Cell-specific prediction and application of drug-induced gene expression .

Neil R. Clark Rachel Hodos Ping Zhang 0016 Hao-Chih Lee Qiaonan Duan Zichen Wang 0002 Neil R. Clark Avi Ma'ayan Fei Wang 0001 Brian A. Kidd Jianying Hu David A. Sontag Joel Dudley Cell-specific prediction and application of drug-induced gene expression . 32-43 2018 PSB http://psb.stanford.edu/psb-online/proceedings/psb18/hodos.pdf conf/psb/2018 db/conf/psb/psb2018.html#HodosZLDWCMWKHS18

Zichen Wang 0002 Neil R. Clark Avi Ma'ayan Drug-induced adverse events prediction with the LINCS L1000 data. 2338-2345 2016 32 Bioinform. 15 https://doi.org/10.1093/bioinformatics/btw168 https://www.wikidata.org/entity/Q31092242 db/journals/bioinformatics/bioinformatics32.html#WangCM16

Avi Ma'ayan Neil R. Clark Large Collection of Diverse Gene Set Search Queries Recapitulate Known Protein-Protein Interactions and Gene-Gene Functional Associations. 2016 abs/1601.01653 CoRR http://arxiv.org/abs/1601.01653 db/journals/corr/corr1601.html#MaayanC16

Zichen Wang 0002 Neil R. Clark Avi Ma'ayan Dynamics of the discovery process of protein-protein interactions from low content studies. 26 2015 9 BMC Syst. Biol. https://doi.org/10.1186/s12918-015-0173-z https://www.wikidata.org/entity/Q28645821 db/journals/bmcsb/bmcsb9.html#WangCM15

Neil R. Clark Maciej Szymkiewicz Zichen Wang 0002 Caroline D. Monteiro Matthew R. Jones Avi Ma'ayan Principle Angle Enrichment Analysis (PAEA): Dimensionally reduced multivariate gene set enrichment analysis tool. 256-262 2015 BIBM https://doi.org/10.1109/BIBM.2015.7359689 https://doi.ieeecomputersociety.org/10.1109/BIBM.2015.7359689 https://www.wikidata.org/entity/Q35915286 conf/bibm/2015 db/conf/bibm/bibm2015.html#ClarkSWMJM15

Neil R. Clark Kevin S. Hu Axel S. Feldmann Yan Kou Edward Y. Chen Qiaonan Duan Avi Ma'ayan The characteristic direction: a geometrical approach to identify differentially expressed genes. 79 2014 15 BMC Bioinform. https://doi.org/10.1186/1471-2105-15-79 https://www.wikidata.org/entity/Q35125871 db/journals/bmcbi/bmcbi15.html#ClarkHFKCDM14

Christopher M. Tan Edward Y. Chen Ruth Dannenfelser Neil R. Clark Avi Ma'ayan Network2Canvas: network visualization on a canvas with enrichment analysis. 1872-1878 2013 29 Bioinform. 15 https://doi.org/10.1093/bioinformatics/btt319 https://www.wikidata.org/entity/Q30541512 db/journals/bioinformatics/bioinformatics29.html#TanCDCM13

Edward Y. Chen Christopher M. Tan Yan Kou Qiaonan Duan Zichen Wang 0002 Gabriela Vaz Meirelles Neil R. Clark Avi Ma'ayan Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. 128 2013 14 BMC Bioinform. https://doi.org/10.1186/1471-2105-14-128 https://www.wikidata.org/entity/Q34668270 db/journals/bmcbi/bmcbi14.html#ChenTKDWMCM13

Yan Kou Edward Y. Chen Neil R. Clark Qiaonan Duan Christopher M. Tan Avi Ma'ayan ChEA2: Gene-Set Libraries from ChIP-X Experiments to Decode the Transcription Regulome. 416-430 2013 CD-ARES https://doi.org/10.1007/978-3-642-40511-2_30 https://www.wikidata.org/entity/Q57009796 conf/IEEEares/2013cd db/conf/IEEEares/cd-ares2013.html#KouCCDTM13

Ruth Dannenfelser Neil R. Clark Avi Ma'ayan Genes2FANs: connecting genes through functional association networks. 156 2012 13 BMC Bioinform. https://doi.org/10.1186/1471-2105-13-156 https://www.wikidata.org/entity/Q34322622 db/journals/bmcbi/bmcbi13.html#DannenfelserCM12

Neil R. Clark Ruth Dannenfelser Christopher M. Tan Michael E. Komosinski Avi Ma'ayan Sets2Networks: network inference from repeated observations of sets. 89 2012 6 BMC Syst. Biol. https://doi.org/10.1186/1752-0509-6-89 https://www.wikidata.org/entity/Q34348473 db/journals/bmcsb/bmcsb6.html#ClarkDTKM12

Amin R. Mazloom Ruth Dannenfelser Neil R. Clark Arsen V. Grigoryan Kathryn M. Linder Timothy Cardozo Julia C. Bond Aislyn D. W. Boran Ravi Iyengar Anna Malovannaya Rainer B. Lanz Avi Ma'ayan Recovering Protein-Protein and Domain-Domain Interactions from Aggregation of IP-MS Proteomics of Coregulator Complexes. 2011 7 PLoS Comput. Biol. 12 https://doi.org/10.1371/journal.pcbi.1002319 https://www.wikidata.org/entity/Q34118997 db/journals/ploscb/ploscb7.html#MazloomDCGLCBBIMLM11

Julia C. Bond Aislyn D. W. Boran Timothy Cardozo Edward Y. Chen Ruth Dannenfelser Qiaonan Duan Joel Dudley Axel S. Feldmann Arsen V. Grigoryan Rachel Hodos Jianying Hu Kevin S. Hu Ravi Iyengar Matthew R. Jones Brian A. Kidd Michael E. Komosinski Yan Kou Rainer B. Lanz Hao-Chih Lee Kathryn M. Linder Avi Ma'ayan Anna Malovannaya Amin R. Mazloom Gabriela Vaz Meirelles Caroline D. Monteiro David A. Sontag Maciej Szymkiewicz Christopher M. Tan Fei Wang 0001 Zichen Wang 0002 Ping Zhang 0016