Joshua M. Stuart

35 papers A* 1A 1Misc 11Journal 19Unranked 3

Year	Rank	Type	Title / Venue / Authors
2021	J	`jnl`	Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel learner integrating multimodal genomic data and pathway knowledge. PLoS Comput. Biol. Vladislav Uzunangelov, Christopher K. Wong, Joshua M. Stuart
2020	J	`jnl`	Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 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 González-Pérez, 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
2020	Misc	`conf`	Using Transcriptional Signatures to Find Cancer Drivers with LURE. PSB David Haan, Ruikang Tao, Verena Friedl, Ioannis N. Anastopoulos, Christopher K. Wong, Alana S. Weinstein, Joshua M. Stuart
2019	Misc	`conf`	PLATYPUS: A Multiple-View Learning Predictive Framework for Cancer Drug Sensitivity Prediction. PSB Kiley Graim, Verena Friedl, Kathleen E. Houlahan, Joshua M. Stuart
2018	J	`jnl`	Germline contamination and leakage in whole genome somatic single nucleotide variant detection. BMC Bioinform. 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
2018	J	`jnl`	Valection: design optimization for validation and verification studies. BMC Bioinform. 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
2017	Misc	`conf`	Tracing Co-Regulatory Network Dynamics in Noisy, Single-Cell Transcriptome Trajectories. PSB Pablo Cordero, Joshua M. Stuart
2016	Misc	`conf`	One-Class Detection of Cell States in Tumor Subtypes. PSB Artem Sokolov, Evan O. Paull, Joshua M. Stuart
2016	J	`jnl`	Pathway-Based Genomics Prediction using Generalized Elastic Net. PLoS Comput. Biol. Artem Sokolov, Daniel E. Carlin, Evan O. Paull, Robert Baertsch, Joshua M. Stuart
2015	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Søren Brunak, Francisco M. de la Vega, Adam A. Margolin, Benjamin J. Raphael, Gunnar Rätsch, Joshua M. Stuart
2015	J	`jnl`	The NIH BD2K center for big data in translational genomics. J. Am. Medical Informatics Assoc. 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
2014	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Søren Brunak, Francisco M. de la Vega, Gunnar Rätsch, Joshua M. Stuart
2013	J	`jnl`	Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE). Bioinform. Evan O. Paull, Daniel E. Carlin, Mario Niepel, Peter K. Sorger, David Haussler, Joshua M. Stuart
2013	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, Trey Ideker, Joel S. Bader
2013	J	`jnl`	The UCSC Cancer Genomics Browser: update 2013. Nucleic Acids Res. Mary Goldman, Brian Craft, Teresa Swatloski, Kyle Ellrott, Melissa S. Cline, Mark Diekhans, Singer Ma, Chris Wilks, Joshua M. Stuart, David Haussler, Jingchun Zhu
2013	J	`jnl`	The UCSC Interaction Browser: multidimensional data views in pathway context. Nucleic Acids Res. Christopher K. Wong, Charles J. Vaske, Sam Ng, J. Zachary Sanborn, Stephen C. Benz, David Haussler, Joshua M. Stuart
2012	J	`jnl`	PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis. Bioinform. Sam Ng, Eric A. Collisson, Artem Sokolov, Theodore Goldstein, Abel González-Pérez, Núria López-Bigas, Christopher Benz, David Haussler, Joshua M. Stuart
2012	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, Joel S. Bader
2011	J	`jnl`	The UCSC cancer genomics browser: update 2011. Nucleic Acids Res. 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
2010	J	`jnl`	Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinform. Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, Joshua M. Stuart
2009	J	`jnl`	A Factor Graph Nested Effects Model To Identify Networks from Genetic Perturbations. PLoS Comput. Biol. Charles J. Vaske, Carrie House, Truong Luu, Bryan Frank, Chen-Hsiang Yeang, Norman H. Lee, Joshua M. Stuart
2009	J	`jnl`	Core stemness mechanisms revealed through homology. BMC Bioinform. Martina Koeva, E. Camilla Forsberg, Joshua M. Stuart
2009	Misc	`conf`	Inferring Disease-Related Pathways Using A Probabilistic Epistasis Model. Pacific Symposium on Biocomputing Pinal N. Kanabar, Charles J. Vaske, Chen-Hsiang Yeang, Fitnat H. Yildiz, Joshua M. Stuart
2008	J	`jnl`	Information-based methods for predicting gene function from systematic gene knock-downs. BMC Bioinform. Matthew T. Weirauch, Christopher K. Wong, Alexandra B. Byrne, Joshua M. Stuart
2007	J	`jnl`	A search engine to identify pathway genes from expression data on multiple organisms. BMC Syst. Biol. Chunnuan Chen, Matthew T. Weirauch, Corey Powell, Alexander C. Zambon, Joshua M. Stuart
2007	J	`jnl`	GenMAPP 2: new features and resources for pathway analysis. BMC Bioinform. 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
2007	Misc	`conf`	Recommending Pathway Genes Using a Compendium of Clustering Solutions. Pacific Symposium on Biocomputing David M. Ng, Marcos H. Woehrmann, Joshua M. Stuart
2007	J	`jnl`	VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. Nucleic Acids Res. Zhenjun Hu, David M. Ng, Takuji Yamada, Chunnuan Chen, Shuichi Kawashima, Joe Mellor, Bolan Linghu, Minoru Kanehisa, Joshua M. Stuart, Charles DeLisi
2005	—	`conf`	A Novel Quartet-Based Method for Phylogenetic Inference. CSB Workshops Corey Powell, Joshua M. Stuart
2005	—	`conf`	Biological Pathway Prediction from Multiple Data Sources Using Iterative Bayesian Updating. CSB Workshops Corey Powell, Joshua M. Stuart
2005	—	`conf`	Discovering Functional Transcription Factor Binding from Superimposed Gene Networks. CSB Workshops Matthew T. Weirauch, Joshua M. Stuart
2002	Misc	`conf`	Ontology Development for a Pharmacogenetics Knowledge Base. Pacific Symposium on Biocomputing Diane E. Oliver, Daniel L. Rubin, Joshua M. Stuart, Micheal Hewett, Teri E. Klein, Russ B. Altman
2002	J	`jnl`	PharmGKB: the Pharmacogenetics Knowledge Base. Nucleic Acids Res. Micheal Hewett, Diane E. Oliver, Daniel L. Rubin, Katrina L. Easton, Joshua M. Stuart, Russ B. Altman, Teri E. Klein
2000	A	`conf`	Pattern Recognition of Genomic Features with Microarrays: Site Typing of Mycobacterium Tuberculosis Strains. ISMB Soumya Raychaudhuri, Joshua M. Stuart, Xuemin Liu, Peter M. Small, Russ B. Altman
1998	A*	`conf`	Learning the Grammar of Dance. ICML Joshua M. Stuart, Elizabeth Bradley