Author Search Results

1

Pathway-based analysis of mutation impact by Stuart, Joshua

Published 2012

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TRACING CO-REGULATORY NETWORK DYNAMICS IN NOISY, SINGLE-CELL TRANSCRIPTOME TRAJECTORIES by Cordero, Pablo, Stuart, Joshua M.

Published 2016

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PRINCIPAL COMPONENTS ANALYSIS TO SUMMARIZE MICROARRAY EXPERIMENTS: APPLICATION TO SPORULATION TIME SERIES by Raychaudhuri, Soumya, Stuart, Joshua M., Altman, Russ B.

Published 2000

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Computational Integration of Homolog and Pathway Gene Module Expression Reveals General Stemness Signatures by Koeva, Martina, Forsberg, E. Camilla, Stuart, Joshua M.

Published 2011

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ONE-CLASS DETECTION OF CELL STATES IN TUMOR SUBTYPES by SOKOLOV, ARTEM, PAULL, EVAN O., STUART, JOSHUA M.

Published 2016

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Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel learner integrating multimodal genomic data and pathway knowledge by Uzunangelov, Vladislav, Wong, Christopher K., Stuart, Joshua M.

Published 2021

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7

VEGA is an interpretable generative model for inferring biological network activity in single-cell transcriptomics by Seninge, Lucas, Anastopoulos, Ioannis, Ding, Hongxu, Stuart, Joshua

Published 2021

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8

Biological process activity transformation of single cell gene expression for cross-species alignment by Ding, Hongxu, Blair, Andrew, Yang, Ying, Stuart, Joshua M.

Published 2019

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PLATYPUS: A Multiple–View Learning Predictive Framework for Cancer Drug Sensitivity Prediction by Graim, Kiley, Friedl, Verena, Houlahan, Kathleen E., Stuart, Joshua M.

Published 2019

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10

Information-based methods for predicting gene function from systematic gene knock-downs by Weirauch, Matthew T, Wong, Christopher K, Byrne, Alexandra B, Stuart, Joshua M

Published 2008

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11

Molecular Pathways: Extracting Medical Knowledge from High Throughput Genomic Data by Goldstein, Theodore, Paull, Evan O., Ellis, Matthew J., Stuart, Joshua M.

Published 2013

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12

Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures by Ding, Hongxu, Anastopoulos, Ioannis, Bailey, Andrew D., Stuart, Joshua, Paten, Benedict

Published 2021

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13

Dual RNA-Seq analysis of SARS-CoV-2 correlates specific human transcriptional response pathways directly to viral expression by Maulding, Nathan D., Seiler, Spencer, Pearson, Alexander, Kreusser, Nicholas, Stuart, Joshua M.

Published 2022

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14

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

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15

Pattern recognition of genomic features with microarrays: site typing of Mycobacterium tuberculosis strains by Raychaudhuri, Soumya, Stuart, Joshua M., Liu, Xuemin, Small, Peter M., Altman, Russ B.

Published 2000

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16

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

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17

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

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18

Pathway-Based Genomics Prediction using Generalized Elastic Net by Sokolov, Artem, Carlin, Daniel E., Paull, Evan O., Baertsch, Robert, Stuart, Joshua M.

Published 2016

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19

Transcriptional Map of Respiratory Versatility in the Hyperthermophilic Crenarchaeon Pyrobaculum aerophilum by Cozen, Aaron E., Weirauch, Matthew T., Pollard, Katherine S., Bernick, David L., Stuart, Joshua M., Lowe, Todd M.

Published 2009

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20

Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE) by Paull, Evan O., Carlin, Daniel E., Niepel, Mario, Sorger, Peter K., Haussler, David, Stuart, Joshua M.

Published 2013

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Search Results - Stuart, Joshua

Pathway-based analysis of mutation impact by Stuart, Joshua

TRACING CO-REGULATORY NETWORK DYNAMICS IN NOISY, SINGLE-CELL TRANSCRIPTOME TRAJECTORIES by Cordero, Pablo, Stuart, Joshua M.

PRINCIPAL COMPONENTS ANALYSIS TO SUMMARIZE MICROARRAY EXPERIMENTS: APPLICATION TO SPORULATION TIME SERIES by Raychaudhuri, Soumya, Stuart, Joshua M., Altman, Russ B.

Computational Integration of Homolog and Pathway Gene Module Expression Reveals General Stemness Signatures by Koeva, Martina, Forsberg, E. Camilla, Stuart, Joshua M.

ONE-CLASS DETECTION OF CELL STATES IN TUMOR SUBTYPES by SOKOLOV, ARTEM, PAULL, EVAN O., STUART, JOSHUA M.

Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel learner integrating multimodal genomic data and pathway knowledge by Uzunangelov, Vladislav, Wong, Christopher K., Stuart, Joshua M.

VEGA is an interpretable generative model for inferring biological network activity in single-cell transcriptomics by Seninge, Lucas, Anastopoulos, Ioannis, Ding, Hongxu, Stuart, Joshua

Biological process activity transformation of single cell gene expression for cross-species alignment by Ding, Hongxu, Blair, Andrew, Yang, Ying, Stuart, Joshua M.

PLATYPUS: A Multiple–View Learning Predictive Framework for Cancer Drug Sensitivity Prediction by Graim, Kiley, Friedl, Verena, Houlahan, Kathleen E., Stuart, Joshua M.

Information-based methods for predicting gene function from systematic gene knock-downs by Weirauch, Matthew T, Wong, Christopher K, Byrne, Alexandra B, Stuart, Joshua M

Molecular Pathways: Extracting Medical Knowledge from High Throughput Genomic Data by Goldstein, Theodore, Paull, Evan O., Ellis, Matthew J., Stuart, Joshua M.

Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures by Ding, Hongxu, Anastopoulos, Ioannis, Bailey, Andrew D., Stuart, Joshua, Paten, Benedict

Dual RNA-Seq analysis of SARS-CoV-2 correlates specific human transcriptional response pathways directly to viral expression by Maulding, Nathan D., Seiler, Spencer, Pearson, Alexander, Kreusser, Nicholas, Stuart, Joshua M.

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

Pattern recognition of genomic features with microarrays: site typing of Mycobacterium tuberculosis strains by Raychaudhuri, Soumya, Stuart, Joshua M., Liu, Xuemin, Small, Peter M., Altman, Russ B.

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.

Toward better benchmarking: challenge-based methods assessment in cancer genomics by Boutros, Paul C, Margolin, Adam A, Stuart, Joshua M, Califano, Andrea, Stolovitzky, Gustavo

Pathway-Based Genomics Prediction using Generalized Elastic Net by Sokolov, Artem, Carlin, Daniel E., Paull, Evan O., Baertsch, Robert, Stuart, Joshua M.

Transcriptional Map of Respiratory Versatility in the Hyperthermophilic Crenarchaeon Pyrobaculum aerophilum by Cozen, Aaron E., Weirauch, Matthew T., Pollard, Katherine S., Bernick, David L., Stuart, Joshua M., Lowe, Todd M.

Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE) by Paull, Evan O., Carlin, Daniel E., Niepel, Mario, Sorger, Peter K., Haussler, David, Stuart, Joshua M.

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