From af7fa7a552648f551baf714e2ba97f9a0bb8414b Mon Sep 17 00:00:00 2001 From: Gregory Way Date: Tue, 12 Aug 2025 13:54:50 -0600 Subject: [PATCH 1/5] add some 2025 pubs --- _data/sources.yaml | 170 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 170 insertions(+) diff --git a/_data/sources.yaml b/_data/sources.yaml index b9774f9..172696a 100644 --- a/_data/sources.yaml +++ b/_data/sources.yaml @@ -1,3 +1,173 @@ +<<<<<<< refs/remotes/origin/update-pubs +======= +- 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: + - image-based profiling + - bioinformatics + - software + - cell morphology + extra-links: + - type: software + link: https://github.com/cytomining/pycytominer + text: GitHub + +- id: 10.1101/2024.09.11.612546 + image: https://www.biorxiv.org/content/biorxiv/early/2024/09/16/2024.09.11.612546/F1.large.jpg + tags: + - image-based profiling + - neurofibromatosis type 1 + - cell morphology + - assay development + extra-links: + - type: software + link: https://github.com/WayScience/nf1_schwann_cell_morphology_signature + text: Analysis code + - type: software + 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 + tags: + - image-based profiling + - pooled cell painting + - cell morphology + extra-links: + - type: source + link: https://github.com/broadinstitute/pooled-cell-painting-image-processing + text: GitHub + +- id: 10.1101/2024.11.16.623947 + image: https://www.biorxiv.org/content/biorxiv/early/2024/11/17/2024.11.16.623947/F1.large.jpg + tags: + - image-based profiling + - cell painting + - data integration + +- id: 10.1186/s44330-024-00014-3 + image: https://github.com/WayScience/phenotypic_profiling/blob/main/7.figures/figures/figure1_panelB.png?raw=true + tags: + - single-cell + - microscopy + - phenotype + extra-links: + - type: source + link: https://github.com/WayScience/phenotypic_profiling/ + text: Analysis + - type: data + link: https://github.com/WayScience/mitocheck_data + text: Data + - type: software + link: https://github.com/WayScience/IDR_Stream + text: IDR_stream Software + +- id: 10.1038/s41467-023-44045-w + image: https://www.biorxiv.org/content/biorxiv/early/2023/01/09/2023.01.09.522731/F1.large.jpg + tags: + - cell painting + - data integration + - cell morphology + +- id: 10.1101/2024.04.01.587631 + 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: 10.7554/eLife.91362 + image: https://raw.githubusercontent.com/broadinstitute/profiling-resistance-mechanisms/master/3.resistance-signature/figures/bortezomib_roc_curve.png + repo: https://github.com/broadinstitute/profiling-resistance-mechanisms + tags: + - cancer resistance + - cell painting + - open science + +- id: 10.1016/j.slasd.2023.08.009 + image: https://ars.els-cdn.com/content/image/1-s2.0-S2472555223000667-gr2.jpg + tags: + - review + - high-content imaging + +- id: 10.1101/2023.08.06.552164 + image: https://www.ncbi.nlm.nih.gov/corecgi/tileshop/tileshop.fcgi?p=PMC3&id=704470&s=171&r=2&c=2 + tags: + - cell painting + - cell morphology + - assay + +- id: https://arxiv.org/abs/2311.13417 + image: https://raw.githubusercontent.com/cytomining/pycytominer/main/logo/just-icon.png + repo: https://github.com/cytomining/pycytominer + tags: + - software + - cell morphology + +- id: 10.7554/eLife.91362 + image: https://raw.githubusercontent.com/broadinstitute/profiling-resistance-mechanisms/master/3.resistance-signature/figures/bortezomib_roc_curve.png + repo: https://github.com/broadinstitute/profiling-resistance-mechanisms + tags: + - cancer resistance + - cell painting + - open science + +- id: doi:10.1016/j.xgen.2023.100340 + image: https://ars.els-cdn.com/content/image/1-s2.0-S2666979X23001155-fx1.jpg + repo: https://github.com/AlexsLemonade/OpenPBTA-analysis + tags: + - pediatric cancer + - brain tumor + - open science + +>>>>>>> local - id: doi:10.1016/j.cels.2022.10.001 image: https://www.cell.com/cms/attachment/55912f54-18d9-4ee9-8374-6f24f9d15bbc/fx1.jpg repo: https://github.com/broadinstitute/lincs-profiling-complementarity From 3cf7a4debc0ced93de63c5adef8fc5e3038962b6 Mon Sep 17 00:00:00 2001 From: Gregory Way Date: Tue, 12 Aug 2025 13:55:25 -0600 Subject: [PATCH 2/5] minor text changes --- research/index.md | 28 +++++++++++----------------- 1 file changed, 11 insertions(+), 17 deletions(-) diff --git a/research/index.md b/research/index.md index 3178cdf..a137a08 100644 --- a/research/index.md +++ b/research/index.md @@ -2,35 +2,29 @@ title: Research nav: order: 1 - tooltip: Published works + tooltip: Overview and published works --- # Research -Cells are building blocks of life. -We are building the next generation of data science methods for cell biology. -This means developing software, reproducible pipelines, and inventing analytical approaches to extract biological insights from microscopy images. +We are building the second generation of high-content microscopy image analysis. -We are interested in several specific research avenues: +We are specifically focused on the following work: -- Live-cell imaging. After tracking cells through time course experiments, can we observe morphology changes over time? Unlike other biological data types, cell morphology can be measured while the cell is still living. Can we observe specific morphological differences of cellular differentiation in different genetic backgrounds? -- Reproducible pipelines for processing high-dimensional morphology readouts. A major bottleneck in analyzing cell morphology is a lack of data provenance and software documentation. We are building infrastructure to support reproducible, large-scale morphology data processing, and developing specific tools like [pycytominer](https://github.com/cytomining/pycytominer) to normalize cell morphology readouts. -- Publicly-available microscopy data. There are growing resources of publicly available microscopy images (e.g. [Image Data Resource](https://idr.openmicroscopy.org/)). We are developing approaches to increase visibility, access, and computability of publicly available resources, while developing methods to leverage the wealth of existing resources. -- Cell health. Cells are constantly in flux, oscillating between different cell cycle stages, and responding to environmental stimuli. We are developing methods to model different variables of cell health to better inform the impacts of chemical and genetic (e.g. CRISPR) perturbations. Can we model the cell health impacts of compounds with polypharmacology and off-target effects? +- **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 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 -How science is performed is sometimes as important as the research topic. -Science hinges on reproducibility, and our procedure maximizes both biological and computational reproducibility. - -Biology is messy, but computational biology need not be! - -We pursue [open science](https://en.wikipedia.org/wiki/Open_science) to the fullest extent possible in every project. -We submit preprints of our work and subsequently publish in peer-reviewed journals to disseminate knowledge more formally around the world. -For each project, we also share project-specific github repositories (representing a lab notebook) to facilitate computational reproducibility. +- **Open science and software.** We perform all of our work in the open and release all of our software as open source. We aim to maximize the impact and reproducibility of our research by making everything we do immediately available for others to build upon. We host all of our code, data, and analysis at [https://github.com/WayScience](https://github.com/WayScience). +- **Scientific publishing.** We submit preprints of our work and subsequently publish in peer-reviewed journals to disseminate knowledge more formally. We use pre-print review services (like [Review Commons](https://www.reviewcommons.org/)) whenever possible to improve the peer-review process. For each project, we also share project-specific github repositories (representing a lab notebook) to facilitate computational reproducibility. We strive for creativity, integrity, inclusivity, and rigor in everything that we do. +See [here](https://scholar.google.com/citations?user=iDKZaA4AAAAJ&hl=en) for a full list of work. + See below for a selection of our recent papers. {% include section.html %} From 1f3e6dd857b38e8ca5110128e565b9818ec1634e Mon Sep 17 00:00:00 2001 From: gwaybio Date: Tue, 12 Aug 2025 19:57:51 +0000 Subject: [PATCH 3/5] Generate citations --- _data/citations.yaml | 117 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 117 insertions(+) diff --git a/_data/citations.yaml b/_data/citations.yaml index 063dbc0..21f200f 100644 --- a/_data/citations.yaml +++ b/_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: From c1e6e675a01b5c977eaca4678ce95e65f202f780 Mon Sep 17 00:00:00 2001 From: Gregory Way Date: Tue, 12 Aug 2025 14:55:47 -0600 Subject: [PATCH 4/5] minor fixes of links --- _data/sources.yaml | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/_data/sources.yaml b/_data/sources.yaml index 172696a..e76b3be 100644 --- a/_data/sources.yaml +++ b/_data/sources.yaml @@ -1,5 +1,3 @@ -<<<<<<< refs/remotes/origin/update-pubs -======= - id: https://arxiv.org/abs/2508.05800 image: https://arxiv.org/static/browse/0.3.4/images/arxiv-logo-one-color-white.svg tags: @@ -50,7 +48,7 @@ - software - cell morphology extra-links: - - type: software + - type: source link: https://github.com/cytomining/pycytominer text: GitHub @@ -62,10 +60,10 @@ - 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 @@ -101,7 +99,7 @@ - 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 @@ -167,7 +165,6 @@ - brain tumor - open science ->>>>>>> local - id: doi:10.1016/j.cels.2022.10.001 image: https://www.cell.com/cms/attachment/55912f54-18d9-4ee9-8374-6f24f9d15bbc/fx1.jpg repo: https://github.com/broadinstitute/lincs-profiling-complementarity From c155ee2c6dc827a2816cfb473acf5ea173b2ee22 Mon Sep 17 00:00:00 2001 From: gwaybio Date: Tue, 12 Aug 2025 20:57:43 +0000 Subject: [PATCH 5/5] Generate citations --- _data/citations.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/_data/citations.yaml b/_data/citations.yaml index 21f200f..2f4dec0 100644 --- a/_data/citations.yaml +++ b/_data/citations.yaml @@ -158,7 +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 @@ -182,10 +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 @@ -272,7 +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