diff --git a/.github/workflows/auto-cite.yaml b/.github/workflows/auto-cite.yaml index 2a5d6b5..8fd8f7b 100644 --- a/.github/workflows/auto-cite.yaml +++ b/.github/workflows/auto-cite.yaml @@ -20,7 +20,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v2 with: - python-version: 3.7 + python-version: 3.12 - name: Install Manubot run: pip install --upgrade manubot - name: Build updated citations diff --git a/_data/citations.yaml b/_data/citations.yaml index 4d6fc7c..063dbc0 100644 --- a/_data/citations.yaml +++ b/_data/citations.yaml @@ -1,15 +1,148 @@ # GENERATED AUTOMATICALLY, DO NOT EDIT -- id: 10.1101/2024.03.13.584858 - title: Toward generalizable phenotype prediction from single-cell morphology representations +- id: 10.1038/s41592-025-02611-8 + title: Reproducible image-based profiling with Pycytominer authors: + - Erik Serrano + - Srinivas Niranj Chandrasekaran + - Dave Bunten + - Kenneth I. Brewer - Jenna Tomkinson - Roshan Kern + - Michael Bornholdt + - Stephen J. Fleming + - Ruifan Pei + - John Arevalo + - Hillary Tsang + - Vincent Rubinetti + - Callum Tromans-Coia + - Tim Becker + - Erin Weisbart + - Charlotte Bunne + - Alexandr A. Kalinin + - Rebecca Senft + - Stephen J. Taylor + - Nasim Jamali + - Adeniyi Adeboye + - Hamdah Shafqat Abbasi + - Allen Goodman + - Juan C. Caicedo + - Anne E. Carpenter + - Beth A. Cimini + - Shantanu Singh + - Gregory P. Way + publisher: Nature Methods + date: '2025-03-03' + link: https://doi.org/g863nc + 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 + title: High-content microscopy and machine learning characterize a cell morphology + signature ofNF1genotype in Schwann cells + authors: + - Jenna Tomkinson - Cameron Mattson + - Michelle Mattson-Hoss + - Herb Sarnoff + - Stephanie J. Bouley + - James A. Walker + - Gregory P. Way + publisher: Cold Spring Harbor Laboratory + date: '2024-09-16' + link: https://doi.org/g863nd + 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 + title: A genome-wide atlas of human cell morphology + authors: + - Meraj Ramezani + - Erin Weisbart + - Julia Bauman + - Avtar Singh + - John Yong + - Maria Lozada + - Gregory P. Way + - Sanam L. Kavari + - Celeste Diaz + - Eddy Leardini + - Gunjan Jetley + - Jenlu Pagnotta + - Marzieh Haghighi + - Thiago M. Batista + - "Joaqu\xEDn P\xE9rez-Schindler" + - Melina Claussnitzer + - Shantanu Singh + - Beth A. Cimini + - Paul C. Blainey + - Anne E. Carpenter + - Calvin H. Jan + - James T. Neal + publisher: Nature Methods + date: '2025-01-27' + link: https://doi.org/g826g9 + 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 + title: Combining NeuroPainting with transcriptomics reveals cell-type-specific morphological + and molecular signatures of the 22q11.2 deletion + authors: + - Matthew Tegtmeyer + - Dhara Liyanage + - Yu Han + - Kathryn B. Hebert + - Ruifan Pei - Gregory P. Way + - Pearl V. Ryder + - Derek Hawes + - Callum Tromans-Coia + - Beth A. Cimini + - Anne E. Carpenter + - Shantanu Singh + - Ralda Nehme publisher: Cold Spring Harbor Laboratory - date: '2024-03-13' - link: https://doi.org/gtrgrh + date: '2024-11-17' + link: https://doi.org/g863nf + 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 + title: Toward generalizable phenotype prediction from single-cell morphology representations + authors: + - Jenna Tomkinson + - Roshan Kern + - Cameron Mattson + - Gregory P. Way + publisher: BMC Methods + date: '2024-12-09' + link: https://doi.org/g863ng image: https://github.com/WayScience/phenotypic_profiling/blob/main/7.figures/figures/figure1_panelB.png?raw=true tags: - single-cell diff --git a/_data/sources.yaml b/_data/sources.yaml index fdb376d..4bc693c 100644 --- a/_data/sources.yaml +++ b/_data/sources.yaml @@ -1,4 +1,50 @@ -- id: 10.1101/2024.03.13.584858 +- 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 diff --git a/_data/tools.yaml b/_data/tools.yaml index 10a1edf..d3954fd 100644 --- a/_data/tools.yaml +++ b/_data/tools.yaml @@ -12,12 +12,19 @@ description: Python package for enabling single-cell microscopy analysis repo: cytomining/cytotable -- name: CytoSnake +- name: coSMicQC group: featured - image: https://raw.githubusercontent.com/wayscience/cytosnake/master/logo/just-icon.png - link: https://github.com/wayscience/cytosnake - description: Python package for orchestrating customized image-based profiling pipelines - repo: wayscience/cytosnake + image: https://raw.githubusercontent.com/wayscience/coSMicQC/main/media/logo/just-icon.png + link: https://github.com/WayScience/coSMicQC + description: Python package for single-cell quality control + repo: wayscience/cosmicqc + +#- name: CytoSnake +# group: featured +# image: https://raw.githubusercontent.com/wayscience/cytosnake/master/logo/just-icon.png +# link: https://github.com/wayscience/cytosnake +# description: Python package for orchestrating customized image-based profiling pipelines +# repo: wayscience/cytosnake - name: BioBombe group: more diff --git a/_includes/gallery.html b/_includes/gallery.html index ca8064e..50f9ba3 100644 --- a/_includes/gallery.html +++ b/_includes/gallery.html @@ -9,8 +9,7 @@ {%- endfor -%}
- {%- for i in (1..100) -%} - + {%- for i in (1..max) -%} {%- assign image = "image" | append: i -%} {%- assign image = include[image] -%} {%- assign tooltip = "tooltip" | append: i -%} @@ -20,13 +19,18 @@ {%- if image -%} {%- endif -%} - {%- endfor -%} -
+ \ No newline at end of file diff --git a/_members/cameron-mattson.md b/_members/cameron-mattson.md index 86a682b..e266b2d 100644 --- a/_members/cameron-mattson.md +++ b/_members/cameron-mattson.md @@ -12,6 +12,7 @@ aliases: links: email: cameron.mattson@cuanschutz.edu github: https://github.com/MattsonCam +group: active --- Cameron graduated with his B.S. in Bioengineering at the University of Colorado, where he implemented and developed physiological models. diff --git a/_members/dave-bunten.md b/_members/dave-bunten.md index 2d20672..78e1e71 100644 --- a/_members/dave-bunten.md +++ b/_members/dave-bunten.md @@ -13,6 +13,7 @@ links: orcid: 0000-0001-6041-3665 email: dave.bunten@cuanschutz.edu github: d33bs +group: active --- Dave Bunten is a software developer with a passion for expanding human potential through software design, collaboration, and innovation. diff --git a/_members/erik-serrano.md b/_members/erik-serrano.md index 35fb1ac..e15ad40 100644 --- a/_members/erik-serrano.md +++ b/_members/erik-serrano.md @@ -15,6 +15,7 @@ links: email: erik.serrano@cuanschutz.com github: axiomcura twitter: axiomcura +group: active --- Erik Serrano is a Computational Bioscience (CPBS) PhD student at the Univeristy of Colorado, Anschutz Medical Campus (CU-AMC). diff --git a/_members/gregory-way.md b/_members/gregory-way.md index 8c6ed45..368d38d 100644 --- a/_members/gregory-way.md +++ b/_members/gregory-way.md @@ -18,7 +18,7 @@ links: email: gregory.way@gmail.com github: gwaybio twitter: gwaybio - google-scholar:: iDKZaA4AAAAJ + google-scholar: iDKZaA4AAAAJ --- diff --git a/_members/jacey-curd.md b/_members/jacey-curd.md index d6945c2..482b069 100644 --- a/_members/jacey-curd.md +++ b/_members/jacey-curd.md @@ -12,6 +12,7 @@ aliases: links: email: julia.curd@cuanschutz.edu github: JaceyBronte +group: active --- 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. diff --git a/_members/jenna-tomkinson.md b/_members/jenna-tomkinson.md index 4b55aab..4039289 100644 --- a/_members/jenna-tomkinson.md +++ b/_members/jenna-tomkinson.md @@ -12,6 +12,7 @@ links: orcid: 0000-0003-2676-5813 email: jenna.tomkinson@ucdenver.edu github: jenna-tomkinson +group: active --- Jenna is a Quantitative Cell Biologist at the Way Lab. diff --git a/_members/mike-lippincott.md b/_members/mike-lippincott.md index b5a81df..06a5bf2 100644 --- a/_members/mike-lippincott.md +++ b/_members/mike-lippincott.md @@ -15,6 +15,7 @@ links: email: michael.lippincott@cuanschutz.com github: MikeLippincott twitter: mike_lippincott +group: active --- Mike Lippincott is a Cell Biology, Stem Cells, and Development (CSD) PhD student at the University of Colorado, Anschutz Medical Campus. diff --git a/_members/roshan-kern.md b/_members/roshan-kern.md index a32e32b..f8632a0 100644 --- a/_members/roshan-kern.md +++ b/_members/roshan-kern.md @@ -12,12 +12,14 @@ links: orcid: 0000-0002-5605-4759 email: roshan.kern@case.edu github: roshankern +group: alum --- -Roshan is a summer intern at the Way Lab. +Roshan was a summer intern at the Way Lab. He is an undergraduate student at [Case Western Reserve University](https://case.edu/) majoring in systems biology. -He is currently focused on the analysis of nuclei morphology features for a generalizable cell cycle model. -He is a major proponent of workflows that are easy to access, interpret, and reproduce. +In the Way Lab, he focused on the analysis of nuclei morphology features for a generalizable cell cycle model. +He published papers related to predicting phenotypes from nuclei images and contributed to the pycytominer software package. +He made several other important contributions to the lab, as it was just getting off the ground. Roshan is a native of the Denver area and enjoys spending time outside hiking or playing a sport. His other interests include spending time with friends, working out, and watching YouTube. \ No newline at end of file diff --git a/images/funding/NHLBI_logo.png b/images/funding/NHLBI_logo.png new file mode 100644 index 0000000..c9abce2 Binary files /dev/null and b/images/funding/NHLBI_logo.png differ diff --git a/images/funding/aha_logo.jpg b/images/funding/aha_logo.jpg new file mode 100644 index 0000000..d8ecc24 Binary files /dev/null and b/images/funding/aha_logo.jpg differ diff --git a/images/funding/alsf_logo.png b/images/funding/alsf_logo.png new file mode 100644 index 0000000..acbe7d3 Binary files /dev/null and b/images/funding/alsf_logo.png differ diff --git a/images/funding/amed_logo.jpg b/images/funding/amed_logo.jpg new file mode 100644 index 0000000..f96af19 Binary files /dev/null and b/images/funding/amed_logo.jpg differ diff --git a/images/funding/gff_logo.jpg b/images/funding/gff_logo.jpg new file mode 100644 index 0000000..efe4010 Binary files /dev/null and b/images/funding/gff_logo.jpg differ diff --git a/index.md b/index.md index a9b0f27..9fceee7 100644 --- a/index.md +++ b/index.md @@ -4,11 +4,11 @@ title: Home Welcome to the Way Lab at [The University of Colorado Anschutz](https://www.cuanschutz.edu/)! -The mission of our lab is to reduce human suffering by integrating biomedical data science and software engineering into drug discovery and translational research. -We develop new computational methods, innovative approaches, assays, and software for analyzing high-dimensional genomic, molecular, and microscopy data. -We focus on pediatric diseases, including pediatric cancer and Neurofibromatosis Type 1 (NF1). +The mission of our lab is to reduce human suffering. +We develop new computational methods and software for analyzing microscopy images of cells. +With our collaborators around the world, we develop innovative assays and approaches for making sense of high-content microscopy. +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. -We perform team science with multidisciplinary collaborators to amplify the impact of our computationally-focused work. We also perform open science, making all of our work immediately open for anyone to use and build upon. {% @@ -37,7 +37,7 @@ We also perform open science, making all of our work immediately open for anyone # Highlights {% capture text %} -We develop computational methods and innovative approaches to find better drugs for pediatric diseases. +We develop computational methods and innovative approaches to analyze high-content microscopy images of cells. [Research focus and publications  →](research) {:.center} @@ -52,7 +52,7 @@ We develop computational methods and innovative approaches to find better drugs %} {% capture text %} -We release public data and open source software to enable reproducible computational biology analyses and workflows. +We release public data and open source software and methods to enable reproducible analysis of microscopy images. [Software  →](software) {:.center} diff --git a/research/index.md b/research/index.md index 0ce05a6..3329fa9 100644 --- a/research/index.md +++ b/research/index.md @@ -7,14 +7,14 @@ nav: # Research -We are building the next generation of data science methods for curing disease. +We are building the second generation of high-content microscopy image analysis. We are specifically focused on the following work: -- **Drug screening for pediatric diseases.** 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. -- **Reproducible software for processing high-dimensional microscopy readouts.** We are building open source software to support reproducible image-based profiling. We develop [pycytominer](https://github.com/cytomining/pycytominer), [CytoTable](https://github.com/cytomining/cytotable), and [CytoSnake](https://github.com/WayScience/cytosnake) to process large-scale microscopy images. Our aim is to improve data processing pipelines, reproducibility, data provenance, and dataset interoperability. -- **Microscopy representations of cell state.** We analyze high-content information from microscopy images, extracting biologically-meaningful and reproducible representations which contain systems biology information. We train artificial intelligence and machine learning (AI/ML) algorithms to predict cell phenotypes from these representations. These phenotypes include various cell health states and cell death mechanisms. Our aim is to use these representations to annotate drug screening data with phenotype and mechanism. -- **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 gene-network-based targets that take advantage of polypharmacology, developing CRISPRi approaches to simulate specific high-dimensional phenotypes, modeling cell resistance to cancer therapies, predicting heart failure subtypes, and more. +- **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. +- **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 diff --git a/team/index.md b/team/index.md index 090aa5f..37e2e6c 100644 --- a/team/index.md +++ b/team/index.md @@ -17,25 +17,25 @@ We define success individually for each team member, and we challenge each other include list.html data="members" component="portrait" - filters="role: pi" + filters="role:pi,group:active" %} {% include list.html data="members" component="portrait" - filters="role: phd" + filters="role:phd,group:active" %} {% include list.html data="members" component="portrait" - filters="role: programmer" + filters="role:programmer,group:active" %} {% include list.html data="members" component="portrait" - filters="role: undergrad" + filters="role:undergrad,group:active" %} {:.center} @@ -55,38 +55,42 @@ We encourage all to apply. {% include section.html %} - + +{% include section.html %} \ No newline at end of file