, Aurora, CO. Won first place with a $1000 cash prize towards any (inter)national conference. $2024-07 ISMB (by the International Society for Computational Biology). Montreal, Canada. Won first place (with a cash prize) for short talks at Evolution and Comparative Genomics. Also, received a registration award. 2024-08 Biomedical Informatics Retreat, Denver, CO 2024-06 qCMB symposium. Fort Collins, CO $2024-04 Rocky Mountain Branch, American Society for Microbiology. Boulder, CO. Won first place (with a cash prize) for postdoc talks. Posters 2026-03 Bioinformatics Symposium, CU Anschutz. Aurora, CO 2025-08 Colorado Immunology \u0026amp; Microbiology Conference. Steamboat Springs, CO 2025-08 Biomedical Informatics Retreat, Aurora, CO 2023-08 Biomedical Informatics Retreat, Aurora, CO ","date":1769904e3,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1769904e3,"objectID":"75f25cd501d73f46346b205070d92299","permalink":"/authors/evan-brenner/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/evan-brenner/","section":"authors","summary":"Accomplishments Fellowships 2023, 2026 NIH NLM Computational Bioscience T15 Postdoctoral Fellowship Awards $2024 First place for talk, University of Colorado Annual Orthopedic Research Symposium \u0026amp; D’Ambrosia Diversity Lectureship $2024 First place for short talks, ISMB, Evolution and Comparative Genomics track $2024 First place for postdoc talks, Rocky Mountain Branch, ASM 2024 ISMB registration award Presentations Talks 2026-03 Bioinformatics Symposium, CU Anschutz. Aurora, CO 2025-05 DBMI Bytes to Bedside Seminar Series, Aurora, CO 2025-02 Pacific Northwest National Laboratory.","tags":null,"title":"Evan Brenner","type":"authors"},{"authors":["admin"],"categories":null,"content":"Accomplishments Recognition 2025 NSF Graduate Research Fellowship Program Honorable Mention 2025 3MT (3-minute thesis) Competition, CU Anschutz — Honorable Mention Presentations Talks 2026-03 Bioinformatics Symposium, CU Anschutz. Aurora, CO 2025-04 3MT Competition, CU Anschutz. Aurora, CO 2025-05 Tattered Cover Book Store STEM series for the public. Denver, CO Posters 2026-03 Bioinformatics Symposium, CU Anschutz. Aurora, CO 2025-08 Colorado Immunology \u0026amp; Microbiology Conference. Steamboat Springs, CO 2025-08 Biomedical Informatics Retreat, Aurora, CO 2025-02 Pacific Northwest National Laboratory. DOE BRAVE symposium. Richland, WA 2024-08 Colorado Immunology \u0026amp; Microbiology Conference. Breckenridge, CO 2024-08 Biomedical Informatics Retreat, Denver, CO 2024-06 qCMB symposium. Fort Collins, CO 2024-04 Rocky Mountain Branch, American Society for Microbiology. Boulder, CO ","date":17604e5,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":17604e5,"objectID":"4bcd2f273e2fa6e351145ff7ef001227","permalink":"/authors/charmie-vang/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/charmie-vang/","section":"authors","summary":"Accomplishments Recognition 2025 NSF Graduate Research Fellowship Program Honorable Mention 2025 3MT (3-minute thesis) Competition, CU Anschutz — Honorable Mention Presentations Talks 2026-03 Bioinformatics Symposium, CU Anschutz. Aurora, CO 2025-04 3MT Competition, CU Anschutz. Aurora, CO 2025-05 Tattered Cover Book Store STEM series for the public. Denver, CO Posters 2026-03 Bioinformatics Symposium, CU Anschutz. Aurora, CO 2025-08 Colorado Immunology \u0026amp; Microbiology Conference. Steamboat Springs, CO 2025-08 Biomedical Informatics Retreat, Aurora, CO 2025-02 Pacific Northwest National Laboratory.","tags":null,"title":"Charmie Vang","type":"authors"},{"authors":["admin"],"categories":null,"content":"Accomplishments Awards 2024 Fully-funded Workshop on Computational Modeling of Proteins for Infectious Disease Researchers. Seattle Children’s Hospital. Seattle, WA. Led by Nobel Laureate David Baker’s Lab. Presentations Talks 2026-03 Bioinformatics Symposium, CU Anschutz. Aurora, CO 2025-09 International Conference on Bioinformatics (hosted by ISCB). Kolkata, India 2025-05 Great Lakes Bioinformatics Conference. Minneapolis, MN 2025-05 DBMI Bytes to Bedside Seminar Series, Aurora, CO 2024-08 Biomedical Informatics Retreat, Aurora, CO Posters 2026-03 Bioinformatics Symposium, CU Anschutz. Aurora, CO 2025-08 Colorado Immunology \u0026amp; Microbiology Conference. Steamboat Springs, CO 2025-08 Biomedical Informatics Retreat, Aurora, CO 2025-04 Rocky Mountain Branch, American Society for Microbiology. Fort Collins, CO 2024-08 Colorado Immunology \u0026amp; Microbiology Conference. Breckenridge, CO ","date":1751846400,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1751846400,"objectID":"1c8df45b15ccb68598e4e148914cd207","permalink":"/authors/abhirupa-ghosh/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/abhirupa-ghosh/","section":"authors","summary":"Accomplishments Awards 2024 Fully-funded Workshop on Computational Modeling of Proteins for Infectious Disease Researchers. Seattle Children’s Hospital. Seattle, WA. Led by Nobel Laureate David Baker’s Lab. Presentations Talks 2026-03 Bioinformatics Symposium, CU Anschutz. Aurora, CO 2025-09 International Conference on Bioinformatics (hosted by ISCB). Kolkata, India 2025-05 Great Lakes Bioinformatics Conference. Minneapolis, MN 2025-05 DBMI Bytes to Bedside Seminar Series, Aurora, CO 2024-08 Biomedical Informatics Retreat, Aurora, CO Posters 2026-03 Bioinformatics Symposium, CU Anschutz.","tags":null,"title":"Abhirupa Ghosh","type":"authors"},{"authors":["admin"],"categories":null,"content":"Accomplishments Scholarships 2025 NIH NHGRI R25 PATH-GREU Scholar (Pathways in Genomics Research Experiences for Undergraduates from Underrepresented Groups) Presentations Talks 2026-03 Bioinformatics Symposium, CU Anschutz. Aurora, CO Posters 2026-03 Bioinformatics Symposium, CU Anschutz. Aurora, CO ","date":1751846400,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1751846400,"objectID":"421194c018e07f6d4eeb780d74476b8d","permalink":"/authors/emily-boyer/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/emily-boyer/","section":"authors","summary":"Accomplishments Scholarships 2025 NIH NHGRI R25 PATH-GREU Scholar (Pathways in Genomics Research Experiences for Undergraduates from Underrepresented Groups) Presentations Talks 2026-03 Bioinformatics Symposium, CU Anschutz. Aurora, CO Posters 2026-03 Bioinformatics Symposium, CU Anschutz. Aurora, CO ","tags":null,"title":"Emily Boyer","type":"authors"},{"authors":["admin"],"categories":null,"content":"Now a PhD student at University of Pittsburgh Medical Center.\nAccomplishments First Place Award in Cell Biology, Genetics, and Genomics, Section 2, University Undergraduate Research and Arts Forum (UURAF) 2024, poster presentation MSU College of Natural Science Summer scholarship (2022) Professorial Assistantship, awarded to the Top 200 incoming undergrads @MSU (2021-2023) Dean\u0026rsquo;s List; Honors College Honorary mention for poster, Intelligent Systems for Molecular Biology, ISMB 2022, EvolCompGen Track Presentations Talks 2024-07 Intelligent Systems for Molecular Biology (ISMB) 2024, International Society for Computational Biology flagship conference. Received travel fellowship award. Posters 2023-09 Midwest Microbial Pathogenesis Conference (MMPC). Chicago, IL 2022-07 Intelligent Systems for Molecular Biology (ISMB) 2022, International Society for Computational Biology flagship conference Madison, WI. Received an honorable mention in the Evolution and Comparative Genomics COSI. Regional 2024-04 University Undergraduate Research and Arts Forum (UURAF) 2023-07 Mid-Michigan Symposium for Undergraduate Research Experience (Mid-SURE) 2023-04 University Undergraduate Research and Arts Forum (UURAF) 2022-07 Mid-Michigan Symposium for Undergraduate Research Experience (Mid-SURE) 2022-04 University Undergraduate Research and Arts Forum (UURAF) ","date":1751846400,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1751846400,"objectID":"c880c6bccfa9814c9827457fca053339","permalink":"/authors/ethan-wolfe/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/ethan-wolfe/","section":"authors","summary":"Now a PhD student at University of Pittsburgh Medical Center.\nAccomplishments First Place Award in Cell Biology, Genetics, and Genomics, Section 2, University Undergraduate Research and Arts Forum (UURAF) 2024, poster presentation MSU College of Natural Science Summer scholarship (2022) Professorial Assistantship, awarded to the Top 200 incoming undergrads @MSU (2021-2023) Dean\u0026rsquo;s List; Honors College Honorary mention for poster, Intelligent Systems for Molecular Biology, ISMB 2022, EvolCompGen Track Presentations Talks 2024-07 Intelligent Systems for Molecular Biology (ISMB) 2024, International Society for Computational Biology flagship conference.","tags":null,"title":"Ethan Wolfe","type":"authors"},{"authors":["admin"],"categories":null,"content":"Now a PhD student at CU Boulder\u0026rsquo;s Computer Science Program, following an internship at NIH NCBI.\nPresentations Talks Bioconductor Conference (BioC) at Harvard University, Boston, MA \u0026ndash; MolevolvR a web-app for protein characterization Great Lakes Bioinformatics Conference (GLBIO) at McGill University in Montreal, Canada Half-day workshop \u0026amp; Talk Posters Rocky Mountain Branch, American Society for Microbiology. Boulder, CO CU Department of Biomedical Informatics Annual retreat. Robust machine learning-based classification of antimicrobial resistance in high-impact pathogens. CU Anschutz, Aurora, CO ","date":1751846400,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1751846400,"objectID":"53b5fdc2ef636dae0663e4217351716c","permalink":"/authors/jacob-krol/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/jacob-krol/","section":"authors","summary":"Now a PhD student at CU Boulder\u0026rsquo;s Computer Science Program, following an internship at NIH NCBI.\nPresentations Talks Bioconductor Conference (BioC) at Harvard University, Boston, MA \u0026ndash; MolevolvR a web-app for protein characterization Great Lakes Bioinformatics Conference (GLBIO) at McGill University in Montreal, Canada Half-day workshop \u0026amp; Talk Posters Rocky Mountain Branch, American Society for Microbiology. Boulder, CO CU Department of Biomedical Informatics Annual retreat. Robust machine learning-based classification of antimicrobial resistance in high-impact pathogens.","tags":null,"title":"Jacob Krol","type":"authors"},{"authors":["admin"],"categories":null,"content":"image credit: https://octodex.github.com\nNow a PhD student in Jay Hesselberth\u0026rsquo;s lab at CU Anschutz.\nRotated with us in Spring 2023.\nPresentations Talks R workshop at Global Alliance for Rapid Diagnostics (GARD) (Mar \u0026lsquo;23) ","date":1751846400,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1751846400,"objectID":"a941f362aa557ea2952c575b092fbe6a","permalink":"/authors/jill-bilodeaux/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/jill-bilodeaux/","section":"authors","summary":"image credit: https://octodex.github.com\nNow a PhD student in Jay Hesselberth\u0026rsquo;s lab at CU Anschutz.\nRotated with us in Spring 2023.\nPresentations Talks R workshop at Global Alliance for Rapid Diagnostics (GARD) (Mar \u0026lsquo;23) ","tags":null,"title":"Jill Bilodeaux","type":"authors"},{"authors":["admin"],"categories":null,"content":"Software Engineer at CRISPR therapeutics from May 2022!\nAccomplishments Dean\u0026rsquo;s List throughout Internship at Apeel Inc (Summer \u0026lsquo;21) MSU Microbiology and Molecular Genetics Undergraduate Award (2022) Presentations Posters American Society of Microbiology Microbe (Jun \u0026lsquo;22; selected but not attending) Midwest Microbial Pathogenesis Conference, MMPC (Sep \u0026lsquo;21) BEACON Congress (Aug \u0026lsquo;21) ","date":1751846400,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1751846400,"objectID":"4d059627e2f304d76c3159382d5376cf","permalink":"/authors/joseph-burke/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/joseph-burke/","section":"authors","summary":"Software Engineer at CRISPR therapeutics from May 2022!\nAccomplishments Dean\u0026rsquo;s List throughout Internship at Apeel Inc (Summer \u0026lsquo;21) MSU Microbiology and Molecular Genetics Undergraduate Award (2022) Presentations Posters American Society of Microbiology Microbe (Jun \u0026lsquo;22; selected but not attending) Midwest Microbial Pathogenesis Conference, MMPC (Sep \u0026lsquo;21) BEACON Congress (Aug \u0026lsquo;21) ","tags":null,"title":"Joseph Burke","type":"authors"},{"authors":["admin"],"categories":null,"content":"image credit: https://octodex.github.com\nNow a PhD student in Arjun Krishnan\u0026rsquo;s lab at CU Anschutz.\nRotated with us in Spring 2023.\n","date":1751846400,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1751846400,"objectID":"bf8d8a9848bba507a7940b243be73549","permalink":"/authors/keenan-manpearl/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/keenan-manpearl/","section":"authors","summary":"image credit: https://octodex.github.com\nNow a PhD student in Arjun Krishnan\u0026rsquo;s lab at CU Anschutz.\nRotated with us in Spring 2023.","tags":null,"title":"Keenan Manpearl","type":"authors"},{"authors":["admin"],"categories":null,"content":"Now a PhD student at CU Anschutz\u0026rsquo;s Computational Bioscience Program (Hirs Fellowship).\nWas co-mentored with Dr. Nina Wale, Michigan State University.\nPresentations Talks 2024 Bioconductor Conference. Grand Rapids, MI 2024 Pathogen Supergroup meeting. Michigan State University, East Lansing, MI Posters 2024 CU Anschutz Biomedical Informatics Retreat. Denver, CO 2024 Quantitative Cell and Molecular Biology (qCMB) symposium. Fort Collins, CO 2024 Rocky Mountain Branch, American Society for Microbiology. Boulder, CO ","date":1751846400,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1751846400,"objectID":"c9ac42c217dd01a66385e6b2540ed13d","permalink":"/authors/raymond-lesiyon/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/raymond-lesiyon/","section":"authors","summary":"Now a PhD student at CU Anschutz\u0026rsquo;s Computational Bioscience Program (Hirs Fellowship).\nWas co-mentored with Dr. Nina Wale, Michigan State University.\nPresentations Talks 2024 Bioconductor Conference. Grand Rapids, MI 2024 Pathogen Supergroup meeting. Michigan State University, East Lansing, MI Posters 2024 CU Anschutz Biomedical Informatics Retreat. Denver, CO 2024 Quantitative Cell and Molecular Biology (qCMB) symposium. Fort Collins, CO 2024 Rocky Mountain Branch, American Society for Microbiology. Boulder, CO ","tags":null,"title":"Raymond L Lesiyon","type":"authors"},{"authors":["vignesh-sridhar"],"categories":null,"content":"Now, Asst. Vice President at BNP Paribas, Canada.\nAccomplishments Best poster award with cash prize, Intelligent Systems for Molecular Biology, ISMB 2021, EvolCompGen Track Presentations Posters 2021-09 Midwest Microbial Pathogenesis Conference (MMPC) 2021-08 BEACON Congress 2021-07 Intelligent Systems for Molecular Biology (ISMB). International Society for Computational Biology flagship conference ","date":1751846400,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1751846400,"objectID":"3170fea6936a92d5a1527a38ab5564c4","permalink":"/authors/vignesh-sridhar/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/vignesh-sridhar/","section":"authors","summary":"Now, Asst. Vice President at BNP Paribas, Canada.\nAccomplishments Best poster award with cash prize, Intelligent Systems for Molecular Biology, ISMB 2021, EvolCompGen Track Presentations Posters 2021-09 Midwest Microbial Pathogenesis Conference (MMPC) 2021-08 BEACON Congress 2021-07 Intelligent Systems for Molecular Biology (ISMB). International Society for Computational Biology flagship conference ","tags":null,"title":"Vignesh Sridhar","type":"authors"},{"authors":["admin"],"categories":null,"content":"Now an MLS intern at Trinity Health\nAccomplishments Professorial Assistantship, awarded to the Top 200 incoming undergrads @MSU (2021-2023) Dean\u0026rsquo;s List; Honors College ","date":1748822400,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1748822400,"objectID":"c4e1966b13d3103836910e8d11010233","permalink":"/authors/amy-tonielli/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/amy-tonielli/","section":"authors","summary":"Now an MLS intern at Trinity Health\nAccomplishments Professorial Assistantship, awarded to the Top 200 incoming undergrads @MSU (2021-2023) Dean\u0026rsquo;s List; Honors College ","tags":null,"title":"Amy Tonielli","type":"authors"},{"authors":["admin"],"categories":null,"content":"Co-mentored by Dr. Arjun Krishnan.\nAccomplishments Thai Scholar 60, scholarship from The National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand MSU College of Natural Science Scholarships for Spring 2020, Summer 2020, Fall 2020, Spring 2021, Fall 2021 L.C. Plant Mathematics Award 2020, MSU Department of Mathematics EnSURE Summer Scholarship 2021 McCartney Math Award 2022 Dean\u0026rsquo;s List throughout Hirs Fellowship, University of Colorado Anschutz Presentations Talks 2025-05 Great Lakes Bioinformatics Conference. Minneapolis, MN 2024-08 Biomedical Informatics Retreat, Denver, CO 2024-06 qCMB symposium. Fort Collins, CO 2023-03 R workshop at Global Alliance for Rapid Diagnostics (GARD) 2021-09 Latin American Congress of Women in Bioinformatics and Data Science 2021-07 Intelligent Systems for Molecular Biology, ISMB 2021, International Society for Computational Biology flagship conference 2021-05 R-Ladies Pune, India Posters 2025-08 Biomedical Informatics Retreat, Denver, CO 2025-04 Computational Bioscience Retreat. Golden, CO $ 2024-04 Rocky Mountain Branch, American Society for Microbiology. Boulder, CO 2024-04 Computational Bioscience Retreat. Golden, CO 2023-11 Genome Informatics. Cold Spring Harbor Laboratories, Long Island, NY 2023-08 Biomedical Informatics Retreat, Denver, CO 2022-08 Colorado Immunology and Microbiology conference, Vail, CO 2022-07 Intelligent Systems for Molecular Biology, ISMB 2022, International Society for Computational Biology flagship conference 2021-05 Great Lakes Bioinformatics Conference 2021-04 University Undergraduate Research and Arts Forum (UURAF), East Lansing, MI 2020-08 Mid-Michigan Symposium for Undergraduate Research Experience, East Lansing, MI ","date":1748822400,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1748822400,"objectID":"92f5f87e312b3f898ac465b0ebad6cc0","permalink":"/authors/kewalin-samart/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/kewalin-samart/","section":"authors","summary":"Co-mentored by Dr. Arjun Krishnan.\nAccomplishments Thai Scholar 60, scholarship from The National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand MSU College of Natural Science Scholarships for Spring 2020, Summer 2020, Fall 2020, Spring 2021, Fall 2021 L.C. Plant Mathematics Award 2020, MSU Department of Mathematics EnSURE Summer Scholarship 2021 McCartney Math Award 2022 Dean\u0026rsquo;s List throughout Hirs Fellowship, University of Colorado Anschutz Presentations Talks 2025-05 Great Lakes Bioinformatics Conference.","tags":null,"title":"Kewalin Samart","type":"authors"},{"authors":["admin"],"categories":null,"content":"Now also an Associate Predictive Modeler at Auto-Owners Insurance, Lansing, MI.\nAccomplishments Alumni Distinguished Scholarship Finalist MSU Professorial Assistantship Herzog Math Competition Finalist Dean’s List; Honors College Presentations Posters University Undergraduate Research and Arts Forum (UURAF) (Apr \u0026lsquo;23) Mid-Michigan Symposium for Undergraduate Research Experiences (Mid-SURE) (Jul \u0026lsquo;23) Talks Division of Nuclear Physics of the American Physical Society (Dec \u0026lsquo;23) ","date":1748822400,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1748822400,"objectID":"e5b9695166b1961085a1b7c8c85d56ab","permalink":"/authors/landon-buskirk/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/landon-buskirk/","section":"authors","summary":"Now also an Associate Predictive Modeler at Auto-Owners Insurance, Lansing, MI.\nAccomplishments Alumni Distinguished Scholarship Finalist MSU Professorial Assistantship Herzog Math Competition Finalist Dean’s List; Honors College Presentations Posters University Undergraduate Research and Arts Forum (UURAF) (Apr \u0026lsquo;23) Mid-Michigan Symposium for Undergraduate Research Experiences (Mid-SURE) (Jul \u0026lsquo;23) Talks Division of Nuclear Physics of the American Physical Society (Dec \u0026lsquo;23) ","tags":null,"title":"Landon Buskirk","type":"authors"},{"authors":["admin"],"categories":null,"content":"Accomplishments Scholarships 2025 NIH NHGRI R25 PATH-GREU Scholar (Pathways in Genomics Research Experiences for Undergraduates from Underrepresented Groups) Presentations Posters Coming soon.\n","date":1748822400,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1748822400,"objectID":"d7ee77dba36027e91fca4d5acd0eaf4e","permalink":"/authors/ling-thang/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/ling-thang/","section":"authors","summary":"Accomplishments Scholarships 2025 NIH NHGRI R25 PATH-GREU Scholar (Pathways in Genomics Research Experiences for Undergraduates from Underrepresented Groups) Presentations Posters Coming soon.","tags":null,"title":"Ling Thang","type":"authors"},{"authors":["admin"],"categories":null,"content":"Currently a software engineer at Amazon Inc (since 2022).\nAccomplishments One of 38 students who got a 4.0 during their Bachelors at MSU! Honors College; Dean’s List throughout Michigan State Scholarship NSF-funded REU-ACRES Summer Scholarship, 2020 Honorable mention for poster at the International conference, ISMB 2020. Presentations Talks BEACON seminar (Mar \u0026lsquo;21) University Undergraduate Research and Arts Forum (UURAF) (Apr \u0026lsquo;21) BEACON Congress (Aug \u0026lsquo;20) Posters Great Lakes Bioinformatics Conference (May \u0026lsquo;21) Mid-Michigan Symposium for Undergraduate Research Experience (Aug ‘20) Intelligent Systems for Molecular Biology, ISMB 2020, International Society for Computational Biology flagship conference (Jul ‘20) ","date":1716940800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1716940800,"objectID":"2218d33caf376b91d2ec75268b5c187f","permalink":"/authors/samuel-chen/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/samuel-chen/","section":"authors","summary":"Currently a software engineer at Amazon Inc (since 2022).\nAccomplishments One of 38 students who got a 4.0 during their Bachelors at MSU! Honors College; Dean’s List throughout Michigan State Scholarship NSF-funded REU-ACRES Summer Scholarship, 2020 Honorable mention for poster at the International conference, ISMB 2020. Presentations Talks BEACON seminar (Mar \u0026lsquo;21) University Undergraduate Research and Arts Forum (UURAF) (Apr \u0026lsquo;21) BEACON Congress (Aug \u0026lsquo;20) Posters Great Lakes Bioinformatics Conference (May \u0026lsquo;21) Mid-Michigan Symposium for Undergraduate Research Experience (Aug ‘20) Intelligent Systems for Molecular Biology, ISMB 2020, International Society for Computational Biology flagship conference (Jul ‘20) ","tags":null,"title":"Samuel Chen","type":"authors"},{"authors":["admin"],"categories":null,"content":"Currently a graduate student at Michigan State University (since 2021).\nPresentations Posters Mid-Michigan Symposium for Undergraduate Research Experience (Aug ‘20) Women in Data Science Symposium East Lansing @ Michigan State University (Apr ‘19) University Undergraduate Research and Arts Forum (UURAF) (Mar ‘19) ","date":1688688e3,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1688688e3,"objectID":"875959d6919ccf791068ac43f5c6f8dd","permalink":"/authors/lo-sosinski/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/lo-sosinski/","section":"authors","summary":"Currently a graduate student at Michigan State University (since 2021).\nPresentations Posters Mid-Michigan Symposium for Undergraduate Research Experience (Aug ‘20) Women in Data Science Symposium East Lansing @ Michigan State University (Apr ‘19) University Undergraduate Research and Arts Forum (UURAF) (Mar ‘19) ","tags":null,"title":"Lo Sosinski","type":"authors"},{"authors":["admin"],"categories":null,"content":"MS in Public Health at the University of British Columbia, Vancouver.\nAccomplishments Mastercard Foundation Scholar Justin S. Morrill Leadership Fellow Food and Nutrition Database Research Center, UG Teaching Assistant Fully funded admits to UC Davis, Purdue University, Emory University for graduate (PhD) programs Mastercard Foundation Scholarship and admit to the University of British Columbia (starting 2021) Contributed to now funded DRN Launch Awards Program grant proposal, 2019 (written with PI, Janani Ravi) Presentations Posters Mid-Michigan Symposium for Undergraduate Research Experience (Aug ‘20) Intelligent Systems for Molecular Biology (ISMB 2020), International Society for Computational Biology flagship conference (Jul ‘20) Women in Data Science Symposium @East Lansing (Apr \u0026lsquo;19) ","date":1636070400,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1636070400,"objectID":"c6634cf5ce8807a20ca9b5351c9b7862","permalink":"/authors/phoebe-tuyishime/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/phoebe-tuyishime/","section":"authors","summary":"MS in Public Health at the University of British Columbia, Vancouver.\nAccomplishments Mastercard Foundation Scholar Justin S. Morrill Leadership Fellow Food and Nutrition Database Research Center, UG Teaching Assistant Fully funded admits to UC Davis, Purdue University, Emory University for graduate (PhD) programs Mastercard Foundation Scholarship and admit to the University of British Columbia (starting 2021) Contributed to now funded DRN Launch Awards Program grant proposal, 2019 (written with PI, Janani Ravi) Presentations Posters Mid-Michigan Symposium for Undergraduate Research Experience (Aug ‘20) Intelligent Systems for Molecular Biology (ISMB 2020), International Society for Computational Biology flagship conference (Jul ‘20) Women in Data Science Symposium @East Lansing (Apr \u0026lsquo;19) ","tags":null,"title":"Phoebe Tuyishime","type":"authors"},{"authors":["admin"],"categories":null,"content":"image credit: https://octodex.github.com\nNow a PhD student in Arjun Krishnan\u0026rsquo;s lab at CU Anschutz.\nRotated with us in Spring 2024.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"c63087054b5b05a4d3a5723d041760b2","permalink":"/authors/aishwarya-mandava/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/aishwarya-mandava/","section":"authors","summary":"image credit: https://octodex.github.com\nNow a PhD student in Arjun Krishnan\u0026rsquo;s lab at CU Anschutz.\nRotated with us in Spring 2024.","tags":null,"title":"Aishwarya Mandava","type":"authors"},{"authors":["admin"],"categories":null,"content":"Accomplishments Scholarships 2025 NIH NHGRI R25 PATH-GREU Scholar (Pathways in Genomics Research Experiences for Undergraduates from Underrepresented Groups) Presentations Posters Coming soon.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"b5698e6c828c905a3299e9886154acf9","permalink":"/authors/clay-griffin-derr/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/clay-griffin-derr/","section":"authors","summary":"Accomplishments Scholarships 2025 NIH NHGRI R25 PATH-GREU Scholar (Pathways in Genomics Research Experiences for Undergraduates from Underrepresented Groups) Presentations Posters Coming soon.","tags":null,"title":"Clay Griffin-Derr","type":"authors"},{"authors":["admin"],"categories":null,"content":"Post-bac student\nAccomplishments Honorary mention for poster, Intelligent Systems for Molecular Biology, ISMB 2021, EvolCompGen Track 2021 NIH R25-funded BRUSH scholarship for summer undergraduate research Presentations Posters Midwest Microbial Pathogenesis Conference, MMPC (Sep \u0026lsquo;21) BEACON Congress (Aug \u0026lsquo;21) National Veterinary Scholars Symposium, AAVMC (Jul \u0026lsquo;21) ISMB, International Society for Computational Biology conference (Jul \u0026lsquo;21) Mid-Michigan Symposium for Undergraduate Research Experience (Jul \u0026lsquo;21) University Undergraduate Research and Arts Forum (UURAF) (Apr \u0026lsquo;21) Mid-Michigan Symposium for Undergraduate Research Experience (Aug ‘20) Talks Phi Zeta Research Symposium, College of Veterinary Medicine, MSU (Oct \u0026lsquo;20) ","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"1c5c5997754bd575a2dcd3e684df5c62","permalink":"/authors/elliot-majlessi/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/elliot-majlessi/","section":"authors","summary":"Post-bac student\nAccomplishments Honorary mention for poster, Intelligent Systems for Molecular Biology, ISMB 2021, EvolCompGen Track 2021 NIH R25-funded BRUSH scholarship for summer undergraduate research Presentations Posters Midwest Microbial Pathogenesis Conference, MMPC (Sep \u0026lsquo;21) BEACON Congress (Aug \u0026lsquo;21) National Veterinary Scholars Symposium, AAVMC (Jul \u0026lsquo;21) ISMB, International Society for Computational Biology conference (Jul \u0026lsquo;21) Mid-Michigan Symposium for Undergraduate Research Experience (Jul \u0026lsquo;21) University Undergraduate Research and Arts Forum (UURAF) (Apr \u0026lsquo;21) Mid-Michigan Symposium for Undergraduate Research Experience (Aug ‘20) Talks Phi Zeta Research Symposium, College of Veterinary Medicine, MSU (Oct \u0026lsquo;20) ","tags":null,"title":"Elliot Majlessi","type":"authors"},{"authors":["admin"],"categories":null,"content":" Accomplishments Professional gymnast ","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"71377078a5ebd26013b84de23444b764","permalink":"/authors/evalyn-resnick/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/evalyn-resnick/","section":"authors","summary":" Accomplishments Professional gymnast ","tags":null,"title":"Evalyn Resnick","type":"authors"},{"authors":["admin"],"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"a2a09f72dc32551e4f6420b6315dce01","permalink":"/authors/ishaq-paktinyar/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/ishaq-paktinyar/","section":"authors","summary":"","tags":null,"title":"Ishaq Paktinyar","type":"authors"},{"authors":["admin"],"categories":null,"content":" Bio: I am a native of Colorado and a first-generation Mexican-American student who aspires to become an expert in Bioinformatics and Computational Biology. I also strive to inspire those in minority groups, such as myself, to pursue a career in STEM, and I hope to set an example for the younger generation of women to pursue research careers. I\u0026rsquo;m a child at heart when it comes to playing sports, but I\u0026rsquo;m particularly fond of soccer, boxing, and volleyball. I also enjoy watching anime and traveling.\nPresentations Posters 2024-04 Rocky Mountain Branch, American Society for Microbiology. Boulder, CO 2023-08 Biomedical Informatics Retreat, Aurora, CO ","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"15e53f08da55c9ebb6be758d3673a06d","permalink":"/authors/karla-vela-lopez/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/karla-vela-lopez/","section":"authors","summary":"Bio: I am a native of Colorado and a first-generation Mexican-American student who aspires to become an expert in Bioinformatics and Computational Biology. I also strive to inspire those in minority groups, such as myself, to pursue a career in STEM, and I hope to set an example for the younger generation of women to pursue research careers. I\u0026rsquo;m a child at heart when it comes to playing sports, but I\u0026rsquo;m particularly fond of soccer, boxing, and volleyball.","tags":null,"title":"Karla Vela Lopez","type":"authors"},{"authors":["admin"],"categories":null,"content":" Accomplishments Selected for NSF-funded REU-ACRES Summer Scholarship, 2020 Honorable mention for poster at the International conference, ISMB 2020. Presentations Talks BEACON Congress (Aug \u0026lsquo;20) Posters Mid-Michigan Symposium for Undergraduate Research Experience (Aug ‘20) Intelligent Systems for Molecular Biology (ISMB 2020), International Society for Computational Biology flagship conference (Jul ‘20) ","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"bb57a5106b98c28e7fa424548270efe9","permalink":"/authors/karn-jongnarangsin/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/karn-jongnarangsin/","section":"authors","summary":" Accomplishments Selected for NSF-funded REU-ACRES Summer Scholarship, 2020 Honorable mention for poster at the International conference, ISMB 2020. Presentations Talks BEACON Congress (Aug \u0026lsquo;20) Posters Mid-Michigan Symposium for Undergraduate Research Experience (Aug ‘20) Intelligent Systems for Molecular Biology (ISMB 2020), International Society for Computational Biology flagship conference (Jul ‘20) ","tags":null,"title":"Karn Jongnarangsin","type":"authors"},{"authors":["admin"],"categories":null,"content":"Accomplishments Fellowships 2025–2027 NIH NLM Computational Bioscience T15 Predoctoral Fellowship Presentations Talks 2026-03 Bioinformatics Symposium, CU Anschutz. Aurora, CO 2025-08 DBMI Bytes to Bedside Seminar Series, Aurora, CO 2025-05 Tattered Cover Book Store STEM series for the public. Denver, CO Posters 2026-03 Bioinformatics Symposium, CU Anschutz. Aurora, CO 2025-08 Colorado Immunology and Microbiology Conference. Steamboat Springs, CO 2025-08 Biomedical Informatics Retreat. Aurora, CO ","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"8dbf7d7558abe4564276b03e7d5c504a","permalink":"/authors/kat-terwelp/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/kat-terwelp/","section":"authors","summary":"Accomplishments Fellowships 2025–2027 NIH NLM Computational Bioscience T15 Predoctoral Fellowship Presentations Talks 2026-03 Bioinformatics Symposium, CU Anschutz. Aurora, CO 2025-08 DBMI Bytes to Bedside Seminar Series, Aurora, CO 2025-05 Tattered Cover Book Store STEM series for the public. Denver, CO Posters 2026-03 Bioinformatics Symposium, CU Anschutz. Aurora, CO 2025-08 Colorado Immunology and Microbiology Conference. Steamboat Springs, CO 2025-08 Biomedical Informatics Retreat. Aurora, CO ","tags":null,"title":"Kat Terwelp","type":"authors"},{"authors":["admin"],"categories":null,"content":"Accomplishments Fellowships 2025 UGC-CSIR NET Junior Research Fellowship, Government of India stipend for PhD candidates Awards 2025 Gold Medal, B.Tech., Cluster Innovation Centre, University of Delhi Presentations Talks 2024 DBMI Seminar Series, Aurora, CO ","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"6d9f7cdf8e13ede7e4aaff9c25358ad4","permalink":"/authors/kritika-verma/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/kritika-verma/","section":"authors","summary":"Accomplishments Fellowships 2025 UGC-CSIR NET Junior Research Fellowship, Government of India stipend for PhD candidates Awards 2025 Gold Medal, B.Tech., Cluster Innovation Centre, University of Delhi Presentations Talks 2024 DBMI Seminar Series, Aurora, CO ","tags":null,"title":"Kritika Verma","type":"authors"},{"authors":["admin"],"categories":null,"content":"PREP program at the University of Pennsylvania.\nAccomplishments 2020 National Summer Undergraduate Research Program (NSURP) BIPOC for microbiology. ","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"08a4c6a897e2f844fc42296cb9159d23","permalink":"/authors/lauryn-brooks/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/lauryn-brooks/","section":"authors","summary":"PREP program at the University of Pennsylvania.\nAccomplishments 2020 National Summer Undergraduate Research Program (NSURP) BIPOC for microbiology. ","tags":null,"title":"Lauryn Brooks","type":"authors"},{"authors":["admin"],"categories":null,"content":"Medical student at the National University of Singapore (with Duke University).\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"ad96243a28e065e871534dbc50aed94e","permalink":"/authors/mary-zhang/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/mary-zhang/","section":"authors","summary":"Medical student at the National University of Singapore (with Duke University).","tags":null,"title":"Mary Zhang","type":"authors"},{"authors":["admin"],"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"be49c892a2189edc0ed9139fc368e8bb","permalink":"/authors/michael-ntrakwa/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/michael-ntrakwa/","section":"authors","summary":"","tags":null,"title":"Michael Ntrakwa","type":"authors"},{"authors":["admin"],"categories":null,"content":"MD at Michigan State University. Now a resident at Ford Hospital in Detroit, MI.\nAccomplishments Accepted to medical school programs \u0026lsquo;21 (Loyola College, MSU College of Human/Osteopathic Medicine, Wayne State University) 2020 NIH R25-funded BRUSH scholarship for summer undergraduate research 2019 SROP summer scholarship for undergraduate research 2019 BEACON fellowship for research Drew Scholar Honors College; Dean’s List Presentations Posters University Undergraduate Research and Arts Forum (UURAF) (Apr \u0026lsquo;21) National Veterinary Scholars Symposium, AAVMC (Aug ‘20) Mid-Michigan Symposium for Undergraduate Research Experience (Aug ‘20) Intelligent Systems for Molecular Biology (ISMB 2020), International Society for Computational Biology flagship conference (Jul ‘20) Phi Zeta Research Symposium, College of Veterinary Medicine, MSU (Oct \u0026lsquo;19) Mid-Michigan Symposium for Undergraduate Research Experiences (Jul ‘19) Talks Phi Zeta Research Symposium, CVM, MSU (Oct \u0026lsquo;20) ","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"c4fec153af382e0126c3584bd00503da","permalink":"/authors/philip-calhoun/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/philip-calhoun/","section":"authors","summary":"MD at Michigan State University. Now a resident at Ford Hospital in Detroit, MI.\nAccomplishments Accepted to medical school programs \u0026lsquo;21 (Loyola College, MSU College of Human/Osteopathic Medicine, Wayne State University) 2020 NIH R25-funded BRUSH scholarship for summer undergraduate research 2019 SROP summer scholarship for undergraduate research 2019 BEACON fellowship for research Drew Scholar Honors College; Dean’s List Presentations Posters University Undergraduate Research and Arts Forum (UURAF) (Apr \u0026lsquo;21) National Veterinary Scholars Symposium, AAVMC (Aug ‘20) Mid-Michigan Symposium for Undergraduate Research Experience (Aug ‘20) Intelligent Systems for Molecular Biology (ISMB 2020), International Society for Computational Biology flagship conference (Jul ‘20) Phi Zeta Research Symposium, College of Veterinary Medicine, MSU (Oct \u0026lsquo;19) Mid-Michigan Symposium for Undergraduate Research Experiences (Jul ‘19) Talks Phi Zeta Research Symposium, CVM, MSU (Oct \u0026lsquo;20) ","tags":null,"title":"Philip Calhoun","type":"authors"},{"authors":["admin"],"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"6bcc39c32f1c62a9cc1122fe342a7921","permalink":"/authors/sana-paktinyar/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/sana-paktinyar/","section":"authors","summary":"","tags":null,"title":"Sana Paktinyar","type":"authors"},{"authors":["admin"],"categories":null,"content":"Accomplishments Fellowships 2025 NSF-funded EURēCA! Summer Fellowship Presentations Posters 2025-08 Rocky Mountain Branch, American Society for Microbiology. Fort Collins, CO 2025-03 Women in STEM. Aurora, CO 2024 Microbial Pathogenesis Symposium. Aurora, CO ","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"a7b6ee89ab12b1f519bd63e9af0b26a2","permalink":"/authors/sarah-mentzer/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/sarah-mentzer/","section":"authors","summary":"Accomplishments Fellowships 2025 NSF-funded EURēCA! Summer Fellowship Presentations Posters 2025-08 Rocky Mountain Branch, American Society for Microbiology. Fort Collins, CO 2025-03 Women in STEM. Aurora, CO 2024 Microbial Pathogenesis Symposium. Aurora, CO ","tags":null,"title":"Sarah Mentzer","type":"authors"},{"authors":["admin"],"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"36354520210447cbccd4a7ee1529e4ba","permalink":"/authors/teresa-smith/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/teresa-smith/","section":"authors","summary":"","tags":null,"title":"Teresa Smith","type":"authors"},{"authors":["admin"],"categories":null,"content":" Accomplishments Colorado Research Experience (CORE) Summer program (Jun–Jul \u0026lsquo;23) ","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"a701710f962fcadc85a08378c07bc202","permalink":"/authors/vy-tran/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/vy-tran/","section":"authors","summary":" Accomplishments Colorado Research Experience (CORE) Summer program (Jun–Jul \u0026lsquo;23) ","tags":null,"title":"Vy 'Andy' Tran","type":"authors"},{"authors":["admin"],"categories":null,"content":"image credit: https://octodex.github.com\nNow a PhD student in Cheryl Ackert-Bicknell\u0026rsquo;s lab at CU Anschutz.\nRotated with us in Spring 2025.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"5bb307884d05474cbfe906285ca394a8","permalink":"/authors/yichi-chen/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/yichi-chen/","section":"authors","summary":"image credit: https://octodex.github.com\nNow a PhD student in Cheryl Ackert-Bicknell\u0026rsquo;s lab at CU Anschutz.\nRotated with us in Spring 2025.","tags":null,"title":"Yichi 'Ella' Chen","type":"authors"},{"authors":["Cristina Penaranda","Evan Brenner","Anne Clatworthy","Lisa Cosimi","Janani Ravi","Deborah Hung"],"categories":["Research"],"content":"CP and EB are co-primary authors. CP, JR, and DH are co-corresponding authors.\n","date":1769904e3,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1769904e3,"objectID":"9380a9e865293905445c2c645ee5a8ba","permalink":"/publication/pseudomonas_diversity/","publishdate":"2026-02-01T00:00:00Z","relpermalink":"/publication/pseudomonas_diversity/","section":"publication","summary":"Pseudomonas aeruginosa is a clinically significant, opportunistic pathogen adept at thriving in both host-associated and environmental settings. We sought to define the extent to which P. aeruginosa isolates specialize across niches using a comprehensive study of whole-genome sequencing with paired phenotypic characterization of 125 P. aeruginosa isolates from diverse clinical and environmental sites. We evaluated virulence-associated traits, including motility, cytotoxicity, biofilm formation, pyocyanin production, and antimicrobial resistance to eight antibiotics. Our results show that genomic diversity does not correlate with isolation source or most virulence phenotypes. Instead, we find that, in agreement with prior studies, the two major P. aeruginosa clades (groups A and B) clearly segregate by cytotoxicity, with group B strains showing significantly higher cytotoxicity than group A. Sequence analysis revealed previously uncharacterized alleles of genes encoding type III secretion effector proteins. We observed high variability among strains and isolation sources in the four assayed virulence phenotypes. Antimicrobial resistance was exclusively observed in clinical isolates, whereas it was absent in environmental isolates, reflecting antibiotic exposure-driven selection. Bacterial genome-wide association studies (GWAS) revealed an association between cytotoxicity and exoU presence, and we identified a novel exoU allelic variant with decreased cytotoxicity, demonstrating that functional diversity of well-characterized virulence factors may influence pathogenic outcomes. Overall, our analysis supports the hypothesis that the ability of P. aeruginosa to thrive across diverse niches is driven not by niche-specific accessory genes but by its core genome.","tags":["pathogenic-features","antimicrobial-resistance","molecular-evolution","compbio-bioinfo"],"title":"Genomic comparison and phenotypic characterization of Pseudomonas aeruginosa isolates across environmental and diverse clinical isolation sites","type":"publication"},{"authors":["Evan Brenner","Charmie Vang","Connah Johnson","Janani Ravi"],"categories":["Research"],"content":"EB, CV are co-primary authors who contributed equally.\n","date":17604e5,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":17604e5,"objectID":"a39b07eac6c4a87536c48ab0a8dbca06","permalink":"/publication/prochlorococcus/","publishdate":"2025-10-14T00:00:00Z","relpermalink":"/publication/prochlorococcus/","section":"publication","summary":"Prochlorococcus is a cyanobacterial genus that exhibits photosynthetic capacity and remarkable genetic diversity. We analyze how Prochlorococcus genomics relate to high vs. low light environment adaptations, applying traditional comparative genomics and machine learning (ML) approaches to connect genotypes to phenotypes. We downloaded nearly 1,000 Prochlorococcus genomes from NCBI with information on their light adaptation ecotype (high-light/low-light) and depth of isolation using metadata through JGI. Average nucleotide identity analysis and traditional pangenome generation tools struggle to capture the cyanobacterial core genome, but despite its scant conservation, we clearly observe a sharp separation of the taxon by its light utilization preferences -- that is, its light ecotypes. A range of classical ML models trained to predict ecotype achieve exceptional binary classification accuracy even when predicting on partial genomes (Matthews Correlation Coefficient = 0.81 - 0.98), while regression models trained to predict the depth of isolation performed poorly, with relatively high root mean square error values (40.8 - 45.3m). For ecotype prediction, top features for the best-performing models included photosynthesis-associated genes and pathways, as well as some novel markers of unknown function. Our research findings recapitulate the extreme genetic versatility in Prochlorococcus and find that variable genetic markers allow excellent classification accuracy, and therefore, ecotype prediction, even for incomplete metagenomic assemblies, emphasizing the specialization and separation among these cyanobacterial ecotypes.","tags":["pathogenic-features","molecular-evolution","machine-learning","compbio-bioinfo"],"title":"Genotype-phenotype modeling of light ecotypes in Prochlorococcus reveals genomic signatures of ecotypic divergence","type":"publication"},{"authors":["Abhirupa Ghosh","Evan Brenner","Charmie Vang","Ethan Wolfe","Emily Boyer","Raymond L Lesiyon","Keenan Manpearl","Vignesh Sridhar","Joseph Burke","Jacob Krol","Jill Bilodeaux","Janani Ravi"],"categories":["Research"],"content":"AG, EB, CV, EW are co-primary authors who contributed equally.\n","date":1751846400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1751846400,"objectID":"fcb88305518732bc0c1dff89639974d2","permalink":"/publication/amr_eskape/","publishdate":"2025-07-07T00:00:00Z","relpermalink":"/publication/amr_eskape/","section":"publication","summary":"Since the clinical introduction of antibiotics in the 1940s, antimicrobial resistance (AMR) has become an increasingly dire threat to global public health. Pathogens acquire AMR much faster than we discover new drugs (antibiotics), warranting innovative methods to better understand its molecular underpinnings. Traditional approaches for detecting AMR in novel bacterial strains are time-consuming and labor-intensive. However, advances in sequencing technology offer a plethora of bacterial genome data, and computational approaches like machine learning (ML) provide an optimistic scope for in silico AMR prediction. Here, we introduce a comprehensive multiscale ML approach to predict AMR phenotypes and identify AMR molecular features associated with a single drug or drug family, stratified by time and geographical locations. As a case study, we focus on a subset of the World Health Organization’s Bacterial Priority Pathogens, the frequently drug-resistant and nosocomial ESKAPE pathogens: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species. We started with sequenced genomes with lab-derived AMR phenotypes, constructed pangenomes, clustered gene and protein sequences, and extracted protein domains to generate pangenomic features across molecular scales. To uncover the molecular mechanisms behind drug-/drug class-specific resistance, we trained logistic regression ML models on our datasets. These yielded ranked lists of AMR-associated genes, proteins, and domains. In addition to recapitulating known AMR features, our models identified novel candidates for experimental validation. The models were performant across molecular scales, data types, and drugs while achieving a median normalized Matthews correlation coefficient of 0.89. Prediction performance showed resilience even when evaluated on geographical and temporal holdouts. We also evaluated model generalizability and cross-resistance across the drug-/drug class-specific models cross-tested on other available drug-/drug class genomes. Finally, we uncovered multiple drug class resistance features using multiclass and multilabel models. Our holistic approach promises reliable prediction of existing and developing resistance in newly sequenced pathogen genomes, while pinpointing the mechanistic molecular contributors of AMR. All our models and results are available at our interactive web app, https://jravilab.org/amr.","tags":["antimicrobial-resistance","pathogenic-features","molecular-evolution","machine-learning","webapp","compbio-bioinfo"],"title":"From sequence to signature: Uncovering multiscale AMR features across bacterial pathogens with supervised machine learning","type":"publication"},{"authors":["Kewalin Samart","Ling Thang","Landon Buskirk","Amy Tonielli","Arjun Krishnan","Janani Ravi"],"categories":["Research"],"content":"AK and JR are co-corresponding authors.\n","date":1748822400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1748822400,"objectID":"437d0e2da3c05a571ecd3d7e0f2ba054","permalink":"/publication/drugrep_tb/","publishdate":"2025-06-02T00:00:00Z","relpermalink":"/publication/drugrep_tb/","section":"publication","summary":"Tuberculosis (TB) remains the second leading cause of infectious disease mortality worldwide, killing over one million people annually. Rising antibiotic resistance has created an urgent need for host-directed therapeutics (HDTs) — preferably by repurposing existing approved drugs — that modulate host immune responses rather than directly targeting the pathogen. Repurposed therapeutics have been successfully identified for cancer and COVID-19 by finding drugs that reverse disease gene expression patterns (an approach called ‘connectivity scoring’), but this approach remains largely unexplored for bacterial infections like TB. The application of transcriptome-based methods to TB faces significant challenges, including dataset heterogeneity across transcriptomics platforms and biological conditions, uncertainty about optimal scoring methods, and lack of systematic approaches to identify robust disease signatures. Here, we developed an integrative computational workflow combining multiple connectivity scoring methods with consensus disease signature construction and used it to systematically identify FDA-approved drugs as promising TB host-directed therapeutics. Our framework integrates six complementary connectivity methods and constructs weighted consensus signatures from 21 TB gene expression datasets spanning microarray and RNA-seq platforms, diverse cell types, and infection conditions. Our approach prioritized 140 high-confidence drug candidates that consistently reverse TB-associated gene expression changes, successfully recovering known HDTs, including statins (atorvastatin, lovastatin, fluvastatin) and vitamin D receptor agonists (calcitriol). We identified promising novel candidates such as niclosamide and tamoxifen, both recently validated in experimental TB models, and revealed enrichment for therapeutically relevant mechanisms, e.g., cholesterol metabolism inhibition and immune modulation pathways. Network analysis of disease-drug interactions identified 10 key bridging genes (including MYD88, RELA, and CXCR2) that represent potential novel druggable targets for TB host-directed therapy. This work establishes transcriptome-based connectivity mapping as a viable approach for systematic HDT discovery in bacterial infections and provides a robust computational framework applicable to other infectious diseases. Our findings offer immediate opportunities for experimental validation of prioritized drug candidates and mechanistic investigation of identified druggable targets in TB pathogenesis.","tags":["host-response","drug-repurposing","disease-signature","mycobacteria","tb","compbio-bioinfo"],"title":"Integrative transcriptome-based drug repurposing in tuberculosis","type":"publication"},{"authors":["Abhirupa Ghosh","Charmie Vang","Evan Brenner","Janani Ravi"],"categories":["Research"],"content":"","date":1748217600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1748217600,"objectID":"b4dfb3a441c13eea87140c197e8273a1","permalink":"/publication/amr_tim/","publishdate":"2025-05-26T00:00:00Z","relpermalink":"/publication/amr_tim/","section":"publication","summary":"The global antimicrobial resistance (AMR) emergency is driven by complex and evolving molecular mechanisms. Cutting-edge machine learning methods and multiomics technologies can help to combat this crisis by predicting novel AMR biomarkers and outcomes with unprecedented precision and speed, offering critical insights into the molecular underpinnings of AMR.","tags":["antimicrobial-resistance","pathogenic-features","host/pathogen","compbio-bioinfo"],"title":"Unlocking antimicrobial resistance with multiomics and machine learning","type":"publication"},{"authors":["Evan Brenner","Abhirupa Ghosh","Ethan Wolfe","Emily Boyer","Charmie Vang","Raymond L Lesiyon","David Mayer","Janani Ravi"],"categories":["Research"],"content":"EB and AG are co-primary authors.\n","date":1735689600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1735689600,"objectID":"aac9969657d78a4fd3d365409e8cacaf","permalink":"/publication/amr_package/","publishdate":"2025-01-01T00:00:00Z","relpermalink":"/publication/amr_package/","section":"publication","summary":"EB and AG are co-primary authors.","tags":["pathogenic-features","antimicrobial-resistance","machine-learning","compbio-bioinfo"],"title":"amR: an R package suite to predict antimicrobial resistance in bacterial pathogens","type":"publication"},{"authors":null,"categories":["Research"],"content":"Summary We develop computational approaches to predict bacterial strain susceptibility to phages and to understand the genomic basis of phage-bacteria coevolution. Our work spans molecular mechanisms of phage defense — including phage defense by deaminase-mediated depletion of deoxynucleotides — to genomic signatures of ecotypic divergence in Prochlorococcus light ecotypes. We are now extending these approaches to systematically predict which bacterial strains are susceptible to which phages, with direct applications to phage-based therapeutic strategies for difficult-to-treat bacterial infections.\n","date":1735689600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1735689600,"objectID":"a70438664d806b29733a5d6066353411","permalink":"/project/phage-bacteria/","publishdate":"2025-01-01T00:00:00Z","relpermalink":"/project/phage-bacteria/","section":"project","summary":"Computational prediction of bacterial susceptibility to phages and genomic signatures of phage-bacteria coevolution.","tags":["phage","phage-bacteria","microbial-genomics","genomics","host-pathogen","ongoing","compbio-bioinfo"],"title":"Phage-bacteria interactions","type":"project"},{"authors":["Janani Ravi","Kewalin Samart","Jason Zwolak"],"categories":["Research"],"content":"","date":1722556800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1722556800,"objectID":"54c472f7f0b83f441493b56c3384d070","permalink":"/publication/start_plos/","publishdate":"2020-09-25T00:00:00Z","relpermalink":"/publication/start_plos/","section":"publication","summary":"Budding yeast, *Saccharomyces cerevisiae*, is widely used as a model organism to study the genetics underlying eukaryotic cellular processes and growth critical to cancer development, such as cell division and cell cycle progression. The budding yeast cell cycle is also one of the best-studied dynamical systems owing to its thoroughly resolved genetics. However, the dynamics underlying the crucial cell cycle decision point called the START transition, at which the cell commits to a new round of DNA replication and cell division, are under-studied. The START machinery involves a central cyclin-dependent kinase; cyclins responsible for starting the transition, bud formation, and initiating DNA synthesis; and their transcriptional regulators. However, evidence has shown that the mechanism is more complicated than a simple irreversible transition switch. Activating a key transcription regulator SBF requires the phosphorylation of its inhibitor, Whi5, or an SBF/MBF monomeric component, Swi6, but not necessarily both. Also, the timing and mechanism of the inhibitor Whi5's nuclear export, while important, are not critical for the timing and execution of START. Therefore, there is a need for a consolidated model for the budding yeast START transition, reconciling regulatory and spatial dynamics. We built a detailed mathematical model (START-BYCC) for the START transition in the budding yeast cell cycle based on established molecular interactions and experimental phenotypes. START-BYCC recapitulates the underlying dynamics and correctly emulates key phenotypic traits of ~150 known START mutants, including regulation of size control, localization of inhibitor/transcription factor complexes, and the nutritional effects on size control. Such a detailed mechanistic understanding of the underlying dynamics gets us closer towards deconvoluting the aberrant cellular development in cancer.","tags":["tbd",null],"title":"Modeling the START transition in the budding yeast cell cycle","type":"publication"},{"authors":["Janani Ravi","Vivek Anantharaman","Samuel Chen","Evan Brenner","Pratik Datta","L Aravind","Maria Gennaro"],"categories":["Research"],"content":"JR, LA, and MG are co-corresponding authors.\n","date":1716940800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1716940800,"objectID":"fc18d224593f709f27d89922b39dfdfc","permalink":"/publication/psp_evolution/","publishdate":"2020-09-25T00:00:00Z","relpermalink":"/publication/psp_evolution/","section":"publication","summary":"Bacterial phage shock protein (PSP) systems stabilize the bacterial cell membrane and protect against envelope stress. These systems have been associated with virulence, but despite their critical roles, PSP components are not well characterized outside proteobacteria. Using comparative genomics and protein sequence-structure-function analyses, we systematically identified and analyzed PSP homologs, phyletic patterns, domain architectures, and gene neighborhoods. This approach underscored the evolutionary significance of the system, revealing that its core protein PspA (Snf7 in ESCRT outside bacteria) was present in the last universal common ancestor and that this ancestral functionality has since diversified into multiple novel, distinct PSP systems across life. Several novel partners of the PSP system were identified: (i) the Toastrack domain, likely facilitating assembly of sub-membrane stress-sensing and signaling complexes, (ii) the newly defined HTH-associated α-helical signaling domain-PadR-like transcriptional regulator pair system, and (iii) multiple independent associations with ATPase, CesT/Tir-like chaperone, and Band-7 domains in proteins thought to mediate sub-membrane dynamics. Our work also uncovered links between the PSP components and other domains, such as novel variants of SHOCT-like domains, suggesting roles in assembling membrane-associated complexes of proteins with disparate biochemical functions. Results are available at our interactive web app, https://jravilab.org/psp.","tags":["stress-response","phylogeny","molecular-evolution","pathogenic-features","host/pathogen","tree-of-life","webapp","compbio-bioinfo","R"],"title":"The phage shock protein (PSP) envelope stress response: discovery of novel partners and evolutionary history","type":"publication"},{"authors":["Joshua Lensmire","Michael Wischer","Lo Sosinski","Elliot Ensink","Jack Dodson","John Shook","Phillip Delekta","Christopher Cooper","Daniel Havlichek Jr","Martha Mulks","Sophia Lunt","Janani Ravi","Neal Hammer"],"categories":["Research"],"content":"","date":1688688e3,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1688688e3,"objectID":"3cf20ddfc507dd8ff181864fe05dc459","permalink":"/publication/ggt_saureus/","publishdate":"2023-07-07T00:00:00Z","relpermalink":"/publication/ggt_saureus/","section":"publication","summary":"Sulfur is an indispensable element for proliferation of bacterial pathogens. Prior studies indicated that the human pathogen, Staphylococcus aureus utilizes glutathione (GSH) as a source of nutrient sulfur; however, mechanisms of GSH acquisition are not defined. Here, we identify a previously uncharacterized five-gene locus comprising a putative ABC-transporter and γ–glutamyl transpeptidase (ggt) that promotes S. aureus proliferation in medium supplemented with either reduced or oxidized GSH (GSSG) as the sole source of nutrient sulfur. Based on these phenotypes, we name this transporter the Glutathione import system (GisABCD). We confirm that Ggt is capable of cleaving GSH and GSSG γ–bonds and that this process is required for their use as nutrient sulfur sources. Additionally, we find that the enzyme is cell associated. Bioinformatic analyses reveal that only Staphylococcus species closely related to S. aureus encode GisABCD-Ggt homologues. Homologues are not detected in Staphylococcus epidermidis. Consequently, we establish that GisABCD-Ggt provides a competitive advantage for S. aureus over S. epidermidis in a GSH-dependent manner. Overall, this study describes the discovery of a nutrient sulfur acquisition system in S. aureus that targets GSH and promotes competition against other staphylococci commonly associated with the human microbiota.","tags":["nutrient-acquisition","pathogenic-features","host/pathogen","molecular-evolution","phylogeny","staphylococcus","compbio-bioinfo"],"title":"The glutathione import system satisfies the Staphylococcus aureus nutrient sulfur requirement and promotes interspecies competition","type":"publication"},{"authors":["Janani Ravi"],"categories":["Research","R"],"content":"Workshop material: https://github.com/jraviLab/2023-glbio\nHosted w/ Jake Krol, Faisal Alquaddoomi\n","date":1684155600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1684155600,"objectID":"ef7890d4b18e0ccaa5b5b7075ae20887","permalink":"/talk/2023-glbio/","publishdate":"2023-05-15T00:00:00Z","relpermalink":"/talk/2023-glbio/","section":"talk","summary":"We recently developed a web application, MolEvolvR, to characterize proteins using molecular evolution and phylogeny. This session will serve as a behind-the-scenes (BTS) sneak peek into what MolEvolvR does, how it does it, and its origin story. The hands-on training component will provide the basic principles of why and how to build a dashboard/web-app for your biological problem of interest with R/Shiny, and when and how you would set up your back-end as an R package.\n\nWorkshop outline | Rationale with hands-on component\n\nWhen are you ready to set up a dashboard? When would you build a simple web-application instead?\nA little bit of bioinformatics: A quick preview of our MolEvolvR web-app. How it came to be, from special cases to a generalized version? How to characterize proteins of interest by identifying the underlying molecular building blocks? Where do these features come from and what does it mean, i.e., how to interpret the results using the lens of evolution?\nHow do you pick your feature list for your web-app? Some lessons and reflections.\nProject management 101: how to set up version-controlled projects and repositories for collaborative computational biology projects (with other dry/wet-lab colleagues)?\nDashboard 101: How to develop a dashboard for your data/visualizations using Rmarkdown/Quarto?\nWeb-app 101: How to develop and host an interactive R/Shiny web application?\nR-package 101: When, why, and how would you create your first R-package?\nQuick tour on how to set up the backend that supports a workflow, data tables and visualizations, for a multi-functional web-app such as MolEvolvR.\n","tags":["compbio-bioinfo","software-tools","R","workshop"],"title":"MolEvolvR BTS: When and how to build a web-app and software package?","type":"talk"},{"authors":["Mary Cantoria","Elaheh Alizadeh","Janani Ravi","Nawat Bunnag","Arminja Kettenbach","Yashi Ahmed","Andrew Paek","John Tyson","Konstantin Doubrovinski","Ethan Lee","Curtis Thorne"],"categories":["Research"],"content":"","date":1673308800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1673308800,"objectID":"af737f6e4237ecce2c9499cc4da7e2cf","permalink":"/publication/wnt_bistability/","publishdate":"2023-01-10T00:00:00Z","relpermalink":"/publication/wnt_bistability/","section":"publication","summary":"Positive feedback within the β-catenin destruction complex gives rise to bistability and memory in response to Wnt stimulation, imparting signal transduction accuracy and insulation.","tags":["dynamical-systems","math-modeling","compbio-bioinfo"],"title":"Feedback in the β-catenin destruction complex imparts bistability and cellular memory","type":"publication"},{"authors":null,"categories":["Research"],"content":"Summary We develop integrative machine learning approaches to predict antimicrobial resistance (AMR) and characterize pathogen genomics across clinical and environmental contexts. Our ML framework associates multi-scale genomic features — genes, protein domains, SNPs, and k-mers — with AMR phenotypes across ESKAPE pathogens, demonstrating that resistance prediction requires integration across sequence scales, with domain-level features often outperforming gene-level markers. Analyses spanning \u0026gt;15,000 genomes reveal that feature importance varies substantially across pathogen species and drug classes, providing mechanistic insights into resistance evolution.\nIn collaboration with the Penaranda lab (National Jewish Health), we characterized the genetic and phenotypic diversity of Pseudomonas aeruginosa across clinical and environmental isolation sites, revealing distinct genomic signatures associated with niche adaptation and novel resistance determinants. We are extending these approaches to predict host specificity in bacterial pathogens, integrating pangenomic features with host-associated metadata to identify molecular determinants of tissue tropism and species barriers.\nEarlier collaborative work with Sreevatsan Lab (while at MSU) identified SNPs in Brazilian Mycobacterium tuberculosis isolates critical for drug resistance, demonstrating how comparative genomics reveals population-specific resistance mechanisms.\n","date":1659312e3,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1659312e3,"objectID":"0ceae3fa76ee2d65b2207df268209088","permalink":"/project/amr-ml/","publishdate":"2022-08-01T00:00:00Z","relpermalink":"/project/amr-ml/","section":"project","summary":"Integrative machine learning to predict AMR and characterize pathogen genomics across clinical and environmental contexts.","tags":["amr","machine-learning","ml","eskape","mycobacteria","microbial-genomics","comparative-genomics","genomics","ongoing","compbio-bioinfo"],"title":"Machine learning \u0026 comparative genomics for antimicrobial resistance","type":"project"},{"authors":["Brian Hsueh","Geoffrey Severin","Clinton Elg","Evan Waldron","Abhiruchi Kant","Alex Wessel","John Dover","Christopher Rhoades","Benjamin Ridenhour","Kristin Parent","Matthew Neiditch","Janani Ravi","Eva Top","Chris Waters"],"categories":["Research"],"content":"BYH and GBS are co-primary authors.\n","date":1658707200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1658707200,"objectID":"96ec9796c10c96b1e2d406b704202090","permalink":"/publication/avcd_vcholerae/","publishdate":"2021-03-31T00:00:00Z","relpermalink":"/publication/avcd_vcholerae/","section":"publication","summary":" ","tags":["phage-defense","pathogenic-features","host/pathogen","molecular-evolution","phylogeny","vibrio","compbio-bioinfo"],"title":"Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria","type":"publication"},{"authors":["Helen Blaine","Joseph Burke","Janani Ravi","Christina Stallings"],"categories":["Research"],"content":"HCB and JTB are co-primary authors. JR and CLS are co-corresponding authors.\n","date":1658620800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1658620800,"objectID":"cf733d3c6cfd4775b4d8c673e42222f3","permalink":"/publication/dcia_evolution/","publishdate":"2022-01-24T00:00:00Z","relpermalink":"/publication/dcia_evolution/","section":"publication","summary":"Despite the fundamental importance of DNA replication for life, this process remains understudied in bacteria outside Escherichia coli and Bacillus subtilis. In particular, most bacteria do not encode the helicase-loading proteins that are essential in E. coli and B. subtilis for DNA replication. Instead, most bacteria encode a DciA homolog that likely constitutes the predominant mechanism of helicase operation in bacteria. However, it is still unknown how DciA structure and function compare across diverse phyla that encode DciA proteins. In this study, we performed computational evolutionary analyses to uncover tremendous diversity among DciA homologs. These studies provide a significant advance in our understanding of an essential component of the bacterial DNA replication machinery.","tags":["helicase-loader","pathogenic-features","host/pathogen","molecular-evolution","phylogeny","mycobacteria","bacteria","compbio-bioinfo"],"title":"DciA Helicase Operators Exhibit Diversity across Bacterial Phyla","type":"publication"},{"authors":["Rocio Joo","Andrea Sanchez-Tapia","Sara Mortara","Yanina Bellini Saibene","Heather Turner","Dorothea Hug Peter","Natalia Soledad Morandeira","Matthias Bannert","Batool Almazrouq","Elizabeth Hare","Laura Acion","Juan Pablo Narvaez-Gomez","Marcela Alfaro Cordoba","Federico Marini","Rita Giordano","Silvia Canelon","Anicet Ebou","Adithi Upadhya","Joselyn Chavez","Janani Ravi"],"categories":["R-Ladies","Resources"],"content":"RJ and AST are co-primary authors. RJ and JR are co-corresponding authors.\n","date":1658620800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1658620800,"objectID":"93146033dd16c6fb5cd26020fc1e82c0","permalink":"/publication/10sr_inclusive_conference/","publishdate":"2022-02-04T00:00:00Z","relpermalink":"/publication/10sr_inclusive_conference/","section":"publication","summary":"Conferences are spaces to meet and network within and across academic and technical fields, learn about new advances, and share our work. They can help define career paths and create long-lasting collaborations and opportunities. However, these opportunities are not equal for all. This article introduces 10 simple rules to host an inclusive conference based on the authors’ recent experience organizing the 2021 edition of the useR! statistical computing conference, which attracted a broad range of participants from academia, industry, government, and the nonprofit sector. Coming from different backgrounds, career stages, and even continents, we embraced the challenge of organizing a high-quality virtual conference in the context of the Coronavirus Disease 2019 (COVID-19) pandemic and making it a kind, inclusive, and accessible experience for as many people as possible. The rules result from our lessons learned before, during, and after the organization of the conference. They have been written mainly for potential organizers and selection committees of conferences and contain multiple practical tips to help a variety of events become more accessible and inclusive. We see this as a starting point for conversations and efforts towards building more inclusive conferences across the world. *Translated versions of the English abstract and the list of rules are available in 10 languages in S1 Text: Arabic, French, German, Italian, Japanese, Korean, Portuguese, Spanish, Tamil, and Thai.","tags":["R","inclusion","diversity","accessibility","rladies"],"title":"Ten simple rules to host an inclusive conference","type":"publication"},{"authors":["Kayla Conner","Joseph Burke","Janani Ravi","Jonathan Hardy"],"categories":["Research"],"content":"KNC and JTB are co-primary authors. JR and JWH are co-corresponding authors.\n","date":1658275200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1658275200,"objectID":"ead23bdec2fa7258929f7cc42b311272","permalink":"/publication/inlp_listeria/","publishdate":"2022-01-19T00:00:00Z","relpermalink":"/publication/inlp_listeria/","section":"publication","summary":"The intracellular bacterial pathogen Listeria monocytogenes can breach protective barriers in the pregnant host, allowing the colonization of the placenta in pregnant people and resulting in numerous adverse pregnancy outcomes. Previous studies aimed at delineating the mechanisms behind placental colonization of L. monocytogenes identified a key virulence factor, internalin P (InlP). The internalin family of proteins has been studied extensively due to their conservation in the genus Listeria and their contribution to virulence and pathogenicity in L. monocytogenes. Still, many questions remain regarding the evolution of internalins and their potential roles in non-pathogenic Listeria. Our work addresses this gap in knowledge by (1) identifying additional InlP homologs in Listeria, including L. ivanovii, L. seeligeri, L. innocua, and L. costaricensis, and (2) characterizing these homologs using computational evolutionary methods to compare their primary sequences, domain architectures, and structural models. Together, our findings contribute to the field by providing insights into the evolution of one key member of the internalin family, as well as serving as a catalyst for future studies of InlP and its role in Listeria pathogenesis.","tags":["internalins","pathogenic-features","host/pathogen","molecular-evolution","phylogeny","listeria","compbio-bioinfo"],"title":"Novel Internalin P homologs in Listeria ivanovii londoniensis and Listeria seeligeri","type":"publication"},{"authors":["Janani Ravi"],"categories":["Research","R"],"content":"","date":1657806300,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1657806300,"objectID":"6d61bc2a6ec78583439127fc8aa7c8f8","permalink":"/talk/2022-ismb/","publishdate":"2022-07-14T00:00:00Z","relpermalink":"/talk/2022-ismb/","section":"talk","summary":"","tags":["phylogeny","molecular-evolution","pathogenic-features","compbio-bioinfo","amr","comparative-genomics","software-tools"],"title":"Cross-database integration using evolution and machine learning to identify multiscale molecular building blocks for antibiotic resistance","type":"talk"},{"authors":["Janani Ravi"],"categories":["R","Resources"],"content":"","date":1653768e3,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1653768e3,"objectID":"386aaea37afaf8f97ce6a11feb38a77d","permalink":"/talk/2022-iscb_academy/","publishdate":"2022-05-28T00:00:00Z","relpermalink":"/talk/2022-iscb_academy/","section":"talk","summary":"This workshop presents how to analyze \u0026 visualize processed transcriptomic data.\n\nThis workshop is divided in 5 parts:\nPart 1: Getting started w/ `readr`\nPart 2: Reshaping data w/ `tidyr`\nPart 3: Data wrangling w/ `dplyr`\nPart 4: Visualizing tidy data w/ `ggplot`\nPart 5: Export and Wrap-up w/ `rmarkdown`\n\nBy the end of this workshop, you will be able to load your transcriptomic dataset, perform basic data tidying \u0026 wrangling, data visualization, and save/export your results using tidyverse! Hopefully, you will also have a newfound appreciation for reproducible research and R!\n","tags":["R","data-science","tidyverse","genomics"],"title":"Using Tidyverse for Genomics","type":"talk"},{"authors":["Faisal Alquaddoomi","Joseph Burke","Lo Sosinski","David Mayer","Evan Brenner","Samuel Chen","Jacob Krol","Ethan Wolfe","Vince Rubinetti","Shaddai Amolitos","Kellen Reason","John Johnston","Janani Ravi"],"categories":["Research","R"],"content":"FSA, JTB, LS are co-primary authors who contributed equally; they are listed alphabetically.\n","date":1645488e3,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1645488e3,"objectID":"afbf4b6194209080ed415a6b3d2aa1cd","permalink":"/publication/molevolvr_webapp/","publishdate":"2022-02-22T00:00:00Z","relpermalink":"/publication/molevolvr_webapp/","section":"publication","summary":"Studying proteins through the lens of evolution can reveal features such as conserved domains, lineage-specific variants, and co-occurring domain architectures in phylogenetic context across all superkingdoms. MolEvolvR enables researchers to conduct such evolution-focused studies to generate testable hypotheses about protein function and evolution. MolEvolvR is a novel web-app allowing researchers to visualize the molecular evolution of their proteins of interest in a phylogenetic context across the tree of life. It accepts multiple input formats – protein/domain sequences, homologous proteins, or domain scans – and, using a general-purpose computational workflow, returns detailed homolog data and dynamic graphical summaries (e.g., phylogenetic trees, multiple sequence alignments, domain architectures, domain proximity networks, phyletic spreads, co-occurrence patterns across lineages). MolEvolvR performs domain-centric searches to capture remote homologs that are missed by full-length searches, integrates domain architecture evolution with phyletic distribution analyses, and provides evolutionary context visualizations that reveal lineage-specific adaptations versus those that are broadly conserved. Thus, MolEvolvR is a powerful, easy-to-use web interface for computational protein characterization. The web-app can be accessed here: https://jravilab.org/molevolvr.","tags":["pathogenic-features","host/pathogen","molecular-evolution","phylogeny","tree-of-life","webapp","compbio-bioinfo","R"],"title":"MolEvolvR: a web-app for characterizing proteins using molecular evolution and phylogeny","type":"publication"},{"authors":["Janani Ravi"],"categories":["R","Resources"],"content":"","date":1645128e3,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1645128e3,"objectID":"ec984f76597569bac966e0ffdb9e063c","permalink":"/talk/2022-lst/","publishdate":"2022-02-17T00:00:00Z","relpermalink":"/talk/2022-lst/","section":"talk","summary":"Key “take home” points: \n1. How to engage and bring together those underrepresented in STEAM?\n2. What are useful formats to engage a diverse audience?\n3. How to identify co-organizers, speakers, sources of funding?\n","tags":["R","data-science","community","inclusion"],"title":"How I teach Life Scientists to Build Inclusive Communities","type":"talk"},{"authors":["Janani Ravi"],"categories":["Research"],"content":"","date":1637611200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1637611200,"objectID":"1e34786c56b338e41001bf15732e7b5b","permalink":"/talk/2021-cu/","publishdate":"2021-11-22T00:00:00Z","relpermalink":"/talk/2021-cu/","section":"talk","summary":"","tags":["compbio-bioinfo","molecular-evolution","pathogenic-features","phylogeny","drug-repurposing","disease-signature","host-response","comparative-genomics","stress-response","software-tools","data-science"],"title":"Computational approaches to study molecular pathogenesis and intervention of infectious diseases","type":"talk"},{"authors":["Kewalin Samart","Phoebe Tuyishime","Arjun Krishnan","Janani Ravi"],"categories":["Research"],"content":"KS and PT are co-primary authors. AK and JR are co-corresponding authors.\n","date":1636070400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1636070400,"objectID":"a32e3d819b127ed8c40e0dfa5516e538","permalink":"/publication/connectivity_scores/","publishdate":"2021-11-05T00:00:00Z","relpermalink":"/publication/connectivity_scores/","section":"publication","summary":"The basis of several recent methods for drug repurposing is the key principle that an efficacious drug will reverse the disease molecular 'signature' with minimal side effects. This principle was defined and popularized by the influential 'connectivity map' study in 2006 regarding reversal relationships between disease- and drug-induced gene expression profiles, quantified by a disease-drug 'connectivity score.' Over the past 15 years, several studies have proposed variations in calculating connectivity scores toward improving accuracy and robustness in light of massive growth in reference drug profiles. However, these variations have been formulated inconsistently using various notations and terminologies even though they are based on a common set of conceptual and statistical ideas. Therefore, we present a systematic reconciliation of multiple disease-drug similarity metrics ($ES$, $css$, $Sum$, $Cosine$, $XSum$, $XCor$, $XSpe$, $XCos$, $EWCos$) and connectivity scores ($CS$, $RGES$, $NCS$, $WCS$, $Tau$, $CSS$, $EMUDRA$) by defining them using consistent notation and terminology. In addition to providing clarity and deeper insights, this coherent definition of connectivity scores and their relationships provides a unified scheme that newer methods can adopt, enabling the computational drug-development community to compare and investigate different approaches easily. To facilitate the continuous and transparent integration of newer methods, this article will be available as a live document (https://jravilab.github.io/connectivity_scores) coupled with a GitHub repository (https://github.com/jravilab/connectivity_scores) that any researcher can build on and push changes to.","tags":["host-response","drug-repurposing","disease-signature","compbio-bioinfo"],"title":"Reconciling Multiple Connectivity Scores for Drug Repurposing","type":"publication"},{"authors":["Janani Ravi"],"categories":["R","Resources"],"content":"","date":1635969600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1635969600,"objectID":"742902875c1790ec4ee2ad8c1fb3b1e9","permalink":"/talk/2021-bioc_asia/","publishdate":"2021-11-03T00:00:00Z","relpermalink":"/talk/2021-bioc_asia/","section":"talk","summary":"","tags":["R","data-science","community","inclusion","AsiaR"],"title":"Strategies to build a strong diverse AsiaR community","type":"talk"},{"authors":["Janani Ravi"],"categories":["Research","R"],"content":"","date":1627416e3,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1627416e3,"objectID":"0a6e38f1dd40f11177de2f5e1fd801e1","permalink":"/talk/2021-ismb/","publishdate":"2021-07-27T00:00:00Z","relpermalink":"/talk/2021-ismb/","section":"talk","summary":"Studying how bacterial pathogenic proteins evolve can help identify lineage-specific and pathogen-specific signatures and variants, and consequently, their functions. We have developed a streamlined computational approach for characterizing the molecular evolution and phylogeny of target proteins, widely applicable across proteins and species of interest. Our approach starts with query protein(s) of interest, identifying their homologs, and characterizing each protein by its domain architecture and phyletic spread. We have developed the MolEvolvR webapp to enable biologists to run our entire workflow on their data by simply uploading a list of their proteins of interest. The webapp accepts inputs in multiple formats: protein/domain sequences, multi-protein operons/homologous proteins, or motif/domain scans. Depending on the input, MolEvolvR returns the complete set of homologs/phylogenetic tree, domain architectures, common partner domains. Users can obtain graphical summaries that include MSA and phylogenetic trees, domain architectures, domain proximity networks, phyletic spreads, co-occurrence patterns, and relative occurrences across lineages. Thus, MolEvolvR provides a powerful, easy-to-use interface for a wide range of protein characterization analyses, including data summarization and dynamic visualization. The webapp can be accessed here: http://jravilab.org/molevolvr. Soon, it will be available as an R-package for use by computational biologists.\n","tags":["phylogeny","molecular-evolution","pathogenic-features","compbio-bioinfo","stress-response","comparative-genomics","software-tools"],"title":"MolEvolvR: A webapp for characterizing proteins using molecular evolution and phylogeny","type":"talk"},{"authors":["Janani Ravi","Matthias Bannert"],"categories":["R","Resources"],"content":"","date":1625860800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1625860800,"objectID":"a7d1699657f8740dae7b67d4f60dc76d","permalink":"/talk/2021-user_rconference/","publishdate":"2021-07-09T00:00:00Z","relpermalink":"/talk/2021-user_rconference/","section":"talk","summary":"The ability to host an entire conference online went from nice-to-have to absolutely essential for many communities within just a bit more than a year. As a consequence, online conference tools were exposed to a wider audience, faced tougher scrutiny, and hauled in more feedback than ever before.\nSo far no clear front runner among conference tools has emerged from the process. Strikingly, all current conference tools used by the open-source community have major deficiencies such as accessibility issues, are bulky to navigate for admins, and/or come with a hefty price tag. The idea of this incubator is to discuss whether and how processes such as registration, abstract evaluation, or submission can be mapped into an R package and the open-source ecosystem. We aim to challenge established processes and walk through possible process changes, e.g., reviews. We also see such a system as an opportunity towards equitable practices in picking topics, forming committees, choosing reviewers, providing feedback to submitters, and selecting contributions. We intend to work on a solution that is easy to reproduce and facilitates knowledge transfer for annual conferences with changing organizers.\n","tags":["R","data-science","community","inclusion","conference"],"title":"Incubator: Stop reinventing the wheel: R package(s) for conference and abstract management","type":"talk"},{"authors":["Janani Ravi"],"categories":["R","Research"],"content":"","date":1625860800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1625860800,"objectID":"0a5bb616f93f75f919eef2808775e79a","permalink":"/talk/2021-user/","publishdate":"2021-07-09T00:00:00Z","relpermalink":"/talk/2021-user/","section":"talk","summary":"Molecular evolution and phylogeny can provide key insights into pathogenic protein families. Studying how these proteins evolve across bacterial lineages can help identify lineage-specific and pathogen-specific signatures and variants, and consequently, their functions. We have developed a streamlined computational approach for characterizing the molecular evolution and phylogeny of target proteins, widely applicable across proteins and species of interest. Our approach starts with query protein(s) of interest, identifying their homologs, and characterizing each protein by its domain architecture and phyletic spread. We have developed the MolEvolvR webapp, written entirely in R and Shiny, to enable biologists to run our entire workflow on their data by simply uploading a list of their proteins of interest. The webapp accepts inputs in multiple formats: protein/domain sequences, multi-protein operons/homologous proteins, or motif/domain scans. Depending on the input, MolEvolvR returns the complete set of homologs/phylogenetic tree, domain architectures, common partner domains. Users can obtain graphical summaries that include multiple sequence alignments and phylogenetic trees, domain architectures, domain proximity networks, phyletic spreads, co-occurrence patterns, and relative occurrences across lineages. Thus, the MolEvolvR webapp provides a powerful, easy-to-use interface for a wide range of protein characterization analyses, starting from homology searches and phylogeny to domain architectures. In addition to this analysis, researchers can use the app for data summarization and dynamic visualization. The webapp can be accessed here: http://jravilab.org/molevolvr. Soon, it will be available as an R-package for use by computational biologists.\n","tags":["R","data-science","stress-response","molecular-evolution","phylogeny","comparative genomics"],"title":"MolEvolvR: Web-app and R-package for characterizing proteins using molecular evolution and phylogeny","type":"talk"},{"authors":["Janani Ravi","Adithi Upadhya"],"categories":["R","Resources"],"content":"","date":1625774400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1625774400,"objectID":"629f99cd4b3e900fcbb809b828b3e9e1","permalink":"/talk/2021-user_asiar/","publishdate":"2021-07-08T00:00:00Z","relpermalink":"/talk/2021-user_asiar/","section":"talk","summary":"R has been a very inclusive community and collective learning has always helped, with many users of R in Asian countries we can as well have a strongly knit community for R’s users. Inspired by the MENA (Middle East and North Africa) R, AfricaR, and LatinR user groups, we propose a similar panel discussion to connect and strengthen the R community in Asia. We aim to target participants who are active R users and/or learners who have not been engaged with any R community and we want to invite panelists who are successful R developers/educators/community leaders in various Asian countries. Our goal is to build a diverse and vibrant R community within Asia. We wish to connect Asian useRs to each other, identify Asian R speakers/participants and facilitate regular webinars, workshops. We want to address the lower participation of Asian, specially Asian Underrepresented Minorities in local meetups and international conferences like useR! 2021, discuss and learn about best practices for nucleating and sustaining an engaged community. We also would like to understand how people from various backgrounds and organisations engage the community for assistance. We also wish to build a strong enough community to host a AsiaR conference in the upcoming years.\n","tags":["R","data-science","community","inclusion"],"title":"Incubator: Strategies to build a strong AsiaR community","type":"talk"},{"authors":["Janani Ravi"],"categories":["Research","R"],"content":"Related: Samuel Z Chen GLBio poster [video])( https://www.youtube.com/watch?v=6rj3eTWxXkg)\n","date":1620936e3,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1620936e3,"objectID":"1e2e22ccd5f86648e06f89e7e031b284","permalink":"/talk/2021-glbio/","publishdate":"2021-05-13T00:00:00Z","relpermalink":"/talk/2021-glbio/","section":"talk","summary":"Background: Studying bacterial physiology, adaptation, and pathogenicity through the lens of evolution requires delineating the phylogenetic history of bacterial proteins and genomes. Moreover, delineating this history of proteins is best done at all three levels, sequence, structure, and function, and comparative pangenomics. However, currently, there are no unified frameworks that experimentalists can avail to seamlessly perform all these analyses for their proteins of their interest. Using these software/tools requires numerous skills/resources: install individual tools; download/preprocess massive datasets; match disparate input-output data formats across different tools; computational resources for efficient analyses; computational know-how to run command-line tools; intuitive result summarization and visualization.\nApproach: To address this challenge, we have developed a computational framework for comprehensive evolutionary analysis that systematically integrates multiple data sources for gleaning sequence-structure-function relationships. Our framework goes beyond simple sequence comparisons by delving into constituent domains, domain architectures, phyletic spreads, and tracing the evolution across the tree of life. By adding a critical step of comparative pangenomics to these analyses, we can pinpoint molecular and genomic features that are unique to bacterial groups of interest (e.g., specific pathogens), which can then help prioritize candidate molecular targets, even in poorly characterized bacterial genomes.\nResults: We have developed a computational approach for molecular evolution and phylogeny that researchers can perform homology searches across the tree of life and reconstructs domain architecture by characterizing the input proteins and each of their homologs by combining: sequence alignment and clustering algorithms for domain detection; profile matching against protein domain/orthology databases; and prediction algorithms for signal peptides, transmembrane regions, cellular localization, and secondary/tertiary structures. We are adding an additional layer of comparative pangenomics to identify unique features for bacterial groups of interest (e.g., pathogens vs nonpathogens). An instance of the web-app, applied to study a large number of Psp stress response proteins (present across the tree of life) can be found here: jravilab.shinyapps.io/psp-evolution. The web-app described here is a general web-server that researchers can use to study any protein(s) of interest. To demonstrate the versatility of this framework, we are currently applying it to zoonotic pathogens causing severe and chronic pathologies in humans and animals, for e.g., host-specific factors in Nontuberculous Mycobacteria, nutrient acquisition systems in Staphylococcus aureus, and surface layer proteins in Bacillus anthracis. We have implemented this computational approach for molecular evolution and phylogeny (MolEvolvR) as open-source software (R-package) and a streamlined easy-to-use web application (jraviilab.org/molevolvr) that will enable us and other researchers to prioritize candidate genetic factors in their application of interest for experimental validation.\n","tags":["compbio-bioinfo","molecular-evolution","pathogenic-features","phylogeny","stress-response","comparative-genomics"],"title":"Using a computational molecular evolution and phylogeny to study pathogenic proteins","type":"talk"},{"authors":["Janani Ravi"],"categories":["R","Resources"],"content":"","date":1620590400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1620590400,"objectID":"06a45fb67b5020e2da3b75b8e416bd0b","permalink":"/talk/2021-rlpune/","publishdate":"2021-05-09T00:00:00Z","relpermalink":"/talk/2021-rlpune/","section":"talk","summary":"","tags":["R","data-science","community","inclusion","rladies"],"title":"Making cool publication quality tables w/ R","type":"talk"},{"authors":["Janani Ravi","Sara Mortara","Jonelle Villar","Haifa Ben Messaoud","Beatriz Milz","Zulemma Bazurto Blacio"],"categories":["R","Resources"],"content":"","date":161964e4,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":161964e4,"objectID":"c63ebd052a3568d111c76f34e15722df","permalink":"/talk/2021-rladies_user/","publishdate":"2021-04-28T00:00:00Z","relpermalink":"/talk/2021-rladies_user/","section":"talk","summary":"This year useR! (https://user2021.r-project.org/) will be a global and entirely remote conference. One of the main goals is to encourage the participation of diverse people (considering diversity in all its forms and all its intersectionalities). The useR! global team is committed to providing inclusive and accessible spaces during the conference, along with extensive waivers, events in different languages (English, Spanish, and French), real-time English captions, and events across different time zones.\n\nIn this meetup, you will have the opportunity to meet RLadies+ from all over the globe. Our panelists will share their useR! experiences to inspire people with different backgrounds, occupations, and paths to participate in this year’s conference. The meetup will be trilingual with a few spots per organizing chapter.\n\n#########\nSchedule\n#########\n- Welcome + Intro | Sara Mortara\n- Panel discussion with:\n- Janani Ravi (East Lansing)\n- Jonelle Villar (Bergen)\n- Haifa Ben Messaoud (Tunis)\n- Beatriz Milz (São Paulo)\n- Zulemma Bazurto Blacio (Guayaquil)\n- Pre-prepared questions\n- Questions from the audience\n\n######################\nCo-organizing chapters\n######################\nR-Ladies+ Vitória\nR-Ladies+ Bangalore\nR-Ladies+ Tunis\nR-Ladies+ East Lansing\nR-Ladies+ Guayaquil\nR-Ladies+ Santa Rosa\nR-Ladies+ Cuernavaca\nR-Ladies+ Den Bosch\n","tags":["R","data-science","community","inclusion","rladies","useR"],"title":"RLadies+ featuring useR! meetup","type":"talk"},{"authors":["Janani Ravi"],"categories":["R","Resources"],"content":"","date":1619294400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1619294400,"objectID":"4d8c72835c9d803e6beec5b65971c64a","permalink":"/talk/2021-rltunis_rlbgl/","publishdate":"2021-04-24T00:00:00Z","relpermalink":"/talk/2021-rltunis_rlbgl/","section":"talk","summary":"This workshop will present how to analyze \u0026 visualize processed genomics data.\n\nThis workshop will be divided in 5 parts:\nPart 1: Getting started w/ readr\nPart 2: Reshaping data w/ tidyr\nPart 3: Data wrangling w/ dplyr\nPart 4: Visualizing tidy data w/ ggplot\nPart 5: Export and Wrap-up w/ rmarkdown\n\nBy the end of this workshop, you will be able to load your genomic dataset, perform basic data tidying \u0026 wrangling, data visualization, and save/export your results using tidyverse! Hopefully, you will also have a newfound appreciation for reproducible research and R!\n","tags":["R","data-science","tidyverse","genomics"],"title":"Using Tidyverse for Genomics","type":"talk"},{"authors":["Janani Ravi","Antonella Fioravanti"],"categories":["Research"],"content":"","date":1618444800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1618444800,"objectID":"3bcbc1b844b155d881b1249d4c95aa11","permalink":"/publication/slps_grampos/","publishdate":"2021-04-15T00:00:00Z","relpermalink":"/publication/slps_grampos/","section":"publication","summary":" ","tags":["pathogenic-features","gram-positive-bacteria","phylogeny","molecular-evolution","compbio-bioinfo","R"],"title":"S-layers: the proteinaceous multifunctional armours of Gram-positive pathogens","type":"publication"},{"authors":["Janani Ravi","Samuel Z Chen"],"categories":["Research","R"],"content":"","date":1616788800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1616788800,"objectID":"0480ef5256f907b368ca3f02d4b07e9f","permalink":"/talk/2021-beacon/","publishdate":"2021-03-26T00:00:00Z","relpermalink":"/talk/2021-beacon/","section":"talk","summary":"We will discuss the alpha version of their new easy-to-use interactive webapp: MolEvolvR, for characterizing proteins using molecular evolution and phylogeny. We will begin by demonstrating the power of MolEvolvR using the panbacterial stress response system, PSP (phage shock protein), as an example. Then, we will anyone can use this app to study their protein(s) of interest.\n\nPSP app: jravilab.shinyapps.io/psp-evolution (bioRxiv 2020)\nMolEvolvR app: jravilab.org/molevolvr (currently, alpha-version)\n","tags":["phylogeny","molecular-evolution","comparative-genomics","pathogenic-features","compbio-bioinfo","software-tools"],"title":"MolEvolvR: a web-app for molecular evolution and phylogeny","type":"talk"},{"authors":["Syeda Anum Hadi","Ida V Kolte","Evan P Brenner","EAT Cunha","V Simonsen","L Ferrazoli","DAM Villela","RS Santos","Janani Ravi","Srinand Sreevatsan","Paulo C Basta"],"categories":["Research"],"content":"","date":1610496e3,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1610496e3,"objectID":"89ee0e520c98fabbd5cee3630c810958","permalink":"/publication/brazil_genomes_mtb/","publishdate":"2021-01-13T00:00:00Z","relpermalink":"/publication/brazil_genomes_mtb/","section":"publication","summary":"After nearly a century of vaccination and six decades of drug therapy, tuberculosis (TB) kills more people annually than any other infectious disease. Substantial challenges to disease eradication remain among vulnerable and underserved populations. The Guarani-Kaiowá people are an indigenous population in Paraguay and the Brazilian state of Mato Grosso do Sul. This community, marginalized in Brazilian society, experiences severe poverty. Like other South American indigenous populations, their TB prevalence is high, but the disease has remained largely unstudied in their communities. Herein, Mycobacterium tuberculosis isolates from local clinics were whole genome sequenced, and a population genetic framework was generated. Phylogenetics show M. tuberculosis isolates in the Guarani-Kaiowá people cluster away from selected reference strains, suggesting divergence. Most cluster in a single group, further characterized as M. tuberculosis sublineage 4.3.3. Closer analysis of SNPs showed numerous variants across the genome, including in drug resistance-associated genes, and with many unique changes fixed in each group. We report that local M. tuberculosis strains have acquired unique polymorphisms in the Guarani-Kaiowá people, and drug resistance characterization is urgently needed to inform public health to ensure proper care and avoid further evolution and spread of drug-resistant TB.","tags":["phylogeny","pathogenic-features","host/pathogen","mycobacteria","tb","compbio-bioinfo"],"title":"Discovery of a predominant and distinct lineage of Mycobacterium tuberculosis in Brazilian indigenous population","type":"publication"},{"authors":null,"categories":["Research"],"content":"Summary We developed MolEvolvR, a web application that integrates sequence analysis, domain architecture mapping, phylogenetic reconstruction, and genomic context visualization to enable systematic study of protein family evolution across the tree of life. MolEvolvR has engaged 45+ trainees worldwide through the Outreachy open-source program; we are developing MolEvolvR 2.0 with a companion R package for programmatic access.\nOur foundational work on the phage shock protein (PSP) envelope stress response exemplifies this approach: discovering that a minimal PSP system was present in the last universal common ancestor and tracing its diversification into novel functional contexts across life, including novel partners (Toastrack domain, HTH-associated signaling domain, ATPase and Band-7 domain associations). We have applied this evolutionary framework broadly to characterize protein families across diverse pathogens — including bacterial phage defense via deoxycytidine deaminases, cell surface S-layer proteins in Gram-positive pathogens, internalins in Listeria, DciA helicase loaders across bacterial phyla, and sulfur acquisition systems in Staphylococcus aureus. This work is foundational to our group\u0026rsquo;s philosophy of using evolutionary genomics to predict protein function with both basic biology and translational impact.\n","date":1602288e3,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1602288e3,"objectID":"46ec08e6f69b2bc92dd60033f43e8696","permalink":"/project/pathogenic-features/","publishdate":"2020-10-10T00:00:00Z","relpermalink":"/project/pathogenic-features/","section":"project","summary":"Characterizing protein families and (patho)genomic features using molecular evolution and phylogenetics, and the MolEvolvR web application.","tags":["molecular-evolution","phylogeny","comparative-genomics","pangenomics","molevolvr","pathogenic-features","tree-of-life","mycobacteria","staphylococci","banthracis","listeria","vibrio","ongoing","compbio-bioinfo"],"title":"Molecular evolution \u0026 comparative pathogenomics","type":"project"},{"authors":null,"categories":["Research"],"content":"Summary We are developing computational approaches to detect unique pathogenic (and host) small RNA in infected hosts (human and non-human).\n","date":1602288e3,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1602288e3,"objectID":"953cc8a819173ef0dde706a231326132","permalink":"/project/srna/","publishdate":"2020-10-10T00:00:00Z","relpermalink":"/project/srna/","section":"project","summary":"Discovering unique pathogenic sRNA in infected hosts","tags":["sRNA","past-work","host-response","pathogen","host/pathogen","mycobacteria","tb","diagnostics","compbio-bioinfo"],"title":"sRNA discovery","type":"project"},{"authors":["Janani Ravi"],"categories":["Teaching"],"content":"","date":1599555600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1599555600,"objectID":"67987749c6ddf4ff8edee89bf58cd419","permalink":"/talk/2020-mmg/","publishdate":"2020-09-10T00:00:00Z","relpermalink":"/talk/2020-mmg/","section":"talk","summary":" ","tags":["phylogeny","molecular-evolution","comparative-genomics","compbio-bioinfo","software-tools"],"title":"Phylogenetics \u0026 Comparative Genomics | MMG801","type":"talk"},{"authors":["Janani Ravi"],"categories":["Research"],"content":"","date":1597335300,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1597335300,"objectID":"99cf3d85d561ff984de829c81ef140db","permalink":"/talk/2020-beacon/","publishdate":"2020-08-13T00:00:00Z","relpermalink":"/talk/2020-beacon/","section":"talk","summary":" ","tags":["phylogeny","molecular-evolution","comparative-genomics","pathogenic-features","compbio-bioinfo","software-tools"],"title":"Computational evolutionary approaches for understanding pathogen proteins and genomes","type":"talk"},{"authors":["Janani Ravi"],"categories":["Research"],"content":"","date":1594695600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1594695600,"objectID":"591e087123597a07b9708dfa7fe76be7","permalink":"/talk/2020-ismb/","publishdate":"2020-07-14T00:00:00Z","relpermalink":"/talk/2020-ismb/","section":"talk","summary":" ","tags":["phylogeny","molecular-evolution","pathogenic-features","compbio-bioinfo","stress-response","software-tools"],"title":"Computational evolutionary approaches to characterize bacterial proteins","type":"talk"},{"authors":["Janani Ravi"],"categories":["Teaching"],"content":"","date":1582794e3,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1582794e3,"objectID":"0da12658b527f4be0a3cac8c84be25f3","permalink":"/talk/2020-cbp/","publishdate":"2020-02-27T00:00:00Z","relpermalink":"/talk/2020-cbp/","section":"talk","summary":" ","tags":["phylogeny","molecular-evolution","compbio-bioinfo","stress-response","software-tools"],"title":"Molecular Evolution and Phylogeny","type":"talk"},{"authors":["Janani Ravi","Rachel Kerwin","Julian Camillo Bello R","Camille Archer"],"categories":["R","Resources"],"content":" ","date":1582567200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1582567200,"objectID":"fe1ca1e5a8840c949808bb66a66cecb2","permalink":"/talk/2020-rmarkdown/","publishdate":"2020-02-24T00:00:00Z","relpermalink":"/talk/2020-rmarkdown/","section":"talk","summary":" ","tags":["R","data-science","software-tools","workshop"],"title":"RLEL Workshop on RMarkdown \u0026 Reproducible Research","type":"talk"},{"authors":["Janani Ravi","Veronica Frans","Julian Camillo Bello R","Camille Archer"],"categories":["R","Resources"],"content":" ","date":1581357600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1581357600,"objectID":"d9d855ade9b9e3ad2aa6670635480fee","permalink":"/talk/2020-rlel-dataviz2.0/","publishdate":"2020-02-10T00:00:00Z","relpermalink":"/talk/2020-rlel-dataviz2.0/","section":"talk","summary":" ","tags":["R","data-science","software-tools","workshop"],"title":"RLEL Workshop on DataViz 2.0","type":"talk"},{"authors":["Janani Ravi"],"categories":["R","Resources","Teaching"],"content":"","date":1580893200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1580893200,"objectID":"ddcdd7f718671fdb5e1abdcd1bd8b692","permalink":"/talk/2020-plb/","publishdate":"2020-02-05T00:00:00Z","relpermalink":"/talk/2020-plb/","section":"talk","summary":" ","tags":["academic","R","compbio-bioinfo","data-science","software-tools","teaching","workshop"],"title":"Tidyverse for Genomics","type":"talk"},{"authors":["Joshua Lensmire","Jack Dodson","Brian Hsueh","Michael Wischer","Phillip Delekta","John Shook","Elizabeth Ottosen","Paige Kies","Janani Ravi","Neal Hammer"],"categories":["Research"],"content":"","date":1575158400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1575158400,"objectID":"d39b395757a1c5f2a425f3b82f1bf07a","permalink":"/publication/tcy_saureus/","publishdate":"2019-12-31T00:00:00Z","relpermalink":"/publication/tcy_saureus/","section":"publication","summary":"","tags":["host/pathogen","molecular-evolution","phylogeny","stress-response","staphylococci","compbio-bioinfo"],"title":"The Staphylococcus aureus cystine transporters, TcyABC and TcyP, facilitate nutrient sulfur acquisition during infection","type":"publication"},{"authors":["Janani Ravi"],"categories":["Research"],"content":"","date":1566903600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1566903600,"objectID":"ccad369d86c10ac2bbe294d0f5f790e4","permalink":"/talk/2019-cocoh/","publishdate":"2019-08-27T00:00:00Z","relpermalink":"/talk/2019-cocoh/","section":"talk","summary":" ","tags":["phylogeny","molecular-evolution","compbio-bioinfo","stress-response","software-tools"],"title":"Computational approaches for understanding host–pathogen biology","type":"talk"},{"authors":["Janani Ravi"],"categories":["Research"],"content":"","date":156411e4,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":156411e4,"objectID":"7f2a727ff5ab3d4fa2c9da19e7b24fea","permalink":"/talk/2019-grampos/","publishdate":"2019-07-26T00:00:00Z","relpermalink":"/talk/2019-grampos/","section":"talk","summary":" ","tags":["phylogeny","molecular-evolution","compbio-bioinfo","stress-response","software-tools"],"title":"Conservation and modularity in the pan-bacterial psp stress response system","type":"talk"},{"authors":["Janani Ravi"],"categories":["Research"],"content":"","date":1557997200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1557997200,"objectID":"b6a078795e784e3ee0b93b8ba126e41b","permalink":"/talk/2019-cbps/","publishdate":"2019-05-16T00:00:00Z","relpermalink":"/talk/2019-cbps/","section":"talk","summary":" ","tags":["phylogeny","molecular-evolution","compbio-bioinfo","stress-response","software-tools"],"title":"An integrative computational evolutionary approach to accelerate the discovery of molecular targets in prevalent under-studied pathogens","type":"talk"},{"authors":["Janani Ravi","Praveena Mathews"],"categories":["R","Resources"],"content":"","date":1551794400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1551794400,"objectID":"b9c8852ece634e754a3ddda1aa0987e5","permalink":"/talk/2019-iitm/","publishdate":"2019-02-15T00:00:00Z","relpermalink":"/talk/2019-iitm/","section":"talk","summary":" ","tags":["R","data-science","compbio-bioinfo","software-tools","teaching","workshop"],"title":"Using Tidyverse for Genomics workshop","type":"talk"},{"authors":["Janani Ravi"],"categories":["R","Resources","Teaching"],"content":"","date":1550048400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1550048400,"objectID":"c44d15c476a7a30f3dbcc15148bdfdc7","permalink":"/talk/2019-plb/","publishdate":"2019-01-15T00:00:00Z","relpermalink":"/talk/2019-plb/","section":"talk","summary":" ","tags":["academic","R","compbio-bioinfo","data-science","software-tools","teaching","workshop"],"title":"Tidyverse workshop","type":"talk"},{"authors":["Janani Ravi"],"categories":["Resources","Research"],"content":"","date":1548331200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1548331200,"objectID":"d517e9ac1a63ba39aeede31c1178198a","permalink":"/talk/2019-cvm/","publishdate":"2019-01-15T00:00:00Z","relpermalink":"/talk/2019-cvm/","section":"talk","summary":" ","tags":["academic","refs","software-tools"],"title":"Simple rules to make an effective scientific presentation","type":"talk"},{"authors":["Janani Ravi"],"categories":["Research"],"content":"Open positions Postdoc | Scientific programmer | Grad students | Undergrads | Visiting scientist\nPostdoctoral Researcher We are looking for a talented and motivated individual to join the JRaviLab (PI: Dr. Janani Ravi) at the Center for Health AI, University of Colorado, Anschutz Medical Campus as a postdoctoral researcher. In our group, we develop/apply computational approaches to analyze and visualize multiscale biological data to study microbial phenotypes and diseases, including genomes, protein sequence-structural features, transcriptomes, and pathway memberships. Postdocs will contribute to this vision by 1) developing new computational approaches to analyze and integrate large collections of biological data, 2) applying these approaches to specific problems in microbiology and infectious diseases, and 3) communicating the methods and discoveries openly to the broader biomedical/clinical community.\nIn addition to participating in ongoing projects, we strongly encourage postdocs to come up with several research ideas, jointly develop them into creative projects, and lead the way in those new directions. We encourage postdocs to apply for federal/foundational fellowships.\nWe are committed to building a diverse team and sustaining an inclusive and supportive environment; we strongly encourage underrepresented minorities in STEM to apply, including but not limited to BIPOC and LGBTQIA+ folks. The position is open to international applicants, in addition to US citizens/permanent residents.\nQualifications A PhD or equivalent, with a strong background in bioinformatics, computational biology, genetics/microbiology, statistics, computer science, machine learning, or other closely related fields. Programming experience in R or Python w/ version control (Git). Experience with handling large datasets in a Unix/Linux environment, high-performance cluster computing is a plus. Familiarity with bioinformatics databases and tools would also be a bonus. Good communication skills, willingness to collaborate openly, give/take constructive feedback, and sustain a friendly and fun lab culture. What will you get Freedom to work on your best ideas broadly aligned with the lab’s vision. Several opportunities to collaborate with fantastic computational, experimental, and clinical researchers at the Center for Health AI and beyond. Resources to develop your own research program and your technical skills as you plan to move to the next stage of your career. Opportunities to mentor students, participate in peer-review and grant-writing, international conferences, and, based on your interests, participate in education and outreach activities. A vibrant, supportive environment: A bunch of really smart and fun colleagues at CHAI and DBMI; Workspace in a contemporary open-office layout in the magnificent new Health Science building with a fabulous view of the Rocky Mountains, easy access to cafeterias; Beautiful campus; Supportive department environment and postdoctoral association (including slack) for professional development; Competitive salary commensurate with experience. Mentoring \u0026amp; support: In addition to being your scientific mentor, my primary responsibility is to help your personal and professional growth by facilitating all of the above. You will always find in me an audience to discuss opportunities/challenges and a strong advocate for your interests. You will also have the option to form a formal mentoring committee. Inclusive, friendly, and supportive environment for underrepresented minorities in STEM and quantitative sciences, and safe space for members across all intersectionalities. Apply | Find out more If you have questions or want to chat about this position, please write to me ( janani.ravi@cuanschutz.edu). If you are interested in something like this, it’s never too early to reach out! To apply, apply to this posting with 1) a detailed CV that includes a link to your Google Scholar page and a list of publications, 2) a cover letter that includes a description of your research accomplishments, how your interests connect with our group’s work, what might be some lines of future work that you are interested in, and what your future professional goals are, and 3) names \u0026amp; contact information for three references.\nBenefits: https://www.cu.edu/employee-services/benefits | postdoc benefits Total Compensation Calculator: https://www.cu.edu/employee-services/total-compensation Diversity and Equity: Please contact hr.adacoordinator@ucdenver.edu for information on disability accommodations.\nScientific Programmer We are looking for coding enthusiasts to join the JRaviLab as scientific programmers. In our group, we develop/apply computational approaches to analyze and visualize multiscale biological data to study microbial phenotypes and diseases, including genomes, protein sequence-structural features, transcriptomes, and pathway memberships.\nThe programmer is expected to contribute most of the code that goes into our analytical pipelines (that utilize high-performance clusters and cloud infrastructure) and production-ready webservers. They are expected to maintain high standards for code documentation, clarity, efficiency, and maintainability. In addition to maintaining these standards in their own code, they should set high expectations for other lab members and share their expertise to improve the code that all members of the lab are writing. We are committed to building a diverse team and sustaining an inclusive and supportive environment; we strongly encourage underrepresented minorities in STEM to apply, including but not limited to BIPOC, LGBTQIA+ folks. The position is open to international applicants, in addition to US citizens/permanent residents.\nQualifications Excellent programming skills in R and/or Python, Unix/Linux, shell scripting, and version controlling (with Git). Familiarity with bioinformatics databases/tools and setting up bioinformatics workflows would be a plus. Experience in web development: R/Shiny, SQL, HTML5, CSS, and JavaScript. It is a plus if you have experience with a) High-performance cluster computing, b) Distributed task queue, c) RESTful web services, d) Docker containers. Have high coding standards for writing efficient, clear, well-documented, version-controlled code (Git). Good communication skills, willingness to collaborate openly, give/take constructive feedback, and sustain a friendly and fun lab culture. What will you get Work on data science / machine learning applied to both pathogen and host research in infectious diseases, supported by ample computational resources. Mentor me, trainees, and students to inculcate high standards of writing and maintaining code. Publish papers on creative tools and pipelines, publish/maintain open-source software projects, and present in scientific meetings/conferences. A vibrant, supportive environment: A bunch of really smart and fun colleagues; Office in a fancy central building with easy access to cafeterias; Beautiful campus; Low cost-of-living; Competitive salary commensurate with experience. Guidance \u0026amp; support: In addition to being your expert partner, my primary responsibility is to help your personal and professional growth. You will always find in me an audience to discuss opportunities/challenges and a strong advocate for your interests. Safe space for underrepresented minorities in STEM and quantitative sciences. Additionally, you will also have the following if you are interested in pursuing a research career.\nFreedom to work on your best ideas broadly aligned with the lab’s vision. Several opportunities to collaborate with other smart computational and experimental researchers at MSU \u0026amp; elsewhere. Resources to develop your own research program and your technical skills as you plan to move to the next stage of your career. Opportunities to mentor students, participate in peer-review and grant-writing, and, based on your interests, participate in teaching, education, and outreach activities. Apply | Find out more If you have questions or want to chat about this position, please write to me. To apply, send me an email with your detailed CV, highlighting your released software, reusable packages, and/or code repositories (GitHub), and names and contact information for three references. If you are interested in something like this, it’s never too early to reach out!\nGraduate Students We are looking for highly motivated graduate students interested in developing computational approaches to study microbial function, phenotypes, and diseases. You will be a perfect fit if you have a background in bioinformatics, computational biology, statistics/biostatistics, computer science, microbiology/immunology, genetics/genomics, or related fields. Having programming experience in R, Python is a huge plus. In addition to these technical qualifications, we are looking for someone who can work well in a team, work hard, and give/take constructive feedback.\nThis research experience will give you the opportunity to i) use data analysis and visualization to address key biological questions as pertaining to molecular evolution, diagnosis, and treatment (using R), ii) present at group meetings, journals, technical workshops and conferences, iii) develop high coding standards for writing efficient, clear, well-documented, version-controlled code, iv) equip yourself professional for your next career step.\nStart a conversation Please send me your latest CV and a cover letter that includes i) a summary of your academic/work experience, ii) description of relevant coursework, research experience (incl. publications, conference talks/posters), iii) a brief note on familiarity in the field of phylogenetics, molecular evolution, and comparative pathogenomics, iv) coding experience, if any. If you are already at MSU, please email me to set a time to meet and discuss your interest.\nWant to rotate? We welcome CU Denver | Anschutz students to rotate with us, esp. those from the Biomedical Sciences Program, Computational Biosciences, Microbiology, Immunology, and Human Medical Genetics and Genomics.\nUndergraduate Students We are looking for highly motivated and quantitatively-minded undergraduate students to work on a research project developing computational approaches to study infectious diseases. Currently, we prefer students coming in with fellowships/scholarships (e.g., SROP, ENSURE, REU-ACRES, BRUSH, Professorial Assistantship, or other department/college-level awards).\nWe are happy to train them in many aspects of data-intensive biology. A keen interest in bioinformatics, computational biology, statistics/biostatistics, computer science, genetics, or related fields, and prior programming experience in R, Python would be a huge plus. As part of this project, they will have the opportunity to work closely with a senior members of the group (and me) and learn to: a) work with large datasets, b) write structured, well-documented code to analyze, integrate, and visualize these datasets, c) interpret the results in the context of pathogenesis, and d) communicate the results in the form of a paper and presentation.\nWe have high expectations for their level of commitment to research, and we are keen on incorporating their contributions into co-authored papers in conferences/journals. As an undergraduate student, if you are interested in discussing research opportunities, please send me an email to set up a time to talk.\nVisiting Scientist We welcome visiting scientists (postbac, postgrad, postdoc, etc) to come and collaborate with us for a short period (6mo–1Y). If you have a burning question or an interesting idea that is directly related to or complements our research project(s), we would be glad to share our space, experience, and resources with you to develop your project and execute it. Having your own funding would be the easiest way to make this happen. There are some funding sources that you can apply to (e.g., CoB). Please send me an email to discuss this opportunity.\nCollaboration If you are interested in any of our specific areas of research or have other great ideas that we could work on together, email me right away!\nContact details\n","date":1547510400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1553472e3,"objectID":"fba6c149775da15c6a5b2adae893dd1c","permalink":"/joinus/","publishdate":"2019-01-15T00:00:00Z","relpermalink":"/joinus/","section":"","summary":"Looking for undergraduate/graduate students, postdocs, and scientific programmer!","tags":["jobs","molecular-evolution","phylogeny","drug-repurposing","data-science","compbio-bioinfo","R"],"title":"Join us!","type":"page"},{"authors":null,"categories":["Books-Blogs"],"content":" Find my latest reads \u0026amp; recommendations on Goodreads!\n2018: #MyYearInBooks Summary Stats Book Read ","date":1546300800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1546300800,"objectID":"ae0e06da576d2483e1b0f498c600da0d","permalink":"/post/goodreads-2018/","publishdate":"2019-01-01T00:00:00Z","relpermalink":"/post/goodreads-2018/","section":"post","summary":"My Year in Books: 2018!","tags":["books"],"title":"2018: Year in Books | Goodreads","type":"post"},{"authors":["Janani Ravi"],"categories":null,"content":"A little background R-Ladies East Lansing welcomes R-enthusiasts of all proficiency levels, including aspiring and experienced R programmers, who are interested in mentoring, networking \u0026amp; expertise upskilling. This non-profit, civil society community is designed to develop members’ R skills \u0026amp; knowledge through social, collaborative learning \u0026amp; sharing. Supporting minority identity access to STEM skills \u0026amp; careers, the Free Software Movement, and contributing to the global R community!\nAnyone and everyone interested in R/Data Science should join the group. We encourage members to actively participate, contributing as learners, teachers, developers or innovators! We encourage women and minority genders to present/lead most sessions, conversations but we have no restrictions whatsoever about who can participate in membership, discussions and other activities. Please join us and bring your R-family \u0026amp; R-friends!\n2019: What’s next? Upcoming Workshops Intro to Statistics w/ R (Spring; workshop series) Intro to RMarkdown (Summer) Intro to Shiny (Summer) Intro to Version Control (Git) w/ R (Summer) Register \u0026amp; RSVP on Meetup: https://meetup.com/rladies-eastlansing\nWould you like to team-lead a workshop? Contact us if you’d to present for 5–10 min slots within the workshop or longer if desired.\nJoin the channels on Slack: #workshop-rstats #workshop-shiny #workshop-rmarkdown OR Email us: eastlansing@rladies.org\nIntroduce a Girl to Engineering (2019-02-16) Register for R-Ladies East Lansing’s activity booth: http://meetu.ps/e/Gfntz/yBMBS/f\nMSU Women in Engg. outreach: http://bit.ly/msu-wie-k12-outreach\nWomen in Data Science Conference (2019-04) https://widsconference.org\nRegister: TBA\nWould like to give a talk/present a poster? Stay tuned on Meetup. Contact us: eastlansing@rladies.org\nR-Ladies East Lansing Bookclub Academic incl. R for Data Science Learning Statistics with R R programming for Data Science Hands-On Programming with R Nonfiction incl. Algorithms to Live by Weapons of Math Destruction Blog posts \u0026amp; Articles incl. Excuse me, do you have a moment to talk about version control? Good enough practices in Scientific Computing Happy Git w/ R Meetup Presentations/Material GitHub | Google Drive | Photos\nYou \u0026amp; R-Ladies East Lansing Join the R-Ladies Community on Slack ( https://bit.ly/rlel-slack-signup)\nLead (or team-lead) presentations/discussions in a meetup\nHelp run the meetup(s) (help R-newbies, help pick up pizza)\nContribute to Blog Entries, Webpage ( https://rladies-eastlansing.github.io)\nBe a Social Butterfly ( Twitter | Facebook | Courier pigeon?)\nSponsor a meeting (OR help find us monthly meeting sponsors; \u0026lt;$75)\nBring in a speaker and/or Bring in fellow R-users!\nSuggest a topic \u0026amp; bring in volunteers from the 200+ Meetup/Slack R-Ladies!\nGetting Involved @ R-Ladies: https://rladies.org/about-us/help/\nHow to be in touch? Access our presentations, R scripts and more on Github and follow us on twitter to stay up to date about R-Ladies news! Join the Meetup group to be notified of our upcoming meetings!\nR-Ladies Global Meetup: https://meetup.com/rladies-east-lansing/ Twitter: @RLadiesELansing \u0026amp; @RLadiesGlobal Slack: https://rladies-eastlansing.slack.com Github: @rladies-eastlansing \u0026amp; @rladies E-mail: eastlansing [at] rladies [dot] org janani [at] rladies [dot] org info [at] rladies [dot] org The Team Organizers: Janani Ravi, Camille Archer\nCo-organizers: Kayla Johnson, Arjun Krishnan (~ Krishnan Lab)\nPS Community Policies \u0026amp; Code of Conduct:\nFull community guidelines are found here: https://github.com/rladies/starter-kit/wiki\n","date":1546300800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1547510400,"objectID":"6e8e427dca699fb8797141b21446567c","permalink":"/post/rlel-2019-upcoming/","publishdate":"2019-01-01T00:00:00Z","relpermalink":"/post/rlel-2019-upcoming/","section":"post","summary":"What's in store for 2019: workshops, conference, bookclubs \u0026 more!","tags":["rladies","software-tools","blogs"],"title":"2019: RLEL Upcoming Events","type":"post"},{"authors":null,"categories":null,"content":"","date":1546300800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1546300800,"objectID":"299a077dcf7d88d57edc9080508f2dd4","permalink":"/bio/","publishdate":"2019-01-01T00:00:00Z","relpermalink":"/bio/","section":"","summary":"Interests \u0026 Experience","tags":null,"title":"Bio","type":"widget_page"},{"authors":null,"categories":["R-Ladies"],"content":" 2019: What’s Next? Upcoming Workshops Introduce a Girl to Engineering (2019-02-16) Women in Data Science Conference (2019-04) R-Ladies East Lansing Bookclub Academic incl. 2018: Year in Review The Team Meetup Presentations/Material 2018 Sponsors 2018 Meetups Kickoff meeting Lightning talks Workshops You \u0026amp; R-Ladies East Lansing How to be in touch? Organizers PS Community Policies \u0026amp; Code of Conduct: Thanks to everyone who attended, participated or sponsored R-Ladies East Lansing in 2018! We had a fantastic start \u0026amp; a very successful first 6mo on campus! We hosted 7 meetups since July 2018 including two very well-attended workshops (70+ attendees) and a DataViz challenge! Help us continue spreading the R \u0026amp; Data Science spirit across MSU in 2019! Contact us eastlansing@rladies.org about co-hosting or sponsoring a meetup/workshop in Spring 2019. As always, R-Ladies events are open to all R-users across all levels of expertise including students, faculty and staff, and non-MSU folks.\n2019: What’s Next? Upcoming Workshops Intro to Statistics w/ R (Spring; workshop series) Intro to RMarkdown (Summer) Intro to Shiny (Summer) Intro to Version Control (Git) w/ R (Summer)\nRegister \u0026amp; RSVP on Meetup: https://meetup.com/rladies-eastlansing Would you like to team-lead a workshop? Contact us if you’d to present for 5–10 min slots within the workshop or longer if desired. Join the channels on Slack: #workshop-rstats #workshop-shiny #workshop-rmarkdown OR Email us: eastlansing@rladies.org\nIntroduce a Girl to Engineering (2019-02-16) Register for R-Ladies East Lansing’s activity booth: http://meetu.ps/e/Gfntz/yBMBS/f MSU Women in Engg. outreach: http://bit.ly/msu-wie-k12-outreach\nWomen in Data Science Conference (2019-04) https://widsconference.org\nRegister: Would like to give a talk/present a poster? Stay tuned on Meetup. Contact us: eastlansing@rladies.org\nR-Ladies East Lansing Bookclub Academic incl. R for Data Science Learning Statistics with R R programming for Data Science Hands-On Programming with R ### Nonfiction incl. Algorithms to Live by Weapons of Math Destruction ### Blog posts \u0026amp; Articles incl. Excuse me, do you have a moment to talk about version control? Good enough practices in Scientific Computing Happy Git w/ R 2018: Year in Review The Team Organizers: Janani Ravi, Camille Archer Other co-organizers: Kayla Johnson, Arjun Krishnan, Nate Davis\nMeetup Presentations/Material GitHub | Google Drive | Photos\n2018 Sponsors INSERT Grand Traverse Pie (2018-12) | Business Analytics (2018-11) | SSDA (2018-10) | Krishnan Lab (2018-09) | College of Veterinary Medicine (2018-09) | BEACON (2018-08) | iCER (2018-07)\n2018 Meetups Kickoff meeting Welcome to RLEL | Who We Are | What We Do | Upcoming Meetups\nPICTURE\nLightning talks Aug 13, 2018 Git \u0026amp; R by Melissa Dale Experimental languages w/ R by Le Ni La Having fun w/ Rcade by Kayla Johnson Websites w/ R by Camille Archer UpSet plots w/ R by Janani Ravi @bigdataignite for their conference promo.\nSep 10, 2018 Morphospaces w/ #Geomorph by Acacia Ackles Integrating Python \u0026amp; R w/ #Reticulate by Anna Yannakopoulos Literature Survey w/ #Bibliometrix by Veronica Frans GLM w/ #glmulti by Lauren Wisnieski Cool #dataviz resources Data-to-Viz RGraph Gallery by Janani Ravi\nSep 24, 2018 Spatial Humanities w/ R Rachael White R/qtl Miranda Haus Hyenas, Microbes \u0026amp; R Connie Rojas Publication quality figures w/ #ggpubr by Taylor Dunivin R+LaTeX=knitr Cara Feldscher\nCOLLAGES\nWorkshops Intro to Tidy Data Workshop: GitHub • Google Drive Data Visualization Workshop: GitHub • Google Drive\nYou \u0026amp; R-Ladies East Lansing Join the R-Ladies Community on Slack (bit.ly/rlel-slack-signup) Lead (or team-lead) presentations/discussions in a meetup Help run the meetup(s) (help R-newbies, help pick up pizza) Contribute to Blog Entries, Webpage (rladies-eastlansing.github.io) Be a Social Butterfly (Twitter | Facebook | Courier pigeon?) Sponsor a meeting (OR help find us monthly meeting sponsors; \u0026lt;$75) Bring in a speaker and/or Bring in fellow R-users! Suggest a topic \u0026amp; bring in volunteers from the 200+ Meetup/Slack R-Ladies!\nGetting Involved @ R-Ladies: https://rladies.org/about-us/help/\nHow to be in touch? Access our presentations, R scripts and more on Github and follow us on twitter to stay up to date about R-Ladies news! Join the Meetup group to be notified of the first meeting in July!\nR-Ladies Global Meetup: https://meetup.com/rladies-east-lansing/ Twitter: @RLadiesELansing \u0026amp; @RLadiesGlobal Slack: https://rladies-eastlansing.slack.com Github: @rladies-eastlansing \u0026amp; @rladies E-mail: eastlansing [at] rladies [dot] org janani [at] rladies [dot] org info [at] rladies [dot] org Organizers Janani Ravi \u0026amp; Camille Archer\nPS Community Policies \u0026amp; Code of Conduct: Full community guidelines are found here: https://github.com/rladies/starter-kit/wiki\n","date":1546300800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1546300800,"objectID":"d0f11bb9cda7b61ef9b63ac93db16795","permalink":"/post/rlel-2018/","publishdate":"2019-01-01T00:00:00Z","relpermalink":"/post/rlel-2018/","section":"post","summary":"Some accomplishments from 2018 \u0026 announcements for 2019!","tags":["rladies","software-tools","blogs"],"title":"R-Ladies East Lansing: 2018, Year in Review","type":"post"},{"authors":null,"categories":["Resources","R"],"content":" My posts with some #useful-resources.\nGreat posts | academic The Awesomest 7-year Postdoc by Radhika Nagpal | Scientific American Matt Might’s Blog Modeler’s Hippocratic oath Bioinformatics Microbial Bioinformatics Starter Kit by Lauren Cowley Microbial genome annotation by Michael Eisen Twitter thread \u0026amp; moment Tools for bacterial comparative genomes by Holt lab R Git, GitHub and R R resources by Paul Vanderlaken Related post: R Tips and Tricks Data Visualization Plotting trees + data by Holt Lab Blogdown, Hugo, Academic \u0026amp; R Markdown Blogdown: Creating websites with R Markdown by Yihui Xie Hugo Hugo discussion forum Hugo Academic by George Cushen Academic R Markdown Building your blog using blogdown by Marie Dussault Blogging tips Lifehacker 6 tips for low-cost academic blogging by Matt Might Ready to start your data science blog? by Maëlle Salmon ","date":1541980800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1541980800,"objectID":"b28671ace434a68e24d75eccaeea9fbc","permalink":"/post/useful-resources/","publishdate":"2018-11-12T00:00:00Z","relpermalink":"/post/useful-resources/","section":"post","summary":"A lazy mixed post: #academic #bioinformatics #r #blog","tags":["academic","blogs","compbio-bioinfo","git","R","refs","software-tools"],"title":"Useful Resources","type":"post"},{"authors":null,"categories":["Research"],"content":"Summary Starting from postdoctoral research at Rutgers University, we have used computational evolutionary approaches to study the phage shock protein (PSP) envelope stress response system across the tree of life. Our work revealed that the minimal PSP system was present in the last universal common ancestor — with its core protein PspA (Snf7 in ESCRT outside bacteria) diversifying into multiple distinct PSP systems across life. Systematic mapping of domain architectures and genomic contexts uncovered novel partners including the Toastrack domain, HTH-associated signaling domain, and ATPase and Band-7 domain associations.\nEarlier work delineated the variations of the Psp system across Actinobacteria, and reconstructed and topologically characterized the sigma factor regulatory network of M. tuberculosis, revealing a master regulator-initiated three-tiered hierarchy with over-represented network motifs including autoregulation and coregulation of sigma/anti-sigma pairs. Results are available at our interactive PSP web app.\n","date":1541548800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1541548800,"objectID":"117895119b7e381b5e410e88e8976a1d","permalink":"/project/stress-response/","publishdate":"2018-11-07T00:00:00Z","relpermalink":"/project/stress-response/","section":"project","summary":"Studying stress response systems using molecular evolution and phylogenetics.","tags":["stress-response","phylogeny","molecular-evolution","tree-of-life","mycobacteria","past-work","compbio-bioinfo"],"title":"Bacterial stress response","type":"project"},{"authors":["Janani Ravi","Nafiseh Haghtalab"],"categories":["R","Resources"],"content":" Workshop material: GitHub • Google Drive\n","date":1541440800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1541440800,"objectID":"f1a624e7a9a4f26355ee7567e7e30c71","permalink":"/talk/2018-rlel-tidydata/","publishdate":"2018-11-05T00:00:00Z","relpermalink":"/talk/2018-rlel-tidydata/","section":"talk","summary":" ","tags":["R","data-science","software-tools","workshop"],"title":"R-Ladies East Lansing | Workshop on Intro to Tidy Data w/ R","type":"talk"},{"authors":["Janani Ravi","Veronica Frans","Kayla Johnson","Cara Feldscher"],"categories":["R","Resources"],"content":" Workshop material: GitHub • Google Drive\n","date":1539021600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1539021600,"objectID":"a18603f0d3b95ce49833d6a7d0dd2ce1","permalink":"/talk/2018-rlel-dataviz/","publishdate":"2018-10-08T00:00:00Z","relpermalink":"/talk/2018-rlel-dataviz/","section":"talk","summary":" ","tags":["R","data-science","software-tools","workshop"],"title":"R-Ladies East Lansing | Workshop on Intro to Data Visualization w/ R","type":"talk"},{"authors":["Janani Ravi","Vivek Anantharaman","L Aravind Iyer","Maria L Gennaro"],"categories":["Research"],"content":"","date":1531151400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1531151400,"objectID":"b11af00340e22728fd14edd229e814c9","permalink":"/talk/2018-ismb/","publishdate":"2017-01-01T00:00:00Z","relpermalink":"/talk/2018-ismb/","section":"talk","summary":"","tags":["phylogeny","molecular-evolution","compbio-bioinfo","stress-response"],"title":"Using computational appraches to understand host-pathogen biology","type":"talk"},{"authors":null,"categories":["R"],"content":" Welcome to our new chapter! What we’re about R-Ladies East Lansing is a local chapter of R-Ladies Global. We meet to discuss, learn, teach, present, work on all things R! Our priority is to provide a safe community space for anyone identifying as a minority gender who is interested in and/or working with R. The group exists to promote gender diversity in the R community worldwide. We are pro-actively inclusive of queer, trans, and all minority identities, with additional sensitivity to intersectional identities.\nWho should join? R-Ladies East Lansing welcomes members of all R proficiency levels, whether you are a new or aspiring R user, or an experienced R programmer interested in mentoring, networking \u0026amp; expert upskilling. Our non-profit, civil society community is designed to develop our members’ R skills \u0026amp; knowledge through social, collaborative learning \u0026amp; sharing. Supporting minority identity access to STEM skills \u0026amp; careers, the Free Software Movement, and contributing to the global R community!\nAnyone and everyone interested in R/Data Science should join our group and participate/contribute in any way you can, be they learners, teachers, developers or innovators! We encourage women and minority genders to present/lead most sessions, conversations but we have no restrictions whatsoever when it comes to membership, participation, and discussions. So, please join us and bring your R-family \u0026amp; R-friends!\nHow to be in touch? Access our presentations, R scripts and more on Github and follow us on twitter to stay up to date about R-Ladies news! Join the Meetup group to be notified of the first meeting in July!\nR-Ladies Global Meetup: https://meetup.com/rladies-east-lansing/ Twitter: @RLadiesELansing \u0026amp; @RLadiesGlobal Slack: https://rladies-eastlansing.slack.com Github: @rladies-eastlansing \u0026amp; @rladies E-mail: eastlansing [at] rladies [dot] org janani [at] rladies [dot] org info [at] rladies [dot] org Organizers Janani Ravi \u0026amp; Camille Archer\nPS Community Policies \u0026amp; Code of Conduct: Full community guidelines are found here: https://github.com/rladies/starter-kit/wiki\n","date":1530403200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1530403200,"objectID":"bca3f4082b3d31472773b2031c008d97","permalink":"/post/rlel-launch/","publishdate":"2018-07-01T00:00:00Z","relpermalink":"/post/rlel-launch/","section":"post","summary":"Welcome to our new chapter: *Who we are \u0026 What we do.*","tags":["rladies","software-tools"],"title":"Launching R-Ladies East Lansing!","type":"post"},{"authors":null,"categories":["Books-Blogs"],"content":"I recently came across the Modeler\u0026rsquo;s Hippocratic Oath while reading Cathy O\u0026rsquo;Neil\u0026rsquo;s \u0026lsquo;Weapons of Math Destruction\u0026rsquo;.\nThis was originally written by Emanuel Derman and Paul Wilmott in the wake of the 2008 financial crisis.\nThe Oath I will remember that I didn’t make the world, and it doesn’t satisfy my equations. Though I will use models boldly to estimate value, I will not be overly impressed by mathematics. I will never sacrifice reality for elegance without explaining why I have done so. Nor will I give the people who use my model false comfort about its accuracy. Instead, I will make explicit its assumptions and oversights. I understand that my work may have enormous effects on society and the economy, many of them beyond my comprehension. ","date":152712e4,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":152712e4,"objectID":"ad2cf3ca6b5a8d0e231ae7a58a0ae0dd","permalink":"/post/modelers-hippocratic-oath/","publishdate":"2018-05-24T00:00:00Z","relpermalink":"/post/modelers-hippocratic-oath/","section":"post","summary":"Simple and sensible pointers laid out by Emanuel Derman \u0026 Paul Wilmott.","tags":["math-modeling","blogs","academic","data-science"],"title":"Modeler's Hippocratic Oath","type":"post"},{"authors":null,"categories":["R","Resources"],"content":" R \u0026amp; R-Ladies East Lansing Posts \u0026amp; Workshops\n","date":1525651200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1525651200,"objectID":"91c538f584ac37453885d68edfd82f2a","permalink":"/project/r/","publishdate":"2018-05-07T00:00:00Z","relpermalink":"/project/r/","section":"project","summary":"Posts, news, \u0026 material pertaining to R \u0026 *R-Ladies East Lansing*","tags":["R","rladies","software-tools","blogs","workshop"],"title":"R \u0026 R-Ladies East Lansing","type":"project"},{"authors":null,"categories":["Books-Blogs"],"content":"Check out my Goodreads profile for my latest reads and recommendations!\n","date":1525651200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1525651200,"objectID":"6da302e29c14c780e10955c05f7c11ad","permalink":"/reading/","publishdate":"2018-05-07T00:00:00Z","relpermalink":"/reading/","section":"","summary":"Posts and updates on [books \u0026 blogs](/categories/Books-Blogs) that caught my eye!","tags":["books","blogs"],"title":"Reading","type":"page"},{"authors":null,"categories":["Resources"],"content":"My posts with some useful resources\nGit, GitHub and R Modeler\u0026rsquo;s Hippocratic oath Great posts | academic The Awesomest 7-year Postdoc by Radhika Nagpal | Scientific American Bioinformatics Microbial Bioinformatics Starter Kit by Lauren Cowley Microbial genome annotation by Michael Eisen Twitter thread \u0026amp; moment Tools for bacterial comparative genomes by Holt lab R R resources by Paul Vanderlaken Related post: R Tips and Tricks Blogdown, Hugo, Academic \u0026amp; R Markdown Blogdown: Creating websites with R Markdown by Yihui Xie Hugo Hugo discussion forum Hugo Academic by George Cushen Academic R Markdown Building your blog using blogdown by Marie Dussault Data Visualization Plotting trees + data by Holt Lab Blogging tips Lifehacker 6 tips for low-cost academic blogging by Matt Might Ready to start your data science blog? by Maëlle Salmon ","date":1525651200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1525651200,"objectID":"c6625328e7b2e36b114847f299065f54","permalink":"/resources/","publishdate":"2018-05-07T00:00:00Z","relpermalink":"/resources/","section":"","summary":"Posts and updates on useful academic blogs \u0026 resources!","tags":["academic","blogs","compbio-bioinfo","git","R","refs"],"title":"Resources","type":"page"},{"authors":null,"categories":["Resources","R"],"content":" See also: My tweet dated: 2017-03-11 Resources for more links related to Blogdown, Rmarkdown \u0026amp; GitHub Git Version control with Git on Software Carpentry Git workflow for beginners Mozilla Git Getting started with Git Git, the simple guide Git exercises GitHowTo Introduction to Git and command line Friendly introduction to Git, Jane Git for humans, slides by Bartlett Learn Git branching Git cheat sheet and best practices Getting yourself out of a Git mess Try Git Git and GitHub GitHub tutorial, Broman New GitHub repo Git \u0026amp; Github | Seankross GitHub on Mac R and Git R with Git and GitHub GitHub Pages, Gists | Jekyll Github pages #1 #2 Creating gists on Github Jekyll GCC Ruby Ruby Gems ","date":1525305600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1525305600,"objectID":"7f313d16696af6326064e0c827364be1","permalink":"/post/git-github-links/","publishdate":"2018-05-03T00:00:00Z","relpermalink":"/post/git-github-links/","section":"post","summary":"... on how to get started, incl. integration with R/RStudio.","tags":["software-tools","refs","git","R"],"title":"Useful Git/GitHub links","type":"post"},{"authors":["Janani Ravi","Vivek Anantharaman","L Aravind","Maria L Gennaro"],"categories":["Research"],"content":"","date":1519689600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1519689600,"objectID":"d31e6e316fcd8f0531685c07b49ae332","permalink":"/publication/psp_actino/","publishdate":"2018-02-27T00:00:00Z","relpermalink":"/publication/psp_actino/","section":"publication","summary":" ","tags":["stress-response","phylogeny","molecular-evolution","actinobacteria","host/pathogen","compbio-bioinfo","R"],"title":"Variations on a theme: evolution of the phage-shock-protein system in Actinobacteria","type":"publication"},{"authors":null,"categories":["Books-Blogs"],"content":" Find my latest reads \u0026amp; recommendations on Goodreads!\n2017: #MyYearInBooks Summary Stats Books Read ","date":1514678400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1514678400,"objectID":"afa976f654666b9490d7ce683ff2570d","permalink":"/post/goodreads-2017/","publishdate":"2017-12-31T00:00:00Z","relpermalink":"/post/goodreads-2017/","section":"post","summary":"My Year in Books: 2017!","tags":["books"],"title":"2017: Year in Books | Goodreads","type":"post"},{"authors":null,"categories":["Books-Blogs"],"content":" Book Review I find myself increasingly drawn to the field of Behavioral Economics (so much so that I was considering a second PhD to channelize my love!), and how beautifully evasive these concepts are in real life. Starting with Daniel Kahneman’s Thinking Fast and Slow, followed by the writings and blogs of Steven Levitt, Dan Ariely, Nate Silver and Barry Schwartz (and still others like Malcolm Gladwell), has set me thinking a lot about how insane and illogical we are. We do see ourselves as logical and reasonably intelligent people who do not fall for the usual traps (OK, maybe you didn’t see me that way, but we’ll let that slide for now…), but how fool-proof are we? What about the narrative fallacy - ‘aah, that makes sense now’ or ‘I thought so’ or confirmation biases?\n‘The Black Swan’ by Nassim Nicholas Taleb (http://fooledbyrandomness.com/) has been on my list ever since I first got infatuated with this topic. I finally finished it last month. Man, is it it well-written! The guy is brilliant, and his wit and humor are unmatchable! Among other things, he leads (and concludes) with our love for everything normal, statistically speaking and otherwise, and how we can’t but help make the obvious blunders of predicting, quite erroneously, based on the past, even though we know fully well that life doesn’t present itself as a series of bell curves stringed together just so that we can get away with some easy math! You’ll hear a lot about epistemology (defined in PS3; truth be told, I hadn’t heard of this word until last month), mediocristan (the Gaussian life) vs extremistan (scale-free distributions encountered more often than not in real-life)\nHere’s a snippet: https://drive.google.com/file/d/0B7_wAV4HsNrkQmdFMndHSHhldFE/view Never mind if you don’t get it. I enjoyed every last bit of the book, and hope that you do too! Give it a try - whether you love it or hate it, it would be time well-spent! :)\nHappy reading!\nPS1. I’ve heard that people either love it or hate it. Clearly, I fall in the bin #1. Do I agree with everything? Well, yeah, almost everything. PS2. Luckily, none of you are directly tied to economics or financial sectors. :D Well, scientists and statisticians have been insulted too, but the elegance of it makes it OK! Lots to think about.:) PS3. Epistemology studies the nature of knowledge, justification, and the rationality of belief. Much of the debate in epistemology centers on four areas: (1) the philosophical analysis of the nature of knowledge and how it relates to such concepts as truth, belief, and justification, (2) various problems of skepticism, (3) the sources and scope of knowledge and justified belief, and (4) the criteria for knowledge and justification.\nTags #behavioraleconomics #books #suggestions #mustread #randomness #economics #business #philosophy\nblurb, review, snapshot below\nBlurb A black swan is a highly improbable event with three principal characteristics: It is unpredictable; it carries a massive impact; and, after the fact, we concoct an explanation that makes it appear less random, and more predictable, than it was.\nThe astonishing success of Google was a black swan; so was 9/11. For Nassim Nicholas Taleb, black swans underlie almost everything about our world, from the rise of religions to events in our own personal lives.\nWhy do we not acknowledge the phenomenon of black swans until after they occur? Part of the answer, according to Taleb, is that humans are hardwired to learn specifics when they should be focused on generalities.\nWe concentrate on things we already know and time and time again fail to take into consideration what we don’t know. We are, therefore, unable to truly estimate opportunities, too vulnerable to the impulse to simplify, narrate, and categorize, and not open enough to rewarding those who can imagine the “impossible.”\nFor years, Taleb has studied how we fool ourselves into thinking we know more than we actually do. We restrict our thinking to the irrelevant and inconsequential, while large events continue to surprise us and shape our world. Now, in this revelatory book, Taleb explains everything we know about what we don’t know. He offers surprisingly simple tricks for dealing with black swans and benefiting from them.\nElegant, startling, and universal in its applications ‘The Black Swan’ will change the way you look at the world. Taleb is a vastly entertaining writer, with wit, irreverence, and unusual stories to tell. He has a polymathic command of subjects ranging from cognitive science to business to probability theory.\n‘The Black Swan’ is a landmark book – itself a black swan.\n","date":1493164800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1493164800,"objectID":"8b40a96d92f81a37e1ff06d49df422fa","permalink":"/post/black-swan-nassim-taleb/","publishdate":"2017-04-26T00:00:00Z","relpermalink":"/post/black-swan-nassim-taleb/","section":"post","summary":"Brief book review/book recommendation.","tags":["books"],"title":"Black Swan by Nassim Taleb","type":"post"},{"authors":["Janani Ravi","Vivek Anantharaman","L Aravind Iyer","Maria L Gennaro"],"categories":["Research"],"content":"","date":1491238800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1491238800,"objectID":"a7e54386f219201ea221cf704105e281","permalink":"/talk/2017-asm-tb/","publishdate":"2017-04-01T00:00:00Z","relpermalink":"/talk/2017-asm-tb/","section":"talk","summary":"","tags":["phylogeny-evolution","compbio-bioinfo"],"title":"Evolution and Conservation of the Psp Envelope Stress-Response System","type":"talk"},{"authors":null,"categories":["Resources"],"content":" Why I’m writing this The initial process, where you read and imbibe! Helpful links: Approximate order of key events \u0026amp; things-to-do Initial set of documents needed for the Indian Consulate attestation Documents to be sent to Indian Home Department Documents to be sent to the other two departments: List of documents Addresses for mailing your packages TN State Department Regional Passport Office (RPO) Additional documents required for police verification Main letters/documents Supporting documents Final set of documents to be sent to the USCIS, Department of State Address for the package to be sent Tracking progress Why I’m writing this I went through this rather painful \u0026amp; ghastly process from Rutgers University, Newark, NJ. My closest consulate was the one in New York (CGNY). I am originally from Chennai, Tamil Nadu (India). So, most of the state department and RPO/police verification guidelines I’ve enlisted below worked for my specific case. Folks from other countries can skip ahead from their consulate to the last step reading some country-specific blogs in-between.\nThe initial process, where you read and imbibe! Helpful links: US govt. websites http://travel.state.gov/content/visas/english/study-exchange/student/residency-waiver.html http://travel.state.gov/content/visas/english/study-exchange/student/residency-waiver/ds-3035-instructions.html https://j1visawaiverrecommendation.state.gov https://j1visawaiverrecommendation.state.gov/accessController.asp?page=26 https://j1visawaiverrecommendation.state.gov/cancelHandler.asp Blogs http://www.sameetmehta.com/2015/01/the-j1-waiver-process-for-indian.html https://sciash.wordpress.com/2016/03/20/j1-waiver-step-by-step-guide/ http://www.immihelp.com/forum/showthread.php/113424-J1-visa-home-residency-requirement-waiver-from-India http://j1.aruppukottai.net/ (old 2009) http://prashanth-jaikumar.blogspot.com/2010/05/how-i-learned-to-stop-worrying-and-love.html (2010 May) Tip: Find specific blogs for your state since the rules and guidelines might be somewhat different. Mine was Tamil Nadu. Other useful PDFs that may include some of the above: The_process Approximate order of key events \u0026amp; things-to-do Read \u0026amp; decipher the resources. It’s a one-time thing. So, do it! Start at least 1–1.5yrs before your current employment ends/your extended J1 expires. The process takes time \u0026amp; patience. Give time for ‘worst case scenarios’! Tip: Talk to your department admin and your university’s international/J1 office. Note: First extend your J1 \u0026amp; then apply for the waiver. You can’t extend once you apply for your waiver. Notarization of your biodata and affidavit (your local bank or other notary publics) Attestation of your biodata and affidavit: Local Indian consulate with the necessary documents Some require passport-sized photo taken within the last 6 mo (CGNY did ‘require’ but they didn’t ’need’ it!!) Call to get their full list and check their website before going Send your packages to the 3 departments back home (web portal/postal mail w/ tracking) Back to the local Indian consulate Take your 3 NORIs and forms to get a NORI that they will forward to the Department of State, US) Send your package to USCIS (w/ tracking) Include all the necessary background documents NORIs from all of the above DS-3035 form Preferably, don’t include what’s not in the govt. list Note: You can migrate your J1 to a different university during your J1’s duration of validity. Talk to both the universities’ J1 departments. This would take 24-48h but can only happen before you terminate your current appointment. Once you are out, you need to process a new J1 and, possibly, go this whole process once again! This could happen even while your J1 is being petitioned. Initial set of documents needed for the Indian Consulate attestation Original Passport + Visa (+ copy) All DS-2019s (+ copy) Latest I-94 (+ copy) https://i94.cbp.dhs.gov/I94 Proof of residence in the US (preferably 2) Cash, money order or cashier’s cheque Biodata \u0026amp; Affidavit unfilled sample: J1-waiver-biodata-affidavit-NY_unfilled.pdf The first page is for New York Consulate General but others could use it as a guide too. Documents to be sent to Indian Home Department Govt. of India Ministry of Human Resource Development (HRD) No Obligation to Return to India http://www.nori.ac.in/ (quite straightforward; trackable (!); they are really fast \u0026amp; responsive)\nBiodata and Affidavit (Notarized \u0026amp; Attested by the Consulate General of India, New York, USA) e-Copy of Passport (New and Old) and J1-Visa e-Copy of all DS-2019s e-Copies of PhD \u0026amp; BTech (other, as applicable) Degree Certificate I don’t remember if I included: Employment letter from the department chair (I needed this somewhere) Proof of current residence in the US Documents to be sent to the other two departments: your state government your Regional Passport Office (likely, where you got your first passport) List of documents Biodata and Affidavit (Notarized \u0026amp; Attested by the Consulate General of India, New York, USA) Copy of Passport (New and Old) and J1-Visa Copy of all DS-2019s Proof of current residence in the US Copies of Ph.D. \u0026amp; B.Tech (other, as applicable) Degree Certificate Cover letter with your request to grant NORI Your correct address \u0026amp; theirs (of course!) including your email ID (you never know!) Where you are studying/working Passport number (new and old) Why you need the waiver (change of job, extending the same one, …) List of attested/enclosed copies of documents Letter of consent from your parent saying that you have no legal obligation to return. Include these details, if possible/applicable Who they are, where they are working/retired from Brief family history Your residential address (India) Your brief educational history When and why you came to the US Your marital \u0026amp; dependent info (briefly) when applicable Your current residential address in the US Why you are requesting the waiver (in their words) And something along these lines (sample below) With regard to the NORI certification, I confirm that all the details stated above are true to the best of my knowledge and all supporting documents have been attached for your perusal (the shipping document list is on the next page). There is no civil or criminal case against my daughter, XYZ. Also, she did not take any educational loan from the Indian or US governments. Therefore, she does not have any commitments here in India for legal, financial or personal reasons.\nI, therefore, request you to kindly provide the necessary NORI certificate that will help her continue working towards her professional and personal goals in the US. The experience and expertise that she gains during her stay there will help her serve India better in the long run.\nAddresses for mailing your packages TN State Department The Secretary Home (Citz II) Department Government of Tamil Nadu Secretariat, Fort St. George Chennai 600 009 Tamil Nadu, India Regional Passport Office (RPO) The Passport Officer Regional Passport Office Royala Towers No. 2 and 3, IV Floor, Old No. 785, New No. 158, Anna Salai, Chennai 600002 Tamil Nadu, India Additional documents required for police verification [At least, I needed it (Chennai, Tamil Nadu)]\nMain letters/documents Consent letter and Pro Forma from the applicant’s parent Letter from the applicant’s spouse Biodata of the applicant Supporting documents Applicant’s: Mark sheets and certificates 10th 12th mark sheets B. Tech. degree certificate Ph.D. degree certificate Applicant’s: Passport and Visa Passport (front/back) J-1 Visa \u0026amp; Certificate of eligibility for exchange visitor (J-1) status (DS-2019) Old passport and old J1 and F1 visas Applicant’s: Graduate assistantship letter for PhD Applicant’s: Employment letter (current place of work) Spouse’s: Mark sheets and certificates 10th, 12th mark sheets B. Tech. degree certificate Ph.D. degree certificate Applicant’s Spouse’s: Passport and Visa Passport (front/back) H1B visa approval notice (I-797) Applicant’s Spouse’s: Employment letter (MSU) Both: Marriage certificate Both: Present address proof (Wells Fargo bank statement) Applicant’s Parents’: Chennai address proof (Ration card, gas bill) Applicant’s Parents’: Aadhar card Final set of documents to be sent to the USCIS, Department of State Read the How to apply for a waiver page on the travel.state.gov website again. DS-3035 \u0026amp; SOR J1 waiver application packet for USCIS and Department of State Application fee Non-refundable — do it at the end cashier’s cheque written out to ’The US Department of State’ Include your name and case number (from the DS-3035 barcode) Waiver review division barcode Statement of reason (below) Sample statement: I am XYZ working at ABC as a PQR. I am currently on J1 visa sponsored by QWERTY. My J1 visa started on 7/19/2013 and ends on 7/19/2018 with a two-year home residency requirement. The main purpose of my J1 visa is to allow me to do research. My research work is progressing well, and it needs more time (longer than 7/19/2018) to complete my research projects. Since I am the lead person in the research projects, my employer and I feel that the opportunity for me to stay here in the US and complete the projects by obtaining the J1 visa waiver will be great. I am requesting a waiver of the two-year home residence requirement to complete my work here on the basis of No Objection certificate. My home country “ABC” has no objection in allowing me to continue working here in the US, and has issued a No Objection certificate to that effect. The ABCian Embassy in the USA will be issuing the No Objection statement to you. I kindly request you to grant me the J1 visa waiver at the earliest.\nThe actual completed DS-3035 https://j1visawaiverrecommendation.state.gov/ If you make a mistake, fill it out from the beginning Passport data page All DS2019s, IAP-66 Degree Certificates (Bachelors, Masters, PhD, …) Statement of Reason Two self-addressed stamped envelopes (legal-size) Your NORI letters from India: i) home department, ii) state department and iii) regional passport office (for police verification) and US (local Indian Consulate, although they would be sending a copy) Address for the package to be sent Postal Service Department of State J-1 Waiver P.O. Box 979037 St. Louis, MO 63197-9000 Courier Service Department of State J-1 Waiver P.O. Box 979037 1005 Convention Plaza St. Louis, MO 63101-1200 Tracking progress https://j1visawaiverrecommendation.state.gov/\n","date":1489449600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1489449600,"objectID":"223d118418c403d60ada80e1aab6621e","permalink":"/post/j1-visa-waiver-nori/","publishdate":"2017-03-14T00:00:00Z","relpermalink":"/post/j1-visa-waiver-nori/","section":"post","summary":"Applying for the J1 visa waiver and No Obligation to Return to India (NORI) certificate from the Indian/US governments.","tags":["refs","India"],"title":"J1 visa waiver | How to obtain your NORI?","type":"post"},{"authors":null,"categories":["Books-Blogs"],"content":" Find my latest reads \u0026amp; recommendations on Goodreads!\n2015: #MyYearInBooks Summary Stats Books Read ","date":1483228800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1483228800,"objectID":"a18c3c61dab73f83c2d1ce79fe4439d8","permalink":"/post/goodreads-2015/","publishdate":"2017-01-01T00:00:00Z","relpermalink":"/post/goodreads-2015/","section":"post","summary":"My Year in Books: 2015!","tags":["books"],"title":"2015: Year in Books | Goodreads","type":"post"},{"authors":null,"categories":["Books-Blogs"],"content":" Find my latest reads \u0026amp; recommendations on Goodreads!\n2016: #MyYearInBooks Summary Stats Books Read ","date":1483228800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1483228800,"objectID":"8eed61fb23a3de1d5d1e07955c7e5524","permalink":"/post/goodreads-2016/","publishdate":"2017-01-01T00:00:00Z","relpermalink":"/post/goodreads-2016/","section":"post","summary":"My Year in Books: 2016!","tags":["books"],"title":"2016: Year in Books | Goodreads","type":"post"},{"authors":null,"categories":["Books-Blogs"],"content":" Becoming Steve Jobs by Brent Schlender is a well-written biography of Steve Jobs \u0026amp; is definitely much better than Walter Isaacson’s ‘official’ one! And yeah, it is much more than a boring compendium of wiki and news articles. :)\nSo, happy reading!\n","date":1475539200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1475539200,"objectID":"57c45de2ebb3dbdc2a22d3a40de0e99d","permalink":"/post/becoming-steve-jobs/","publishdate":"2016-10-04T00:00:00Z","relpermalink":"/post/becoming-steve-jobs/","section":"post","summary":"Book recommendation","tags":["books"],"title":"Becoming Steve Jobs by Brent Schlender","type":"post"},{"authors":["Janani Ravi","Vivek Anantharaman","L Aravind Iyer","Maria L Gennaro"],"categories":null,"content":"","date":1466261100,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1466261100,"objectID":"7d1b66cfaa6602959075f195b872ded1","permalink":"/talk/2016-asm/","publishdate":"2016-06-18T00:00:00Z","relpermalink":"/talk/2016-asm/","section":"talk","summary":"","tags":["phylogeny-evolution","compbio-bioinfo"],"title":"Microbial Mechanosensing: Phage Shock Protein Response System in Gram-positive Bacteria","type":"talk"},{"authors":null,"categories":["Books-Blogs"],"content":" Background Matt Might has an awesome easy-to-read blog that has inspired us in many ways! Matt is a tenured CS professor at Utah and a visiting professor at HMS (Harvard Medical School). He’s the dad of 3 kids, one of whom has a very rare genetic disorder. He \u0026amp; his wife have spent a good part of their lives educating themselves and others about the disease.\nSome of his useful blog posts Health | Strength-training | JustDoIt HOWTO: Gain strength and muscle Least resistance weight loss Path of least resistance Handling repetitive strain injury (e.g. carpal tunnel syndrome) Efficiency | Productivity | work-life-balance Productivity tips for academics How to send and reply to email Tips for work-life balance Travel hacks 12 resolutions for programmers Academic | Professorship Academic job hunt advice HOWTO: Get tenure … = lots more where this came from!\n","date":1464220800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1464220800,"objectID":"9d17b8f4d6440fffe59a2512c8ff5155","permalink":"/post/matt-might-blog/","publishdate":"2016-05-26T00:00:00Z","relpermalink":"/post/matt-might-blog/","section":"post","summary":"Compilation of some useful posts *by* Matt Might.","tags":["blogs","academic"],"title":"Matt Might's Blog","type":"post"},{"authors":null,"categories":["Books-Blogs"],"content":" Authors: Janani Ravi, Arjun Krishnan\nSrinivasa Ramanujan has been noted as one of the classic ‘genius-mathematicians’ of all time! Hailing from the same state/country as him, Arjun Krishnan and I have always looked up to him \u0026amp; his elegant math as a source of inspiration right through our formative years!\nThe Movie Recent movie that has drastically increased Ramanujan’s international visibility The Man Who Knew Infinity by Matthew Brown.\nThe Play We watched this beautiful play in the University of Virginia campus during our grad school. Such unmistakable passion for math, that’s almost art-like or was it art!\nA Disappearing Number by Simon McBurney The Book Here is a great companion book to better understand the Man and little bit of the Math!\nThe Man Who Knew Infinity: A Life of the Genius Ramanujan by Robert Kanigel The People Without the help of the following people (and many more we haven’t mentioned here), Ramanujan would have remained an unknown \u0026amp; obsolete genius!\nGH Hardy: Collaborator, Mentor Hardy was an English mathematician who brought Ramanujan to Cambridge, encouraged his professional growth and helped publish his many theorems and elegant solutions.\nMatthew Brown: The Director The director of the new Ramanujan movie, The Man Who Knew Infinity\nManjul Bhargava: Math advisor \u0026amp; associate producer Princeton number theorist, winner of the Field’s medal, and Associate Producer of the movie.\nVideo made for Manjul Bhargava Princeton\nKen Ono: Math advisor \u0026amp; associate producer Ken Ono is this very accomplished mathematician who’s central research questions revolve around the work of Ramanujan. He is also a fantastic and sincere communicator, teacher and author so much so that you can read/listen to almost anything that he has to say.\nHere’s a great video of a conversation he had with another mathematician where he talks about Ramanujan and his connection with him.\nSteven Strogatz: Applied mathematician Famous applied mathematician and author of superb books \u0026amp; articles on mathematics.\nSteven Strogatz, Manjul Bhargava \u0026amp; Matt Brown Video\nSome more interesting articles Ramanujan surprises again| plus.maths.org Remembering Ramanujan: India Celebrates Its Famous Mathematical Son December 22, 2012, marks the 125th anniversary of the birth of legendary Indian mathematician Srinivasa Ramanujan. An intuitive mathematical genius, Ramanujan’s discoveries have influenced several areas of mathematics, but he is probably most famous for his contributions to number theory and infinite series, among them fascinating formulas that can be used to calculate digits of pi in unusual ways.\nMore\n","date":1460678400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1460678400,"objectID":"414d8a30b594a49873b3cd0b12a48018","permalink":"/post/ramanujan/","publishdate":"2016-04-15T00:00:00Z","relpermalink":"/post/ramanujan/","section":"post","summary":"... one of the greatest mathematicians of all time!","tags":["math-modeling","India","books"],"title":"A dedication to Ramanujan","type":"post"},{"authors":["Rinki Chauhan","Janani Ravi","Pratik Datta","Tian Chen","Dirk Schnappinger","Kevin Bassler","Gabor Balázsi","Maria Gennaro"],"categories":["Research"],"content":"","date":1456790400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1456790400,"objectID":"09920d7cf7b22b20e21576c6002af4ad","permalink":"/publication/sigfac_mtb/","publishdate":"2016-03-01T00:00:00Z","relpermalink":"/publication/sigfac_mtb/","section":"publication","summary":"Accessory sigma factors, which reprogram RNA polymerase to transcribe specific gene sets, activate bacterial adaptive responses to noxious environments. Here we reconstruct the complete sigma factor regulatory network of the human pathogen Mycobacterium tuberculosis by an integrated approach. The approach combines identification of direct regulatory interactions between M. tuberculosis sigma factors in an E. coli model system, validation of selected links in M. tuberculosis, and extensive literature review. The resulting network comprises 41 direct interactions among all 13 sigma factors. Analysis of network topology reveals (i) a three-tiered hierarchy initiating at master regulators, (ii) high connectivity and (iii) distinct communities containing multiple sigma factors. These topological features are likely associated with multi-layer signal processing and specialized stress responses involving multiple sigma factors. Moreover, the identification of overrepresented network motifs, such as autoregulation and coregulation of sigma and anti-sigma factor pairs, provides structural information that is relevant for studies of network dynamics.","tags":["stress-response","mycobacteria","tb","network","compbio-bioinfo","host/pathogen","R"],"title":"Reconstruction and topological characterization of the sigma factor regulatory network of Mycobacterium tuberculosis","type":"publication"},{"authors":null,"categories":["Research"],"content":"Summary We develop computational approaches to study host responses to infection and identify host-directed therapeutic interventions. We unified and standardized computational metrics for quantifying reversal of disease gene signatures by candidate therapeutics, addressing critical reproducibility issues in connectivity score methodologies. Our framework reconciles multiple scoring approaches (GSEA, KS, cosine, XSum) and provides quantitative guidance for method selection based on data characteristics.\nBuilding on this, we developed an integrative drug repurposing pipeline for tuberculosis that combines transcriptomic signatures from diverse infection models with multi-database screening (LINCS L1000, CMap). Consensus approaches across multiple connectivity scores improve prediction of drugs with known anti-TB efficacy and identify novel repurposed candidates.\n","date":145152e4,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":145152e4,"objectID":"3882814436694d859783c078ae4d3571","permalink":"/project/host-response/","publishdate":"2015-12-31T00:00:00Z","relpermalink":"/project/host-response/","section":"project","summary":"Computational approaches to study host responses to infection and identify host-directed therapeutic interventions.","tags":["host-response","drug-repurposing","disease-signature","host-directed-intervention","tb","mycobacteria","ongoing","compbio-bioinfo"],"title":"Host respones and therapeutic interventions","type":"project"},{"authors":null,"categories":["Research"],"content":"Summary We also studied host responses to M. tuberculosis infection using computational approaches:\ncharacterizing the transcriptional response in infected macrophages under various small molecule perturbations using RNA-Seq analysis; understanding the dysregulation of lipid metabolism in M. tuberculosis-infected macrophages using dynamic Bayesian model and statistical analyses of heterogeneous single-cell populations. ","date":145152e4,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":145152e4,"objectID":"c439d133997be1849ed0fea9a682b78b","permalink":"/project/lipid-metabolism/","publishdate":"2015-12-31T00:00:00Z","relpermalink":"/project/lipid-metabolism/","section":"project","summary":"Summary We also studied host responses to M. tuberculosis infection using computational approaches:\ncharacterizing the transcriptional response in infected macrophages under various small molecule perturbations using RNA-Seq analysis; understanding the dysregulation of lipid metabolism in M. tuberculosis-infected macrophages using dynamic Bayesian model and statistical analyses of heterogeneous single-cell populations. ","tags":["lipid-metabolism","host/pathogen","tb","past-work","compbio-bioinfo"],"title":"Studying lipid metabolism deregulation in TB","type":"project"},{"authors":null,"categories":["Research"],"content":"","date":1446723900,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1446723900,"objectID":"1836d0fca7e4c0db37c9167dd78ffd38","permalink":"/talk/2015-rutgers-symp/","publishdate":"2015-11-05T00:00:00Z","relpermalink":"/talk/2015-rutgers-symp/","section":"talk","summary":"","tags":["host/pathogen","compbio-bioinfo","lipid-metabolism"],"title":"Stochastic nature of adipogenic and inflammatory responses in tuberculous macrophages","type":"talk"},{"authors":["Pratik Datta","Janani Ravi","Valentina Guerrini","Rinki Chauhan","Matthew Neiditch","Scarlet Shell","Sarah Fortune","Baris Hancioglu","Oleg Igoshin","Maria Gennaro"],"categories":["Research"],"content":"","date":143856e4,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":143856e4,"objectID":"2304dd5c03c49d6f87a39e277074e406","permalink":"/publication/psp_mtb/","publishdate":"2015-08-03T00:00:00Z","relpermalink":"/publication/psp_mtb/","section":"publication","summary":"The bacterial envelope integrates essential stress-sensing and adaptive functions; thus, envelope-preserving functions are important for survival. In Gram-negative bacteria, envelope integrity during stress is maintained by the multi-gene Psp response. Mycobacterium tuberculosis was thought to lack the Psp system since it encodes only pspA and no other psp ortholog. Intriguingly, pspA maps downstream from clgR, which encodes a transcription factor regulated by the MprAB-σ(E) envelope-stress-signaling system. clgR inactivation lowered ATP concentration during stress and protonophore treatment-induced clgR-pspA expression, suggesting that these genes express Psp-like functions. We identified a four-gene set - clgR, pspA (rv2744c), rv2743c, rv2742c - that is regulated by clgR and in turn regulates ClgR activity. Regulatory and protein-protein interactions within the set and a requirement of the four genes for functions associated with envelope integrity and surface-stress tolerance indicate that a Psp-like system has evolved in mycobacteria. Among Actinobacteria, the four-gene module occurred only in tuberculous mycobacteria and was required for intramacrophage growth, suggesting links between its function and mycobacterial virulence. Additionally, the four-gene module was required for MprAB-σ(E) stress-signaling activity. The positive feedback between envelope-stress-sensing and envelope-preserving functions allows sustained responses to multiple, envelope-perturbing signals during chronic infection, making the system uniquely suited to tuberculosis pathogenesis.","tags":["stress-response","phylogeny","molecular-evolution","host/pathogen","mycobacteria","tb","compbio-bioinfo","R"],"title":"The Psp system of Mycobacterium tuberculosis integrates envelope stress-sensing and envelope-preserving functions","type":"publication"},{"authors":null,"categories":["Research"],"content":"","date":1414760400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1414760400,"objectID":"f6b4f57dd933a921edaddda1e9ecd788","permalink":"/talk/2014-imsc/","publishdate":"2014-10-31T00:00:00Z","relpermalink":"/talk/2014-imsc/","section":"talk","summary":"","tags":["math-modeling"],"title":"Mathematical modeling of pathways involved in cell cycle regulation and Differentiation","type":"talk"},{"authors":["Hugh Salamon","Natalie Bruiners","Karim Lakehal","Lanbo Shi","Janani Ravi","Ken D Yamaguchi","Richard Pine","Maria L Gennaro"],"categories":["Research"],"content":"","date":1404172800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1404172800,"objectID":"605cb9dc5a1258eccc8208939236204d","permalink":"/publication/jimm/","publishdate":"2014-07-01T00:00:00Z","relpermalink":"/publication/jimm/","section":"publication","summary":" ","tags":["tb","transcriptomics","host-response","compbio-bioinfo","host/pathogen"],"title":"Cutting edge: Vitamin D regulates lipid metabolism in Mycobacterium tuberculosis infection","type":"publication"},{"authors":null,"categories":["Research"],"content":"Summary We developed mathematical models that capture dynamic aspects of cellular regulatory systems. A detailed model (~100 molecular species, ~150 parameters) of the START transition in budding yeast reconciles diverse experimental findings on mechanisms and timing of transcriptional, post-translational, and localization events, and addresses the nutritional effect on size control. Consistent with ~200 experimental phenotypes, the model successfully predicts whether novel mutants rescue or induce cell cycle arrest; many predictions have been experimentally validated. Interactive model simulations are available for the research community to explore START dynamics.\nWe also built a simplified model of the Wnt signaling pathway demonstrating that incorporating key feedback regulatory interactions enables bistable behavior, reconciling theoretical predictions with experimental observations of cellular memory in differentiation decisions. In bacterial systems, network analysis of the M. tuberculosis sigma factor regulatory network revealed a master regulator-initiated three-tiered hierarchy and distinct sigma factor communities with over-represented network motifs including autoregulation and coregulation of sigma/anti-sigma pairs.\n+++\n","date":1322697600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1322697600,"objectID":"714e3c9462a90768eb4d56c90714f71d","permalink":"/project/dynamical-systems/","publishdate":"2011-12-01T00:00:00Z","relpermalink":"/project/dynamical-systems/","section":"project","summary":"Mathematical modeling of pathways involved in cell cycle regulation and differentiation","tags":["dynamical-systems","math-modeling","compbio-bioinfo","past-work"],"title":"Dynamical systems \u0026 modeling","type":"project"},{"authors":null,"categories":["Research"],"content":"","date":1301421600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1301421600,"objectID":"e80cb395f19766ec4eced6b8f142853d","permalink":"/talk/2011-cshl/","publishdate":"2011-03-29T00:00:00Z","relpermalink":"/talk/2011-cshl/","section":"talk","summary":"","tags":["math-modeling"],"title":"Modeling the START transition in the budding yeast cell cycle","type":"talk"},{"authors":null,"categories":["Research"],"content":"","date":1246798800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1246798800,"objectID":"abe5043793937d3a5368aa191c94e394","permalink":"/talk/2009-grc/","publishdate":"2009-05-05T00:00:00Z","relpermalink":"/talk/2009-grc/","section":"talk","summary":"","tags":["math-modeling"],"title":"Modeling the START transition in the budding yeast cell cycle","type":"talk"},{"authors":null,"categories":["Research"],"content":"","date":1237899600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1237899600,"objectID":"32f0f3d3c853bafe6bd9e3367ec8fa3e","permalink":"/talk/2009-cshl/","publishdate":"2009-01-01T00:00:00Z","relpermalink":"/talk/2009-cshl/","section":"talk","summary":"","tags":["math-modeling"],"title":"Modeling the START transition and size control in budding yeast","type":"talk"},{"authors":null,"categories":["Research"],"content":"","date":1235912400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1235912400,"objectID":"b16942501164b097278f3ac42414d4c9","permalink":"/talk/2009-vt-symp/","publishdate":"2009-03-01T00:00:00Z","relpermalink":"/talk/2009-vt-symp/","section":"talk","summary":"","tags":["math-modeling"],"title":"Modeling the START transition and size control in budding yeast","type":"talk"}]