We Accelerate Discovery

You are here

Illuminating the Druggable Genome (47)
Publication TitleAuthorsJournalPublication DatePage NoPubMedID
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
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
?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
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
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
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


Up to Top