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

Autor Cordero, Pablo, Stuart, Joshua M.
Vydáno v Pac Symp Biocomput (2016)

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

Autor Raychaudhuri, Soumya, Stuart, Joshua M., Altman, Russ B.
Vydáno 2000

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

Autor Koeva, Martina, Forsberg, E. Camilla, Stuart, Joshua M.
Vydáno 2011

ONE-CLASS DETECTION OF CELL STATES IN TUMOR SUBTYPES

Autor SOKOLOV, ARTEM, PAULL, EVAN O., STUART, JOSHUA M.
Vydáno v Pac Symp Biocomput (2016)

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

Autor Uzunangelov, Vladislav, Wong, Christopher K., Stuart, Joshua M.
Vydáno v PLoS Comput Biol (2021)

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

Autor Ding, Hongxu, Blair, Andrew, Yang, Ying, Stuart, Joshua M.
Vydáno v Nat Commun (2019)

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

Autor Graim, Kiley, Friedl, Verena, Houlahan, Kathleen E., Stuart, Joshua M.
Vydáno v Pac Symp Biocomput (2019)

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

Autor Weirauch, Matthew T, Wong, Christopher K, Byrne, Alexandra B, Stuart, Joshua M
Vydáno 2008

Molecular Pathways: Extracting Medical Knowledge from High Throughput Genomic Data

Autor Goldstein, Theodore, Paull, Evan O., Ellis, Matthew J., Stuart, Joshua M.
Vydáno 2013

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

Autor Chen, Chunnuan, Weirauch, Matthew T, Powell, Corey C, Zambon, Alexander C, Stuart, Joshua M
Vydáno 2007

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

Autor Raychaudhuri, Soumya, Stuart, Joshua M., Liu, Xuemin, Small, Peter M., Altman, Russ B.
Vydáno 2000

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

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

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

Autor Boutros, Paul C, Margolin, Adam A, Stuart, Joshua M, Califano, Andrea, Stolovitzky, Gustavo
Vydáno v Genome Biol (2014)

Pathway-Based Genomics Prediction using Generalized Elastic Net

Autor Sokolov, Artem, Carlin, Daniel E., Paull, Evan O., Baertsch, Robert, Stuart, Joshua M.
Vydáno v PLoS Comput Biol (2016)

Transcriptional Map of Respiratory Versatility in the Hyperthermophilic Crenarchaeon Pyrobaculum aerophilum

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

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

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

Exploring Integrative Analysis Using the BioMedical Evidence Graph

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

RADIA: RNA and DNA Integrated Analysis for Somatic Mutation Detection

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

Using Transcriptional Signatures to Find Cancer Drivers with LURE

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

Prioritizing transcriptional factors in gene regulatory networks with PageRank

Autor Ding, Hongxu, Yang, Ying, Xue, Yuanqing, Seninge, Lucas, Gong, Henry, Safavi, Rojin, Califano, Andrea, Stuart, Joshua M.
Vydáno v iScience (2020)