©2019 by Gregory Way

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

Paper: https://doi.org/10.1101/566455

Software: https://github.com/marislab/pdx-classification

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

Gregory P. Way, Casey S. Greene

Paper: https://peerj.com/preprints/27229/

Peer Reviewed

30 November 2018

Bayesian deep learning for single-cell analysis

Nature Methods

Gregory P. Way, Casey S. Greene

Paper: https://doi.org/10.1038/s41592-018-0230-9

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

Paper: https://doi.org/10.1186/s13040-018-0175-7

Software: https://github.com/greenelab/PathCORE-T-analysis

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

Paper: https://doi.org/10.1016/j.cell.2018.03.035

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

Paper: https://doi.org/10.1098/rsif.2017.0387

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

Paper: https://doi.org/10.1038/ejhg.2017.108

Software: https://github.com/greenelab/tad_pathways

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

Paper: https://doi.org/10.1007/s40471-017-0115-y

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

Paper: https://doi.org/10.1186/s12864-017-3519-7

Software: https://github.com/greenelab/nf1_inactivation

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

Paper: https://doi.org/10.1534/g3.116.033514

Software: https://github.com/greenelab/hgsc_subtypes