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2020 – today
- 2023
[d1]John N. Weinstein, Eric A. Collisson, Gordon B. Mills, Kenna R. Mills Shaw, Brad A. Ozenberger, Kyle Ellrott, Ilya Shmulevich, Chris Sander, Joshua M. Stuart:
TCGA Kidney Cancers. UCI Machine Learning Repository, 2023
- 2021
- [j19]Vladislav Uzunangelov
, Christopher K. Wong, Joshua M. Stuart:
Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel learner integrating multimodal genomic data and pathway knowledge. PLoS Comput. Biol. 17(4) (2021) - 2020
- [j18]Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah Wala, Ofer Shapira, Grace Tiao, Henrik Hornshøj, Julian M. Hess, Randi Istrup Juul, Ziao Lin, Lars Feuerbach, Radhakrishnan Sabarinathan, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andrés Lanzós, Carl Herrmann, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin, Pratiti Bandopadhayay, Johanna Bertl, Keith A. Boroevich, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, David Craft, Priyanka Dhingra, Klev Diamanti, Nuno A. Fonseca, Abel Gonzalez-Perez, Qianyun Guo, Mark P. Hamilton, Nicholas J. Haradhvala, Chen Hong, Keren Isaev, Todd A. Johnson, Malene Juul, André Kahles, Abdullah Kahraman, Youngwook Kim, Jan Komorowski, Kiran Kumar, Sushant Kumar, Donghoon Lee, Kjong-Van Lehmann, Yilong Li, Eric Minwei Liu, Lucas Lochovsky, Keunchil Park, Oriol Pich, Nicola D. Roberts, Gordon Saksena, Steven E. Schumacher, Nikos Sidiropoulos, Lina Sieverling, Nasa Sinnott-Armstrong, Chip Stewart, David Tamborero, Jose M. C. Tubio, Husen M. Umer, Liis Uusküla-Reimand, Claes Wadelius, Lina Wadi, Xiaotong Yao, Cheng-Zhong Zhang, Jing Zhang, James E. Haber, Asger Hobolth, Marcin Imielinski, Manolis Kellis, Michael S. Lawrence, Christian von Mering, Hidewaki Nakagawa, Benjamin J. Raphael, Mark A. Rubin, Chris Sander, Lincoln D. Stein, Joshua M. Stuart, Tatsuhiko Tsunoda, David A. Wheeler, Rory Johnson, Jüri Reimand, Mark Gerstein, Ekta Khurana, Peter J. Campbell, Núria López-Bigas, Gary D. Bader, Jonathan Barenboim, Rameen Beroukhim, Søren Brunak, Ken Chen, Jung Kyoon Choi, Jordi Deu-Pons, J. Lynn Fink, Joan Frigola, Carlo Gambacorti Passerini, Dale W. Garsed, Gad Getz, Ivo Glynne Gut, David Haan, Arif Ozgun Harmanci, Mohamed Helmy, Ermin Hodzic, José M. G. Izarzugaza, Jong K. Kim, Jan O. Korbel, Erik Larsson, Shantao Li, Xiaotong Li, Shaoke Lou, Kathleen Marchal, Iñigo Martincorena, Alexander Martínez-Fundichely, Patrick D. McGillivray, William Meyerson, Ferran Muiños, Marta Paczkowska, Kiejung Park, Jakob Skou Pedersen, Tirso Pons, Sergio Pulido-Tamayo, Iker Reyes-Salazar, Matthew A. Reyna, Carlota Rubio-Perez, Süleyman Cenk Sahinalp, Leonidas Salichos, Mark Shackleton, Raunak Shrestha, Alfonso Valencia, Miguel Vazquez, Lieven P. C. Verbeke, Jiayin Wang, Jonathan Warrell, Sebastian M. Waszak, Joachim Weischenfeldt, Guanming Wu, Jun Yu, Xuanping Zhang, Yan Zhang, Zhongming Zhao, Lihua Zou, Kadir C. Akdemir, Eva G. Alvarez, Adrian Baez-Ortega, Paul C. Boutros, David D. L. Bowtell, Benedikt Brors, Kathleen H. Burns, Kin Chan, Isidro Cortés-Ciriano, Ana Dueso-Barroso, Andrew J. Dunford, Paul A. Edwards, Xavier Estivill, Dariush Etemadmoghadam, Milana Frenkel-Morgenstern, Dmitry A. Gordenin, Barbara Hutter, David T. W. Jones, Young Seok Ju, Marat D. Kazanov, Leszek J. Klimczak, Youngil Koh, Eunjung Alice Lee, Jake June-Koo Lee, Andy G. Lynch, Geoff MacIntyre, Florian Markowetz, Matthew Meyerson, Satoru Miyano, Fabio C. P. Navarro, Stephan Ossowski, Peter J. Park, John V. Pearson, Montserrat Puiggròs, Karsten Rippe, Steven A. Roberts, Bernardo Rodriguez-Martin, Ralph Scully, David Torrents, Izar Villasante, Nicola Waddell, Jeremiah A. Wala, Lixing Yang, Sung-Soo Yoon, Jorge Zamora:
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 578(7793): 102-111 (2020) - [c16]David Haan, Ruikang Tao, Verena Friedl, Ioannis N. Anastopoulos, Christopher K. Wong, Alana S. Weinstein, Joshua M. Stuart:
Using Transcriptional Signatures to Find Cancer Drivers with LURE. PSB 2020: 343-354
2010 – 2019
- 2019
- [c15]Kiley Graim, Verena Friedl, Kathleen E. Houlahan, Joshua M. Stuart:
PLATYPUS: A Multiple-View Learning Predictive Framework for Cancer Drug Sensitivity Prediction. PSB 2019: 136-147 - 2018
- [j17]Dorota H. Sendorek, Cristian Caloian, Kyle Ellrott, J. Christopher Bare, Takafumi N. Yamaguchi, Adam D. Ewing, Kathleen E. Houlahan, Thea C. Norman, Adam A. Margolin, Joshua M. Stuart, Paul C. Boutros:
Germline contamination and leakage in whole genome somatic single nucleotide variant detection. BMC Bioinform. 19(1): 28:1-28:9 (2018) - [j16]Christopher I Cooper, Delia Yao, Dorota H. Sendorek, Takafumi N. Yamaguchi, Christine P'ng, Kathleen E. Houlahan, Cristian Caloian, Michael Fraser, Kyle Ellrott, Adam A. Margolin, Robert G. Bristow, Joshua M. Stuart, Paul C. Boutros:
Valection: design optimization for validation and verification studies. BMC Bioinform. 19(1): 339:1-339:11 (2018) - 2017
- [c14]Pablo Cordero, Joshua M. Stuart:
Tracing Co-Regulatory Network Dynamics in Noisy, Single-Cell Transcriptome Trajectories. PSB 2017: 576-587 - 2016
- [j15]Artem Sokolov, Daniel E. Carlin, Evan O. Paull, Robert Baertsch, Joshua M. Stuart:
Pathway-Based Genomics Prediction using Generalized Elastic Net. PLoS Comput. Biol. 12(3) (2016) - [c13]Artem Sokolov, Evan O. Paull, Joshua M. Stuart:
One-Class Detection of Cell States in Tumor Subtypes. PSB 2016: 405-416 - 2015
- [j14]Benedict Paten, Mark Diekhans, Brian J. Druker, Stephen H. Friend, Justin Guinney, Nadine Gassner, Mitchell Guttman, W. James Kent, Patrick Mantey, Adam A. Margolin, Matt Massie, Adam M. Novak, Frank A. Nothaft, Lior Pachter, David A. Patterson, Maciej Smuga-Otto, Joshua M. Stuart, Laura J. van't Veer, Barbara J. Wold, David Haussler:
The NIH BD2K center for big data in translational genomics. J. Am. Medical Informatics Assoc. 22(6): 1143-1147 (2015) - [c12]Søren Brunak, Francisco M. de la Vega, Adam A. Margolin, Benjamin J. Raphael, Gunnar Rätsch, Joshua M. Stuart:
Session Introduction. Pacific Symposium on Biocomputing 2015: 8-9 - 2014
- [c11]Søren Brunak, Francisco M. de la Vega, Gunnar Rätsch, Joshua M. Stuart:
Session Introduction. Pacific Symposium on Biocomputing 2014: 1-2 - 2013
- [j13]Evan O. Paull, Daniel E. Carlin, Mario Niepel, Peter K. Sorger, David Haussler, Joshua M. Stuart:
Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE). Bioinform. 29(21): 2757-2764 (2013) - [j12]Mary Goldman, Brian Craft, Teresa Swatloski, Kyle Ellrott, Melissa S. Cline, Mark Diekhans, Singer Ma, Chris Wilks, Joshua M. Stuart, David Haussler, Jingchun Zhu:
The UCSC Cancer Genomics Browser: update 2013. Nucleic Acids Res. 41(Database-Issue): 949-954 (2013) - [j11]Christopher K. Wong, Charles J. Vaske, Sam Ng, J. Zachary Sanborn, Stephen C. Benz, David Haussler, Joshua M. Stuart:
The UCSC Interaction Browser: multidimensional data views in pathway context. Nucleic Acids Res. 41(Webserver-Issue): 218-224 (2013) - [c10]Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, Trey Ideker, Joel S. Bader:
Session Introduction. Pacific Symposium on Biocomputing 2013: 103-110 - 2012
- [j10]Sam Ng, Eric A. Collisson, Artem Sokolov, Theodore Goldstein, Abel Gonzalez-Perez, Núria López-Bigas, Christopher Benz, David Haussler, Joshua M. Stuart:
PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis. Bioinform. 28(18): 640-646 (2012) - [c9]Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, Joel S. Bader:
Session Introduction. Pacific Symposium on Biocomputing 2012: 1-6 - 2011
- [j9]J. Zachary Sanborn, Stephen C. Benz, Brian Craft, Christopher Szeto, Kord M. Kober, Laurence R. Meyer, Charles J. Vaske, Mary Goldman, Kayla E. Smith, Robert M. Kuhn, Donna Karolchik, W. James Kent, Joshua M. Stuart, David Haussler, Jingchun Zhu:
The UCSC cancer genomics browser: update 2011. Nucleic Acids Res. 39(Database-Issue): 951-959 (2011) - 2010
- [j8]Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, Joshua M. Stuart:
Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinform. 26(12): 237-245 (2010)
2000 – 2009
- 2009
- [j7]Martina Koeva, E. Camilla Forsberg, Joshua M. Stuart:
Core stemness mechanisms revealed through homology. BMC Bioinform. 10(S-13): 0 (2009) - [j6]Charles J. Vaske, Carrie House, Truong Luu, Bryan Frank, Chen-Hsiang Yeang, Norman H. Lee, Joshua M. Stuart:
A Factor Graph Nested Effects Model To Identify Networks from Genetic Perturbations. PLoS Comput. Biol. 5(1) (2009) - [c8]Pinal N. Kanabar, Charles J. Vaske, Chen-Hsiang Yeang, Fitnat H. Yildiz, Joshua M. Stuart:
Inferring Disease-Related Pathways Using A Probabilistic Epistasis Model. Pacific Symposium on Biocomputing 2009: 480-491 - 2008
- [j5]Matthew T. Weirauch, Christopher K. Wong, Alexandra B. Byrne, Joshua M. Stuart:
Information-based methods for predicting gene function from systematic gene knock-downs. BMC Bioinform. 9 (2008) - 2007
- [j4]Nathan Salomonis, Kristina Hanspers, Alexander C. Zambon, Karen Vranizan, Steven C. Lawlor, Kam D. Dahlquist, Scott Doniger, Joshua M. Stuart, Bruce R. Conklin, Alexander R. Pico:
GenMAPP 2: new features and resources for pathway analysis. BMC Bioinform. 8 (2007) - [j3]Chunnuan Chen, Matthew T. Weirauch, Corey Powell, Alexander C. Zambon, Joshua M. Stuart:
A search engine to identify pathway genes from expression data on multiple organisms. BMC Syst. Biol. 1: 20 (2007) - [j2]Zhenjun Hu, David M. Ng, Takuji Yamada, Chunnuan Chen, Shuichi Kawashima, Joe Mellor, Bolan Linghu, Minoru Kanehisa, Joshua M. Stuart, Charles DeLisi:
VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. Nucleic Acids Res. 35(Web-Server-Issue): 625-632 (2007) - [c7]David M. Ng, Marcos H. Woehrmann, Joshua M. Stuart:
Recommending Pathway Genes Using a Compendium of Clustering Solutions. Pacific Symposium on Biocomputing 2007: 379-390 - 2005
- [c6]Corey Powell, Joshua M. Stuart:
A Novel Quartet-Based Method for Phylogenetic Inference. CSB Workshops 2005: 59-60 - [c5]Corey Powell, Joshua M. Stuart:
Biological Pathway Prediction from Multiple Data Sources Using Iterative Bayesian Updating. CSB Workshops 2005: 159-160 - [c4]Matthew T. Weirauch, Joshua M. Stuart:
Discovering Functional Transcription Factor Binding from Superimposed Gene Networks. CSB Workshops 2005: 178-179 - 2002
- [j1]Micheal Hewett, Diane E. Oliver, Daniel L. Rubin, Katrina L. Easton, Joshua M. Stuart, Russ B. Altman, Teri E. Klein:
PharmGKB: the Pharmacogenetics Knowledge Base. Nucleic Acids Res. 30(1): 163-165 (2002) - [c3]Diane E. Oliver, Daniel L. Rubin, Joshua M. Stuart, Micheal Hewett, Teri E. Klein, Russ B. Altman:
Ontology Development for a Pharmacogenetics Knowledge Base. Pacific Symposium on Biocomputing 2002: 65-76 - 2000
- [c2]Soumya Raychaudhuri, Joshua M. Stuart, Xuemin Liu, Peter M. Small, Russ B. Altman:
Pattern Recognition of Genomic Features with Microarrays: Site Typing of Mycobacterium Tuberculosis Strains. ISMB 2000: 286-295
1990 – 1999
- 1998
- [c1]Joshua M. Stuart, Elizabeth Bradley:
Learning the Grammar of Dance. ICML 1998: 547-555
Coauthor Index
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