Illuminating the Druggable Genome (101)
Publication TitleAuthorsJournalPublication DatePage NoPubMedID
Podocyte-Specific Induction of Krüppel-Like Factor 15 Restores Differentiation Markers and Attenuates Kidney Injury in Proteinuric Kidney Disease.Guo, Yiqing; Pace, Jesse; Li, Zhengzhe; Ma'ayan, Avi; Wang, Zichen; Revelo, Monica P; Chen, Edward; Gu, Xiangchen; Attalah, Ahmed; Yang, Yaqi; Estrada, Chelsea; Yang, Vincent W; He, John C; Mallipattu, Sandeep KJournal of the American Society of Nephrology : JASN.2018 Aug 24;30143559
eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks.Clarke, Daniel J B; Kuleshov, Maxim V; Schilder, Brian M; Torre, Denis; Duffy, Mary E; Keenan, Alexandra B; Lachmann, Alexander; Feldmann, Axel S; Gundersen, Gregory W; Silverstein, Moshe C; Wang, Zichen; Ma'ayan, AviNucleic acids research.2018 Jul 02;29800326
Proteomic analysis defines kinase taxonomies specific for subtypes of breast cancer.Collins, Kyla A L; Stuhlmiller, Timothy J; Zawistowski, Jon S; East, Michael P; Pham, Trang T; Hall, Claire R; Goulet, Daniel R; Bevill, Samantha M; Angus, Steven P; Velarde, Sara H; Sciaky, Noah; Oprea, Tudor I; Graves, Lee M; Johnson, Gary L; Gomez, Shawn MOncotarget.2018 Mar 20;29643987
Massive mining of publicly available RNA-seq data from human and mouse.Lachmann, Alexander; Torre, Denis; Keenan, Alexandra B; Jagodnik, Kathleen M; Lee, Hoyjin J; Wang, Lily; Silverstein, Moshe C; Ma'ayan, AviNature communications.;29636450
Unexplored therapeutic opportunities in the human genome.Oprea, Tudor I; Bologa, Cristian G; Brunak, Søren; Campbell, Allen; Gan, Gregory N; Gaulton, Anna; Gomez, Shawn M; Guha, Rajarshi; Hersey, Anne; Holmes, Jayme; Jadhav, Ajit; Jensen, Lars Juhl; Johnson, Gary L; Karlson, Anneli; Leach, Andrew R; Ma'ayan, Avi; Malovannaya, Anna; Mani, Subramani; Mathias, Stephen L; McManus, Michael T; Meehan, Terrence F; von Mering, Christian; Muthas, Daniel; Nguyen, Dac-Trung; Overington, John P; Papadatos, George; Qin, Jun; Reich, Christian; Roth, Bryan L; Schürer, Stephan C; Simeonov, Anton; Sklar, Larry A; Southall, Noel; Tomita, Susumu; Tudose, Ilinca; Ursu, Oleg; Vidovic, Du?ica; Waller, Anna; Westergaard, David; Yang, Jeremy J; Zahoránszky-Köhalmi, GergelyNature reviews. Drug discovery.2018 May;29472638
L1000FWD: fireworks visualization of drug-induced transcriptomic signatures.Wang, Zichen; Lachmann, Alexander; Keenan, Alexandra B; Ma'ayan, AviBioinformatics (Oxford, England).;29420694
Structure-inspired design of ?-arrestin-biased ligands for aminergic GPCRs.McCorvy, John D; Butler, Kyle V; Kelly, Brendan; Rechsteiner, Katie; Karpiak, Joel; Betz, Robin M; Kormos, Bethany L; Shoichet, Brian K; Dror, Ron O; Jin, Jian; Roth, Bryan LNature chemical biology.2017 Dec 11;29227473
Cell-specific prediction and application of drug-induced gene expression profiles.Hodos, Rachel; Zhang, Ping; Lee, Hao-Chih; Duan, Qiaonan; Wang, Zichen; Clark, Neil R; Ma'ayan, Avi; Wang, Fei; Kidd, Brian; Hu, Jianying; Sontag, David; Dudley, JoelPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.2018;29218867
Predicting age by mining electronic medical records with deep learning characterizes differences between chronological and physiological age.Wang, Zichen; Li, Li; Glicksberg, Benjamin S; Israel, Ariel; Dudley, Joel T; Ma'ayan, AviJournal of biomedical informatics.2017 Dec;29113935
Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling.Niepel, Mario; Hafner, Marc; Duan, Qiaonan; Wang, Zichen; Paull, Evan O; Chung, Mirra; Lu, Xiaodong; Stuart, Joshua M; Golub, Todd R; Subramanian, Aravind; Ma'ayan, Avi; Sorger, Peter KNature communications.2017 Oct 30;29084964
Identification and Optimization of 4-Anilinoquinolines as Inhibitors of Cyclin?G Associated Kinase.Asquith, Christopher R M; Laitinen, Tuomo; Bennett, James M; Godoi, Paulo H; East, Michael P; Tizzard, Graham J; Graves, Lee M; Johnson, Gary L; Dornsife, Ronna E; Wells, Carrow I; Elkins, Jonathan M; Willson, Timothy M; Zuercher, William JChemMedChem.2018 Jan 08;29072804
Discovery of new GPCR ligands to illuminate new biology.Roth, Bryan L; Irwin, John J; Shoichet, Brian KNature chemical biology.2017 Nov;29045379
Biased signaling of the proton-sensing receptor OGR1 by benzodiazepines.Pera, Tonio; Deshpande, Deepak A; Ippolito, Michael; Wang, Bin; Gavrila, Adelina; Michael, James V; Nayak, Ajay P; Tompkins, Eric; Farrell, Eleni; Kroeze, Wesley K; Roth, Bryan L; Panettieri Jr, Reynold A; Benovic, Jeffrey L; An, Steven S; Dulin, Nickolai O; Penn, Raymond BFASEB journal : official publication of the Federation of American Societies for Experimental Biology.;29042451
Report and Application of a Tool Compound Data Set.Butler, Kyle V; MacDonald, Ian A; Hathaway, Nathaniel A; Jin, JianJournal of chemical information and modeling.2017 Nov 02;29035535
Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data.Fernandez, Nicolas F; Gundersen, Gregory W; Rahman, Adeeb; Grimes, Mark L; Rikova, Klarisa; Hornbeck, Peter; Ma'ayan, AviScientific data.2017 Oct 10;28994825
Complex systems biology.Ma'ayan, AviJournal of the Royal Society, Interface.2017 Sep;28931638
A high-conductance chemo-optogenetic system based on the vertebrate channel Trpa1b.Lam, Pui-Ying; Mendu, Suresh K; Mills, Robert W; Zheng, Baohui; Padilla, Hugo; Milan, David J; Desai, Bimal N; Peterson, Randall TScientific reports.2017 Sep 19;28928472
Assembly rules for GABAA receptor complexes in the brain.Martenson, James S;Yamasaki, Tokiwa;Chaudhury, Nashid H;Albrecht, David;Tomita, SusumueLife28816653
Intracoronary Imaging, Cholesterol Efflux, and Transcriptomics after Intensive Statin Treatment in Diabetes.Chamaria, Surbhi; Johnson, Kipp W; Vengrenyuk, Yuliya; Baber, Usman; Shameer, Khader; Divaraniya, Aparna A; Glicksberg, Benjamin S; Li, Li; Bhatheja, Samit; Moreno, Pedro; Maehara, Akiko; Mehran, Roxana; Dudley, Joel T; Narula, Jagat; Sharma, Samin K; Kini, Annapoorna SScientific reports.2017 Aug 01;28765529
How Ligands Illuminate GPCR Molecular Pharmacology.Wacker, Daniel; Stevens, Raymond C; Roth, Bryan LCell.2017 Jul 27;28753422
From flamingo dance to (desirable) drug discovery: a nature-inspired approach.Sánchez-Rodríguez, Aminael; Pérez-Castillo, Yunierkis; Schürer, Stephan C; Nicolotti, Orazio; Mangiatordi, Giuseppe Felice; Borges, Fernanda; Cordeiro, M Natalia D S; Tejera, Eduardo; Medina-Franco, José L; Cruz-Monteagudo, MaykelDrug discovery today.2017 Jun 15;28624633
Activation of tumor suppressor protein PP2A inhibits KRAS-driven tumor growth.Sangodkar, Jaya; Perl, Abbey; Tohme, Rita; Kiselar, Janna; Kastrinsky, David B; Zaware, Nilesh; Izadmehr, Sudeh; Mazhar, Sahar; Wiredja, Danica D; O'Connor, Caitlin M; Hoon, Divya; Dhawan, Neil S; Schlatzer, Daniela; Yao, Shen; Leonard, Daniel; Borczuk, AThe Journal of clinical investigation.2017 Jun 01;28504649
A mouse tissue transcription factor atlas.Zhou, Quan; Liu, Mingwei; Xia, Xia; Gong, Tongqing; Feng, Jinwen; Liu, Wanlin; Liu, Yang; Zhen, Bei; Wang, Yi; Ding, Chen; Qin, JunNature communications.2017 Apr 21;28429721
L1000CDS(2): LINCS L1000 characteristic direction signatures search engine.Duan, Qiaonan; Reid, St Patrick; Clark, Neil R; Wang, Zichen; Fernandez, Nicolas F; Rouillard, Andrew D; Readhead, Ben; Tritsch, Sarah R; Hodos, Rachel; Hafner, Marc; Niepel, Mario; Sorger, Peter K; Dudley, Joel T; Bavari, Sina; Panchal, Rekha G; Ma'ayan, AviNPJ systems biology and applications.2016;28413689
In silico design of novel probes for the atypical opioid receptor MRGPRX2.Lansu, Katherine; Karpiak, Joel; Liu, Jing; Huang, Xi-Ping; McCorvy, John D; Kroeze, Wesley K; Che, Tao; Nagase, Hiroshi; Carroll, Frank I; Jin, Jian; Shoichet, Brian K; Roth, Bryan LNature chemical biology.2017 May;28288109
GARLH Family Proteins Stabilize GABAA Receptors at Synapses.Yamasaki, Tokiwa; Hoyos-Ramirez, Erika; Martenson, James S; Morimoto-Tomita, Megumi; Tomita, SusumuNeuron.2017 Mar 08;28279354
Systemic QSAR and phenotypic virtual screening: chasing butterflies in drug discovery.Cruz-Monteagudo, Maykel; Schürer, Stephan; Tejera, Eduardo; Pérez-Castillo, Yunierkis; Medina-Franco, José L; Sánchez-Rodríguez, Aminael; Borges, FernandaDrug discovery today.2017 Mar 06;28274840
A Whole-Genome RNA Interference Screen Reveals a Role for Spry2 in Insulin Transcription and the Unfolded Protein Response.Pappalardo, Zachary; Gambhir Chopra, Deeksha; Hennings, Thomas G; Richards, Hunter; Choe, Justin; Yang, Katherine; Baeyens, Luc; Ang, Kenny; Chen, Steven; Arkin, Michelle; German, Michael S; McManus, Michael T; Ku, Gregory MDiabetes.2017 Jun;28246293
Protamine is an antagonist of apelin receptor, and its activity is reversed by heparin.Le Gonidec, Sophie; Chaves-Almagro, Carline; Bai, Yushi; Kang, Hye Jin; Smith, Allyson; Wanecq, Estelle; Huang, Xi-Ping; Prats, Hervé; Knibiehler, Bernard; Roth, Bryan L; Barak, Larry S; Caron, Marc G; Valet, Philippe; Audigier, Yves; Masri, BernardFASEB journal : official publication of the Federation of American Societies for Experimental Biology.2017 06;28242772
Differential cytokine contributions of perivascular haematopoietic stem cell niches.Asada, Noboru; Kunisaki, Yuya; Pierce, Halley; Wang, Zichen; Fernandez, Nicolas F; Birbrair, Alexander; Ma'ayan, Avi; Frenette, Paul SNature cell biology.2017 Mar;28218906
Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning.Shameer, Khader; Glicksberg, Benjamin S; Hodos, Rachel; Johnson, Kipp W; Badgeley, Marcus A; Readhead, Ben; Tomlinson, Max S; O'Connor, Timothy; Miotto, Riccardo; Kidd, Brian A; Chen, Rong; Ma'ayan, Avi; Dudley, Joel TBriefings in bioinformatics.2017 Feb 15;28200013
Automated cell type discovery and classification through knowledge transfer.Lee, Hao-Chih; Kosoy, Roman; Becker, Christine E; Dudley, Joel T; Kidd, Brian ABioinformatics (Oxford, England).2017 Jun 01;28158442
Protein biomarker druggability profiling.Mani, Subramani; Cannon, Daniel; Ohls, Robin; Oprea, Tudor; Mathias, Stephen; Ballard, Karri; Ursu, Oleg; Bologa, CristianJournal of biomedical informatics.2017 Feb;28131723
Integrative Analysis of Disease Signatures Shows Inflammation Disrupts Juvenile Experience-Dependent Cortical Plasticity.Smith, Milo R; Burman, Poromendro; Sadahiro, Masato; Kidd, Brian A; Dudley, Joel T; Morishita, HirofumieNeuro.2016 Nov-Dec;28101530
Novel Therapeutics Identification for Fibrosis in Renal Allograft Using Integrative Informatics Approach.Li, Li; Greene, Ilana; Readhead, Benjamin; Menon, Madhav C; Kidd, Brian A; Uzilov, Andrew V; Wei, Chengguo; Philippe, Nimrod; Schroppel, Bernd; He, John Cijiang; Chen, Rong; Dudley, Joel T; Murphy, BarbaraScientific reports.2017 Jan 04;28051114
Nrf2 mitigates LRRK2- and α-synuclein-induced neurodegeneration by modulating proteostasis.Gaia Skibinski, Vicky Hwang, Dale Michael Ando, Aaron Daub, Alicia K. Lee, Abinaya Ravisankar, Sara Modan, Mariel M. Finucane, Benjamin A. Shaby, and Steven FinkbeinerProceedings of the National Academy of Sciences of the United States of America.2017 Jan 31;1165–117028028237
Genomic Analysis of Kidney Allograft Injury Identifies Hematopoietic Cell Kinase as a Key Driver of Renal Fibrosis.Wei, Chengguo; Li, Li; Menon, Madhav C; Zhang, Weijia; Fu, Jia; Kidd, Brian; Keung, Karen L; Woytovich, Christopher; Greene, Ilana; Xiao, Wenzhen; Salem, Fadi; Yi, Zhengzi; He, John Cijiang; Dudley, Joel T; Murphy, BarbaraJournal of the American Society of Nephrology : JASN.2017 May;27927780
A comprehensive map of molecular drug targets.Santos, Rita; Ursu, Oleg; Gaulton, Anna; Bento, A Patrícia; Donadi, Ramesh S; Bologa, Cristian G; Karlsson, Anneli; Al-Lazikani, Bissan; Hersey, Anne; Oprea, Tudor I; Overington, John PNature reviews. Drug discovery.2017 01;27910877
Pharos: Collating protein information to shed light on the druggable genome.Nguyen, Dac-Trung; Mathias, Stephen; Bologa, Cristian; Brunak, Soren; Fernandez, Nicolas; Gaulton, Anna; Hersey, Anne; Holmes, Jayme; Jensen, Lars Juhl; Karlsson, Anneli; Liu, Guixia; Ma'ayan, Avi; Mandava, Geetha; Mani, Subramani; Mehta, Saurabh; Overington, John; Patel, Juhee; Rouillard, Andrew D; Schürer, Stephan; Sheils, Timothy; Simeonov, Anton; Sklar, Larry A; Southall, Noel; Ursu, Oleg; Vidovic, Dusica; Waller, Anna; Yang, Jeremy; Jadhav, Ajit; Oprea, Tudor I; Guha, RajarshiNucleic acids research.2017 Jan 4;27903890
EXPLORING THE REPRODUCIBILITY OF PROBABILISTIC CAUSAL MOLECULAR NETWORK MODELS.Cohain, Ariella; Divaraniya, Aparna A; Zhu, Kuixi; Scarpa, Joseph R; Kasarskis, Andrew; Zhu, Jun; Chang, Rui; Dudley, Joel T; Schadt, Eric EPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.2016;27896968
EXPLORING BRAIN TRANSCRIPTOMIC PATTERNS: A TOPOLOGICAL ANALYSIS USING SPATIAL EXPRESSION NETWORKS.Kuncheva, Zhana; Krishnan, Michelle L; Montana, GiovanniPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.2016;27896963
GEN3VA: aggregation and analysis of gene expression signatures from related studies.Gundersen, Gregory W; Jagodnik, Kathleen M; Woodland, Holly; Fernandez, Nicholas F; Sani, Kevin; Dohlman, Anders B; Ung, Peter Man-Un; Monteiro, Caroline D; Schlessinger, Avner; Ma'ayan, AviBMC bioinformatics.2016 Nov 15;27846806
DrugCentral: online drug compendium.Ursu, Oleg; Holmes, Jayme; Knockel, Jeffrey; Bologa, Cristian G; Yang, Jeremy J; Mathias, Stephen L; Nelson, Stuart J; Oprea, Tudor INucleic acids research.2017 Jan 4;27789690
Discovery and Characterization of Novel GPR39 Agonists Allosterically Modulated by Zinc.Sato, Seiji; Huang, Xi-Ping; Kroeze, Wesley K; Roth, Bryan LMolecular pharmacology.2016 Dec;27754899
Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd.Wang, Zichen; Monteiro, Caroline D; Jagodnik, Kathleen M; Fernandez, Nicolas F; Gundersen, Gregory W; Rouillard, Andrew D; Jenkins, Sherry L; Feldmann, Axel S; Hu, Kevin S; McDermott, Michael G; Duan, Qiaonan; Clark, Neil R; Jones, Matthew R; Kou, Yan; Goff, Troy; Woodland, Holly; Amaral, Fabio M R; Szeto, Gregory L; Fuchs, Oliver; Schüssler-Fiorenza Rose, Sophia M; Sharma, Shvetank; Schwartz, Uwe; Bausela, Xabier Bengoetxea; Szymkiewicz, Maciej; Maroulis, Vasileios; Salykin, Anton; Barra, Carolina M; Kruth, Candice D; Bongio, Nicholas J; Mathur, Vaibhav; Todoric, Radmila D; Rubin, Udi E; Malatras, Apostolos; Fulp, Carl T; Galindo, John A; Motiejunaite, Ruta; Jüschke, Christoph; Dishuck, Philip C; Lahl, Katharina; Jafari, Mohieddin; Aibar, Sara; Zaravinos, Apostolos; Steenhuizen, Linda H; Allison, Lindsey R; Gamallo, Pablo; de Andres Segura, Fernando; Dae Devlin, Tyler; Pérez-García, Vicente; Ma'ayan, AviNature communications.2016 Sep 26;27667448
Replicating Cardiovascular Condition-Birth Month Associations.Li, Li; Boland, Mary Regina; Miotto, Riccardo; Tatonetti, Nicholas P; Dudley, Joel TScientific reports.2016 Sep 14;27624541
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.Wang, Zichen; Ma'ayan, AviF1000Research.2016 Jul 5;27583132
Non-Substrate Based, Small Molecule Inhibitors of the Human Isoprenylcysteine Carboxyl Methyltransferase.Butler, Kyle V; Bohn, Kelsey; Hrycyna, Christine A; Jin, JianMedChemComm.2016 May 1;27547295
Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration.von Schimmelmann, Melanie; Feinberg, Philip A; Sullivan, Josefa M; Ku, Stacy M; Badimon, Ana; Duff, Mary Kaye; Wang, Zichen; Lachmann, Alexander; Dewell, Scott; Ma'ayan, Avi; Han, Ming-Hu; Tarakhovsky, Alexander; Schaefer, AnneNature neuroscience.2016 Oct;27526204
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins.Rouillard, Andrew D; Gundersen, Gregory W; Fernandez, Nicolas F; Wang, Zichen; Monteiro, Caroline D; McDermott, Michael G; Ma'ayan, AviDatabase : the journal of biological databases and curation.2016;27374120
Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks.Glicksberg, Benjamin S; Li, Li; Badgeley, Marcus A; Shameer, Khader; Kosoy, Roman; Beckmann, Noam D; Pho, Nam; Hakenberg, Jörg; Ma, Meng; Ayers, Kristin L; Hoffman, Gabriel E; Dan Li, Shuyu; Schadt, Eric E; Patel, Chirag J; Chen, Rong; Dudley, Joel TBioinformatics (Oxford, England).2016 Jun 15;27307606
Krüppel-Like Factor 15 Mediates Glucocorticoid-Induced Restoration of Podocyte Differentiation Markers.Mallipattu, Sandeep K; Guo, Yiqing; Revelo, Monica P; Roa-Peña, Lucia; Miller, Timothy; Ling, Jason; Shankland, Stuart J; Bialkowska, Agnieszka B; Ly, Victoria; Estrada, Chelsea; Jain, Mukesh K; Lu, Yuan; Ma'ayan, Avi; Mehrotra, Anita; Yacoub, Rabi; Nord, Edward P; Woroniecki, Robert P; Yang, Vincent W; He, John CJournal of the American Society of Nephrology : JASN.2016 Jun 10;27288011
Cognitive Machine-Learning Algorithm for Cardiac Imaging: A Pilot Study for Differentiating Constrictive Pericarditis From Restrictive Cardiomyopathy.Sengupta, Partho P; Huang, Yen-Min; Bansal, Manish; Ashrafi, Ali; Fisher, Matt; Shameer, Khader; Gall, Walt; Dudley, Joel TCirculation. Cardiovascular imaging.2016 Jun;27266599
?1 receptor ligands control a switch between passive and active threat responses.Rennekamp, Andrew J; Huang, Xi-Ping; Wang, You; Patel, Samir; Lorello, Paul J; Cade, Lindsay; Gonzales, Andrew P W; Yeh, Jing-Ruey Joanna; Caldarone, Barbara J; Roth, Bryan L; Kokel, David; Peterson, Randall TNature chemical biology.2016 Jul;27239788
Zebrafish behavioral profiling identifies multitarget antipsychotic-like compounds.Bruni, Giancarlo; Rennekamp, Andrew J; Velenich, Andrea; McCarroll, Matthew; Gendelev, Leo; Fertsch, Ethan; Taylor, Jack; Lakhani, Parth; Lensen, Dennis; Evron, Tama; Lorello, Paul J; Huang, Xi-Ping; Kolczewski, Sabine; Carey, Galen; Caldarone, Barbara J; Prinssen, Eric; Roth, Bryan L; Keiser, Michael J; Peterson, Randall T; Kokel, DavidNature chemical biology.2016 Jul;27239787
Badapple: promiscuity patterns from noisy evidence.Yang, Jeremy J; Ursu, Oleg; Lipinski, Christopher A; Sklar, Larry A; Oprea, Tudor I; Bologa, Cristian GJournal of cheminformatics.2016;27239230
Glucocorticoid receptor isoforms direct distinct mitochondrial programs to regulate ATP production.Morgan, David J; Poolman, Toryn M; Williamson, Andrew J K; Wang, Zichen; Clark, Neil R; Ma'ayan, Avi; Whetton, Anthony D; Brass, Andrew; Matthews, Laura C; Ray, David WScientific reports.2016;27226058
Cre dependent DREADD (designer receptors exclusively activated by designer drugs) mice.Zhu, Hu; Aryal, Dipendra K; Olsen, Reid H J; Urban, Daniel J; Swearingen, Amanda; Forbes, Stacy; Roth, Bryan L; Hochgeschwender, UteGenesis (New York, N.Y. : 2000).2016 May 19;27194399
Deep Patient: An Unsupervised Representation to Predict the Future of Patients from the Electronic Health Records.Miotto, Riccardo; Li, Li; Kidd, Brian A; Dudley, Joel TScientific reports.2016 May 17;27185194
BDDCS, the Rule of 5 and drugability.Benet, Leslie Z; Hosey, Chelsea M; Ursu, Oleg; Oprea, Tudor IAdvanced drug delivery reviews.2016 Jun 1;27182629
Drug-induced adverse events prediction with the LINCS L1000 data.Wang, Zichen; Clark, Neil R; Ma'ayan, AviBioinformatics (Oxford, England).2016 Aug 1;27153606
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update.Kuleshov, Maxim V; Jones, Matthew R; Rouillard, Andrew D; Fernandez, Nicolas F; Duan, Qiaonan; Wang, Zichen; Koplev, Simon; Jenkins, Sherry L; Jagodnik, Kathleen M; Lachmann, Alexander; McDermott, Michael G; Monteiro, Caroline D; Gundersen, Gregory W; Ma'ayan, AviNucleic acids research.2016 Jul 8;27141961
In silico methods for drug repurposing and pharmacology.Hodos, Rachel A; Kidd, Brian A; Shameer, Khader; Readhead, Ben P; Dudley, Joel TWiley interdisciplinary reviews. Systems biology and medicine.2016 May;27080087
Discovery of a specific inhibitor of human GLUT5 by virtual screening and in vitro transport evaluationGeorge-Thompson AM, Ursu O, Babkin P, Iancu CV, Whang A, Oprea TI, Choe JYScientific ReportsEpub 2016 Apr 14.27074918
Integrative network modeling approaches to personalized cancer medicineKidd BA, Readhead BP, Eden C, Parekh S, Dudley JTPersonalized Medicine2015 Jun 112(3):245-25727019658
Integrative network modeling approaches to personalized cancer medicine.Kidd BA, Readhead BP, Eden C, Parekh S, Dudley JT.Personalized Medicine2015 Jun 112(3):245-257.27019658
Evaluation of direct-to-consumer low-volume lab tests in healthy adultsKidd BA, Hoffman G, Zimmerman N, Li L, Morgan JW, Glowe PK, Botwin GJ, Parekh S, Babic N, Doust MW, Stock GB, Schadt EE, Dudley JTJ Clin Invest2016 Mar 28pii: 86318. doi: 10.1172/JCI86318. [Epub ahead of print]27018593
Signaling Networks among Stem Cell Precursors, Transit-Amplifying Progenitors, and their Niche in Developing Hair Follicles.Rezza, Amélie; Wang, Zichen; Sennett, Rachel; Qiao, Wenlian; Wang, Dongmei; Heitman, Nicholas; Mok, Ka Wai; Clavel, Carlos; Yi, Rui; Zandstra, Peter; Ma'ayan, Avi; Rendl, MichaelCell reports.2016 Mar 29;27009580
Polygenic overlap between schizophrenia risk and antipsychotic response: a genomic medicine approach.Ruderfer, Douglas M; Charney, Alexander W; Readhead, Ben; Kidd, Brian A; Kähler, Anna K; Kenny, Paul J; Keiser, Michael J; Moran, Jennifer L; Hultman, Christina M; Scott, Stuart A; Sullivan, Patrick F; Purcell, Shaun M; Dudley, Joel T; Sklar, PamelaThe lancet. Psychiatry.2016 Apr;26915512
Translational bioinformatics in the era of real-time biomedical, health care and wellness data streamsShameer K, Badgeley MA, Miotto R, Glicksberg BS, Morgan JW, Dudley JTBrief Bioinform2016 Feb 14pii: bbv118. [Epub ahead of print]26876889
Integrative radiogenomic analysis for multicentric radiophenotype in glioblastomaKong DS, Kim J, Lee IH, Kim ST, Seol HJ, Lee JI, Park WY, Ryu G, Wang Z, Ma'ayan A, Nam DHOncotarget2016 Feb 1doi: 10.18632/oncotarget.7115. [Epub ahead of print]26863628
Principal Angle Enrichment Analysis (PAEA): Dimensionally Reduced Multivariate Gene Set Enrichment Analysis Tool.Clark, Neil R; Szymkiewicz, Maciej; Wang, Zichen; Monteiro, Caroline D; Jones, Matthew R; Ma'ayan, AviProceedings. IEEE International Conference on Bioinformatics and Biomedicine.2015 Nov;256-26226848405
A three-groups model for high-throughput survival screens.Shaby, Benjamin A; Skibinski, Gaia; Ando, Michael; LaDow, Eva S; Finkbeiner, StevenBiometrics.2016 Jan 28;26821783
Fetal liver hematopoietic stem cell niches associate with portal vessels.Khan, Jalal A; Mendelson, Avital; Kunisaki, Yuya; Birbrair, Alexander; Kou, Yan; Arnal-Estapé, Anna; Pinho, Sandra; Ciero, Paul; Nakahara, Fumio; Ma'ayan, Avi; Bergman, Aviv; Merad, Miriam; Frenette, Paul SScience (New York, N.Y.).2016 Jan 8;176-8026634440
Mapping the effects of drugs on the immune system.Kidd, Brian A; Wroblewska, Aleksandra; Boland, Mary R; Agudo, Judith; Merad, Miriam; Tatonetti, Nicholas P; Brown, Brian D; Dudley, Joel TNature biotechnology.2016 Jan;47-5426619012
Molecular systems evaluation of oligomerogenic APP(E693Q) and fibrillogenic APP(KM670/671NL)/PSEN1(?exon9) mouse models identifies shared features with human Alzheimer's brain molecular pathology.Readhead, B; Haure-Mirande, J-V; Zhang, B; Haroutunian, V; Gandy, S; Schadt, E E; Dudley, J T; Ehrlich, M EMolecular psychiatry.2015 Nov 10;26552589
Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65.Huang, Xi-Ping; Karpiak, Joel; Kroeze, Wesley K; Zhu, Hu; Chen, Xin; Moy, Sheryl S; Saddoris, Kara A; Nikolova, Viktoriya D; Farrell, Martilias S; Wang, Sheng; Mangano, Thomas J; Deshpande, Deepak A; Jiang, Alice; Penn, Raymond B; Jin, Jian; Koller, BeverNature.2015 Nov 26;477-8326550826
Identification of type 2 diabetes subgroups through topological analysis of patient similarity.Li, Li; Cheng, Wei-Yi; Glicksberg, Benjamin S; Gottesman, Omri; Tamler, Ronald; Chen, Rong; Bottinger, Erwin P; Dudley, Joel TScience translational medicine.2015 Oct 28;311ra17426511511
Noribogaine is a G-protein biased ?-opioid receptor agonist.Maillet, Emeline L; Milon, Nicolas; Heghinian, Mari D; Fishback, James; Schürer, Stephan C; Garamszegi, Nandor; Mash, Deborah CNeuropharmacology.2015 Dec;675-8826302653
Reprint of ''Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction''.Rouillard, Andrew D; Wang, Zichen; Ma'ayan, AviComputational biology and chemistry.2015 Dec;123-3826297300
An Integrated Transcriptome Atlas of Embryonic Hair Follicle Progenitors, Their Niche, and the Developing Skin.Sennett, Rachel; Wang, Zichen; Rezza, Amélie; Grisanti, Laura; Roitershtein, Nataly; Sicchio, Cristina; Mok, Ka Wai; Heitman, Nicholas J; Clavel, Carlos; Ma'ayan, Avi; Rendl, MichaelDevelopmental cell.2015 Sep 14;577-9126256211
Computational and Practical Aspects of Drug Repositioning.Oprea, Tudor I; Overington, John PAssay and drug development technologies.2015 Jul-Aug;299-30626241209
Comprehensive comparison of large-scale tissue expression datasetsSantos A, Tsafou K, Stolte C, Pletscher-Frankild S, O'Donoghue SI, Jensen LJ.Peer J2015 June 3026157623
Morphine Regulated Synaptic Networks Revealed by Integrated Proteomics and Network Analysis.Stockton Jr, Steven D; Gomes, Ivone; Liu, Tong; Moraje, Chandrakala; Hipólito, Lucia; Jones, Matthew R; Ma'ayan, Avi; Morón, Jose A; Li, Hong; Devi, Lakshmi AMolecular & cellular proteomics : MCP.2015 Oct;2564-7626149443
Publisher?s Note:Abstraction for data integration:Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction.Rouillard, Andrew D; Wang, Zichen; Ma'ayan, AviComputational biology and chemistry.2015 Oct;104-1926101093
Integrated Approaches for Genome-wide Interrogation of the Druggable Non-olfactory G Protein-coupled Receptor Superfamily.Roth, Bryan L; Kroeze, Wesley KThe Journal of biological chemistry.2015 Aug 7;19471-726100629
Dynamics of the discovery process of protein-protein interactions from low content studies.Wang, Zichen; Clark, Neil R; Ma'ayan, AviBMC systems biology.2015;2626048415
Choosing the Right Tool for the Job: RNAi, TALEN, or CRISPR.Boettcher, Michael; McManus, Michael TMolecular cell.2015 May 21;575-8526000843
GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions.Gundersen, Gregory W; Jones, Matthew R; Rouillard, Andrew D; Kou, Yan; Monteiro, Caroline D; Feldmann, Axel S; Hu, Kevin S; Ma'ayan, AviBioinformatics (Oxford, England).2015 Sep 15;3060-225971742
PRESTO-Tango as an open-source resource for interrogation of the druggable human GPCRome.Kroeze, Wesley K; Sassano, Maria F; Huang, Xi-Ping; Lansu, Katherine; McCorvy, John D; Giguère, Patrick M; Sciaky, Noah; Roth, Bryan LNature structural & molecular biology.2015 May;362-925895059
Inhibition of Lapatinib-Induced Kinome Reprogramming in ERBB2-Positive Breast Cancer by Targeting BET Family Bromodomains.Stuhlmiller, Timothy J; Miller, Samantha M; Zawistowski, Jon S; Nakamura, Kazuhiro; Beltran, Adriana S; Duncan, James S; Angus, Steven P; Collins, Kyla A L; Granger, Deborah A; Reuther, Rachel A; Graves, Lee M; Gomez, Shawn M; Kuan, Pei-Fen; Parker, Joel Cell reports.2015 Apr 21;390-40425865888
Cell-Based Screening: Extracting Meaning from Complex DataFinkbeiner S., Frumkin M., Kassner PDNeuron 2015 Apr 886(1):160-17425856492
Genome-wide significant loci: how important are they? Systems genetics to understand heritability of coronary artery disease and other common complex disorders.Björkegren, Johan L M; Kovacic, Jason C; Dudley, Joel T; Schadt, Eric EJournal of the American College of Cardiology.2015 Mar 3;830-4525720628
Genomic and network patterns of schizophrenia genetic variation in human evolutionary accelerated regions.Xu, Ke; Schadt, Eric E; Pollard, Katherine S; Roussos, Panos; Dudley, Joel TMolecular biology and evolution.2015 May;1148-6025681384
Computational and experimental advances in drug repositioning for accelerated therapeutic stratificationShameer K, Readhead B, Dudley JT. Current Topics in Medicinal Chemistry201525579574
REDD1 functions at the crossroads between the therapeutic and adverse effects of topical glucocorticoids.Baida, Gleb; Bhalla, Pankaj; Kirsanov, Kirill; Lesovaya, Ekaterina; Yakubovskaya, Marianna; Yuen, Kit; Guo, Shuchi; Lavker, Robert M; Readhead, Ben; Dudley, Joel T; Budunova, IrinaEMBO molecular medicine.2015 Jan;42-5825504525
The TLQP-21 peptide activates the G-protein-coupled receptor C3aR1 via a folding-upon-binding mechanismCero C, Vostrikov VV, Verardi R, Severini C, Gopinath T, Braun PD, Sassano MF, Gurney A, Roth BL, Vulchanova L, Possenti R, Veglia G, Bartolomucci A.Structure2014 Dec 222(12):1744-53. 25456411
Lean Big Data integration in systems biology and systems pharmacology.Ma'ayan, Avi; Rouillard, Andrew D; Clark, Neil R; Wang, Zichen; Duan, Qiaonan; Kou, YanTrends in pharmacological sciences2014 Sep450-46025109570
Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets.Duan, Qiaonan; Wang, Zichen; Fernandez, Nicolas F; Rouillard, Andrew D; Tan, Christopher M; Benes, Cyril H; Ma'ayan, AviBioinformatics (Oxford, England).2014 Nov 15;3289-9025100688
Autophagy induction enhances TDP43 turnover and survival in neuronal ALS models.Barmada, Sami J; Serio, Andrea; Arjun, Arpana; Bilican, Bilada; Daub, Aaron; Ando, D Michael; Tsvetkov, Andrey; Pleiss, Michael; Li, Xingli; Peisach, Daniel; Shaw, Christopher; Chandran, Siddharthan; Finkbeiner, StevenNature chemical biology.2014 Aug;24974230
LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures.Duan, Qiaonan; Flynn, Corey; Niepel, Mario; Hafner, Marc; Muhlich, Jeremy L; Fernandez, Nicolas F; Rouillard, Andrew D; Tan, Christopher M; Chen, Edward Y; Golub, Todd R; Sorger, Peter K; Subramanian, Aravind; Ma'ayan, AviNucleic acids research2014 JulW449-6024906883