Publications
Preprints
30 March 2019
Jo Lynne Rokita, Komal S. Rathi, Maria F. Cardenas, Kristen A. Upton, Joy Jayaseelan, Katherine L. Cross, Jacob Pfeil, Laura E. Ritenour, Apexa Modi, Alvin Farrel, Gregory P. Way, Nathan M. Kendsersky, Khushbu Patel, Gonzalo Lopez, Zalman Vaksman, Chelsea Mayoh, Jonas Nance, Kristyn McCoy, Michelle Haber, Kathryn Evans, Hannah McCalmont, Katerina Bendak, Julia W. Böhm, Glenn M. Marshall, Vanessa Tyrrell, Karthik Kalletla, Frank K. Braun, Lin Qi, Yunchen Du, Huiyuan Zhang, Holly B. Lindsay, Sibo Zhao, Jack Shu, Patricia Baxter, Christopher Morton, Dias Kurmashev, Siyuan Zheng, Yidong Chen, Jay Bowen, Anthony C. Bryan, Kristen M. Leraas, Sara E. Coppens, HarshaVardhan Doddapaneni, Zeineen Momin, Wendong Zhang, Gregory I. Sacks, Lori S. Hart, Kateryna Krytska, Yael P. Mosse, GregorJ. Gatto, Yolanda Sanchez, Casey S. Greene, Sharon J. Diskin, Olena Morozova Vaske, David Haussler, Julie M. Gastier-Foster, E. Anders Kolb, Richard Gorlick, Xiao-Nan Li, C. Patrick Reynolds, Raushan T. Kurmasheva, Peter J. Houghton, Malcolm A. Smith, Richard B. Lock, Pichai Raman, David A. Wheeler, John M. Maris
11 March 2019
Sequential compression across latent space dimensions enhances gene expression signatures
Gregory P. Way, Michael Zietz, Daniel S. Himmelstein, Casey S. Greene
Paper: https://doi.org/10.1101/573782
Software: https://github.com/greenelab/BioBombe
28 February 2019
Integrated phosphoproteomics and transcriptional classifiers reveal hidden RAS signaling dynamics in multiple myeloma
Yu-Hsiu Tony 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
Paper: https://doi.org/10.1101/563312
Software: https://github.com/greenelab/multiple-myeloma-classifier
20 September 2018
Discovering pathway and cell-type signatures in transcriptomic compendia with machine learning
Peer Reviewed
30 November 2018
Bayesian deep learning for single-cell analysis
3 July 2018
PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia
BioData Mining
Kathleen M. Chen, Jie Tan, Gregory P. Way, Georgia Doing, Deborah A. Hogan, Casey S. Greene
5 April 2018
Oncogenic signaling pathways in the cancer genome atlas
Cell
Francisco Sanchez-Vega, Marco Mina, Joshua Armenia, Walid K. Chatila, Augustin Luna, Konnor C. La, Sofia Dimitriadoy, David L. Liu, Havish S. Kantheti, Sadegh Saghafinia, Debyani Chakravarty, Foysal Daian, Qingsong Gao, Matthew H. Bailey, Wen-Wei Liang, Steven M. Foltz, Ilya Shmulevich, Li Ding, Zachary Heins, Angelica Ochoa, Benjamin Gross, Jianjiong Gao, Hongxin Zhang, Ritika Kundra, Cyriac Kandoth, Istemi Bahceci, Leonard Dervishi, Ugur Dogrusoz, Wanding Zhou, Hui Shen, Peter W. Laird, Gregory P. Way, Casey S. Greene, Han Liang, Yonghong Xiao, Chen Wang, Antonio Iavarone, Alice H. Berger, Trever G Bivona, Alexander J. Lazar, Gary D Hammer, Thomas Giordano, Lawrence N Kwong, Grant McArthur, Chenfei Huang, Aaron D. Tward, Mitchell J Frederick, Frank McCormick, Matthew Meyerson, Eliezer M. Van Allen, Andrew D. Cherniack Giovanni Ciriello, Chris Sander, Nikolaus Schultz
4 April 2018
Opportunities and obstacles for deep learning in biology and medicine
Journal of the Royal Society Interface
Travers Ching, 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
3 April 2018
Genomic and molecular landscape of DNA damage repair deficiency across The Cancer Genome Atlas
Cell Reports
Theo A. Knijnenburg, Linghua Wang, Michael T. Zimmermann, Nyasha Chambwe, Galen F. Gao, Andrew D. Cherniack, Huihui Fan, Hui Shen, Gregory P. Way, Casey S. Greene, Yuexin Liu, Rehan Akbani, Bin Feng, Lawrence A. Donehower, Chase Miller, Yang Shen, Mostafa Karimi, Haoran Chen, Pora Kim, Peilin Jia, Eve Shinbrot, Shaojun Zhang, Jianfang Liu, Hai Hu, Matthew H. Bailey, Christina Yau, Denise Wolf, Zhongming Zhao, John N. Weinstein, Lei Li, Li Ding, Gordon B. Mills, Peter W. Laird, David A. Wheeler, Ilya Shmulevich, Raymond J. Monnat Jr., Yonghong Xiao, Chen Wang
Paper: https://doi.org/10.1016/j.celrep.2018.03.076
Classifier Software: https://github.com/greenelab/pancancer
3 April 2018
Machine learning detects pan-cancer Ras pathway activation in The Cancer Genome Atlas
Cell Reports
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
Paper: https://doi.org/10.1016/j.celrep.2018.03.046
Software: https://github.com/greenelab/pancancer
3 January 2018
Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders
Proceedings of the Pacific Symposium on Biocomputing
Gregory P. Way, Casey S. Greene
Paper: https://doi.org/10.1142/9789813235533_0008
Software: https://github.com/greenelab/tybalt/
3 January 2018
Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses
Proceedings of the Pacific Symposium on Biocomputing
Lia X. Harrington, Gregory P. Way, Jennifer A. Doherty, Casey S. Greene
Paper: https://doi.org/10.1142/9789813235533_0015
Software: https://github.com/greenelab/GEA_Community_Detection
25 November 2017
Implicating candidate genes at GWAS signals by leveraging topologically associating domains
European Journal of Human Genetics
Gregory P. Way, Daniel W. Youngstrom, Kurt D. Hankenson, Casey S. Greene, Struan F.A. Grant
14 September 2017
Deconvolution of DNA methylation identifies differentially methylated gene regions on 1p36 across breast cancer subtypes
Scientific Reports
Alexander J. Titus, Gregory P. Way, Kevin C. Johnson, Brock C. Christensen
Paper: https://doi.org/10.1038/s41598-017-10199-z
Software: https://github.com/Christensen-Lab-Dartmouth/brca_lowstage_DMGRs
1 September 2017
Challenges and opportunities in studying the epidemiology of ovarian cancer subtypes
Current Epidemiology Reports
Jennifer A. Doherty, Lauren C. Peres, Chen Wang, Gregory P. Way, Casey S. Greene, Joellen M. Schildkraut
6 Februrary 2017
A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma
BMC Genomics
Gregory P. Way, Robert J. Allaway, Stephanie J. Bouley, Camilo E. Fadul, Yolanda Sanchez, Casey S. Greene
1 December 2016
Comprehensive cross-population analysis of high-grade serous ovarian cancer supports no more than three subtypes
Gregory P. Way, James Rudd, Chen Wang, Habib Hamidi, Brooke L. Fridley, Gottfried E. Konecny, Ellen L. Goode, Casey S. Greene, Jennifer A. Doherty