Computational Integration of Homolog and Pathway Gene Module Expression Reveals General Stemness Signatures

by Koeva, Martina, Forsberg, E. Camilla, Stuart, Joshua M.
Published 2011

A search engine to identify pathway genes from expression data on multiple organisms

by Chen, Chunnuan, Weirauch, Matthew T, Powell, Corey C, Zambon, Alexander C, Stuart, Joshua M
Published 2007

Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies

by Tripp, H. James, Hewson, Ian, Boyarsky, Sam, Stuart, Joshua M., Zehr, Jonathan P.
Published 2011

Pathway-Based Genomics Prediction using Generalized Elastic Net

by Sokolov, Artem, Carlin, Daniel E., Paull, Evan O., Baertsch, Robert, Stuart, Joshua M.
Published 2016

Toward better benchmarking: challenge-based methods assessment in cancer genomics

by Boutros, Paul C, Margolin, Adam A, Stuart, Joshua M, Califano, Andrea, Stolovitzky, Gustavo
Published 2014

The UCSC Interaction Browser: multidimensional data views in pathway context

by Wong, Christopher K., Vaske, Charles J., Ng, Sam, Sanborn, J. Zachary, Benz, Stephen C., Haussler, David, Stuart, Joshua M.
Published 2013

RADIA: RNA and DNA Integrated Analysis for Somatic Mutation Detection

by Radenbaugh, Amie J., Ma, Singer, Ewing, Adam, Stuart, Joshua M., Collisson, Eric A., Zhu, Jingchun, Haussler, David
Published 2014

VisANT 3.0: new modules for pathway visualization, editing, prediction and construction

by Hu, Zhenjun, Ng, David M., Yamada, Takuji, Chen, Chunnuan, Kawashima, Shuichi, Mellor, Joe, Linghu, Bolan, Kanehisa, Minoru, Stuart, Joshua M., DeLisi, Charles
Published 2007

PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis

by Ng, Sam, Collisson, Eric A., Sokolov, Artem, Goldstein, Theodore, Gonzalez-Perez, Abel, Lopez-Bigas, Nuria, Benz, Christopher, Haussler, David, Stuart, Joshua M.
Published 2012

Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla

by Waltman, Peter H., Guo, Jian, Reistetter, Emily Nahas, Purvine, Samuel, Ansong, Charles K., van Baren, Marijke J., Wong, Chee-Hong, Wei, Chia-Lin, Smith, Richard D., Callister, Stephen J., Stuart, Joshua M., Worden, Alexandra Z.
Published 2016

TNF-α modulates genome-wide redistribution of ΔNp63α/TAp73 and NF-κB c-REL interactive binding on TP53 and AP-1 motifs to promote an oncogenic gene program in squamous cancer

by Si, Han, Lu, Hai, Yang, Xinping, Mattox, Austin, Jang, Minyoung, Bian, Yansong, Sano, Eleanor, Viadiu, Hector, Yan, Bin, Yau, Christina, Ng, Sam, Lee, Steven K., Romano, Rose-Anne, Davis, Sean, Walker, Robert L., Xiao, Wenming, Sun, Hongwei, Wei, Lai, Sinha, Satrajit, Benz, Christopher C, Stuart, Joshua M., Meltzer, Paul S., Van Waes, Carter, Chen, Zhong
Published 2016

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection

by Ewing, Adam D, Houlahan, Kathleen E, Hu, Yin, Ellrott, Kyle, Caloian, Cristian, Yamaguchi, Takafumi N, Bare, J Christopher, P’ng, Christine, Waggott, Daryl, Sabelnykova, Veronica Y, Kellen, Michael R, Norman, Thea C, Haussler, David, Friend, Stephen H, Stolovitzky, Gustavo, Margolin, Adam A, Stuart, Joshua M, Boutros, Paul C
Published 2015

Inferring causal molecular networks: empirical assessment through a community-based effort

by Hill, Steven M., Heiser, Laura M., Cokelaer, Thomas, Unger, Michael, Nesser, Nicole K., Carlin, Daniel E., Zhang, Yang, Sokolov, Artem, Paull, Evan O., Wong, Chris K., Graim, Kiley, Bivol, Adrian, Wang, Haizhou, Zhu, Fan, Afsari, Bahman, Danilova, Ludmila V., Favorov, Alexander V., Lee, Wai Shing, Taylor, Dane, Hu, Chenyue W., Long, Byron L., Noren, David P., Bisberg, Alexander J., Mills, Gordon B., Gray, Joe W., Kellen, Michael, Norman, Thea, Friend, Stephen, Qutub, Amina A., Fertig, Elana J., Guan, Yuanfang, Song, Mingzhou, Stuart, Joshua M., Spellman, Paul T., Koeppl, Heinz, Stolovitzky, Gustavo, Saez-Rodriguez, Julio, Mukherjee, Sach
Published 2016

Whole Genome Analysis Informs Breast Cancer Response to Aromatase Inhibition

by Ellis, Matthew J., Ding, Li, Shen, Dong, Luo, Jingqin, Suman, Vera J., Wallis, John W., Van Tine, Brian A., Hoog, Jeremy, Goiffon, Reece J., Goldstein, Theodore C., Ng, Sam, Lin, Li, Crowder, Robert, Snider, Jacqueline, Ballman, Karla, Weber, Jason, Chen, Ken, Koboldt, Daniel C., Kandoth, Cyriac, Schierding, William S., McMichael, Joshua F., Miller, Christopher A., Lu, Charles, Harris, Christopher C., McLellan, Michael D., Wendl, Michael C., DeSchryver, Katherine, Allred, D. Craig, Esserman, Laura, Unzeitig, Gary, Margenthaler, Julie, Babiera, G.V., Marcom, P. Kelly, Guenther, J.M., Leitch, Marilyn, Hunt, Kelly, Olson, John, Tao, Yu, Maher, Christopher A., Fulton, Lucinda L., Fulton, Robert S., Harrison, Michelle, Oberkfell, Ben, Du, Feiyu, Demeter, Ryan, Vickery, Tammi L., Elhammali, Adnan, Piwnica-Worms, Helen, McDonald, Sandra, Watson, Mark, Dooling, David J., Ota, David, Chang, Li-Wei, Bose, Ron, Ley, Timothy J., Piwnica-Worms, David, Stuart, Joshua M., Wilson, Richard K., Mardis, Elaine R.
Published 2012