citations.yaml

# GENERATED AUTOMATICALLY, DO NOT EDIT

- id: 10.1038/s44320-026-00197-7
  title: Progress and new challenges in image-based profiling
  authors:
  - Erik Serrano
  - John Peters
  - Jesko Wagner
  - Rebecca E Graham
  - Zhenghao Chen
  - Brian Y 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: Molecular Systems Biology
  date: '2026-03-27'
  link: https://doi.org/hbxfz5
  tags:
  - image-based profiling
  - review
  image: https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs44320-026-00197-7/MediaObjects/44320_2026_197_Fig1_HTML.png?as=webp
- id: 10.64898/2026.04.15.718737
  title: Single-cell hit calling in high-content imaging screens with Buscar
  authors:
  - Erik Serrano
  - Wei-shan Li
  - Gregory Way
  publisher: openRxiv
  date: '2026-04-19'
  link: https://doi.org/hb35zs
  tags:
  - software
  - hit calling
  - high-content screening
  - single-cell
  image: https://raw.githubusercontent.com/WayScience/buscar/main/logo/just-icon.png
  extra-links:
  - type: source
    link: https://github.com/WayScience/Buscar
    text: GitHub
- id: 10.1101/2025.11.14.688518
  title: Characterizing the landscape of gene process dependencies in cancer
  authors:
  - Julia B. Curd
  - Gregory P. Way
  publisher: openRxiv
  date: '2025-11-16'
  link: https://doi.org/hb35zt
  tags:
  - cancer
  - gene dependencies
  - CRISPR
  extra-links:
  - type: source
    link: https://github.com/WayScience/gene_dependency_representations
    text: Analysis code
- id: 10.1101/2025.10.23.684203
  title: High-content live-cell time-lapse imaging predicts cells about to die via
    apoptosis
  authors:
  - Michael J. Lippincott
  - Jenna Tomkinson
  - Ibrahim Bilem
  - Mahomi Suzuki
  - Akiko Nakde
  - Toshiaki Endou
  - Simon Mathien
  - Felix Lavoie-Perusse
  - "Carla Basualto-Alarc\xF3n"
  - Gregory P. Way
  publisher: openRxiv
  date: '2025-10-24'
  link: https://doi.org/hb35zv
  tags:
  - live-cell imaging
  - apoptosis
  - cell death
  - time-lapse
- id: 10.1101/2025.10.14.682427
  title: Stellar quality control for single-cell image-based profiling with coSMicQC
  authors:
  - Jenna Tomkinson
  - Dave Bunten
  - Gregory P. Way
  publisher: openRxiv
  date: '2025-10-15'
  link: https://doi.org/hb35zw
  tags:
  - software
  - quality control
  - single-cell
  - image-based profiling
  extra-links:
  - type: source
    link: https://github.com/WayScience/coSMicQC
    text: GitHub
  image: https://raw.githubusercontent.com/cytomining/cosmicqc/main/media/logo/just-icon.png
- id: 10.1016/j.patter.2026.101514
  title: Scalable data harmonization for single-cell image-based profiling with CytoTable
  authors:
  - Dave Bunten
  - Jenna Tomkinson
  - Erik Serrano
  - Michael J. Lippincott
  - Kenneth I. Brewer
  - Vince Rubinetti
  - Faisal Alquaddoomi
  - Gregory P. Way
  publisher: Patterns
  date: '2026-05-01'
  link: https://doi.org/hbvg3p
  image: https://raw.githubusercontent.com/cytomining/cytotable/master/logo/just-icon.png
  tags:
  - software
  - image-based profiling
  - single-cell
  - data harmonization
  extra-links:
  - type: source
    link: https://github.com/cytomining/CytoTable
    text: GitHub
- id: 10.1038/s41467-025-61547-x
  title: Combining phenomics 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: Nature Communications
  date: '2025-07-09'
  link: https://doi.org/hb35zx
  tags:
  - cell morphology
  - transcriptomics
  - 22q11.2
  - phenotyping
- 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:
  - 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: source
    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 of<i>NF1</i>genotype 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: source
    link: https://github.com/WayScience/nf1_schwann_cell_morphology_signature
    text: Analysis code
  - type: source
    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: '2024-11-17'
  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
  - 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: source
    link: https://github.com/WayScience/IDR_Stream
    text: IDR_stream Software
- id: 10.1038/s41467-023-44045-w
  title: High-dimensional phenotyping to define the genetic basis of cellular morphology
  authors:
  - Matthew Tegtmeyer
  - Jatin Arora
  - Samira Asgari
  - Beth A. Cimini
  - Ajay Nadig
  - Emily Peirent
  - Dhara Liyanage
  - Gregory P. Way
  - Erin Weisbart
  - Aparna Nathan
  - Tiffany Amariuta
  - Kevin Eggan
  - Marzieh Haghighi
  - Steven A. McCarroll
  - "Luke O\u2019Connor"
  - Anne E. Carpenter
  - Shantanu Singh
  - Ralda Nehme
  - Soumya Raychaudhuri
  publisher: Nature Communications
  date: '2024-01-06'
  link: https://doi.org/gtct77
  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: 10.7554/eLife.91362
  title: High-content microscopy reveals a morphological signature of bortezomib resistance
  authors:
  - Megan E Kelley
  - Adi Y Berman
  - David R Stirling
  - Beth A Cimini
  - Yu Han
  - Shantanu Singh
  - Anne E Carpenter
  - Tarun M Kapoor
  - Gregory P Way
  publisher: eLife
  date: '2023-09-27'
  link: https://doi.org/gtcgdd
  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
  title: Evolution and impact of high content imaging
  authors:
  - Gregory P. Way
  - Heba Sailem
  - Steven Shave
  - Richard Kasprowicz
  - Neil O. Carragher
  publisher: SLAS Discovery
  date: '2023-10-01'
  link: https://doi.org/gtcgfv
  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
  title: A genome-wide atlas of human cell morphology
  authors:
  - Meraj Ramezani
  - Julia Bauman
  - Avtar Singh
  - Erin Weisbart
  - John Yong
  - Maria Lozada
  - Gregory P. Way
  - Sanam L. Kavari
  - Celeste Diaz
  - 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: Cold Spring Harbor Laboratory
  date: '2023-08-07'
  link: https://doi.org/gszn2s
  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: 10.1101/2023.11.01.565179
  title: Molecular subtypes of high-grade serous ovarian cancer across racial groups
    and gene expression platforms
  authors:
  - Natalie R. Davidson
  - Mollie E. Barnard
  - Ariel A. Hippen
  - Amy Campbell
  - Courtney E. Johnson
  - Gregory P. Way
  - Brian K. Dalley
  - Andrew Berchuck
  - Lucas A. Salas
  - Lauren C. Peres
  - Jeffrey R. Marks
  - Joellen M. Schildkraut
  - Casey S. Greene
  - Jennifer A. Doherty
  publisher: openRxiv
  date: '2023-11-04'
  link: https://doi.org/gs3vwj
  tags:
  - ovarian cancer
  - molecular subtypes
  - racial disparities
  - genomics
- id: doi:10.1016/j.xgen.2023.100340
  title: 'OpenPBTA: The Open Pediatric Brain Tumor Atlas'
  authors:
  - Joshua A. Shapiro
  - Krutika S. Gaonkar
  - Stephanie J. Spielman
  - Candace L. Savonen
  - Chante J. Bethell
  - Run Jin
  - Komal S. Rathi
  - Yuankun Zhu
  - Laura E. Egolf
  - Bailey K. Farrow
  - Daniel P. Miller
  - Yang Yang
  - Tejaswi Koganti
  - Nighat Noureen
  - Mateusz P. Koptyra
  - Nhat Duong
  - Mariarita Santi
  - Jung Kim
  - Shannon Robins
  - Phillip B. Storm
  - Stephen C. Mack
  - Jena V. Lilly
  - Hongbo M. Xie
  - Payal Jain
  - Pichai Raman
  - Brian R. Rood
  - Rishi R. Lulla
  - Javad Nazarian
  - Adam A. Kraya
  - Zalman Vaksman
  - Allison P. Heath
  - Cassie Kline
  - Laura Scolaro
  - Angela N. Viaene
  - Xiaoyan Huang
  - Gregory P. Way
  - Steven M. Foltz
  - Bo Zhang
  - Anna R. Poetsch
  - Sabine Mueller
  - Brian M. Ennis
  - Michael Prados
  - Sharon J. Diskin
  - Siyuan Zheng
  - Yiran Guo
  - Shrivats Kannan
  - Angela J. Waanders
  - Ashley S. Margol
  - Meen Chul Kim
  - Derek Hanson
  - Nicholas Van Kuren
  - Jessica Wong
  - Rebecca S. Kaufman
  - Noel Coleman
  - Christopher Blackden
  - Kristina A. Cole
  - Jennifer L. Mason
  - Peter J. Madsen
  - Carl J. Koschmann
  - Douglas R. Stewart
  - Eric Wafula
  - Miguel A. Brown
  - Adam C. Resnick
  - Casey S. Greene
  - Jo Lynne Rokita
  - Jaclyn N. Taroni
  publisher: Cell Genomics
  date: '2023-05-01'
  link: https://doi.org/gr92p6
  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
- id: doi:10.1016/j.cels.2022.10.001
  title: Morphology and gene expression profiling provide complementary information
    for mapping cell state
  authors:
  - Gregory P. Way
  - Ted Natoli
  - Adeniyi Adeboye
  - Lev Litichevskiy
  - Andrew Yang
  - Xiaodong Lu
  - Juan C. Caicedo
  - Beth A. Cimini
  - Kyle Karhohs
  - David J. Logan
  - Mohammad H. Rohban
  - Maria Kost-Alimova
  - Kate Hartland
  - Michael Bornholdt
  - Srinivas Niranj Chandrasekaran
  - Marzieh Haghighi
  - Erin Weisbart
  - Shantanu Singh
  - Aravind Subramanian
  - Anne E. Carpenter
  publisher: Cell Systems
  date: '2022-10-01'
  link: https://doi.org/gq6hbw
  image: https://www.cell.com/cms/attachment/55912f54-18d9-4ee9-8374-6f24f9d15bbc/fx1.jpg
  repo: https://github.com/broadinstitute/lincs-profiling-complementarity
  extra-links:
  - type: data
    link: broadinstitute/lincs-cell-painting
    text: Reproducible data pipeline
  - type: data
    link: https://idr.github.io/idr0125-way-cellpainting/
    text: Publicly-available Cell Painting images
  - type: data
    link: https://doi.org/10.6084/m9.figshare.13181966.v2
    text: Publicly-available L1000 profiles
  tags:
  - cell painting
  - drug discovery
  - gene expression
  - deep learning
  - reproducibility
- id: doi:10.1371/journal.pcbi.1009888
  title: Predicting drug polypharmacology from cell morphology readouts using variational
    autoencoder latent space arithmetic
  authors:
  - Yuen Ler Chow
  - Shantanu Singh
  - Anne E. Carpenter
  - Gregory P. Way
  publisher: PLOS Computational Biology
  date: '2022-02-25'
  link: https://doi.org/gq6hbx
  image: https://docs.google.com/drawings/d/e/2PACX-1vRzFGkZMf9ZfXb_q1rE1D9gAAczySfYZ4zyVl93l-zcRXv7sNtJpZTNp__9fmyaTl5MyccvtHh74i-I/pub?w=345&h=321
  repo: broadinstitute/cell-painting-vae
  extra-links:
  - type: data
    link: https://doi.org/10.5281/zenodo.5348067
    text: Zenodo archive
  tags:
  - variational autoencoder
  - cell painting
  - drug discovery
  - latent space arithmetic
- id: doi:10.1371/journal.pbio.3001419
  title: A field guide to cultivating computational biology
  authors:
  - Gregory P Way
  - Anne E Carpenter
  - Casey S Greene
  - Piero Carnici
  - Benilton S Carvalho
  - Michiel de Hoon
  - Stacey Finley
  - Sara JC Gosline
  - Kim-Anh Le Cao
  - Jerry SH Lee
  - Luigi Marchionni
  - Suzanne Sindi
  - Fabian J Theis
  - Jean YH Yang
  - Elana J Fertig
  publisher: PLOS Biology
  date: '2021-10-07'
  link: https://doi.org/gm3hdh
  image: https://raw.githubusercontent.com/WayScience/waysciencelab.com/main/_posts/analysis/cultivating_compbio_map_us_centric.png
  tags:
  - open science
  - essay
  - call to action
- id: doi:10.1002/1873-3468.14067
  title: 'Sharing biological data: why, when, and how'
  authors:
  - Samantha L. Wilson
  - Gregory P. Way
  - Wout Bittremieux
  - "Jean\u2010Paul Armache"
  - Melissa A. Haendel
  - Michael M. Hoffman
  publisher: FEBS Letters
  date: '2021-04-11'
  link: https://doi.org/gmmq7d
  image: https://febs.onlinelibrary.wiley.com/cms/asset/4a3a1cde-1265-471c-87af-f7556d28db36/feb213824-toc-0001-m.jpg
  tags:
  - open science
  - microscopy data
- id: doi:10.1091/mbc.E20-12-0784
  title: Predicting cell health phenotypes using image-based morphology profiling
  authors:
  - Gregory P. Way
  - Maria Kost-Alimova
  - Tsukasa Shibue
  - William F. Harrington
  - Stanley Gill
  - Federica Piccioni
  - Tim Becker
  - Hamdah Shafqat-Abbasi
  - William C. Hahn
  - Anne E. Carpenter
  - Francisca Vazquez
  - Shantanu Singh
  publisher: Molecular Biology of the Cell
  date: '2021-04-19'
  link: https://doi.org/gmmq7f
  image: https://www.molbiolcell.org/cms/10.1091/mbc.E20-12-0784/asset/images/medium/mbc-32-995-g001.gif
  repo: broadinstitute/cell-health
  extra-links:
  - type: preprint
    link: https://www.biorxiv.org/content/10.1101/2020.07.08.193938v2
  - type: source
    link: https://github.com/broadinstitute/cell-health
    text: Analysis
  tags:
  - image-based profiling
  - cell biology
- id: doi:10.1186/s13059-020-02021-3
  title: Compressing gene expression data using multiple latent space dimensionalities
    learns complementary biological representations
  authors:
  - Gregory P. Way
  - Michael Zietz
  - Vincent Rubinetti
  - Daniel S. Himmelstein
  - Casey S. Greene
  publisher: Genome Biology
  date: '2020-05-11'
  link: https://doi.org/gg2mjh
  image: https://raw.githubusercontent.com/greenelab/BioBombe/master/docs/favicon-192x192.png
  repo: greenelab/biobombe
  extra-links:
  - type: preprint
    link: https://doi.org/10.1101/573782
  - type: source
    link: https://github.com/greenelab/biobombe
    text: Analysis
  - type: data
    link: https://greenelab.github.io/BioBombe/
    text: Embeddings
  tags:
  - biological representations
  - unsupervised learning
  - cancer
- id: 10.1016/j.xgen.2023.100346
  title: Discovering cellular programs of intrinsic and extrinsic drivers of metabolic
    traits using LipocyteProfiler
  authors:
  - Samantha Laber
  - Sophie Strobel
  - Josep M. Mercader
  - Hesam Dashti
  - Felipe R.C. dos Santos
  - Phil Kubitz
  - Maya Jackson
  - Alina Ainbinder
  - Julius Honecker
  - Saaket Agrawal
  - Garrett Garborcauskas
  - David R. Stirling
  - Aaron Leong
  - Katherine Figueroa
  - Nasa Sinnott-Armstrong
  - Maria Kost-Alimova
  - Giacomo Deodato
  - Alycen Harney
  - Gregory P. Way
  - Alham Saadat
  - Sierra Harken
  - Saskia Reibe-Pal
  - Hannah Ebert
  - Yixin Zhang
  - Virtu Calabuig-Navarro
  - Elizabeth McGonagle
  - Adam Stefek
  - "Jos\xE9e Dupuis"
  - Beth A. Cimini
  - Hans Hauner
  - Miriam S. Udler
  - Anne E. Carpenter
  - Jose C. Florez
  - Cecilia Lindgren
  - Suzanne B.R. Jacobs
  - Melina Claussnitzer
  publisher: Cell Genomics
  date: '2023-06-01'
  link: https://doi.org/gsff72
  image: https://www.biorxiv.org/content/biorxiv/early/2021/07/19/2021.07.17.452050/F1.large.jpg
  tags:
  - image-based profiling
  - metabolism
  - variant to function
- id: 10.1038/s41597-020-0458-y
  title: Epigenomic profiling of neuroblastoma cell lines
  authors:
  - Kristen Upton
  - Apexa Modi
  - Khushbu Patel
  - Nathan M. Kendsersky
  - Karina L. Conkrite
  - Robyn T. Sussman
  - Gregory P. Way
  - Rebecca N. Adams
  - Gregory I. Sacks
  - Paolo Fortina
  - Sharon J. Diskin
  - John M. Maris
  - Jo Lynne Rokita
  publisher: Scientific Data
  date: '2020-04-14'
  link: https://doi.org/gmndmm
  image: https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41597-020-0458-y/MediaObjects/41597_2020_458_Fig1_HTML.png?as=webp
  tags:
  - gene regulation
  - pediatric cancer
- id: 10.1186/s40478-019-0803-6
  title: Immune landscapes associated with different glioblastoma molecular subtypes
  authors:
  - Maria Martinez-Lage
  - Timothy M. Lynch
  - Yingtao Bi
  - Carolina Cocito
  - Gregory P. Way
  - Sharmistha Pal
  - Josephine Haller
  - Rachel E. Yan
  - Amy Ziober
  - Aivi Nguyen
  - Manoj Kandpal
  - "Donald M. O\u2019Rourke"
  - Jeffrey P. Greenfield
  - Casey S. Greene
  - Ramana V. Davuluri
  - Nadia Dahmane
  publisher: Acta Neuropathologica Communications
  date: '2019-11-29'
  link: https://doi.org/gg7qrr
  image: https://media.springernature.com/full/springer-static/image/art%3A10.1186%2Fs40478-019-0803-6/MediaObjects/40478_2019_803_Fig1_HTML.png?as=webp
  repo: greenelab/gbm_immune_validation
  extra-links:
  - type: data
    link: https://doi.org/10.5281/zenodo.195238
    text: Zenodo archive
  tags:
  - gene expression deconvolution
  - cancer
  - glioblastoma
- id: 10.1182/bloodadvances.2019000303
  title: Integrated phosphoproteomics and transcriptional classifiers reveal hidden
    RAS signaling dynamics in multiple myeloma
  authors:
  - Yu-Hsiu T. Lin
  - Gregory P. Way
  - Benjamin G. Barwick
  - Margarette C. Mariano
  - Makeba Marcoulis
  - Ian D. Ferguson
  - Christoph Driessen
  - Lawrence H. Boise
  - Casey S. Greene
  - Arun P. Wiita
  publisher: Blood Advances
  date: '2019-11-12'
  link: https://doi.org/gg7m56
  image: https://ash.silverchair-cdn.com/ash/content_public/journal/bloodadvances/3/21/10.1182_bloodadvances.2019000303/6/advancesadv2019000303absf1.png?Expires=1632888317&Signature=gyxBCxLAJuFoJyUnY-Re3Tx7FjQJW3eGp8O5R58Nf9ivPWiKomDxz198mYlFFrCs6t-gu0ROAi9Ka4pdaBM5iltSUr~Ert9N85mYKB3NdQ9VHUXLAb-~4igHfF~azabT~UGLx2g44C3qP3RGw1X45kCm-wcOkGLwppiFdBeO-kB-llMFDPHIUtWz4JijMZi3bkYcNe5e9zFW2aPQifNun-76wWa4cDmI4XUqi1VOFPATlMdNXbI5JNMkRwyAESfqA__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA
  repo: greenelab/multiple-myeloma-classifier
  extra-links:
  - type: data
    link: https://doi.org/10.5281/zenodo.2566059
    text: Zenodo archive
  tags:
  - NF1
  - RAS pathway
  - cancer
  - multiple myeloma
- id: 10.1016/j.celrep.2019.09.071
  title: Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to
    Enable Rational Clinical Trial Design
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  - Kristen A. Upton
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  - Gonzalo Lopez
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  - Hannah McCalmont
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  - "Julia W. B\xF6hm"
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  - Wendong Zhang
  - Gregory I. Sacks
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  - Yael P. Mosse
  - Gregory J. Gatto
  - Yolanda Sanchez
  - Casey S. Greene
  - Sharon J. Diskin
  - Olena Morozova Vaske
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  - John M. Maris
  publisher: Cell Reports
  date: '2019-11-01'
  link: https://doi.org/gg596n
  image: https://ars.els-cdn.com/content/image/1-s2.0-S2211124719312689-gr1.jpg
  repo: marislab/pdx-classification
  extra-links:
  - type: data
    link: https://doi.org/10.5281/Zenodo.1475249
    text: Zenodo archive
  tags:
  - pediatric cancer
- id: 10.1146/annurev-biodatasci-072018-021348
  title: Discovering Pathway and Cell Type Signatures in Transcriptomic Compendia
    with Machine Learning
  authors:
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  - Casey S. Greene
  publisher: Annual Review of Biomedical Data Science
  date: '2019-07-20'
  link: https://doi.org/ggns8p
  image: https://d3i71xaburhd42.cloudfront.net/1faf6f4ced4693d61acbbdc592d349eb09dbe32c/19-Figure1.1-1.png
  extra-links:
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    link: https://doi.org/10.7287/peerj.preprints.27229v1
    text: preprint
  tags:
  - review
- id: 10.1038/s41592-018-0230-9
  title: Bayesian deep learning for single-cell analysis
  authors:
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  - Casey S. Greene
  publisher: Nature Methods
  date: '2018-11-30'
  link: https://doi.org/ggjn34
  image: https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41592-018-0230-9/MediaObjects/41592_2018_230_Fig1_HTML.png
  tags:
  - news and views
- id: 10.1016/j.cell.2018.03.035
  title: Oncogenic Signaling Pathways in The Cancer Genome Atlas
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  - Mirella Marino
  - Roberta Merola
  - Ronald de Krijger
  - Anne-Paule Gimenez-Roqueplo
  - "Alain Pich\xE9"
  - Simone Chevalier
  - Ginette McKercher
  - Kivanc Birsoy
  - Gene Barnett
  - Cathy Brewer
  - Carol Farver
  - Theresa Naska
  - Nathan A. Pennell
  - Daniel Raymond
  - Cathy Schilero
  - Kathy Smolenski
  - Felicia Williams
  - Carl Morrison
  - Jeffrey A. Borgia
  - Michael J. Liptay
  - Mark Pool
  - Christopher W. Seder
  - Kerstin Junker
  - Larsson Omberg
  - Mikhail Dinkin
  - George Manikhas
  - Domenico Alvaro
  - Maria Consiglia Bragazzi
  - Vincenzo Cardinale
  - Guido Carpino
  - Eugenio Gaudio
  - David Chesla
  - Sandra Cottingham
  - Michael Dubina
  - Fedor Moiseenko
  - Renumathy Dhanasekaran
  - Karl-Friedrich Becker
  - Klaus-Peter Janssen
  - Julia Slotta-Huspenina
  - Mohamed H. Abdel-Rahman
  - Dina Aziz
  - Sue Bell
  - Colleen M. Cebulla
  - Amy Davis
  - Rebecca Duell
  - J. Bradley Elder
  - Joe Hilty
  - Bahavna Kumar
  - James Lang
  - Norman L. Lehman
  - Randy Mandt
  - Phuong Nguyen
  - Robert Pilarski
  - Karan Rai
  - Lynn Schoenfield
  - Kelly Senecal
  - Paul Wakely
  - Paul Hansen
  - Ronald Lechan
  - James Powers
  - Arthur Tischler
  - William E. Grizzle
  - Katherine C. Sexton
  - Alison Kastl
  - Joel Henderson
  - Sima Porten
  - Jens Waldmann
  - Martin Fassnacht
  - Sylvia L. Asa
  - Dirk Schadendorf
  - Marta Couce
  - Markus Graefen
  - Hartwig Huland
  - Guido Sauter
  - Thorsten Schlomm
  - Ronald Simon
  - Pierre Tennstedt
  - Oluwole Olabode
  - Mark Nelson
  - Oliver Bathe
  - Peter R. Carroll
  - June M. Chan
  - Philip Disaia
  - Pat Glenn
  - Robin K. Kelley
  - Charles N. Landen
  - Joanna Phillips
  - Michael Prados
  - Jeffry Simko
  - Karen Smith-McCune
  - Scott VandenBerg
  - Kevin Roggin
  - Ashley Fehrenbach
  - Ady Kendler
  - Suzanne Sifri
  - Ruth Steele
  - Antonio Jimeno
  - Francis Carey
  - Ian Forgie
  - Massimo Mannelli
  - Michael Carney
  - Brenda Hernandez
  - Benito Campos
  - Christel Herold-Mende
  - Christin Jungk
  - Andreas Unterberg
  - Andreas von Deimling
  - Aaron Bossler
  - Joseph Galbraith
  - Laura Jacobus
  - Michael Knudson
  - Tina Knutson
  - Deqin Ma
  - Mohammed Milhem
  - Rita Sigmund
  - Andrew K. Godwin
  - Rashna Madan
  - Howard G. Rosenthal
  - Clement Adebamowo
  - Sally N. Adebamowo
  - Alex Boussioutas
  - David Beer
  - Thomas Giordano
  - Anne-Marie Mes-Masson
  - Fred Saad
  - Therese Bocklage
  - Lisa Landrum
  - Robert Mannel
  - Kathleen Moore
  - Katherine Moxley
  - Russel Postier
  - Joan Walker
  - Rosemary Zuna
  - Michael Feldman
  - Federico Valdivieso
  - Rajiv Dhir
  - James Luketich
  - Edna M. Mora Pinero
  - Mario Quintero-Aguilo
  - Carlos Gilberto Carlotti
  - "Jose Sebasti\xE3o Dos Santos"
  - Rafael Kemp
  - Ajith Sankarankuty
  - Daniela Tirapelli
  - James Catto
  - Kathy Agnew
  - Elizabeth Swisher
  - Jenette Creaney
  - Bruce Robinson
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  - Eryn M. Godwin
  - Sara Kendall
  - Cassaundra Shipman
  - Carol Bradford
  - Thomas Carey
  - Andrea Haddad
  - Jeffey Moyer
  - Lisa Peterson
  - Mark Prince
  - Laura Rozek
  - Gregory Wolf
  - Rayleen Bowman
  - Kwun M. Fong
  - Ian Yang
  - Robert Korst
  - W. Kimryn Rathmell
  - J. Leigh Fantacone-Campbell
  - Jeffrey A. Hooke
  - Albert J. Kovatich
  - Craig D. Shriver
  - John DiPersio
  - Bettina Drake
  - Ramaswamy Govindan
  - Sharon Heath
  - Timothy Ley
  - Brian Van Tine
  - Peter Westervelt
  - Mark A. Rubin
  - Jung Il Lee
  - "Nat\xE1lia D. Aredes"
  - Armaz Mariamidze
  publisher: Cell
  date: '2018-04-01'
  link: https://doi.org/gc7r9b
  image: https://ars.els-cdn.com/content/image/1-s2.0-S0092867418303593-fx1_lrg.jpg
- id: 10.1098/rsif.2017.0387
  title: Opportunities and obstacles for deep learning in biology and medicine
  authors:
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  - Daniel S. Himmelstein
  - Brett K. Beaulieu-Jones
  - Alexandr A. Kalinin
  - Brian T. Do
  - Gregory P. Way
  - Enrico Ferrero
  - Paul-Michael Agapow
  - Michael Zietz
  - Michael M. Hoffman
  - Wei Xie
  - Gail L. Rosen
  - Benjamin J. Lengerich
  - Johnny Israeli
  - Jack Lanchantin
  - Stephen Woloszynek
  - Anne E. Carpenter
  - Avanti Shrikumar
  - Jinbo Xu
  - Evan M. Cofer
  - Christopher A. Lavender
  - Srinivas C. Turaga
  - Amr M. Alexandari
  - Zhiyong Lu
  - David J. Harris
  - Dave DeCaprio
  - Yanjun Qi
  - Anshul Kundaje
  - Yifan Peng
  - Laura K. Wiley
  - Marwin H. S. Segler
  - Simina M. Boca
  - S. Joshua Swamidass
  - Austin Huang
  - Anthony Gitter
  - Casey S. Greene
  publisher: Journal of The Royal Society Interface
  date: '2018-04-04'
  link: https://doi.org/gddkhn
  image: https://royalsocietypublishing.org/cms/asset/1aee5837-745c-40ad-a398-00dc5655466c/rsif20170387f01.jpg
  repo: greenelab/deep-review
  tags:
  - review
- id: 10.1016/j.celrep.2018.03.076
  title: Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The
    Cancer Genome Atlas
  authors:
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  - Linghua Wang
  - Michael T. Zimmermann
  - Nyasha Chambwe
  - Galen F. Gao
  - Andrew D. Cherniack
  - Huihui Fan
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  - Gregory P. Way
  - Casey S. Greene
  - Yuexin Liu
  - Rehan Akbani
  - Bin Feng
  - Lawrence A. Donehower
  - Chase Miller
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  - Mostafa Karimi
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  - Eve Shinbrot
  - Shaojun Zhang
  - Jianfang Liu
  - Hai Hu
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  - Lei Li
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  - Ilya Shmulevich
  - Raymond J. Monnat
  - Yonghong Xiao
  - Chen Wang
  - Samantha J. Caesar-Johnson
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  - Heidi J. Sofia
  - Roy Tarnuzzer
  - Zhining Wang
  - Liming Yang
  - Jean C. Zenklusen
  - Jiashan (Julia) Zhang
  - Sudha Chudamani
  - Jia Liu
  - Laxmi Lolla
  - Rashi Naresh
  - Todd Pihl
  - Qiang Sun
  - Yunhu Wan
  - Ye Wu
  - Juok Cho
  - Timothy DeFreitas
  - Scott Frazer
  - Nils Gehlenborg
  - Gad Getz
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  - Jaegil Kim
  - Michael S. Lawrence
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  - Gordon Saksena
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  - Varsha Dhankani
  - Theo Knijnenburg
  - Roger Kramer
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  - Yuexin Liu
  - Michael Miller
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  - Francisco Sanchez-Vega
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  - Hongxin Zhang
  - Pavana Anur
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  - Yi Han
  - Jianhong Hu
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  - Lora Lewis
  - Wei Li
  - Xiuping Liu
  - Margaret Morgan
  - Donna Morton
  - Donna Muzny
  - Jireh Santibanez
  - Margi Sheth
  - Eve Shinbrot
  - Linghua Wang
  - Min Wang
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  - Mikhail Tavobilov
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  - Karen Devine
  - Jordonna Fulop
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  - Kristen Shimmel
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  - Agostino De Rose
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  - Marc Goodman
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  - Brenda Deyarmin
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  - Leonid Kvecher
  - Caroline Larson
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  - Tomas Zelinka
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  - Brenda Rabeno
  - Patricia Swanson
  - Mathieu Latour
  - Louis Lacombe
  - "Bernard T\xEAtu"
  - Alain Bergeron
  - Mary McGraw
  - Susan M. Staugaitis
  - John Chabot
  - Hanina Hibshoosh
  - Antonia Sepulveda
  - Tao Su
  - Timothy Wang
  - Olga Potapova
  - Olga Voronina
  - Laurence Desjardins
  - Odette Mariani
  - Sergio Roman-Roman
  - Xavier Sastre
  - Marc-Henri Stern
  - Feixiong Cheng
  - Sabina Signoretti
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  - Alan Pickens
  - Suresh Ramalingam
  - Dong M. Shin
  - Gabriel Sica
  - Erwin G. Van Meir
  - Hongzheng Zhang
  - Wil Eijckenboom
  - Ad Gillis
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  - Leendert Looijenga
  - Wolter Oosterhuis
  - Hans Stoop
  - Kim E. van Kessel
  - Ellen C. Zwarthoff
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  - Lucia Cuppini
  - Stefania Cuzzubbo
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  - Gaetano Finocchiaro
  - Luca Mattei
  - Alessandro Perin
  - Bianca Pollo
  - Chu Chen
  - John Houck
  - Pawadee Lohavanichbutr
  - Arndt Hartmann
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  - Robert Stoehr
  - Helge Taubert
  - Sven Wach
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  - Witold Kycler
  - Dawid Murawa
  - Maciej Wiznerowicz
  - Ki Chung
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  - Julie Martin
  - Eric Baudin
  - Glenn Bubley
  - Raphael Bueno
  - Assunta De Rienzo
  - William G. Richards
  - Steven Kalkanis
  - Tom Mikkelsen
  - Houtan Noushmehr
  - Lisa Scarpace
  - Nicolas Girard
  - Marta Aymerich
  - Elias Campo
  - "Eva Gin\xE9"
  - "Armando L\xF3pez Guillermo"
  - Nguyen Van Bang
  - Phan Thi Hanh
  - Bui Duc Phu
  - Yufang Tang
  - Howard Colman
  - Kimberley Evason
  - Peter R. Dottino
  - John A. Martignetti
  - Hani Gabra
  - Hartmut Juhl
  - Teniola Akeredolu
  - Serghei Stepa
  - Dave Hoon
  - Keunsoo Ahn
  - Koo Jeong Kang
  - Felix Beuschlein
  - Anne Breggia
  - Michael Birrer
  - Debra Bell
  - Mitesh Borad
  - Alan H. Bryce
  - Erik Castle
  - Vishal Chandan
  - John Cheville
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  - Nasra Giama
  - Thai Ho
  - Michael Kendrick
  - Jean-Pierre Kocher
  - Karla Kopp
  - Catherine Moser
  - David Nagorney
  - "Daniel O\u2019Brien"
  - "Brian Patrick O\u2019Neill"
  - Tushar Patel
  - Gloria Petersen
  - Florencia Que
  - Michael Rivera
  - Lewis Roberts
  - Robert Smallridge
  - Thomas Smyrk
  - Melissa Stanton
  - R. Houston Thompson
  - Michael Torbenson
  - Ju Dong Yang
  - Lizhi Zhang
  - Fadi Brimo
  - Jaffer A. Ajani
  - Ana Maria Angulo Gonzalez
  - Carmen Behrens
  - Jolanta Bondaruk
  - Russell Broaddus
  - Bogdan Czerniak
  - Bita Esmaeli
  - Junya Fujimoto
  - Jeffrey Gershenwald
  - Charles Guo
  - Alexander J. Lazar
  - Christopher Logothetis
  - Funda Meric-Bernstam
  - Cesar Moran
  - Lois Ramondetta
  - David Rice
  - Anil Sood
  - Pheroze Tamboli
  - Timothy Thompson
  - Patricia Troncoso
  - Anne Tsao
  - Ignacio Wistuba
  - Candace Carter
  - Lauren Haydu
  - Peter Hersey
  - Valerie Jakrot
  - Hojabr Kakavand
  - Richard Kefford
  - Kenneth Lee
  - Georgina Long
  - Graham Mann
  - Michael Quinn
  - Robyn Saw
  - Richard Scolyer
  - Kerwin Shannon
  - Andrew Spillane
  - Jonathan Stretch
  - Maria Synott
  - John Thompson
  - James Wilmott
  - Hikmat Al-Ahmadie
  - Timothy A. Chan
  - Ronald Ghossein
  - Anuradha Gopalan
  - Douglas A. Levine
  - Victor Reuter
  - Samuel Singer
  - Bhuvanesh Singh
  - Nguyen Viet Tien
  - Thomas Broudy
  - Cyrus Mirsaidi
  - Praveen Nair
  - Paul Drwiega
  - Judy Miller
  - Jennifer Smith
  - Howard Zaren
  - Joong-Won Park
  - Nguyen Phi Hung
  - Electron Kebebew
  - W. Marston Linehan
  - Adam R. Metwalli
  - Karel Pacak
  - Peter A. Pinto
  - Mark Schiffman
  - Laura S. Schmidt
  - Cathy D. Vocke
  - Nicolas Wentzensen
  - Robert Worrell
  - Hannah Yang
  - Marc Moncrieff
  - Chandra Goparaju
  - Jonathan Melamed
  - Harvey Pass
  - Natalia Botnariuc
  - Irina Caraman
  - Mircea Cernat
  - Inga Chemencedji
  - Adrian Clipca
  - Serghei Doruc
  - Ghenadie Gorincioi
  - Sergiu Mura
  - Maria Pirtac
  - Irina Stancul
  - Diana Tcaciuc
  - Monique Albert
  - Iakovina Alexopoulou
  - Angel Arnaout
  - John Bartlett
  - Jay Engel
  - Sebastien Gilbert
  - Jeremy Parfitt
  - Harman Sekhon
  - George Thomas
  - Doris M. Rassl
  - Robert C. Rintoul
  - Carlo Bifulco
  - Raina Tamakawa
  - Walter Urba
  - Nicholas Hayward
  - Henri Timmers
  - Anna Antenucci
  - Francesco Facciolo
  - Gianluca Grazi
  - Mirella Marino
  - Roberta Merola
  - Ronald de Krijger
  - Anne-Paule Gimenez-Roqueplo
  - "Alain Pich\xE9"
  - Simone Chevalier
  - Ginette McKercher
  - Kivanc Birsoy
  - Gene Barnett
  - Cathy Brewer
  - Carol Farver
  - Theresa Naska
  - Nathan A. Pennell
  - Daniel Raymond
  - Cathy Schilero
  - Kathy Smolenski
  - Felicia Williams
  - Carl Morrison
  - Jeffrey A. Borgia
  - Michael J. Liptay
  - Mark Pool
  - Christopher W. Seder
  - Kerstin Junker
  - Larsson Omberg
  - Mikhail Dinkin
  - George Manikhas
  - Domenico Alvaro
  - Maria Consiglia Bragazzi
  - Vincenzo Cardinale
  - Guido Carpino
  - Eugenio Gaudio
  - David Chesla
  - Sandra Cottingham
  - Michael Dubina
  - Fedor Moiseenko
  - Renumathy Dhanasekaran
  - Karl-Friedrich Becker
  - Klaus-Peter Janssen
  - Julia Slotta-Huspenina
  - Mohamed H. Abdel-Rahman
  - Dina Aziz
  - Sue Bell
  - Colleen M. Cebulla
  - Amy Davis
  - Rebecca Duell
  - J. Bradley Elder
  - Joe Hilty
  - Bahavna Kumar
  - James Lang
  - Norman L. Lehman
  - Randy Mandt
  - Phuong Nguyen
  - Robert Pilarski
  - Karan Rai
  - Lynn Schoenfield
  - Kelly Senecal
  - Paul Wakely
  - Paul Hansen
  - Ronald Lechan
  - James Powers
  - Arthur Tischler
  - William E. Grizzle
  - Katherine C. Sexton
  - Alison Kastl
  - Joel Henderson
  - Sima Porten
  - Jens Waldmann
  - Martin Fassnacht
  - Sylvia L. Asa
  - Dirk Schadendorf
  - Marta Couce
  - Markus Graefen
  - Hartwig Huland
  - Guido Sauter
  - Thorsten Schlomm
  - Ronald Simon
  - Pierre Tennstedt
  - Oluwole Olabode
  - Mark Nelson
  - Oliver Bathe
  - Peter R. Carroll
  - June M. Chan
  - Philip Disaia
  - Pat Glenn
  - Robin K. Kelley
  - Charles N. Landen
  - Joanna Phillips
  - Michael Prados
  - Jeffry Simko
  - Karen Smith-McCune
  - Scott VandenBerg
  - Kevin Roggin
  - Ashley Fehrenbach
  - Ady Kendler
  - Suzanne Sifri
  - Ruth Steele
  - Antonio Jimeno
  - Francis Carey
  - Ian Forgie
  - Massimo Mannelli
  - Michael Carney
  - Brenda Hernandez
  - Benito Campos
  - Christel Herold-Mende
  - Christin Jungk
  - Andreas Unterberg
  - Andreas von Deimling
  - Aaron Bossler
  - Joseph Galbraith
  - Laura Jacobus
  - Michael Knudson
  - Tina Knutson
  - Deqin Ma
  - Mohammed Milhem
  - Rita Sigmund
  - Andrew K. Godwin
  - Rashna Madan
  - Howard G. Rosenthal
  - Clement Adebamowo
  - Sally N. Adebamowo
  - Alex Boussioutas
  - David Beer
  - Thomas Giordano
  - Anne-Marie Mes-Masson
  - Fred Saad
  - Therese Bocklage
  - Lisa Landrum
  - Robert Mannel
  - Kathleen Moore
  - Katherine Moxley
  - Russel Postier
  - Joan Walker
  - Rosemary Zuna
  - Michael Feldman
  - Federico Valdivieso
  - Rajiv Dhir
  - James Luketich
  - Edna M. Mora Pinero
  - Mario Quintero-Aguilo
  - Carlos Gilberto Carlotti
  - "Jose Sebasti\xE3o Dos Santos"
  - Rafael Kemp
  - Ajith Sankarankuty
  - Daniela Tirapelli
  - James Catto
  - Kathy Agnew
  - Elizabeth Swisher
  - Jenette Creaney
  - Bruce Robinson
  - Carl Simon Shelley
  - Eryn M. Godwin
  - Sara Kendall
  - Cassaundra Shipman
  - Carol Bradford
  - Thomas Carey
  - Andrea Haddad
  - Jeffey Moyer
  - Lisa Peterson
  - Mark Prince
  - Laura Rozek
  - Gregory Wolf
  - Rayleen Bowman
  - Kwun M. Fong
  - Ian Yang
  - Robert Korst
  - W. Kimryn Rathmell
  - J. Leigh Fantacone-Campbell
  - Jeffrey A. Hooke
  - Albert J. Kovatich
  - Craig D. Shriver
  - John DiPersio
  - Bettina Drake
  - Ramaswamy Govindan
  - Sharon Heath
  - Timothy Ley
  - Brian Van Tine
  - Peter Westervelt
  - Mark A. Rubin
  - Jung Il Lee
  - "Nat\xE1lia D. Aredes"
  - Armaz Mariamidze
  publisher: Cell Reports
  date: '2018-04-01'
  link: https://doi.org/gfspsc
  image: https://ars.els-cdn.com/content/image/1-s2.0-S2211124718304376-fx1_lrg.jpg
  repo: greenelab/pancancer
- id: 10.1142/9789813235533_0008
  title: Extracting a biologically relevant latent space from cancer transcriptomes
    with variational autoencoders
  authors:
  - Gregory P. Way
  - Casey S. Greene
  publisher: World Scientific Pub Co Pte Lt
  date: '2018-01-01'
  link: https://doi.org/gfspsd
  image: https://hpc.nih.gov/apps/tybalt/tsne_adage.png
  repo: greenelab/tybalt
  extra-links:
  - type: preprint
    link: https://doi.org/10.1101/174474
    text: preprint
  - type: source
    link: https://github.com/greenelab/tybalt
    text: Analysis
- id: 10.1016/j.celrep.2018.03.046
  title: Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer
    Genome Atlas
  authors:
  - Gregory P. Way
  - Francisco Sanchez-Vega
  - Konnor La
  - Joshua Armenia
  - Walid K. Chatila
  - Augustin Luna
  - Chris Sander
  - Andrew D. Cherniack
  - Marco Mina
  - Giovanni Ciriello
  - Nikolaus Schultz
  - Yolanda Sanchez
  - Casey S. Greene
  - Samantha J. Caesar-Johnson
  - John A. Demchok
  - Ina Felau
  - Melpomeni Kasapi
  - Martin L. Ferguson
  - Carolyn M. Hutter
  - Heidi J. Sofia
  - Roy Tarnuzzer
  - Zhining Wang
  - Liming Yang
  - Jean C. Zenklusen
  - Jiashan (Julia) Zhang
  - Sudha Chudamani
  - Jia Liu
  - Laxmi Lolla
  - Rashi Naresh
  - Todd Pihl
  - Qiang Sun
  - Yunhu Wan
  - Ye Wu
  - Juok Cho
  - Timothy DeFreitas
  - Scott Frazer
  - Nils Gehlenborg
  - Gad Getz
  - David I. Heiman
  - Jaegil Kim
  - Michael S. Lawrence
  - Pei Lin
  - Sam Meier
  - Michael S. Noble
  - Gordon Saksena
  - Doug Voet
  - Hailei Zhang
  - Brady Bernard
  - Nyasha Chambwe
  - Varsha Dhankani
  - Theo Knijnenburg
  - Roger Kramer
  - Kalle Leinonen
  - Yuexin Liu
  - Michael Miller
  - Sheila Reynolds
  - Ilya Shmulevich
  - Vesteinn Thorsson
  - Wei Zhang
  - Rehan Akbani
  - Bradley M. Broom
  - Apurva M. Hegde
  - Zhenlin Ju
  - Rupa S. Kanchi
  - Anil Korkut
  - Jun Li
  - Han Liang
  - Shiyun Ling
  - Wenbin Liu
  - Yiling Lu
  - Gordon B. Mills
  - Kwok-Shing Ng
  - Arvind Rao
  - Michael Ryan
  - Jing Wang
  - John N. Weinstein
  - Jiexin Zhang
  - Adam Abeshouse
  - Joshua Armenia
  - Debyani Chakravarty
  - Walid K. Chatila
  - Ino de Bruijn
  - Jianjiong Gao
  - Benjamin E. Gross
  - Zachary J. Heins
  - Ritika Kundra
  - Konnor La
  - Marc Ladanyi
  - Augustin Luna
  - Moriah G. Nissan
  - Angelica Ochoa
  - Sarah M. Phillips
  - Ed Reznik
  - Francisco Sanchez-Vega
  - Chris Sander
  - Nikolaus Schultz
  - Robert Sheridan
  - S. Onur Sumer
  - Yichao Sun
  - Barry S. Taylor
  - Jioajiao Wang
  - Hongxin Zhang
  - Pavana Anur
  - Myron Peto
  - Paul Spellman
  - Christopher Benz
  - Joshua M. Stuart
  - Christopher K. Wong
  - Christina Yau
  - D. Neil Hayes
  - Joel S. Parker
  - Matthew D. Wilkerson
  - Adrian Ally
  - Miruna Balasundaram
  - Reanne Bowlby
  - Denise Brooks
  - Rebecca Carlsen
  - Eric Chuah
  - Noreen Dhalla
  - Robert Holt
  - Steven J.M. Jones
  - Katayoon Kasaian
  - Darlene Lee
  - Yussanne Ma
  - Marco A. Marra
  - Michael Mayo
  - Richard A. Moore
  - Andrew J. Mungall
  - Karen Mungall
  - A. Gordon Robertson
  - Sara Sadeghi
  - Jacqueline E. Schein
  - Payal Sipahimalani
  - Angela Tam
  - Nina Thiessen
  - Kane Tse
  - Tina Wong
  - Ashton C. Berger
  - Rameen Beroukhim
  - Andrew D. Cherniack
  - Carrie Cibulskis
  - Stacey B. Gabriel
  - Galen F. Gao
  - Gavin Ha
  - Matthew Meyerson
  - Steven E. Schumacher
  - Juliann Shih
  - Melanie H. Kucherlapati
  - Raju S. Kucherlapati
  - Stephen Baylin
  - Leslie Cope
  - Ludmila Danilova
  - Moiz S. Bootwalla
  - Phillip H. Lai
  - Dennis T. Maglinte
  - David J. Van Den Berg
  - Daniel J. Weisenberger
  - J. Todd Auman
  - Saianand Balu
  - Tom Bodenheimer
  - Cheng Fan
  - Katherine A. Hoadley
  - Alan P. Hoyle
  - Stuart R. Jefferys
  - Corbin D. Jones
  - Shaowu Meng
  - Piotr A. Mieczkowski
  - Lisle E. Mose
  - Amy H. Perou
  - Charles M. Perou
  - Jeffrey Roach
  - Yan Shi
  - Janae V. Simons
  - Tara Skelly
  - Matthew G. Soloway
  - Donghui Tan
  - Umadevi Veluvolu
  - Huihui Fan
  - Toshinori Hinoue
  - Peter W. Laird
  - Hui Shen
  - Wanding Zhou
  - Michelle Bellair
  - Kyle Chang
  - Kyle Covington
  - Chad J. Creighton
  - Huyen Dinh
  - HarshaVardhan Doddapaneni
  - Lawrence A. Donehower
  - Jennifer Drummond
  - Richard A. Gibbs
  - Robert Glenn
  - Walker Hale
  - Yi Han
  - Jianhong Hu
  - Viktoriya Korchina
  - Sandra Lee
  - Lora Lewis
  - Wei Li
  - Xiuping Liu
  - Margaret Morgan
  - Donna Morton
  - Donna Muzny
  - Jireh Santibanez
  - Margi Sheth
  - Eve Shinbrot
  - Linghua Wang
  - Min Wang
  - David A. Wheeler
  - Liu Xi
  - Fengmei Zhao
  - Julian Hess
  - Elizabeth L. Appelbaum
  - Matthew Bailey
  - Matthew G. Cordes
  - Li Ding
  - Catrina C. Fronick
  - Lucinda A. Fulton
  - Robert S. Fulton
  - Cyriac Kandoth
  - Elaine R. Mardis
  - Michael D. McLellan
  - Christopher A. Miller
  - Heather K. Schmidt
  - Richard K. Wilson
  - Daniel Crain
  - Erin Curley
  - Johanna Gardner
  - Kevin Lau
  - David Mallery
  - Scott Morris
  - Joseph Paulauskis
  - Robert Penny
  - Candace Shelton
  - Troy Shelton
  - Mark Sherman
  - Eric Thompson
  - Peggy Yena
  - Jay Bowen
  - Julie M. Gastier-Foster
  - Mark Gerken
  - Kristen M. Leraas
  - Tara M. Lichtenberg
  - Nilsa C. Ramirez
  - Lisa Wise
  - Erik Zmuda
  - Niall Corcoran
  - Tony Costello
  - Christopher Hovens
  - Andre L. Carvalho
  - Ana C. de Carvalho
  - "Jos\xE9 H. Fregnani"
  - Adhemar Longatto-Filho
  - Rui M. Reis
  - Cristovam Scapulatempo-Neto
  - Henrique C.S. Silveira
  - Daniel O. Vidal
  - Andrew Burnette
  - Jennifer Eschbacher
  - Beth Hermes
  - Ardene Noss
  - Rosy Singh
  - Matthew L. Anderson
  - Patricia D. Castro
  - Michael Ittmann
  - David Huntsman
  - Bernard Kohl
  - Xuan Le
  - Richard Thorp
  - Chris Andry
  - Elizabeth R. Duffy
  - Vladimir Lyadov
  - Oxana Paklina
  - Galiya Setdikova
  - Alexey Shabunin
  - Mikhail Tavobilov
  - Christopher McPherson
  - Ronald Warnick
  - Ross Berkowitz
  - Daniel Cramer
  - Colleen Feltmate
  - Neil Horowitz
  - Adam Kibel
  - Michael Muto
  - Chandrajit P. Raut
  - Andrei Malykh
  - Jill S. Barnholtz-Sloan
  - Wendi Barrett
  - Karen Devine
  - Jordonna Fulop
  - Quinn T. Ostrom
  - Kristen Shimmel
  - Yingli Wolinsky
  - Andrew E. Sloan
  - Agostino De Rose
  - Felice Giuliante
  - Marc Goodman
  - Beth Y. Karlan
  - Curt H. Hagedorn
  - John Eckman
  - Jodi Harr
  - Jerome Myers
  - Kelinda Tucker
  - Leigh Anne Zach
  - Brenda Deyarmin
  - Hai Hu
  - Leonid Kvecher
  - Caroline Larson
  - Richard J. Mural
  - Stella Somiari
  - Ales Vicha
  - Tomas Zelinka
  - Joseph Bennett
  - Mary Iacocca
  - Brenda Rabeno
  - Patricia Swanson
  - Mathieu Latour
  - Louis Lacombe
  - "Bernard T\xEAtu"
  - Alain Bergeron
  - Mary McGraw
  - Susan M. Staugaitis
  - John Chabot
  - Hanina Hibshoosh
  - Antonia Sepulveda
  - Tao Su
  - Timothy Wang
  - Olga Potapova
  - Olga Voronina
  - Laurence Desjardins
  - Odette Mariani
  - Sergio Roman-Roman
  - Xavier Sastre
  - Marc-Henri Stern
  - Feixiong Cheng
  - Sabina Signoretti
  - Andrew Berchuck
  - Darell Bigner
  - Eric Lipp
  - Jeffrey Marks
  - Shannon McCall
  - Roger McLendon
  - Angeles Secord
  - Alexis Sharp
  - Madhusmita Behera
  - Daniel J. Brat
  - Amy Chen
  - Keith Delman
  - Seth Force
  - Fadlo Khuri
  - Kelly Magliocca
  - Shishir Maithel
  - Jeffrey J. Olson
  - Taofeek Owonikoko
  - Alan Pickens
  - Suresh Ramalingam
  - Dong M. Shin
  - Gabriel Sica
  - Erwin G. Van Meir
  - Hongzheng Zhang
  - Wil Eijckenboom
  - Ad Gillis
  - Esther Korpershoek
  - Leendert Looijenga
  - Wolter Oosterhuis
  - Hans Stoop
  - Kim E. van Kessel
  - Ellen C. Zwarthoff
  - Chiara Calatozzolo
  - Lucia Cuppini
  - Stefania Cuzzubbo
  - Francesco DiMeco
  - Gaetano Finocchiaro
  - Luca Mattei
  - Alessandro Perin
  - Bianca Pollo
  - Chu Chen
  - John Houck
  - Pawadee Lohavanichbutr
  - Arndt Hartmann
  - Christine Stoehr
  - Robert Stoehr
  - Helge Taubert
  - Sven Wach
  - Bernd Wullich
  - Witold Kycler
  - Dawid Murawa
  - Maciej Wiznerowicz
  - Ki Chung
  - W. Jeffrey Edenfield
  - Julie Martin
  - Eric Baudin
  - Glenn Bubley
  - Raphael Bueno
  - Assunta De Rienzo
  - William G. Richards
  - Steven Kalkanis
  - Tom Mikkelsen
  - Houtan Noushmehr
  - Lisa Scarpace
  - Nicolas Girard
  - Marta Aymerich
  - Elias Campo
  - "Eva Gin\xE9"
  - "Armando L\xF3pez Guillermo"
  - Nguyen Van Bang
  - Phan Thi Hanh
  - Bui Duc Phu
  - Yufang Tang
  - Howard Colman
  - Kimberley Evason
  - Peter R. Dottino
  - John A. Martignetti
  - Hani Gabra
  - Hartmut Juhl
  - Teniola Akeredolu
  - Serghei Stepa
  - Dave Hoon
  - Keunsoo Ahn
  - Koo Jeong Kang
  - Felix Beuschlein
  - Anne Breggia
  - Michael Birrer
  - Debra Bell
  - Mitesh Borad
  - Alan H. Bryce
  - Erik Castle
  - Vishal Chandan
  - John Cheville
  - John A. Copland
  - Michael Farnell
  - Thomas Flotte
  - Nasra Giama
  - Thai Ho
  - Michael Kendrick
  - Jean-Pierre Kocher
  - Karla Kopp
  - Catherine Moser
  - David Nagorney
  - "Daniel O\u2019Brien"
  - "Brian Patrick O\u2019Neill"
  - Tushar Patel
  - Gloria Petersen
  - Florencia Que
  - Michael Rivera
  - Lewis Roberts
  - Robert Smallridge
  - Thomas Smyrk
  - Melissa Stanton
  - R. Houston Thompson
  - Michael Torbenson
  - Ju Dong Yang
  - Lizhi Zhang
  - Fadi Brimo
  - Jaffer A. Ajani
  - Ana Maria Angulo Gonzalez
  - Carmen Behrens
  - Jolanta Bondaruk
  - Russell Broaddus
  - Bogdan Czerniak
  - Bita Esmaeli
  - Junya Fujimoto
  - Jeffrey Gershenwald
  - Charles Guo
  - Alexander J. Lazar
  - Christopher Logothetis
  - Funda Meric-Bernstam
  - Cesar Moran
  - Lois Ramondetta
  - David Rice
  - Anil Sood
  - Pheroze Tamboli
  - Timothy Thompson
  - Patricia Troncoso
  - Anne Tsao
  - Ignacio Wistuba
  - Candace Carter
  - Lauren Haydu
  - Peter Hersey
  - Valerie Jakrot
  - Hojabr Kakavand
  - Richard Kefford
  - Kenneth Lee
  - Georgina Long
  - Graham Mann
  - Michael Quinn
  - Robyn Saw
  - Richard Scolyer
  - Kerwin Shannon
  - Andrew Spillane
  - Jonathan Stretch
  - Maria Synott
  - John Thompson
  - James Wilmott
  - Hikmat Al-Ahmadie
  - Timothy A. Chan
  - Ronald Ghossein
  - Anuradha Gopalan
  - Douglas A. Levine
  - Victor Reuter
  - Samuel Singer
  - Bhuvanesh Singh
  - Nguyen Viet Tien
  - Thomas Broudy
  - Cyrus Mirsaidi
  - Praveen Nair
  - Paul Drwiega
  - Judy Miller
  - Jennifer Smith
  - Howard Zaren
  - Joong-Won Park
  - Nguyen Phi Hung
  - Electron Kebebew
  - W. Marston Linehan
  - Adam R. Metwalli
  - Karel Pacak
  - Peter A. Pinto
  - Mark Schiffman
  - Laura S. Schmidt
  - Cathy D. Vocke
  - Nicolas Wentzensen
  - Robert Worrell
  - Hannah Yang
  - Marc Moncrieff
  - Chandra Goparaju
  - Jonathan Melamed
  - Harvey Pass
  - Natalia Botnariuc
  - Irina Caraman
  - Mircea Cernat
  - Inga Chemencedji
  - Adrian Clipca
  - Serghei Doruc
  - Ghenadie Gorincioi
  - Sergiu Mura
  - Maria Pirtac
  - Irina Stancul
  - Diana Tcaciuc
  - Monique Albert
  - Iakovina Alexopoulou
  - Angel Arnaout
  - John Bartlett
  - Jay Engel
  - Sebastien Gilbert
  - Jeremy Parfitt
  - Harman Sekhon
  - George Thomas
  - Doris M. Rassl
  - Robert C. Rintoul
  - Carlo Bifulco
  - Raina Tamakawa
  - Walter Urba
  - Nicholas Hayward
  - Henri Timmers
  - Anna Antenucci
  - Francesco Facciolo
  - Gianluca Grazi
  - Mirella Marino
  - Roberta Merola
  - Ronald de Krijger
  - Anne-Paule Gimenez-Roqueplo
  - "Alain Pich\xE9"
  - Simone Chevalier
  - Ginette McKercher
  - Kivanc Birsoy
  - Gene Barnett
  - Cathy Brewer
  - Carol Farver
  - Theresa Naska
  - Nathan A. Pennell
  - Daniel Raymond
  - Cathy Schilero
  - Kathy Smolenski
  - Felicia Williams
  - Carl Morrison
  - Jeffrey A. Borgia
  - Michael J. Liptay
  - Mark Pool
  - Christopher W. Seder
  - Kerstin Junker
  - Larsson Omberg
  - Mikhail Dinkin
  - George Manikhas
  - Domenico Alvaro
  - Maria Consiglia Bragazzi
  - Vincenzo Cardinale
  - Guido Carpino
  - Eugenio Gaudio
  - David Chesla
  - Sandra Cottingham
  - Michael Dubina
  - Fedor Moiseenko
  - Renumathy Dhanasekaran
  - Karl-Friedrich Becker
  - Klaus-Peter Janssen
  - Julia Slotta-Huspenina
  - Mohamed H. Abdel-Rahman
  - Dina Aziz
  - Sue Bell
  - Colleen M. Cebulla
  - Amy Davis
  - Rebecca Duell
  - J. Bradley Elder
  - Joe Hilty
  - Bahavna Kumar
  - James Lang
  - Norman L. Lehman
  - Randy Mandt
  - Phuong Nguyen
  - Robert Pilarski
  - Karan Rai
  - Lynn Schoenfield
  - Kelly Senecal
  - Paul Wakely
  - Paul Hansen
  - Ronald Lechan
  - James Powers
  - Arthur Tischler
  - William E. Grizzle
  - Katherine C. Sexton
  - Alison Kastl
  - Joel Henderson
  - Sima Porten
  - Jens Waldmann
  - Martin Fassnacht
  - Sylvia L. Asa
  - Dirk Schadendorf
  - Marta Couce
  - Markus Graefen
  - Hartwig Huland
  - Guido Sauter
  - Thorsten Schlomm
  - Ronald Simon
  - Pierre Tennstedt
  - Oluwole Olabode
  - Mark Nelson
  - Oliver Bathe
  - Peter R. Carroll
  - June M. Chan
  - Philip Disaia
  - Pat Glenn
  - Robin K. Kelley
  - Charles N. Landen
  - Joanna Phillips
  - Michael Prados
  - Jeffry Simko
  - Karen Smith-McCune
  - Scott VandenBerg
  - Kevin Roggin
  - Ashley Fehrenbach
  - Ady Kendler
  - Suzanne Sifri
  - Ruth Steele
  - Antonio Jimeno
  - Francis Carey
  - Ian Forgie
  - Massimo Mannelli
  - Michael Carney
  - Brenda Hernandez
  - Benito Campos
  - Christel Herold-Mende
  - Christin Jungk
  - Andreas Unterberg
  - Andreas von Deimling
  - Aaron Bossler
  - Joseph Galbraith
  - Laura Jacobus
  - Michael Knudson
  - Tina Knutson
  - Deqin Ma
  - Mohammed Milhem
  - Rita Sigmund
  - Andrew K. Godwin
  - Rashna Madan
  - Howard G. Rosenthal
  - Clement Adebamowo
  - Sally N. Adebamowo
  - Alex Boussioutas
  - David Beer
  - Thomas Giordano
  - Anne-Marie Mes-Masson
  - Fred Saad
  - Therese Bocklage
  - Lisa Landrum
  - Robert Mannel
  - Kathleen Moore
  - Katherine Moxley
  - Russel Postier
  - Joan Walker
  - Rosemary Zuna
  - Michael Feldman
  - Federico Valdivieso
  - Rajiv Dhir
  - James Luketich
  - Edna M. Mora Pinero
  - Mario Quintero-Aguilo
  - Carlos Gilberto Carlotti
  - "Jose Sebasti\xE3o Dos Santos"
  - Rafael Kemp
  - Ajith Sankarankuty
  - Daniela Tirapelli
  - James Catto
  - Kathy Agnew
  - Elizabeth Swisher
  - Jenette Creaney
  - Bruce Robinson
  - Carl Simon Shelley
  - Eryn M. Godwin
  - Sara Kendall
  - Cassaundra Shipman
  - Carol Bradford
  - Thomas Carey
  - Andrea Haddad
  - Jeffey Moyer
  - Lisa Peterson
  - Mark Prince
  - Laura Rozek
  - Gregory Wolf
  - Rayleen Bowman
  - Kwun M. Fong
  - Ian Yang
  - Robert Korst
  - W. Kimryn Rathmell
  - J. Leigh Fantacone-Campbell
  - Jeffrey A. Hooke
  - Albert J. Kovatich
  - Craig D. Shriver
  - John DiPersio
  - Bettina Drake
  - Ramaswamy Govindan
  - Sharon Heath
  - Timothy Ley
  - Brian Van Tine
  - Peter Westervelt
  - Mark A. Rubin
  - Jung Il Lee
  - "Nat\xE1lia D. Aredes"
  - Armaz Mariamidze
  publisher: Cell Reports
  date: '2018-04-01'
  link: https://doi.org/gfspsb
  image: https://ars.els-cdn.com/content/image/1-s2.0-S2211124718303899-fx1_lrg.jpg
  repo: greenelab/pancancer
- id: 10.1186/s12864-017-3519-7
  title: A machine learning classifier trained on cancer transcriptomes detects NF1
    inactivation signal in glioblastoma
  authors:
  - Gregory P. Way
  - Robert J. Allaway
  - Stephanie J. Bouley
  - Camilo E. Fadul
  - Yolanda Sanchez
  - Casey S. Greene
  publisher: BMC Genomics
  date: '2017-02-06'
  link: https://doi.org/gg7qr9
  image: https://media.springernature.com/full/springer-static/image/art%3A10.1186%2Fs12864-017-3519-7/MediaObjects/12864_2017_3519_Fig2_HTML.gif?as=webp
  repo: greenelab/nf1_inactivation
  extra-links:
  - type: preprint
    link: https://www.biorxiv.org/content/10.1101/075382v3
    text: preprint
  - type: source
    link: https://github.com/greenelab/nf1_inactivation
    text: analysis
  - type: data
    link: https://doi.org/10.5281/zenodo.200713
    text: Zenodo archive
  - type: data
    link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE85033
    text: GEO data
- id: 10.1038/ejhg.2017.108
  title: Implicating candidate genes at GWAS signals by leveraging topologically associating
    domains
  authors:
  - Gregory P Way
  - Daniel W Youngstrom
  - Kurt D Hankenson
  - Casey S Greene
  - Struan FA Grant
  publisher: European Journal of Human Genetics
  date: '2017-08-09'
  link: https://doi.org/gbq2j6
  image: https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fejhg.2017.108/MediaObjects/41431_2017_Article_BFejhg2017108_Fig1_HTML.jpg?as=webp
  extra-links:
  - type: preprint
    link: https://doi.org/10.1101/087718
    text: preprint
  - type: source
    link: https://github.com/greenelab/tad_pathways_pipeline
    text: analysis
  - type: data
    link: https://doi.org/10.5281/zenodo.254190
    text: Zenodo archive
  - type: data
    link: https://static-content.springer.com/esm/art%3A10.1038%2Fejhg.2017.108/MediaObjects/41431_2017_BFejhg2017108_MOESM464_ESM.mp4
    text: download video
- id: 10.1038/s41598-017-10199-z
  title: Deconvolution of DNA methylation identifies differentially methylated gene
    regions on 1p36 across breast cancer subtypes
  authors:
  - Alexander J. Titus
  - Gregory P. Way
  - Kevin C. Johnson
  - Brock C. Christensen
  publisher: Scientific Reports
  date: '2017-09-14'
  link: https://doi.org/gbxv64
  image: https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41598-017-10199-z/MediaObjects/41598_2017_10199_Fig2_HTML.jpg?as=webp
  repo: Christensen-Lab-Dartmouth/brca_lowstage_DMGRs
  extra-links:
  - type: source
    link: https://github.com/Christensen-Lab-Dartmouth/brca_lowstage_DMGRs
    text: analysis
- id: 10.1007/s40471-017-0115-y
  title: Challenges and Opportunities in Studying the Epidemiology of Ovarian Cancer
    Subtypes
  authors:
  - Jennifer Anne Doherty
  - Lauren Cole Peres
  - Chen Wang
  - Gregory P. Way
  - Casey S. Greene
  - Joellen M. Schildkraut
  publisher: Current Epidemiology Reports
  date: '2017-07-10'
  link: https://doi.org/gg7qrv
  image: https://d3i71xaburhd42.cloudfront.net/b177abd3b27ac7d4fe17ced5eae4dd2e902c2f8a/6-Figure1-1.png
- id: 10.1534/g3.116.033514
  title: Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer
    Supports No More Than Three Subtypes
  authors:
  - Gregory P Way
  - James Rudd
  - Chen Wang
  - Habib Hamidi
  - Brooke L Fridley
  - Gottfried E Konecny
  - Ellen L Goode
  - Casey S Greene
  - Jennifer A Doherty
  publisher: G3 Genes|Genomes|Genetics
  date: '2016-12-01'
  link: https://doi.org/gg7qsd
  image: https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/g3journal/6/12/10.1534_g3.116.033514/4/4097f3.gif?Expires=1633369396&Signature=0EsDFIHM0bshy381PKGunZ9vgQcuMi2YqhUrJe-ldF3c3qPYLQgt9OWnrf1Qr2dTrEfX6smibB7Utg8cGOGgrzYyN9-7~B59JzmUAyeufyyu0PLXF0mkGzy7jW9y4T87swqTT-f1zs2upNFh6kfvMWHTf7kn3q3gizSL49CiexMWB1IACnZc3DKWv6bRguNdbj33spOjzRmRrKTOgiXpWhW9p-29eEszXKycUYLsUNRlo7vhaX3u6U-iUrp48UXftXhjUls0T7sDQSpZTaHsT~gckgmf3ImSHa5VAvbhHWKJJL6yVp2Ov6mkJ760n4xCBspUKiMiYkgNu-N2UiBQ0Q__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA
  repo: greenelab/hgsc_subtypes
  extra-links:
  - type: source
    link: https://github.com/greenelab/hgsc_subtypes
    text: analysis
  - type: data
    link: https://doi.org/10.5281/zenodo.61245
    text: Zenodo archive
- id: 10.1089/zeb.2014.1025
  title: A Comparison of Methodologies to Test Aggression in Zebrafish
  authors:
  - Gregory P. Way
  - Nathan Ruhl
  - Jennifer L. Snekser
  - Alexis L. Kiesel
  - Scott P. McRobert
  publisher: Zebrafish
  date: '2015-04-01'
  link: https://doi.org/f65dgg
  image: https://www.liebertpub.com/cms/10.1089/zeb.2014.1025/asset/images/medium/figure1.gif
  tags:
  - zebrafish
- id: 10.1016/j.beproc.2014.12.014
  title: Sex differences in a shoaling-boldness behavioral syndrome, but no link with
    aggression
  authors:
  - Gregory P. Way
  - Alexis L. Kiesel
  - Nathan Ruhl
  - Jennifer L. Snekser
  - Scott P. McRobert
  publisher: Behavioural Processes
  date: '2015-04-01'
  link: https://doi.org/f67cwk
  image: https://ars.els-cdn.com/content/image/1-s2.0-S0376635714003258-gr1.jpg
  tags:
  - zebrafish