A Machine-Learning Tool Concurrently Models Single Omics and Phenome Data for Functional Subtyping and Personalized Cancer Medicine

by Gift Nyamundanda, Katherine Eason, Justin Guinney, Christopher J. Lord, Anguraj Sadanandam
Published 2020-09-01

Probing the chemical–biological relationship space with the Drug Target Explorer

by Robert J. Allaway, Salvatore La Rosa, Justin Guinney, Sara J. C. Gosline
Published 2018-08-01

Modeling cancer progression via pathway dependencies.

by Elena J Edelman, Justin Guinney, Jen-Tsan Chi, Phillip G Febbo, Sayan Mukherjee
Published 2008-02-01

CRI iAtlas: an interactive portal for immuno-oncology research [version 1; peer review: 2 approved]

by James A. Eddy, Vésteinn Thorsson, Andrew E. Lamb, David L. Gibbs, Carolina Heimann, Jia Xin Yu, Verena Chung, Yooree Chae, Kristen Dang, Benjamin G. Vincent, Ilya Shmulevich, Justin Guinney
Published 2020-08-01

Integrative Analysis Identifies Candidate Tumor Microenvironment and Intracellular Signaling Pathways that Define Tumor Heterogeneity in NF1

by Jineta Banerjee, Robert J Allaway, Jaclyn N Taroni, Aaron Baker, Xiaochun Zhang, Chang In Moon, Christine A Pratilas, Jaishri O Blakeley, Justin Guinney, Angela Hirbe, Casey S Greene, Sara JC Gosline
Published 2020-02-01

Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges

by Kyle Ellrott, Alex Buchanan, Allison Creason, Michael Mason, Thomas Schaffter, Bruce Hoff, James Eddy, John M. Chilton, Thomas Yu, Joshua M. Stuart, Julio Saez-Rodriguez, Gustavo Stolovitzky, Paul C. Boutros, Justin Guinney
Published 2019-09-01

Society for Immunotherapy of Cancer clinical and biomarkers data sharing resource document: Volume II—practical challenges

by Ena Wang, Alessandra Cesano, Beatrix Kotlan, Mohan Karkada, Nicholas Tschernia, Aung Naing, Bruno Gomes, Anne Monette, Vésteinn Thórsson, Sergio Rutella, Vaios Karanikas, Michael A Cannarile, Justin Guinney, Giuseppe V Masucci, Els Meeusen, Daniel K Wells, Timothy L Wyant
Published 2020-07-01

The evolution and multi-molecular properties of NF1 cutaneous neurofibromas originating from C-fiber sensory endings and terminal Schwann cells at normal sites of sensory terminati...

by Frank L Rice, George Houk, James P Wymer, Sara J C Gosline, Justin Guinney, Jianqiang Wu, Nancy Ratner, Michael P Jankowski, Salvo La Rosa, Marilyn Dockum, James R Storey, Steven L Carroll, Phillip J Albrecht, Vincent M Riccardi
Published 2019-01-01

CTCF Haploinsufficiency Destabilizes DNA Methylation and Predisposes to Cancer

by Christopher J. Kemp, James M. Moore, Russell Moser, Brady Bernard, Matt Teater, Leslie E. Smith, Natalia A. Rabaia, Kay E. Gurley, Justin Guinney, Stephanie E. Busch, Rita Shaknovich, Victor V. Lobanenkov, Denny Liggitt, Ilya Shmulevich, Ari Melnick, Galina N. Filippova
Published 2014-05-01

Bayesian multi-source regression and monocyte-associated gene expression predict BCL-2 inhibitor resistance in acute myeloid leukemia

by Brian S. White, Suleiman A. Khan, Mike J. Mason, Muhammad Ammad-ud-din, Swapnil Potdar, Disha Malani, Heikki Kuusanmäki, Brian J. Druker, Caroline Heckman, Olli Kallioniemi, Stephen E. Kurtz, Kimmo Porkka, Cristina E. Tognon, Jeffrey W. Tyner, Tero Aittokallio, Krister Wennerberg, Justin Guinney
Published 2021-07-01

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells

by Theodoros I. Roumeliotis, Steven P. Williams, Emanuel Gonçalves, Clara Alsinet, Martin Del Castillo Velasco-Herrera, Nanne Aben, Fatemeh Zamanzad Ghavidel, Magali Michaut, Michael Schubert, Stacey Price, James C. Wright, Lu Yu, Mi Yang, Rodrigo Dienstmann, Justin Guinney, Pedro Beltrao, Alvis Brazma, Mercedes Pardo, Oliver Stegle, David J. Adams, Lodewyk Wessels, Julio Saez-Rodriguez, Ultan McDermott, Jyoti S. Choudhary
Published 2017-08-01

Improving breast cancer survival analysis through competition-based multidimensional modeling.

by Erhan Bilal, Janusz Dutkowski, Justin Guinney, In Sock Jang, Benjamin A Logsdon, Gaurav Pandey, Benjamin A Sauerwine, Yishai Shimoni, Hans Kristian Moen Vollan, Brigham H Mecham, Oscar M Rueda, Jorg Tost, Christina Curtis, Mariano J Alvarez, Vessela N Kristensen, Samuel Aparicio, Anne-Lise Børresen-Dale, Carlos Caldas, Andrea Califano, Stephen H Friend, Trey Ideker, Eric E Schadt, Gustavo A Stolovitzky, Adam A Margolin
Published 2013-01-01

Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection

by Anna Y. Lee, Adam D. Ewing, Kyle Ellrott, Yin Hu, Kathleen E. Houlahan, J. Christopher Bare, Shadrielle Melijah G. Espiritu, Vincent Huang, Kristen Dang, Zechen Chong, Cristian Caloian, Takafumi N. Yamaguchi, ICGC-TCGA DREAM Somatic Mutation Calling Challenge Participants, Michael R. Kellen, Ken Chen, Thea C. Norman, Stephen H. Friend, Justin Guinney, Gustavo Stolovitzky, David Haussler, Adam A. Margolin, Joshua M. Stuart, Paul C. Boutros
Published 2018-11-01

Crowdsourced mapping of unexplored target space of kinase inhibitors

by Anna Cichońska, Balaguru Ravikumar, Robert J. Allaway, Fangping Wan, Sungjoon Park, Olexandr Isayev, Shuya Li, Michael Mason, Andrew Lamb, Ziaurrehman Tanoli, Minji Jeon, Sunkyu Kim, Mariya Popova, Stephen Capuzzi, Jianyang Zeng, Kristen Dang, Gregory Koytiger, Jaewoo Kang, Carrow I. Wells, Timothy M. Willson, The IDG-DREAM Drug-Kinase Binding Prediction Challenge Consortium, Tudor I. Oprea, Avner Schlessinger, David H. Drewry, Gustavo Stolovitzky, Krister Wennerberg, Justin Guinney, Tero Aittokallio
Published 2021-06-01

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

by Michael P. Menden, Dennis Wang, Mike J. Mason, Bence Szalai, Krishna C. Bulusu, Yuanfang Guan, Thomas Yu, Jaewoo Kang, Minji Jeon, Russ Wolfinger, Tin Nguyen, Mikhail Zaslavskiy, AstraZeneca-Sanger Drug Combination DREAM Consortium, In Sock Jang, Zara Ghazoui, Mehmet Eren Ahsen, Robert Vogel, Elias Chaibub Neto, Thea Norman, Eric K. Y. Tang, Mathew J. Garnett, Giovanni Y. Di Veroli, Stephen Fawell, Gustavo Stolovitzky, Justin Guinney, Jonathan R. Dry, Julio Saez-Rodriguez
Published 2019-06-01

Predictive genes in adjacent normal tissue are preferentially altered by sCNV during tumorigenesis in liver cancer and may rate limiting.

by John R Lamb, Chunsheng Zhang, Tao Xie, Kai Wang, Bin Zhang, Ke Hao, Eugene Chudin, Hunter B Fraser, Joshua Millstein, Mark Ferguson, Christine Suver, Irena Ivanovska, Martin Scott, Ulrike Philippar, Dimple Bansal, Zhan Zhang, Julja Burchard, Ryan Smith, Danielle Greenawalt, Michele Cleary, Jonathan Derry, Andrey Loboda, James Watters, Ronnie T P Poon, Sheung T Fan, Chun Yeung, Nikki P Y Lee, Justin Guinney, Cliona Molony, Valur Emilsson, Carolyn Buser-Doepner, Jun Zhu, Stephen Friend, Mao Mao, Peter M Shaw, Hongyue Dai, John M Luk, Eric E Schadt
Published 2011-01-01

Traditional and systems biology based drug discovery for the rare tumor syndrome neurofibromatosis type 2.

by Synodos for NF2 Consortium, Robert Allaway, Steve P Angus, Roberta L Beauchamp, Jaishri O Blakeley, Marga Bott, Sarah S Burns, Annemarie Carlstedt, Long-Sheng Chang, Xin Chen, D Wade Clapp, Patrick A Desouza, Serkan Erdin, Cristina Fernandez-Valle, Justin Guinney, James F Gusella, Stephen J Haggarty, Gary L Johnson, Salvatore La Rosa, Helen Morrison, Alejandra M Petrilli, Scott R Plotkin, Abhishek Pratap, Vijaya Ramesh, Noah Sciaky, Anat Stemmer-Rachamimov, Tim J Stuhlmiller, Michael E Talkowski, D Bradley Welling, Charles W Yates, Jon S Zawistowski, Wen-Ning Zhao
Published 2018-01-01

Brigatinib causes tumor shrinkage in both NF2-deficient meningioma and schwannoma through inhibition of multiple tyrosine kinases but not ALK.

by Long-Sheng Chang, Janet L Oblinger, Abbi E Smith, Marc Ferrer, Steven P Angus, Eric Hawley, Alejandra M Petrilli, Roberta L Beauchamp, Lars Björn Riecken, Serkan Erdin, Ming Poi, Jie Huang, Waylan K Bessler, Xiaohu Zhang, Rajarshi Guha, Craig Thomas, Sarah S Burns, Thomas S K Gilbert, Li Jiang, Xiaohong Li, Qingbo Lu, Jin Yuan, Yongzheng He, Shelley A H Dixon, Andrea Masters, David R Jones, Charles W Yates, Stephen J Haggarty, Salvatore La Rosa, D Bradley Welling, Anat O Stemmer-Rachamimov, Scott R Plotkin, James F Gusella, Justin Guinney, Helen Morrison, Vijaya Ramesh, Cristina Fernandez-Valle, Gary L Johnson, Jaishri O Blakeley, D Wade Clapp, Synodos for NF2 Consortium
Published 2021-01-01