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March 2025 Updates (#30)
* add roshan to alum group * troubleshoot rendering * more rendering troubleshooting * more rendering troubleshooting * add cosmic qc * fix typo in link * update research language * more team troubleshooting * modify home page * update pubs * bump auto-cite python version * Generate citations * add funding * fix funders * update funding * add grid content * fix gallery * fix typo * fix logos * fix links --------- Co-authored-by: gwaybio <[email protected]>
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‎.github/workflows/auto-cite.yaml

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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: 3.7
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python-version: 3.12
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- name: Install Manubot
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run: pip install --upgrade manubot
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- name: Build updated citations

‎_data/citations.yaml

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# GENERATED AUTOMATICALLY, DO NOT EDIT
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- id: 10.1101/2024.03.13.584858
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title: Toward generalizable phenotype prediction from single-cell morphology representations
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- id: 10.1038/s41592-025-02611-8
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title: Reproducible image-based profiling with Pycytominer
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authors:
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- Erik Serrano
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- Srinivas Niranj Chandrasekaran
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- Dave Bunten
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- Kenneth I. Brewer
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- Jenna Tomkinson
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- Roshan Kern
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- Michael Bornholdt
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- Stephen J. Fleming
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- Ruifan Pei
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- John Arevalo
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- Hillary Tsang
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- Vincent Rubinetti
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- Callum Tromans-Coia
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- Tim Becker
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- Erin Weisbart
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- Charlotte Bunne
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- Alexandr A. Kalinin
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- Rebecca Senft
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- Stephen J. Taylor
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- Nasim Jamali
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- Adeniyi Adeboye
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- Hamdah Shafqat Abbasi
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- Allen Goodman
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- Juan C. Caicedo
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- Anne E. Carpenter
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- Beth A. Cimini
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- Shantanu Singh
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- Gregory P. Way
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publisher: Nature Methods
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date: '2025-03-03'
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link: https://doi.org/g863nc
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image: https://raw.githubusercontent.com/cytomining/pycytominer/master/logo/just-icon.png
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tags:
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- image-based profiling
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- bioinformatics
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- software
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- cell morphology
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extra-links:
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- type: software
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link: https://github.com/cytomining/pycytominer
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text: GitHub
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- id: 10.1101/2024.09.11.612546
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title: High-content microscopy and machine learning characterize a cell morphology
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signature of<i>NF1</i>genotype in Schwann cells
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authors:
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- Jenna Tomkinson
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- Cameron Mattson
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- Michelle Mattson-Hoss
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- Herb Sarnoff
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- Stephanie J. Bouley
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- James A. Walker
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- Gregory P. Way
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publisher: Cold Spring Harbor Laboratory
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date: '2024-09-16'
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link: https://doi.org/g863nd
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image: https://www.biorxiv.org/content/biorxiv/early/2024/09/16/2024.09.11.612546/F1.large.jpg
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tags:
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- image-based profiling
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- neurofibromatosis type 1
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- cell morphology
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- assay development
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extra-links:
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- type: software
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link: https://github.com/WayScience/nf1_schwann_cell_morphology_signature
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text: Analysis code
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- type: software
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link: https://github.com/WayScience/nf1_schwann_cell_painting_data
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text: Data processing code
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- id: 10.1038/s41592-024-02537-7
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title: A genome-wide atlas of human cell morphology
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authors:
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- Meraj Ramezani
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- Erin Weisbart
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- Julia Bauman
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- Avtar Singh
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- John Yong
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- Maria Lozada
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- Gregory P. Way
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- Sanam L. Kavari
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- Celeste Diaz
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- Eddy Leardini
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- Gunjan Jetley
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- Jenlu Pagnotta
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- Marzieh Haghighi
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- Thiago M. Batista
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- "Joaqu\xEDn P\xE9rez-Schindler"
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- Melina Claussnitzer
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- Shantanu Singh
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- Beth A. Cimini
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- Paul C. Blainey
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- Anne E. Carpenter
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- Calvin H. Jan
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- James T. Neal
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publisher: Nature Methods
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date: '2025-01-27'
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link: https://doi.org/g826g9
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image: https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41592-024-02537-7/MediaObjects/41592_2024_2537_Fig1_HTML.png
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tags:
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- image-based profiling
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- pooled cell painting
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- cell morphology
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extra-links:
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- type: source
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link: https://github.com/broadinstitute/pooled-cell-painting-image-processing
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text: GitHub
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- id: 10.1101/2024.11.16.623947
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title: Combining NeuroPainting with transcriptomics reveals cell-type-specific morphological
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and molecular signatures of the 22q11.2 deletion
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authors:
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- Matthew Tegtmeyer
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- Dhara Liyanage
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- Yu Han
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- Kathryn B. Hebert
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- Ruifan Pei
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- Gregory P. Way
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- Pearl V. Ryder
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- Derek Hawes
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- Callum Tromans-Coia
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- Beth A. Cimini
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- Anne E. Carpenter
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- Shantanu Singh
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- Ralda Nehme
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publisher: Cold Spring Harbor Laboratory
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date: '2024-03-13'
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link: https://doi.org/gtrgrh
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date: '2024-11-17'
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link: https://doi.org/g863nf
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image: https://www.biorxiv.org/content/biorxiv/early/2024/11/17/2024.11.16.623947/F1.large.jpg
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tags:
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- image-based profiling
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- cell painting
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- data integration
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- id: 10.1186/s44330-024-00014-3
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title: Toward generalizable phenotype prediction from single-cell morphology representations
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authors:
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- Jenna Tomkinson
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- Roshan Kern
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- Cameron Mattson
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- Gregory P. Way
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publisher: BMC Methods
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date: '2024-12-09'
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link: https://doi.org/g863ng
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image: https://github.com/WayScience/phenotypic_profiling/blob/main/7.figures/figures/figure1_panelB.png?raw=true
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tags:
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- single-cell

‎_data/sources.yaml

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- id: 10.1101/2024.03.13.584858
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- id: 10.1038/s41592-025-02611-8
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image: https://raw.githubusercontent.com/cytomining/pycytominer/master/logo/just-icon.png
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tags:
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- image-based profiling
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- bioinformatics
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- software
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- cell morphology
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extra-links:
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- type: software
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link: https://github.com/cytomining/pycytominer
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text: GitHub
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- id: 10.1101/2024.09.11.612546
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image: https://www.biorxiv.org/content/biorxiv/early/2024/09/16/2024.09.11.612546/F1.large.jpg
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tags:
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- image-based profiling
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- neurofibromatosis type 1
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- cell morphology
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- assay development
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extra-links:
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- type: software
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link: https://github.com/WayScience/nf1_schwann_cell_morphology_signature
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text: Analysis code
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- type: software
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link: https://github.com/WayScience/nf1_schwann_cell_painting_data
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text: Data processing code
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- id: 10.1038/s41592-024-02537-7
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image: https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41592-024-02537-7/MediaObjects/41592_2024_2537_Fig1_HTML.png
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tags:
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- image-based profiling
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- pooled cell painting
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- cell morphology
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extra-links:
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- type: source
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link: https://github.com/broadinstitute/pooled-cell-painting-image-processing
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text: GitHub
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- id: 10.1101/2024.11.16.623947
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image: https://www.biorxiv.org/content/biorxiv/early/2024/11/17/2024.11.16.623947/F1.large.jpg
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tags:
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- image-based profiling
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- cell painting
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- data integration
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- id: 10.1186/s44330-024-00014-3
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image: https://github.com/WayScience/phenotypic_profiling/blob/main/7.figures/figures/figure1_panelB.png?raw=true
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tags:
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- single-cell

‎_data/tools.yaml

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description: Python package for enabling single-cell microscopy analysis
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repo: cytomining/cytotable
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- name: CytoSnake
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- name: coSMicQC
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group: featured
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image: https://raw.githubusercontent.com/wayscience/cytosnake/master/logo/just-icon.png
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link: https://github.com/wayscience/cytosnake
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description: Python package for orchestrating customized image-based profiling pipelines
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repo: wayscience/cytosnake
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image: https://raw.githubusercontent.com/wayscience/coSMicQC/main/media/logo/just-icon.png
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link: https://github.com/WayScience/coSMicQC
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description: Python package for single-cell quality control
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repo: wayscience/cosmicqc
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#- name: CytoSnake
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# group: featured
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# image: https://raw.githubusercontent.com/wayscience/cytosnake/master/logo/just-icon.png
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# link: https://github.com/wayscience/cytosnake
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# description: Python package for orchestrating customized image-based profiling pipelines
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# repo: wayscience/cytosnake
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- name: BioBombe
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group: more

‎_includes/gallery.html

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{%- endfor -%}
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<div class="gallery" data-style="{{ include.style }}" data-number="{{ max }}">
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{%- for i in (1..100) -%}
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{%- for i in (1..max) -%}
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{%- assign image = "image" | append: i -%}
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{%- assign image = include[image] -%}
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{%- assign tooltip = "tooltip" | append: i -%}
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{%- if image -%}
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<a
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{% if link %}href="{{ link | relative_url }}"{% endif %}
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{% if link %}
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{% if link contains "http" %}
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href="{{ link }}"
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{% else %}
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href="{{ link | relative_url }}"
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{% endif %}
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{% endif %}
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class="gallery_item"
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data-tooltip="{{ tooltip }}"
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{% if tooltip %}data-tooltip="{{ tooltip }}"{% endif %}
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>
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<img src="{{ image | relative_url }}" loading="lazy">
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</a>
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{%- endif -%}
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</div>
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</div>

‎_members/cameron-mattson.md

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email: [email protected]
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github: https://github.com/MattsonCam
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group: active
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---
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Cameron graduated with his B.S. in Bioengineering at the University of Colorado, where he implemented and developed physiological models.

‎_members/dave-bunten.md

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orcid: 0000-0001-6041-3665
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group: active
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---
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Dave Bunten is a software developer with a passion for expanding human potential through software design, collaboration, and innovation.

‎_members/erik-serrano.md

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group: active
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Erik Serrano is a Computational Bioscience (CPBS) PhD student at the Univeristy of Colorado, Anschutz Medical Campus (CU-AMC).

‎_members/gregory-way.md

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google-scholar:: iDKZaA4AAAAJ
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google-scholar: iDKZaA4AAAAJ
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---
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‎_members/jacey-curd.md

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Jacey graduated with B.S. degrees in Computer Science and Biology from Duke University, where she worked in Dr. Raluca Gordan’s lab on CRISPR and MutS.

‎_members/jenna-tomkinson.md

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Jenna is a Quantitative Cell Biologist at the Way Lab.

‎_members/mike-lippincott.md

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group: active
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Mike Lippincott is a Cell Biology, Stem Cells, and Development (CSD) PhD student at the University of Colorado, Anschutz Medical Campus.

‎_members/roshan-kern.md

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Roshan is a summer intern at the Way Lab.
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Roshan was a summer intern at the Way Lab.
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He is an undergraduate student at [Case Western Reserve University](https://case.edu/) majoring in systems biology.
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He is currently focused on the analysis of nuclei morphology features for a generalizable cell cycle model.
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He is a major proponent of workflows that are easy to access, interpret, and reproduce.
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In the Way Lab, he focused on the analysis of nuclei morphology features for a generalizable cell cycle model.
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He published papers related to predicting phenotypes from nuclei images and contributed to the pycytominer software package.
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He made several other important contributions to the lab, as it was just getting off the ground.
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Roshan is a native of the Denver area and enjoys spending time outside hiking or playing a sport.
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His other interests include spending time with friends, working out, and watching YouTube.

‎images/funding/NHLBI_logo.png

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‎index.md

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Welcome to the Way Lab at [The University of Colorado Anschutz](https://www.cuanschutz.edu/)!
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The mission of our lab is to reduce human suffering by integrating biomedical data science and software engineering into drug discovery and translational research.
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We develop new computational methods, innovative approaches, assays, and software for analyzing high-dimensional genomic, molecular, and microscopy data.
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We focus on pediatric diseases, including pediatric cancer and Neurofibromatosis Type 1 (NF1).
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The mission of our lab is to reduce human suffering.
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We develop new computational methods and software for analyzing microscopy images of cells.
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With our collaborators around the world, we develop innovative assays and approaches for making sense of high-content microscopy.
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We focus on pediatric diseases, including pediatric cancer and Neurofibromatosis Type 1 (NF1), and we also have applications in discovering new treatments for cardiac fibrosis.
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We perform team science with multidisciplinary collaborators to amplify the impact of our computationally-focused work.
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We also perform open science, making all of our work immediately open for anyone to use and build upon.
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# Highlights
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We develop computational methods and innovative approaches to find better drugs for pediatric diseases.
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We develop computational methods and innovative approaches to analyze high-content microscopy images of cells.
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[Research focus and publications &nbsp;→](research)
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%}
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We release public data and open source software to enable reproducible computational biology analyses and workflows.
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We release public data and open source software and methods to enable reproducible analysis of microscopy images.
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[Software &nbsp;→](software)
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{:.center}

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