Update pubs and tweak research language

_data/citations.yaml

@@ -1,5 +1,122 @@
 # GENERATED AUTOMATICALLY, DO NOT EDIT
 
+- id: https://arxiv.org/abs/2508.05800
+  title: Progress and new challenges in image-based profiling
+  authors:
+  - Erik Serrano
+  - John Peters
+  - Jesko Wagner
+  - Rebecca E. Graham
+  - Zhenghao Chen
+  - Brian Feng
+  - Gisele Miranda
+  - Alexandr A. Kalinin
+  - Loan Vulliard
+  - Jenna Tomkinson
+  - Cameron Mattson
+  - Michael J. Lippincott
+  - Ziqi Kang
+  - Divya Sitani
+  - Dave Bunten
+  - Srijit Seal
+  - Neil O. Carragher
+  - Anne E. Carpenter
+  - Shantanu Singh
+  - Paula A. Marin Zapata
+  - Juan C. Caicedo
+  - Gregory P. Way
+  publisher: arXiv
+  date: '2025-08-07'
+  link: http://arxiv.org/abs/2508.05800
+  image: https://arxiv.org/static/browse/0.3.4/images/arxiv-logo-one-color-white.svg
+  tags:
+  - image-based profiling
+  - review
+- id: 10.1161/CIRCULATIONAHA.124.071956
+  title: Cell Painting and Machine Learning Distinguish Fibroblasts From Nonfailing
+    and Failing Human Hearts
+  authors:
+  - Joshua G. Travers
+  - Jenna Tomkinson
+  - Marcello Rubino
+  - Marion Delaunay
+  - Michael R. Bristow
+  - Gregory P. Way
+  - Timothy A. McKinsey
+  publisher: Circulation
+  date: '2025-04-22'
+  link: https://doi.org/g9wt6s
+  image: https://www.ahajournals.org/cms/10.1161/CIRCULATIONAHA.124.071956/asset/eb5df843-0afb-4f37-bf75-265f17c7ec93/assets/graphic/circulationaha.124.071956.fig01.jpg
+  tags:
+  - high-content microscopy
+  - cell painting
+  - cardiac fibrosis
+  extra-links:
+  - type: source
+    link: https://github.com/WayScience/cellpainting_predicts_cardiac_fibrosis
+    text: Analysis code
+- id: 10.1091/mbc.E25-03-0119
+  title: A morphology and secretome map of pyroptosis
+  authors:
+  - Michael J. Lippincott
+  - Jenna Tomkinson
+  - Dave Bunten
+  - Milad Mohammadi
+  - Johanna Kastl
+  - Johannes Knop
+  - Ralf Schwandner
+  - Jiamin Huang
+  - Grant Ongo
+  - Nathaniel Robichaud
+  - Milad Dagher
+  - "Andr\xE9s Mansilla-Soto"
+  - Cynthia Saravia-Estrada
+  - Masafumi Tsuboi
+  - "Carla Basualto-Alarc\xF3n"
+  - Gregory P. Way
+  publisher: Molecular Biology of the Cell
+  date: '2025-06-01'
+  link: https://doi.org/g9wt6t
+  image: https://www.molbiolcell.org/cms/10.1091/mbc.E25-03-0119/asset/images/large/mbc-36-ar63-g001.jpeg
+  tags:
+  - cell death
+  - high-content microscopy
+  - multimodal data
+  extra-links:
+  - type: source
+    link: https://github.com/WayScience/pyroptosis_signature_image_profiling
+    text: Data processing
+  - type: source
+    link: https://github.com/WayScience/pyroptosis_signature_data_analysis
+    text: Analysis code
+- id: 10.1038/s41467-025-60306-2
+  title: A versatile information retrieval framework for evaluating profile strength
+    and similarity
+  authors:
+  - Alexandr A. Kalinin
+  - John Arevalo
+  - Erik Serrano
+  - Loan Vulliard
+  - Hillary Tsang
+  - Michael Bornholdt
+  - "Al\xE1n F. Mu\xF1oz"
+  - Suganya Sivagurunathan
+  - Bartek Rajwa
+  - Anne E. Carpenter
+  - Gregory P. Way
+  - Shantanu Singh
+  publisher: Nature Communications
+  date: '2025-06-04'
+  link: https://doi.org/g9wt6v
+  image: https://www.biorxiv.org/content/biorxiv/early/2024/04/02/2024.04.01.587631/F1.large.jpg
+  tags:
+  - drug screening metric
+  - software
+  - profiling
+  extra-links:
+  - type: source
+    link: https://github.com/cytomining/copairs
+    text: Software
 - id: 10.1038/s41592-025-02611-8
   title: Reproducible image-based profiling with Pycytominer
   authors:
@@ -41,7 +158,7 @@
   - software
   - cell morphology
   extra-links:
-  - type: software
+  - type: source
     link: https://github.com/cytomining/pycytominer
     text: GitHub
 - id: 10.1101/2024.09.11.612546
@@ -65,10 +182,10 @@
   - cell morphology
   - assay development
   extra-links:
-  - type: software
+  - type: source
     link: https://github.com/WayScience/nf1_schwann_cell_morphology_signature
     text: Analysis code
-  - type: software
+  - type: source
     link: https://github.com/WayScience/nf1_schwann_cell_painting_data
     text: Data processing code
 - id: 10.1038/s41592-024-02537-7
@@ -155,7 +272,7 @@
   - type: data
     link: https://github.com/WayScience/mitocheck_data
     text: Data
-  - type: software
+  - type: source
     link: https://github.com/WayScience/IDR_Stream
     text: IDR_stream Software
 - id: 10.1038/s41467-023-44045-w

_data/sources.yaml

@@ -1,3 +1,45 @@
+- id: https://arxiv.org/abs/2508.05800
+  image: https://arxiv.org/static/browse/0.3.4/images/arxiv-logo-one-color-white.svg
+  tags:
+    - image-based profiling
+    - review
+
+- id: 10.1161/CIRCULATIONAHA.124.071956
+  image: https://www.ahajournals.org/cms/10.1161/CIRCULATIONAHA.124.071956/asset/eb5df843-0afb-4f37-bf75-265f17c7ec93/assets/graphic/circulationaha.124.071956.fig01.jpg
+  tags:
+    - high-content microscopy
+    - cell painting
+    - cardiac fibrosis
+  extra-links:
+    - type: source
+      link: https://github.com/WayScience/cellpainting_predicts_cardiac_fibrosis
+      text: Analysis code
+
+- id: 10.1091/mbc.E25-03-0119
+  image: https://www.molbiolcell.org/cms/10.1091/mbc.E25-03-0119/asset/images/large/mbc-36-ar63-g001.jpeg
+  tags:
+    - cell death
+    - high-content microscopy
+    - multimodal data
+  extra-links:
+    - type: source
+      link: https://github.com/WayScience/pyroptosis_signature_image_profiling
+      text: Data processing
+    - type: source
+      link: https://github.com/WayScience/pyroptosis_signature_data_analysis
+      text: Analysis code
+
+- id: 10.1038/s41467-025-60306-2
+  image: https://www.biorxiv.org/content/biorxiv/early/2024/04/02/2024.04.01.587631/F1.large.jpg
+  tags:
+    - drug screening metric
+    - software
+    - profiling
+  extra-links:
+    - type: source
+      link: https://github.com/cytomining/copairs
+      text: Software
+
 - id: 10.1038/s41592-025-02611-8
   image: https://raw.githubusercontent.com/cytomining/pycytominer/master/logo/just-icon.png
   tags:
@@ -6,7 +48,7 @@
     - software
     - cell morphology
   extra-links:
-    - type: software
+    - type: source
       link: https://github.com/cytomining/pycytominer
       text: GitHub
 
@@ -18,13 +60,12 @@
     - cell morphology
     - assay development
   extra-links:
-    - type: software
+    - type: source
       link: https://github.com/WayScience/nf1_schwann_cell_morphology_signature
       text: Analysis code
-    - type: software
+    - type: source
       link: https://github.com/WayScience/nf1_schwann_cell_painting_data
       text: Data processing code
-
 
 - id: 10.1038/s41592-024-02537-7
   image: https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41592-024-02537-7/MediaObjects/41592_2024_2537_Fig1_HTML.png
@@ -57,7 +98,7 @@
     - type: data
       link: https://github.com/WayScience/mitocheck_data
       text: Data
-    - type: software
+    - type: source
       link: https://github.com/WayScience/IDR_Stream
       text: IDR_stream Software
 

research/index.md

@@ -13,7 +13,7 @@ We are specifically focused on the following work:
 
 - **Reproducible software and methods for high-content microscopy analysis.** We are building open source software to support reproducible microscopy image analysis. We develop [pycytominer](https://github.com/cytomining/pycytominer), [CytoTable](https://github.com/cytomining/cytotable), and [coSMicQC](https://github.com/WayScience/cosmicqc) to analyze and process large-scale microscopy images. Our aim is to improve data processing pipelines, reproducibility, data provenance, and dataset interoperability. We are also innovating new methods and software for analyzing microscopy images across space and time.
 - **Predicting cell phenotypes.** We extract biologically-meaningful and reproducible representations which contain information about cell phenotypes. We train artificial intelligence and machine learning (AI/ML) algorithms (e.g., virtual staining) to predict cell phenotypes and other markers from these images. These phenotypes include various cell health states, cell death mechanisms, and other important biological processes (e.g., nuclear speckles). Our aim is to use these representations to characterize and discover new biological processes and to annotate drug screening data with cell phenotypes.
-- **Drug screening for pediatric diseases and cardiac fibrosis.** We perform microscopy-based, _in vitro_ drug screens to identify promising drug candidates. Our goal is to identify new therapeutic options for children with diseases like Neurofibromatosis Type 1 (NF1), neuroblastoma, and pediatric high grade glioma. We also have drug screening applications to discover innovative treatments for cardiac fibrosis.
+- **Drug screening for pediatric cancers, Neurofibromatosis Type 1, and cardiac fibrosis.** We perform microscopy-based, _in vitro_ phenotypic drug screening to prioritize promising drug candidates and new targets. We are also developing patient-derived organoid phenotypic drug screening. Our goal is to identify new therapeutic strategies for diseases with urgent unmet needs.
 - **Innovative method development for drug screening and translational research.** We develop new assays and computational methods to improve human health. This includes modeling NF1 and other pediatric diseases using patient-derived organoids, developing CRISPRi approaches to simulate specific high-dimensional phenotypes, modeling cell resistance to cancer therapies, and pioneering the concept we call "multi-gene dependencies", which we believe will revolutionize precision medicine for cancer patients.
 
 ## How we do science