TRACING CO-REGULATORY NETWORK DYNAMICS IN NOISY, SINGLE-CELL TRANSCRIPTOME TRAJECTORIES

av Cordero, Pablo, Stuart, Joshua M.
I publikationen Pac Symp Biocomput (2016)

PRINCIPAL COMPONENTS ANALYSIS TO SUMMARIZE MICROARRAY EXPERIMENTS: APPLICATION TO SPORULATION TIME SERIES

av Raychaudhuri, Soumya, Stuart, Joshua M., Altman, Russ B.
Publicerad 2000

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

av Koeva, Martina, Forsberg, E. Camilla, Stuart, Joshua M.
Publicerad 2011

ONE-CLASS DETECTION OF CELL STATES IN TUMOR SUBTYPES

av SOKOLOV, ARTEM, PAULL, EVAN O., STUART, JOSHUA M.
I publikationen Pac Symp Biocomput (2016)

Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel learner integrating multimodal genomic data and pathway knowledge

av Uzunangelov, Vladislav, Wong, Christopher K., Stuart, Joshua M.
I publikationen PLoS Comput Biol (2021)

Biological process activity transformation of single cell gene expression for cross-species alignment

av Ding, Hongxu, Blair, Andrew, Yang, Ying, Stuart, Joshua M.
I publikationen Nat Commun (2019)

PLATYPUS: A Multiple–View Learning Predictive Framework for Cancer Drug Sensitivity Prediction

av Graim, Kiley, Friedl, Verena, Houlahan, Kathleen E., Stuart, Joshua M.
I publikationen Pac Symp Biocomput (2019)

Information-based methods for predicting gene function from systematic gene knock-downs

av Weirauch, Matthew T, Wong, Christopher K, Byrne, Alexandra B, Stuart, Joshua M
Publicerad 2008

Molecular Pathways: Extracting Medical Knowledge from High Throughput Genomic Data

av Goldstein, Theodore, Paull, Evan O., Ellis, Matthew J., Stuart, Joshua M.
Publicerad 2013

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

av Chen, Chunnuan, Weirauch, Matthew T, Powell, Corey C, Zambon, Alexander C, Stuart, Joshua M
Publicerad 2007

Pattern recognition of genomic features with microarrays: site typing of Mycobacterium tuberculosis strains

av Raychaudhuri, Soumya, Stuart, Joshua M., Liu, Xuemin, Small, Peter M., Altman, Russ B.
Publicerad 2000

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

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

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

av Boutros, Paul C, Margolin, Adam A, Stuart, Joshua M, Califano, Andrea, Stolovitzky, Gustavo
I publikationen Genome Biol (2014)

Pathway-Based Genomics Prediction using Generalized Elastic Net

av Sokolov, Artem, Carlin, Daniel E., Paull, Evan O., Baertsch, Robert, Stuart, Joshua M.
I publikationen PLoS Comput Biol (2016)

Transcriptional Map of Respiratory Versatility in the Hyperthermophilic Crenarchaeon Pyrobaculum aerophilum

av Cozen, Aaron E., Weirauch, Matthew T., Pollard, Katherine S., Bernick, David L., Stuart, Joshua M., Lowe, Todd M.
Publicerad 2009

Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE)

av Paull, Evan O., Carlin, Daniel E., Niepel, Mario, Sorger, Peter K., Haussler, David, Stuart, Joshua M.
Publicerad 2013

Exploring Integrative Analysis Using the BioMedical Evidence Graph

av Struck, Adam, Walsh, Brian, Buchanan, Alexander, Lee, Jordan A., Spangler, Ryan, Stuart, Joshua M., Ellrott, Kyle
I publikationen JCO Clin Cancer Inform (2020)

RADIA: RNA and DNA Integrated Analysis for Somatic Mutation Detection

av Radenbaugh, Amie J., Ma, Singer, Ewing, Adam, Stuart, Joshua M., Collisson, Eric A., Zhu, Jingchun, Haussler, David
I publikationen PLoS One (2014)

Using Transcriptional Signatures to Find Cancer Drivers with LURE

av Haan, David, Tao, Ruikang, Friedl, Verena, Anastopoulos, Ioannis N, Wong, Christopher K, Weinstein, Alana S, Stuart, Joshua M
I publikationen Pac Symp Biocomput (2020)

Prioritizing transcriptional factors in gene regulatory networks with PageRank

av Ding, Hongxu, Yang, Ying, Xue, Yuanqing, Seninge, Lucas, Gong, Henry, Safavi, Rojin, Califano, Andrea, Stuart, Joshua M.
I publikationen iScience (2020)