Avi Ma'ayan, Ph.D. - Publications

2006 Icahn School of Medicine at Mount Sinai, New York, NY, United States 
Cellular signaling systems

191 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Piret SE, Guo Y, Attallah AA, Horne SJ, Zollman A, Owusu D, Henein J, Sidorenko VS, Revelo MP, Hato T, Ma'ayan A, He JC, Mallipattu SK. Krüppel-like factor 6-mediated loss of BCAA catabolism contributes to kidney injury in mice and humans. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34074766 DOI: 10.1073/pnas.2024414118  0.6
2021 Kuleshov MV, Xie Z, London ABK, Yang J, Evangelista JE, Lachmann A, Shu I, Torre D, Ma'ayan A. KEA3: improved kinase enrichment analysis via data integration. Nucleic Acids Research. PMID 34019655 DOI: 10.1093/nar/gkab359  1
2021 Sevilla A, Papatsenko D, Mazloom AR, Xu H, Vasileva A, Unwin RD, LeRoy G, Chen EY, Garrett-Bakelman FE, Lee DF, Trinite B, Webb RL, Wang Z, Su J, Gingold J, et al. An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feed Forward Loop Interactions. Frontiers in Cell and Developmental Biology. 9: 630067. PMID 33816475 DOI: 10.3389/fcell.2021.630067  1
2021 Austin E, Koo E, Merleev A, Torre D, Marusina A, Luxardi G, Mamalis A, Isseroff RR, Ma'ayan A, Maverakis E, Jagdeo J. Transcriptome analysis of human dermal fibroblasts following red light phototherapy. Scientific Reports. 11: 7315. PMID 33795767 DOI: 10.1038/s41598-021-86623-2  0.76
2021 Kropiwnicki E, Evangelista JE, Stein DJ, Clarke DJB, Lachmann A, Kuleshov MV, Jeon M, Jagodnik KM, Ma'ayan A. Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning. Database : the Journal of Biological Databases and Curation. 2021. PMID 33787872 DOI: 10.1093/database/baab017  1
2021 Xie Z, Bailey A, Kuleshov MV, Clarke DJB, Evangelista JE, Jenkins SL, Lachmann A, Wojciechowicz ML, Kropiwnicki E, Jagodnik KM, Jeon M, Ma'ayan A. Gene Set Knowledge Discovery with Enrichr. Current Protocols. 1: e90. PMID 33780170 DOI: 10.1002/cpz1.90  1
2021 Clarke DJB, Rebman AW, Bailey A, Wojciechowicz ML, Jenkins SL, Evangelista JE, Danieletto M, Fan J, Eshoo MW, Mosel MR, Robinson W, Ramadoss N, Bobe J, Soloski MJ, Aucott JN, et al. Predicting Lyme Disease From Patients' Peripheral Blood Mononuclear Cells Profiled With RNA-Sequencing. Frontiers in Immunology. 12: 636289. PMID 33763080 DOI: 10.3389/fimmu.2021.636289  0.76
2021 Clarke DJB, Jeon M, Stein DJ, Moiseyev N, Kropiwnicki E, Dai C, Xie Z, Wojciechowicz ML, Litz S, Hom J, Evangelista JE, Goldman L, Zhang S, Yoon C, Ahamed T, et al. Appyters: Turning Jupyter Notebooks into data-driven web apps. Patterns (New York, N.Y.). 2: 100213. PMID 33748796 DOI: 10.1016/j.patter.2021.100213  1
2021 Jeon M, Jagodnik KM, Kropiwnicki E, Stein DJ, Ma'ayan A. Prioritizing Pain-Associated Targets with Machine Learning. Biochemistry. PMID 33606503 DOI: 10.1021/acs.biochem.0c00930  0.72
2020 Zhang L, Wang Z, Liu R, Li Z, Lin J, Wojciechowicz ML, Huang J, Lee K, Ma'ayan A, He JC. Connectivity Mapping Identifies BI-2536 as a Potential Drug to Treat Diabetic Kidney Disease. Diabetes. PMID 33067313 DOI: 10.2337/db20-0580  1
2020 Eberlein J, Davenport B, Nguyen TT, Victorino F, Jhun K, van der Heide V, Kuleshov M, Ma'ayan A, Kedl R, Homann D. Chemokine Signatures of Pathogen-Specific T Cells I: Effector T Cells. Journal of Immunology (Baltimore, Md. : 1950). PMID 32948687 DOI: 10.4049/Jimmunol.2000253  0.56
2020 Davenport B, Eberlein J, Nguyen TT, Victorino F, van der Heide V, Kuleshov M, Ma'ayan A, Kedl R, Homann D. Chemokine Signatures of Pathogen-Specific T Cells II: Memory T Cells in Acute and Chronic Infection. Journal of Immunology (Baltimore, Md. : 1950). PMID 32948682 DOI: 10.4049/Jimmunol.2000254  0.56
2020 Kuleshov MV, Stein DJ, Clarke DJB, Kropiwnicki E, Jagodnik KM, Bartal A, Evangelista JE, Hom J, Cheng M, Bailey A, Zhou A, Ferguson LB, Lachmann A, Ma'ayan A. The COVID-19 Drug and Gene Set Library. Patterns (New York, N.Y.). 100090. PMID 32838343 DOI: 10.1016/j.patter.2020.100090  1
2020 Kuleshov MV, Clarke DJB, Kropiwnicki E, Jagodnik KM, Bartal A, Evangelista JE, Zhou A, Ferguson LB, Lachmann A, Ma'ayan A. The COVID-19 Gene and Drug Set Library. Research Square. PMID 32702729 DOI: 10.21203/rs.3.rs-28582/v1  1
2020 Chen Z, Herting CJ, Ross JL, Gabanic B, Puigdelloses Vallcorba M, Szulzewsky F, Wojciechowicz ML, Cimino PJ, Ezhilarasan R, Sulman EP, Ying M, Ma'ayan A, Read RD, Hambardzumyan D. Genetic driver mutations introduced in identical cell-of-origin in murine glioblastoma reveal distinct immune landscapes but similar response to checkpoint blockade. Glia. PMID 32639068 DOI: 10.1002/Glia.23883  0.76
2020 Borziak K, Qi T, Evangelista JE, Clarke DJB, Ma'ayan A, Finkelstein J. Towards Intelligent Integration and Sharing of Stem Cell Research Data. Studies in Health Technology and Informatics. 272: 334-337. PMID 32604670 DOI: 10.3233/Shti200563  0.72
2020 Wojciechowicz ML, Ma'ayan A. GPR84: an immune response dial? Nature Reviews. Drug Discovery. 19: 374. PMID 32494048 DOI: 10.1038/D41573-020-00029-9  0.76
2020 Edwards JJ, Rouillard AD, Fernandez NF, Wang Z, Lachmann A, Shankaran SS, Bisgrove BW, Demarest B, Turan N, Srivastava D, Bernstein D, Deanfield J, Giardini A, Porter G, Kim R, et al. Systems Analysis Implicates WAVE2 Complex in the Pathogenesis of Developmental Left-Sided Obstructive Heart Defects. Jacc. Basic to Translational Science. 5: 376-386. PMID 32368696 DOI: 10.1016/J.Jacbts.2020.01.012  1
2020 Bartal A, Lachmann A, Clarke DJB, Seiden AH, Jagodnik KM, Ma'ayan A. EnrichrBot: Twitter Bot Tracking Tweets About Human Genes. Bioinformatics (Oxford, England). PMID 32277816 DOI: 10.1093/Bioinformatics/Btaa240  1
2020 Bernitz JM, Rapp K, Daniel MG, Shcherbinin D, Yuan Y, Gomes A, Waghray A, Brosh R, Lachmann A, Ma'ayan A, Papatsenko D, Moore KA. Memory of Divisional History Directs the Continuous Process of Primitive Hematopoietic Lineage Commitment. Stem Cell Reports. PMID 32243840 DOI: 10.1016/J.Stemcr.2020.03.005  1
2020 Lachmann A, Clarke DJB, Torre D, Xie Z, Ma'ayan A. Interoperable RNA-Seq analysis in the cloud. Biochimica Et Biophysica Acta. Gene Regulatory Mechanisms. 194521. PMID 32156561 DOI: 10.1016/J.Bbagrm.2020.194521  1
2019 Heitman N, Sennett R, Mok KW, Saxena N, Srivastava D, Martino P, Grisanti L, Wang Z, Ma'ayan A, Rompolas P, Rendl M. Dermal sheath contraction powers stem cell niche relocation during hair cycle regression. Science (New York, N.Y.). PMID 31857493 DOI: 10.1126/Science.Aax9131  1
2019 Stathias V, Turner J, Koleti A, Vidovic D, Cooper D, Fazel-Najafabadi M, Pilarczyk M, Terryn R, Chung C, Umeano A, Clarke DJB, Lachmann A, Evangelista JE, Ma'ayan A, Medvedovic M, et al. LINCS Data Portal 2.0: next generation access point for perturbation-response signatures. Nucleic Acids Research. PMID 31701147 DOI: 10.1093/Nar/Gkz1023  1
2019 Clarke DJB, Wang L, Jones A, Wojciechowicz ML, Torre D, Jagodnik KM, Jenkins SL, McQuilton P, Flamholz Z, Silverstein MC, Schilder BM, Robasky K, Castillo C, Idaszak R, Ahalt SC, et al. FAIRshake: Toolkit to Evaluate the FAIRness of Research Digital Resources. Cell Systems. PMID 31677972 DOI: 10.1016/J.Cels.2019.09.011  0.76
2019 Ochsner SA, Abraham D, Martin K, Ding W, McOwiti A, Kankanamge W, Wang Z, Andreano K, Hamilton RA, Chen Y, Hamilton A, Gantner ML, Dehart M, Qu S, Hilsenbeck SG, et al. The Signaling Pathways Project, an integrated 'omics knowledgebase for mammalian cellular signaling pathways. Scientific Data. 6: 252. PMID 31672983 DOI: 10.1038/S41597-019-0193-4  1
2019 Duncan A, Heyer MP, Ishikawa M, Caligiuri SPB, Liu XA, Chen Z, Vittoria Micioni Di Bonaventura M, Elayouby KS, Ables JL, Howe WM, Bali P, Fillinger C, Williams M, O'Connor RM, Wang Z, et al. Habenular TCF7L2 links nicotine addiction to diabetes. Nature. 574: 372-377. PMID 31619789 DOI: 10.1038/S41586-019-1653-X  1
2019 Fernandez DM, Rahman AH, Fernandez NF, Chudnovskiy A, Amir ED, Amadori L, Khan NS, Wong CK, Shamailova R, Hill CA, Wang Z, Remark R, Li JR, Pina C, Faries C, et al. Single-cell immune landscape of human atherosclerotic plaques. Nature Medicine. PMID 31591603 DOI: 10.1038/S41591-019-0590-4  1
2019 Keenan AB, Torre D, Lachmann A, Leong AK, Wojciechowicz ML, Utti V, Jagodnik KM, Kropiwnicki E, Wang Z, Ma'ayan A. ChEA3: transcription factor enrichment analysis by orthogonal omics integration. Nucleic Acids Research. PMID 31114921 DOI: 10.1093/Nar/Gkz446  1
2019 Lachmann A, Schilder BM, Wojciechowicz ML, Torre D, Kuleshov MV, Keenan AB, Ma'ayan A. Geneshot: search engine for ranking genes from arbitrary text queries. Nucleic Acids Research. PMID 31114885 DOI: 10.1093/Nar/Gkz393  1
2019 Kuleshov MV, Diaz JEL, Flamholz ZN, Keenan AB, Lachmann A, Wojciechowicz ML, Cagan RL, Ma'ayan A. modEnrichr: a suite of gene set enrichment analysis tools for model organisms. Nucleic Acids Research. PMID 31069376 DOI: 10.1093/Nar/Gkz347  1
2019 Nakahara F, Borger DK, Wei Q, Pinho S, Maryanovich M, Zahalka AH, Suzuki M, Cruz CD, Wang Z, Xu C, Boulais PE, Ma'ayan A, Greally JM, Frenette PS. Engineering a haematopoietic stem cell niche by revitalizing mesenchymal stromal cells. Nature Cell Biology. PMID 30988422 DOI: 10.1038/S41556-019-0308-3  1
2019 Ellis RJ, Wang Z, Genes N, Ma'ayan A. Predicting opioid dependence from electronic health records with machine learning. Biodata Mining. 12: 3. PMID 30728857 DOI: 10.1186/S13040-019-0193-0  1
2018 Mok KW, Saxena N, Heitman N, Grisanti L, Srivastava D, Muraro MJ, Jacob T, Sennett R, Wang Z, Su Y, Yang LM, Ma'ayan A, Ornitz DM, Kasper M, Rendl M. Dermal Condensate Niche Fate Specification Occurs Prior to Formation and Is Placode Progenitor Dependent. Developmental Cell. PMID 30595537 DOI: 10.1016/J.Devcel.2018.11.034  1
2018 Wang Z, Lachmann A, Ma'ayan A. Mining data and metadata from the gene expression omnibus. Biophysical Reviews. PMID 30594974 DOI: 10.1007/S12551-018-0490-8  1
2018 Breen MS, Ozcan S, Ramsey JM, Wang Z, Ma'ayan A, Rustogi N, Gottschalk MG, Webster MJ, Weickert CS, Buxbaum JD, Bahn S. Temporal proteomic profiling of postnatal human cortical development. Translational Psychiatry. 8: 267. PMID 30518843 DOI: 10.1038/S41398-018-0306-4  1
2018 Gomes AM, Kurochkin I, Chang B, Daniel M, Law K, Satija N, Lachmann A, Wang Z, Ferreira L, Ma'ayan A, Chen BK, Papatsenko D, Lemischka IR, Moore KA, Pereira CF. Cooperative Transcription Factor Induction Mediates Hemogenic Reprogramming. Cell Reports. 25: 2821-2835.e7. PMID 30517869 DOI: 10.1016/J.Celrep.2018.11.032  1
2018 Torre D, Lachmann A, Ma'ayan A. BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud. Cell Systems. PMID 30447998 DOI: 10.1016/J.Cels.2018.10.007  1
2018 Wang Z, He E, Sani K, Jagodnik KM, Silverstein M, Ma'ayan A. Drug Gene Budger (DGB): An application for ranking drugs to modulate a specific gene based on transcriptomic signatures. Bioinformatics (Oxford, England). PMID 30169739 DOI: 10.1093/Bioinformatics/Bty763  1
2018 Strub T, Ghiraldini FG, Carcamo S, Li M, Wroblewska A, Singh R, Goldberg MS, Hasson D, Wang Z, Gallagher SJ, Hersey P, Ma'ayan A, Long GV, Scolyer RA, Brown B, et al. SIRT6 haploinsufficiency induces BRAF melanoma cell resistance to MAPK inhibitors via IGF signalling. Nature Communications. 9: 3440. PMID 30143629 DOI: 10.1038/S41467-018-05966-Z  1
2018 Guo Y, Pace J, Li Z, Ma'ayan A, Wang Z, Revelo MP, Chen E, Gu X, Attalah A, Yang Y, Estrada C, Yang VW, He JC, Mallipattu SK. Podocyte-Specific Induction of Krüppel-Like Factor 15 Restores Differentiation Markers and Attenuates Kidney Injury in Proteinuric Kidney Disease. Journal of the American Society of Nephrology : Jasn. PMID 30143559 DOI: 10.1681/Asn.2018030324  1
2018 Han S, Tan C, Ding J, Wang J, Ma'ayan A, Gouon-Evans V. Endothelial cells instruct liver specification of embryonic stem cell-derived endoderm through endothelial VEGFR2 signaling and endoderm epigenetic modifications. Stem Cell Research. 30: 163-170. PMID 29936335 DOI: 10.1016/J.Scr.2018.06.004  0.44
2018 Stathias V, Koleti A, Vidović D, Cooper DJ, Jagodnik KM, Terryn R, Forlin M, Chung C, Torre D, Ayad N, Medvedovic M, Ma'ayan A, Pillai A, Schürer SC. Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center. Scientific Data. 5: 180117. PMID 29917015 DOI: 10.1038/Sdata.2018.117  0.76
2018 Clarke DJB, Kuleshov MV, Schilder BM, Torre D, Duffy ME, Keenan AB, Lachmann A, Feldmann AS, Gundersen GW, Silverstein MC, Wang Z, Ma'ayan A. eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks. Nucleic Acids Research. PMID 29800326 DOI: 10.1093/Nar/Gky458  1
2018 Grimes M, Hall B, Foltz L, Levy T, Rikova K, Gaiser J, Cook W, Smirnova E, Wheeler T, Clark NR, Lachmann A, Zhang B, Hornbeck P, Ma'ayan A, Comb M. Integration of protein phosphorylation, acetylation, and methylation data sets to outline lung cancer signaling networks. Science Signaling. 11. PMID 29789295 DOI: 10.1126/Scisignal.Aaq1087  1
2018 Lachmann A, Torre D, Keenan AB, Jagodnik KM, Lee HJ, Wang L, Silverstein MC, Ma'ayan A. Massive mining of publicly available RNA-seq data from human and mouse. Nature Communications. 9: 1366. PMID 29636450 DOI: 10.1038/S41467-018-03751-6  1
2018 Czarnowicki T, Dohlman AB, Malik K, Antonini D, Bissonnette R, Chan TC, Zhou L, Wen HC, Estrada Y, Xu H, Bryson C, Shen J, Lala D, Ma'ayan A, McGeehan G, et al. Short-term LXR activation improves epidermal barrier features in mild-to-moderate atopic dermatitis: a randomized controlled trial. Annals of Allergy, Asthma & Immunology : Official Publication of the American College of Allergy, Asthma, & Immunology. PMID 29567358 DOI: 10.1016/J.Anai.2018.03.013  1
2018 Torre D, Krawczuk P, Jagodnik KM, Lachmann A, Wang Z, Wang L, Kuleshov MV, Ma'ayan A. Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses. Scientific Data. 5: 180023. PMID 29485625 DOI: 10.1038/Sdata.2018.23  1
2018 Wang Z, Lachmann A, Keenan AB, Ma'ayan A, Stegle O. L1000FWD: Fireworks visualization of drug-induced transcriptomic signatures. Bioinformatics (Oxford, England). PMID 29420694 DOI: 10.1093/Bioinformatics/Bty060  1
2018 Koplev S, Lin K, Dohlman AB, Ma'ayan A. Integration of pan-cancer transcriptomics with RPPA proteomics reveals mechanisms of epithelial-mesenchymal transition. Plos Computational Biology. 14: e1005911. PMID 29293502 DOI: 10.1371/journal.pcbi.1005911  0.48
2018 Hodos R, Zhang P, Lee HC, Duan Q, Wang Z, Clark NR, Ma'ayan A, Wang F, Kidd B, Hu J, Sontag D, Dudley J. Cell-specific prediction and application of drug-induced gene expression profiles. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 23: 32-43. PMID 29218867  1
2018 Keenan AB, Jenkins SL, Jagodnik KM, Koplev S, He E, Torre D, Wang Z, Dohlman AB, Silverstein MC, Lachmann A, Kuleshov MV, Ma'ayan A, Stathias V, Terryn R, Cooper D, et al. The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations. Cell Systems. 6: 13-24. PMID 29199020 DOI: 10.1016/J.Cels.2017.11.001  1
2017 Koleti A, Terryn R, Stathias V, Chung C, Cooper DJ, Turner JP, Vidovic D, Forlin M, Kelley TT, D'Urso A, Allen BK, Torre D, Jagodnik KM, Wang L, Jenkins SL, et al. Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data. Nucleic Acids Research. PMID 29140462 DOI: 10.1093/Nar/Gkx1063  0.76
2017 Wang Z, Li L, Glicksberg BS, Israel A, Dudley JT, Ma'ayan A. Predicting Age by Mining Electronic Medical Records with Deep Learning Characterizes Differences between Chronological and Physiological Age. Journal of Biomedical Informatics. PMID 29113935 DOI: 10.1016/J.Jbi.2017.11.003  1
2017 Fu J, Wang Z, Lee K, Wei C, Liu Z, Zhang M, Zhou M, Cai M, Zhang W, Chuang PY, Ma'ayan A, He JC, Liu Z. Transcriptomic analysis uncovers novel synergistic mechanisms in combination therapy for lupus nephritis. Kidney International. PMID 29102373 DOI: 10.1016/J.Kint.2017.08.031  1
2017 Niepel M, Hafner M, Duan Q, Wang Z, Paull EO, Chung M, Lu X, Stuart JM, Golub TR, Subramanian A, Ma'ayan A, Sorger PK. Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling. Nature Communications. 8: 1186. PMID 29084964 DOI: 10.1038/S41467-017-01383-W  1
2017 Fernandez NF, Gundersen GW, Rahman A, Grimes ML, Rikova K, Hornbeck P, Ma'ayan A. Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data. Scientific Data. 4: 170151. PMID 28994825 DOI: 10.7490/F1000Research.1113430.1  0.52
2017 Sangodkar J, Perl A, Tohme R, Kiselar J, Kastrinsky DB, Zaware N, Izadmehr S, Mazhar S, Wiredja DD, O'Connor CM, Hoon D, Dhawan NS, Schlatzer D, Yao S, Leonard D, et al. Activation of tumor suppressor protein PP2A inhibits KRAS-driven tumor growth. The Journal of Clinical Investigation. PMID 28504649 DOI: 10.1172/Jci89548  1
2017 Jagodnik KM, Koplev S, Jenkins S, Ohno-Machado L, Paten B, Schurer SC, Dumontier M, Verborgh R, Bui A, Ping P, McKenna NJ, Madduri R, Pillai A, Ma'ayan A. Developing a Framework for Digital Objects in the Big Data to Knowledge (BD2K) Commons: Report from the Commons Framework Pilots Workshop. Journal of Biomedical Informatics. PMID 28501646 DOI: 10.1016/J.Jbi.2017.05.006  0.72
2017 Asada N, Kunisaki Y, Pierce H, Wang Z, Fernandez NF, Birbrair A, Ma'ayan A, Frenette PS. Differential cytokine contributions of perivascular haematopoietic stem cell niches. Nature Cell Biology. PMID 28218906 DOI: 10.1038/Ncb3475  1
2017 Shameer K, Glicksberg BS, Hodos R, Johnson KW, Badgeley MA, Readhead B, Tomlinson MS, O'Connor T, Miotto R, Kidd BA, Chen R, Ma'ayan A, Dudley JT. Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning. Briefings in Bioinformatics. PMID 28200013 DOI: 10.1093/Bib/Bbw136  0.52
2017 Niepel M, Hafner M, Duan Q, Subramanian A, Ma'ayan A, Sorger PK. Abstract IA05: New methods and better theory for pre-clinical cancer pharmacogenomics Cancer Research. 77. DOI: 10.1158/1538-7445.Epso16-Ia05  1
2016 Duan Q, Reid SP, Clark NR, Wang Z, Fernandez NF, Rouillard AD, Readhead B, Tritsch SR, Hodos R, Hafner M, Niepel M, Sorger PK, Dudley JT, Bavari S, Panchal RG, et al. L1000CDS(2): LINCS L1000 characteristic direction signatures search engine. Npj Systems Biology and Applications. 2. PMID 28413689 DOI: 10.1038/npjsba.2016.15  1
2016 Pfau ML, Purushothaman I, Feng J, Golden SA, Aleyasin H, Lorsch ZS, Cates HM, Flanigan ME, Menard C, Heshmati M, Wang Z, Ma'ayan A, Shen L, Hodes GE, Russo SJ. Integrative Analysis of Sex-Specific microRNA Networks Following Stress in Mouse Nucleus Accumbens. Frontiers in Molecular Neuroscience. 9: 144. PMID 28066174 DOI: 10.3389/Fnmol.2016.00144  1
2016 Nguyen DT, Mathias S, Bologa C, Brunak S, Fernandez N, Gaulton A, Hersey A, Holmes J, Jensen LJ, Karlsson A, Liu G, Ma'ayan A, Mandava G, Mani S, Mehta S, et al. Pharos: Collating protein information to shed light on the druggable genome. Nucleic Acids Research. PMID 27903890 DOI: 10.1093/Nar/Gkw1072  0.84
2016 Gundersen GW, Jagodnik KM, Woodland H, Fernandez NF, Sani K, Dohlman AB, Ung PM, Monteiro CD, Schlessinger A, Ma'ayan A. GEN3VA: aggregation and analysis of gene expression signatures from related studies. Bmc Bioinformatics. 17: 461. PMID 27846806 DOI: 10.1186/S12859-016-1321-1  0.72
2016 Wang Z, Monteiro CD, Jagodnik KM, Fernandez NF, Gundersen GW, Rouillard AD, Jenkins SL, Feldmann AS, Hu KS, McDermott MG, Duan Q, Clark NR, Jones MR, Kou Y, Goff T, et al. Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd. Nature Communications. 7: 12846. PMID 27667448 DOI: 10.7490/F1000Research.1113422.1  1
2016 Wang Z, Ma'ayan A. An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study. F1000research. 5: 1574. PMID 27583132 DOI: 10.12688/F1000Research.9110.1  1
2016 von Schimmelmann M, Feinberg PA, Sullivan JM, Ku SM, Badimon A, Duff MK, Wang Z, Lachmann A, Dewell S, Ma'ayan A, Han MH, Tarakhovsky A, Schaefer A. Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration. Nature Neuroscience. PMID 27526204 DOI: 10.1038/Nn.4360  1
2016 Rouillard AD, Gundersen GW, Fernandez NF, Wang Z, Monteiro CD, McDermott MG, Ma'ayan A. The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. Database : the Journal of Biological Databases and Curation. 2016. PMID 27374120 DOI: 10.1093/Database/Baw100  1
2016 Mallipattu SK, Guo Y, Revelo MP, Roa-Peña L, Miller T, Ling J, Shankland SJ, Bialkowska AB, Ly V, Estrada C, Jain MK, Lu Y, Ma'ayan A, Mehrotra A, Yacoub R, et al. Krüppel-Like Factor 15 Mediates Glucocorticoid-Induced Restoration of Podocyte Differentiation Markers. Journal of the American Society of Nephrology : Jasn. PMID 27288011 DOI: 10.1681/Asn.2015060672  0.6
2016 Morgan DJ, Poolman TM, Williamson AJ, Wang Z, Clark NR, Ma'ayan A, Whetton AD, Brass A, Matthews LC, Ray DW. Glucocorticoid receptor isoforms direct distinct mitochondrial programs to regulate ATP production. Scientific Reports. 6: 26419. PMID 27226058 DOI: 10.1038/Srep26419  1
2016 Wang Z, Clark NR, Ma'ayan A. Drug-induced adverse events prediction with the LINCS L1000 data. Bioinformatics (Oxford, England). PMID 27153606 DOI: 10.1093/Bioinformatics/Btw168  1
2016 Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, Koplev S, Jenkins SL, Jagodnik KM, Lachmann A, McDermott MG, Monteiro CD, Gundersen GW, Ma'ayan A. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Research. PMID 27141961 DOI: 10.1093/Nar/Gkw377  1
2016 Rezza A, Wang Z, Sennett R, Qiao W, Wang D, Heitman N, Mok KW, Clavel C, Yi R, Zandstra P, Ma'ayan A, Rendl M. Signaling Networks among Stem Cell Precursors, Transit-Amplifying Progenitors, and their Niche in Developing Hair Follicles. Cell Reports. PMID 27009580 DOI: 10.1016/J.Celrep.2016.02.078  1
2016 Kong DS, Kim J, Lee IH, Kim ST, Seol HJ, Lee JI, Park WY, Ryu G, Wang Z, Ma'ayan A, Nam DH. Integrative radiogenomic analysis for multicentric radiophenotype in glioblastoma. Oncotarget. PMID 26863628 DOI: 10.18632/Oncotarget.7115  1
2016 Dohlman A, Zaman S, Duan Q, Wang Z, Iyengar R, Abernethy D, Ma'ayan A. Predicting adverse cardiovascular events for tyrosine kinase inhibitors from molecular features F1000research. 5. DOI: 10.7490/F1000Research.1113434.1  1
2016 Gundersen GW, Jagodnik KM, Woodland H, Fernandez NF, Sani K, Dohlman AB, Ung PM, Monteiro CD, Schlessinger A, Ma'ayan A. GEN3VA: aggregation and analysis of gene expression signatures from related studies F1000research. 5. DOI: 10.7490/F1000Research.1113433.1  0.72
2016 Kuleshov MV, Ma'ayan A. Dashboard visualization and tool integration for Enrichr F1000research. 5. DOI: 10.7490/F1000Research.1113431.1  0.8
2016 Lachmann A, Goff T, Monteiro CD, Koplev S, Ma'ayan A. Cloud-based drag-and-drop scalable RNA sequencing pipeline F1000research. 5. DOI: 10.7490/F1000Research.1113424.1  1
2016 Wang Z, Ma'ayan A. RNA-seq pipeline tutorial with an example of reprocessing data from a recent Zika virus study F1000research. 5. DOI: 10.7490/F1000Research.1113423.1  1
2016 Jenkins S, Schürer S, Medvedovic M, Ma'ayan A. Community training and outreach activities of the BD2K-LINCS data coordination and integration center (DCIC) F1000research. 5. DOI: 10.7490/F1000Research.1113421.1  0.36
2016 Torre D, Lachmann A, Kuleshov M, Wang Z, He E, Monteiro CD, Jenkins SL, Ohno-Machado L, Ma'ayan A. Datasets2Tools: enriching DataMed with canned analyses F1000research. 5. DOI: 10.7490/F1000Research.1113420.1  1
2015 Clark NR, Szymkiewicz M, Wang Z, Monteiro CD, Jones MR, Ma'ayan A. Principal Angle Enrichment Analysis (PAEA): Dimensionally Reduced Multivariate Gene Set Enrichment Analysis Tool. Proceedings. Ieee International Conference On Bioinformatics and Biomedicine. 2015: 256-262. PMID 26848405 DOI: 10.1109/BIBM.2015.7359689  1
2015 Rouillard AD, Wang Z, Ma'ayan A. Reprint of "Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction". Computational Biology and Chemistry. PMID 26297300 DOI: 10.1016/J.Compbiolchem.2015.08.005  1
2015 Sennett R, Wang Z, Rezza A, Grisanti L, Roitershtein N, Sicchio C, Mok KW, Heitman NJ, Clavel C, Ma'ayan A, Rendl M. An Integrated Transcriptome Atlas of Embryonic Hair Follicle Progenitors, Their Niche, and the Developing Skin. Developmental Cell. PMID 26256211 DOI: 10.1016/J.Devcel.2015.06.023  1
2015 Stockton SD, Gomes I, Liu T, Moraje C, Hipólito L, Jones MR, Ma'ayan A, Morón JA, Li H, Devi LA. Morphine Regulated Synaptic Networks Revealed by Integrated Proteomics and Network Analysis. Molecular & Cellular Proteomics : McP. PMID 26149443 DOI: 10.1074/Mcp.M115.047977  1
2015 Rouillard AD, Wang Z, Ma'ayan A. Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction. Computational Biology and Chemistry. 58: 104-119. PMID 26101093 DOI: 10.1016/j.compbiolchem.2015.06.003  1
2015 Wang Z, Clark NR, Ma'ayan A. Dynamics of the discovery process of protein-protein interactions from low content studies. Bmc Systems Biology. 9: 26. PMID 26048415 DOI: 10.1186/S12918-015-0173-Z  1
2015 Gundersen GW, Jones MR, Rouillard AD, Kou Y, Monteiro CD, Feldmann AS, Hu KS, Ma'ayan A. GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions. Bioinformatics (Oxford, England). PMID 25971742 DOI: 10.1093/bioinformatics/btv297  1
2015 Mallipattu SK, Horne SJ, D'Agati V, Narla G, Liu R, Frohman MA, Dickman K, Chen EY, Ma'ayan A, Bialkowska AB, Ghaleb AM, Nandan MO, Jain MK, Daehn I, Chuang PY, et al. Krüppel-like factor 6 regulates mitochondrial function in the kidney. The Journal of Clinical Investigation. 125: 1347-61. PMID 25689250 DOI: 10.1172/Jci77084  1
2015 Scheckel C, Drapeau E, Frias MA, Park CY, Fak J, Zucker-Scharff I, Kou Y, Haroutunian V, Ma'ayan A, Buxbaum JD, Darnell RB. Author response: Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain Elife. DOI: 10.7554/Elife.10421.041  0.84
2015 Hafner M, Niepel M, Duan Q, Lu X, Subramanian A, Ma'ayan A, Sorger PK. Abstract PR16: Transcriptional landscape of drug response guides the design of specific and potent drug combinations Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-Pr16  1
2015 Gundersen GW, Jones MR, Ma'ayan A. Abstract B1-28: GEO2Enrichr: A Google Chrome extension to extract gene sets from the Gene Expression Omnibus and analyze these lists for common biological functions Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-B1-28  0.68
2015 Rouillard AD, Ma'ayan A. Abstract B1-25: Data integration for illuminating the druggable genome Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-B1-25  0.84
2015 Duarte LF, Young ARJ, Wang Z, Wu H, Panda T, Kou Y, Kapoor A, Hasson D, Mills NR, Ma'ayan A, Narita M, Bernstein E. Abstract SY10-04: Histone tail alterations in cellular senescence Cancer Research. 75. DOI: 10.1158/1538-7445.Am2015-Sy10-04  1
2015 Hafner M, Niepel M, Duan Q, Paull E, Stuart J, Subramanian A, Ma'ayan A, Sorger P. Abstract B20: Transcriptional landscape of drug response guides the design of specific and potent drug combinations Molecular Cancer Therapeutics. 14. DOI: 10.1158/1535-7163.Targ-15-B20  1
2014 Duarte LF, Young AR, Wang Z, Wu HA, Panda T, Kou Y, Kapoor A, Hasson D, Mills NR, Ma'ayan A, Narita M, Bernstein E. Histone H3.3 and its proteolytically processed form drive a cellular senescence programme. Nature Communications. 5: 5210. PMID 25394905 DOI: 10.1038/Ncomms6210  1
2014 De Rubeis S, He X, Goldberg AP, Poultney CS, Samocha K, Cicek AE, Kou Y, Liu L, Fromer M, Walker S, Singh T, Klei L, Kosmicki J, Shih-Chen F, Aleksic B, et al. Synaptic, transcriptional and chromatin genes disrupted in autism. Nature. 515: 209-15. PMID 25363760 DOI: 10.1038/Nature13772  1
2014 Ma'ayan A, Duan Q. A blueprint of cell identity. Nature Biotechnology. 32: 1007-8. PMID 25299921 DOI: 10.1038/Nbt.3035  1
2014 Xu H, Ang YS, Sevilla A, Lemischka IR, Ma'ayan A. Construction and validation of a regulatory network for pluripotency and self-renewal of mouse embryonic stem cells. Plos Computational Biology. 10: e1003777. PMID 25122140 DOI: 10.1371/Journal.Pcbi.1003777  1
2014 Ma'ayan A, Rouillard AD, Clark NR, Wang Z, Duan Q, Kou Y. Lean Big Data integration in systems biology and systems pharmacology. Trends in Pharmacological Sciences. 35: 450-60. PMID 25109570 DOI: 10.1016/J.Tips.2014.07.001  1
2014 Duan Q, Wang Z, Fernandez NF, Rouillard AD, Tan CM, Benes CH, Ma'ayan A. Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets. Bioinformatics (Oxford, England). 30: 3289-90. PMID 25100688 DOI: 10.1093/Bioinformatics/Btu526  0.56
2014 Hays T, Ma'ayan A, Clark NR, Tan CM, Teixeira A, Teixeira A, Choi JW, Burdis N, Jung SY, Bajaj AO, O'Malley BW, He JC, Hyink DP, Klotman PE. Proteomics analysis of the non-muscle myosin heavy chain IIa-enriched actin-myosin complex reveals multiple functions within the podocyte. Plos One. 9: e100660. PMID 24949636 DOI: 10.1371/Journal.Pone.0100660  1
2014 Duan Q, Flynn C, Niepel M, Hafner M, Muhlich JL, Fernandez NF, Rouillard AD, Tan CM, Chen EY, Golub TR, Sorger PK, Subramanian A, Ma'ayan A. LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. Nucleic Acids Research. 42: W449-60. PMID 24906883 DOI: 10.1093/Nar/Gku476  1
2014 Clark NR, Hu KS, Feldmann AS, Kou Y, Chen EY, Duan Q, Ma'ayan A. The characteristic direction: A geometrical approach to identify differentially expressed genes Bmc Bioinformatics. 15. PMID 24650281 DOI: 10.1186/1471-2105-15-79  1
2014 Liu L, Lei J, Sanders SJ, Willsey AJ, Kou Y, Cicek AE, Klei L, Lu C, He X, Li M, Muhle RA, Ma'ayan A, Noonan JP, Sestan N, McFadden KA, et al. DAWN: a framework to identify autism genes and subnetworks using gene expression and genetics. Molecular Autism. 5: 22. PMID 24602502 DOI: 10.1186/2040-2392-5-22  1
2014 Baker SJ, Ma'ayan A, Lieu YK, John P, Reddy MV, Chen EY, Duan Q, Snoeck HW, Reddy EP. B-myb is an essential regulator of hematopoietic stem cell and myeloid progenitor cell development. Proceedings of the National Academy of Sciences of the United States of America. 111: 3122-7. PMID 24516162 DOI: 10.1073/Pnas.1315464111  1
2014 Azeloglu EU, Hardy SV, Eungdamrong NJ, Chen Y, Jayaraman G, Chuang PY, Fang W, Xiong H, Neves SR, Jain MR, Li H, Ma'ayan A, Gordon RE, He JC, Iyengar R. Interconnected network motifs control podocyte morphology and kidney function. Science Signaling. 7: ra12. PMID 24497609 DOI: 10.1126/Scisignal.2004621  1
2014 Kleensang A, Maertens A, Rosenberg M, Fitzpatrick S, Lamb J, Auerbach S, Brennan R, Crofton KM, Gordon B, Fornace AJ, Gaido K, Gerhold D, Haw R, Henney A, Ma'ayan A, et al. t4 workshop report: Pathways of Toxicity. Altex. 31: 53-61. PMID 24127042 DOI: 10.14573/Altex.1309261  1
2013 Poultney CS, Goldberg AP, Drapeau E, Kou Y, Harony-Nicolas H, Kajiwara Y, De Rubeis S, Durand S, Stevens C, Rehnström K, Palotie A, Daly MJ, Ma'ayan A, Fromer M, Buxbaum JD. Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder. American Journal of Human Genetics. 93: 607-19. PMID 24094742 DOI: 10.1016/J.Ajhg.2013.09.001  1
2013 Jakubzick C, Gautier EL, Gibbings SL, Sojka DK, Schlitzer A, Johnson TE, Ivanov S, Duan Q, Bala S, Condon T, van Rooijen N, Grainger JR, Belkaid Y, Ma'ayan A, Riches DW, et al. Minimal differentiation of classical monocytes as they survey steady-state tissues and transport antigen to lymph nodes. Immunity. 39: 599-610. PMID 24012416 DOI: 10.1016/J.Immuni.2013.08.007  1
2013 Duan Q, Kou Y, Clark NR, Gordonov S, Ma'ayan A. Metasignatures identify two major subtypes of breast cancer. Cpt: Pharmacometrics & Systems Pharmacology. 2: e35. PMID 23836026 DOI: 10.1038/psp.2013.11  1
2013 Xu H, Baroukh C, Dannenfelser R, Chen EY, Tan CM, Kou Y, Kim YE, Lemischka IR, Ma'ayan A. ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells. Database : the Journal of Biological Databases and Curation. 2013: bat045. PMID 23794736 DOI: 10.1093/Database/Bat045  1
2013 Pereira CF, Chang B, Qiu J, Niu X, Papatsenko D, Hendry CE, Clark NR, Nomura-Kitabayashi A, Kovacic JC, Ma'ayan A, Schaniel C, Lemischka IR, Moore K. Induction of a hemogenic program in mouse fibroblasts. Cell Stem Cell. 13: 205-18. PMID 23770078 DOI: 10.1016/J.Stem.2013.05.024  1
2013 Tan CM, Chen EY, Dannenfelser R, Clark NR, Ma'ayan A. Network2Canvas: network visualization on a canvas with enrichment analysis. Bioinformatics (Oxford, England). 29: 1872-8. PMID 23749960 DOI: 10.1093/Bioinformatics/Btt319  1
2013 Sillivan SE, Whittard JD, Jacobs MM, Ren Y, Mazloom AR, Caputi FF, Horvath M, Keller E, Ma'ayan A, Pan YX, Chiang LW, Hurd YL. ELK1 transcription factor linked to dysregulated striatal mu opioid receptor signaling network and OPRM1 polymorphism in human heroin abusers. Biological Psychiatry. 74: 511-9. PMID 23702428 DOI: 10.1016/J.Biopsych.2013.04.012  1
2013 Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, Clark NR, Ma'ayan A. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. Bmc Bioinformatics. 14: 128. PMID 23586463 DOI: 10.1186/1471-2105-14-128  1
2013 Zhong Y, Chen EY, Liu R, Chuang PY, Mallipattu SK, Tan CM, Clark NR, Deng Y, Klotman PE, Ma'ayan A, He JC. Renoprotective effect of combined inhibition of angiotensin-converting enzyme and histone deacetylase. Journal of the American Society of Nephrology : Jasn. 24: 801-11. PMID 23559582 DOI: 10.1681/Asn.2012060590  1
2013 Jenkins SL, Ma'ayan A. Systems pharmacology meets predictive, preventive, personalized and participatory medicine. Pharmacogenomics. 14: 119-22. PMID 23327571 DOI: 10.2217/pgs.12.186  0.6
2013 Mallipattu SK, Liu R, Zhong Y, Chen EY, D'Agati V, Kaufman L, Ma'ayan A, Klotman PE, Chuang PY, He JC. Expression of HIV transgene aggravates kidney injury in diabetic mice. Kidney International. 83: 626-34. PMID 23325078 DOI: 10.1038/Ki.2012.445  1
2013 Rabinowitz KM, Wang Y, Chen EY, Hovhannisyan Z, Chiang D, Berin MC, Dahan S, Chaussabel D, Ma'ayan A, Mayer L. Transforming growth factor β signaling controls activities of human intestinal CD8(+)T suppressor cells. Gastroenterology. 144: 601-612.e1. PMID 23232296 DOI: 10.1053/J.Gastro.2012.12.001  1
2013 Xu H, Papatsenko D, Ma'ayan A, Lemischka I. Biological and Quantitative Models for Stem Cell Self-Renewal and Differentiation Handbook of Systems Biology. 427-441. DOI: 10.1016/B978-0-12-385944-0.00022-8  1
2013 Kou Y, Chen EY, Clark NR, Duan Q, Tan CM, Ma'ayan A. ChEA2: Gene-set libraries from ChIP-X experiments to decode the transcription regulome Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 8127: 416-430. DOI: 10.1007/978-3-642-40511-2_30  1
2012 Ma'ayan A. Colliding dynamical complex network models: biological attractors versus attractors from material physics. Biophysical Journal. 103: 1816-7. PMID 23199907 DOI: 10.1016/j.bpj.2012.09.019  1
2012 Clavel C, Grisanti L, Zemla R, Rezza A, Barros R, Sennett R, Mazloom AR, Chung CY, Cai X, Cai CL, Pevny L, Nicolis S, Ma'ayan A, Rendl M. Sox2 in the dermal papilla niche controls hair growth by fine-tuning BMP signaling in differentiating hair shaft progenitors. Developmental Cell. 23: 981-94. PMID 23153495 DOI: 10.1016/J.Devcel.2012.10.013  1
2012 MacArthur BD, Sevilla A, Lenz M, Müller FJ, Schuldt BM, Schuppert AA, Ridden SJ, Stumpf PS, Fidalgo M, Ma'ayan A, Wang J, Lemischka IR. Nanog-dependent feedback loops regulate murine embryonic stem cell heterogeneity. Nature Cell Biology. 14: 1139-47. PMID 23103910 DOI: 10.1038/Ncb2603  1
2012 Gautiar EL, Shay T, Miller J, Greter M, Jakubzick C, Ivanov S, Helft J, Chow A, Elpek KG, Gordonov S, Mazloom AR, Ma'Ayan A, Chua WJ, Hansen TH, Turley SJ, et al. Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages Nature Immunology. 13: 1118-1128. PMID 23023392 DOI: 10.1038/Ni.2419  1
2012 Zhou Q, Lv H, Mazloom AR, Xu H, Ma'ayan A, Gallo JM. Activation of alternate prosurvival pathways accounts for acquired sunitinib resistance in U87MG glioma xenografts. The Journal of Pharmacology and Experimental Therapeutics. 343: 509-19. PMID 22869928 DOI: 10.1124/Jpet.112.196097  1
2012 Lee DF, Su J, Ang YS, Carvajal-Vergara X, Mulero-Navarro S, Pereira CF, Gingold J, Wang HL, Zhao R, Sevilla A, Darr H, Williamson AJ, Chang B, Niu X, Aguilo F, et al. Regulation of embryonic and induced pluripotency by aurora kinase-p53 signaling. Cell Stem Cell. 11: 179-94. PMID 22862944 DOI: 10.1016/J.Stem.2012.05.020  1
2012 Clark NR, Dannenfelser R, Tan CM, Komosinski ME, Ma'ayan A. Sets2Networks: network inference from repeated observations of sets. Bmc Systems Biology. 6: 89. PMID 22824380 DOI: 10.1186/1752-0509-6-89  1
2012 Dannenfelser R, Clark NR, Ma'ayan A. Genes2FANs: connecting genes through functional association networks. Bmc Bioinformatics. 13: 156. PMID 22748121 DOI: 10.1186/1471-2105-13-156  1
2012 Kou Y, Betancur C, Xu H, Buxbaum JD, Ma'ayan A. Network- and attribute-based classifiers can prioritize genes and pathways for autism spectrum disorders and intellectual disability. American Journal of Medical Genetics. Part C, Seminars in Medical Genetics. 160: 130-42. PMID 22499558 DOI: 10.1002/Ajmg.C.31330  1
2012 Neale BM, Kou Y, Liu L, Ma'ayan A, Samocha KE, Sabo A, Lin CF, Stevens C, Wang LS, Makarov V, Polak P, Yoon S, Maguire J, Crawford EL, Campbell NG, et al. Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature. 485: 242-5. PMID 22495311 DOI: 10.1038/Nature11011  1
2012 Mallipattu SK, Liu R, Zheng F, Narla G, Ma'ayan A, Dikman S, Jain MK, Saleem M, D'Agati V, Klotman P, Chuang PY, He JC. Kruppel-like factor 15 (KLF15) is a key regulator of podocyte differentiation. The Journal of Biological Chemistry. 287: 19122-35. PMID 22493483 DOI: 10.1074/Jbc.M112.345983  1
2012 Jin Y, Ratnam K, Chuang PY, Fan Y, Zhong Y, Dai Y, Mazloom AR, Chen EY, D'Agati V, Xiong H, Ross MJ, Chen N, Ma'ayan A, He JC. A systems approach identifies HIPK2 as a key regulator of kidney fibrosis. Nature Medicine. 18: 580-8. PMID 22406746 DOI: 10.1038/Nm.2685  1
2012 Rozenfeld R, Bushlin I, Gomes I, Tzavaras N, Gupta A, Neves S, Battini L, Gusella GL, Lachmann A, Ma'ayan A, Blitzer RD, Devi LA. Receptor heteromerization expands the repertoire of cannabinoid signaling in rodent neurons. Plos One. 7: e29239. PMID 22235275 DOI: 10.1371/Journal.Pone.0029239  1
2012 Ding J, Xu H, Faiola F, Ma'ayan A, Wang J. Oct4 links multiple epigenetic pathways to the pluripotency network. Cell Research. 22: 155-67. PMID 22083510 DOI: 10.1038/Cr.2011.179  1
2012 Chen EY, Xu H, Gordonov S, Lim MP, Perkins MH, Ma'ayan A. Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers. Bioinformatics (Oxford, England). 28: 105-11. PMID 22080467 DOI: 10.1093/Bioinformatics/Btr625  1
2012 He JC, Chuang PY, Ma'ayan A, Iyengar R. Systems biology of kidney diseases. Kidney International. 81: 22-39. PMID 21881558 DOI: 10.1038/Ki.2011.314  1
2012 Gordonov S, Ma'Ayan A. Connecting clusters of patient to drug responses of cell lines to suggest personalized therapeutics for breast cancer Proceedings - 2012 Ieee International Conference On Bioinformatics and Biomedicine Workshops, Bibmw 2012. 529-534. DOI: 10.1109/BIBMW.2012.6470378  1
2012 Xiao K, Sun J, Kim J, Rajagopal S, Zhai B, Villén J, Haas W, Kovacs JJ, Shukla AK, Hara MR, Hernandez M, Lachmann A, Zhao S, Lin Y, Cheng Y, et al. Global phosphorylation analysis of β-arrestin-mediated signaling downstream of a seven transmembrane receptor (7TMR) (Proceedings of the National Academy of Sciences of the United States of America (2010) 107, 34 (15299-15304) doi:10.1073/pnas.1008461107) Proceedings of the National Academy of Sciences of the United States of America. 109: 13464. DOI: 10.1073/Pnas.1211889109  1
2012 Dannenfelser R, Xu H, Raimond C, Ma'Ayan A. Network pharmacology to aid the drug discovery process New Frontiers of Network Analysis in Systems Biology. 161-172. DOI: 10.1007/978-94-007-4330-4_9  1
2012 Ma'ayan A, MacArthur BD. New Frontiers of network analysis in systems biology New Frontiers of Network Analysis in Systems Biology. 1-199. DOI: 10.1007/978-94-007-4330-4  1
2011 Mazloom AR, Dannenfelser R, Clark NR, Grigoryan AV, Linder KM, Cardozo TJ, Bond JC, Boran AD, Iyengar R, Malovannaya A, Lanz RB, Ma'ayan A. Recovering protein-protein and domain-domain interactions from aggregation of IP-MS proteomics of coregulator complexes. Plos Computational Biology. 7: e1002319. PMID 22219718 DOI: 10.1371/Journal.Pcbi.1002319  1
2011 Abul-Husn NS, Annangudi SP, Ma'ayan A, Ramos-Ortolaza DL, Stockton SD, Gomes I, Sweedler JV, Devi LA. Chronic morphine alters the presynaptic protein profile: identification of novel molecular targets using proteomics and network analysis. Plos One. 6: e25535. PMID 22043286 DOI: 10.1371/Journal.Pone.0025535  0.48
2011 Baroukh C, Jenkins SL, Dannenfelser R, Ma'ayan A. Genes2WordCloud: a quick way to identify biological themes from gene lists and free text. Source Code For Biology and Medicine. 6: 15. PMID 21995939 DOI: 10.1186/1751-0473-6-15  1
2011 Ma'ayan A. Introduction to network analysis in systems biology. Science Signaling. 4: tr5. PMID 21917719 DOI: 10.1126/scisignal.2001965  1
2011 Clark NR, Ma'ayan A. Introduction to statistical methods for analyzing large data sets: gene-set enrichment analysis. Science Signaling. 4: tr4. PMID 21917718 DOI: 10.1126/Scisignal.2001966  1
2011 Clark NR, Ma'ayan A. Introduction to statistical methods to analyze large data sets: principal components analysis. Science Signaling. 4: tr3. PMID 21917717 DOI: 10.1126/Scisignal.2001967  1
2011 Webb RL, Ma'ayan A. Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format. Source Code For Biology and Medicine. 6: 5. PMID 21418653 DOI: 10.1186/1751-0473-6-5  1
2011 Dannenfelser R, Lachmann A, Szenk M, Ma'ayan A. FNV: light-weight flash-based network and pathway viewer. Bioinformatics (Oxford, England). 27: 1181-2. PMID 21349871 DOI: 10.1093/Bioinformatics/Btr098  1
2011 Xu H, Ma'ayan A. Visualization of patient samples by dimensionality reduction of genome-wide measurements Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7058: 15-22. DOI: 10.1007/978-3-642-25364-5_2  1
2010 Hernandez M, Lachmann A, Zhao S, Xiao K, Ma'ayan A. Inferring the Sign of Kinase-Substrate Interactions by Combining Quantitative Phosphoproteomics with a Literature-Based Mammalian Kinome Network. Proceedings / Annual Ieee International Symposium On Bioinformatics and Bioengineering (Bibe). Ieee International Symposium On Bioinformatics and Bioengineering. 2010: 180-184. PMID 21552464 DOI: 10.1109/BIBE.2010.75  1
2010 Xu H, Lemischka IR, Ma'ayan A. SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells. Bmc Systems Biology. 4: 173. PMID 21176149 DOI: 10.1186/1752-0509-4-173  1
2010 Carcea I, Ma'ayan A, Mesias R, Sepulveda B, Salton SR, Benson DL. Flotillin-mediated endocytic events dictate cell type-specific responses to semaphorin 3A. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 30: 15317-29. PMID 21068336 DOI: 10.1523/Jneurosci.1821-10.2010  1
2010 Xu H, Schaniel C, Lemischka IR, Ma'ayan A. Toward a complete in silico, multi-layered embryonic stem cell regulatory network. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 2: 708-33. PMID 20890967 DOI: 10.1002/Wsbm.93  1
2010 Lachmann A, Xu H, Krishnan J, Berger SI, Mazloom AR, Ma'ayan A. ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinformatics (Oxford, England). 26: 2438-44. PMID 20709693 DOI: 10.1093/Bioinformatics/Btq466  1
2010 Méndez-Ferrer S, Michurina TV, Ferraro F, Mazloom AR, Macarthur BD, Lira SA, Scadden DT, Ma'ayan A, Enikolopov GN, Frenette PS. Mesenchymal and haematopoietic stem cells form a unique bone marrow niche. Nature. 466: 829-34. PMID 20703299 DOI: 10.1038/Nature09262  0.32
2010 Ma'ayan A, He JC. Protein kinase target discovery from genome-wide messenger RNA expression profiling. The Mount Sinai Journal of Medicine, New York. 77: 345-9. PMID 20687179 DOI: 10.1002/Msj.20192  1
2010 Xiao K, Sun J, Kim J, Rajagopal S, Zhai B, Villén J, Haas W, Kovacs JJ, Shukla AK, Hara MR, Hernandez M, Lachmann A, Zhao S, Lin Y, Cheng Y, et al. Global phosphorylation analysis of beta-arrestin-mediated signaling downstream of a seven transmembrane receptor (7TMR). Proceedings of the National Academy of Sciences of the United States of America. 107: 15299-304. PMID 20686112 DOI: 10.1073/Pnas.1008461107  1
2010 MacArthur BD, Sánchez-García RJ, Ma'ayan A. Microdynamics and criticality of adaptive regulatory networks. Physical Review Letters. 104: 168701. PMID 20482087 DOI: 10.1103/PhysRevLett.104.168701  1
2010 Berger SI, Ma'ayan A, Iyengar R. Systems pharmacology of arrhythmias. Science Signaling. 3: ra30. PMID 20407125 DOI: 10.1126/Scisignal.2000723  1
2010 Lachmann A, Ma'ayan A. Lists2Networks: integrated analysis of gene/protein lists. Bmc Bioinformatics. 11: 87. PMID 20152038 DOI: 10.1186/1471-2105-11-87  1
2010 MacArthur BD, Lachmann A, Lemischka IR, Ma'ayan A. GATE: software for the analysis and visualization of high-dimensional time series expression data. Bioinformatics (Oxford, England). 26: 143-4. PMID 19892805 DOI: 10.1093/Bioinformatics/Btp628  1
2009 Lu R, Markowetz F, Unwin RD, Leek JT, Airoldi EM, MacArthur BD, Lachmann A, Rozov R, Ma'ayan A, Boyer LA, Troyanskaya OG, Whetton AD, Lemischka IR. Systems-level dynamic analyses of fate change in murine embryonic stem cells. Nature. 462: 358-62. PMID 19924215 DOI: 10.1038/Nature08575  0.32
2009 Cordeddu V, Di Schiavi E, Pennacchio LA, Ma'ayan A, Sarkozy A, Fodale V, Cecchetti S, Cardinale A, Martin J, Schackwitz W, Lipzen A, Zampino G, Mazzanti L, Digilio MC, Martinelli S, et al. Mutation of SHOC2 promotes aberrant protein N-myristoylation and causes Noonan-like syndrome with loose anagen hair. Nature Genetics. 41: 1022-6. PMID 19684605 DOI: 10.1038/Ng.425  1
2009 Abul-Husn NS, Bushlin I, Morón JA, Jenkins SL, Dolios G, Wang R, Iyengar R, Ma'ayan A, Devi LA. Systems approach to explore components and interactions in the presynapse. Proteomics. 9: 3303-15. PMID 19562802 DOI: 10.1002/Pmic.200800767  1
2009 Lachmann A, Ma'ayan A. KEA: kinase enrichment analysis. Bioinformatics (Oxford, England). 25: 684-6. PMID 19176546 DOI: 10.1093/Bioinformatics/Btp026  1
2009 Ma'ayan A, Jenkins SL, Barash A, Iyengar R. Neuro2A differentiation by Galphai/o pathway. Science Signaling. 2: cm1. PMID 19155528 DOI: 10.1126/Scisignal.254Cm1  1
2009 Ma'ayan A, Jenkins SL, Webb RL, Berger SI, Purushothaman SP, Abul-Husn NS, Posner JM, Flores T, Iyengar R. SNAVI: Desktop application for analysis and visualization of large-scale signaling networks. Bmc Systems Biology. 3: 10. PMID 19154595 DOI: 10.1186/1752-0509-3-10  1
2009 Ma'ayan A. Insights into the organization of biochemical regulatory networks using graph theory analyses. The Journal of Biological Chemistry. 284: 5451-5. PMID 18940806 DOI: 10.1074/Jbc.R800056200  1
2009 Xu H, Ma'ayan A. Visualization of the Phosphoproteomic Data from AfCS with the Google Motion Chart Gadget Nature Precedings. 4: 1-1. DOI: 10.1038/Npre.2009.3074.1  1
2008 MacArthur BD, Ma'ayan A, Lemischka IR. Toward stem cell systems biology: from molecules to networks and landscapes. Cold Spring Harbor Symposia On Quantitative Biology. 73: 211-5. PMID 19329576 DOI: 10.1101/Sqb.2008.73.061  1
2008 Ma'ayan A. Network integration and graph analysis in mammalian molecular systems biology. Iet Systems Biology. 2: 206-21. PMID 19045817 DOI: 10.1049/Iet-Syb:20070075  1
2008 Ma'ayan A, Cecchi GA, Wagner J, Rao AR, Iyengar R, Stolovitzky G. Ordered cyclic motifs contribute to dynamic stability in biological and engineered networks. Proceedings of the National Academy of Sciences of the United States of America. 105: 19235-40. PMID 19033453 DOI: 10.1073/Pnas.0805344105  1
2008 Ma'ayan A, Lipshtat A, Iyengar R, Sontag ED. Proximity of intracellular regulatory networks to monotone systems. Iet Systems Biology. 2: 103-12. PMID 18537452 DOI: 10.1049/Iet-Syb:20070036  1
2008 Bromberg KD, Ma'ayan A, Neves SR, Iyengar R. Design logic of a cannabinoid receptor signaling network that triggers neurite outgrowth. Science (New York, N.Y.). 320: 903-9. PMID 18487186 DOI: 10.1126/Science.1152662  1
2008 Ma'ayan A. PubMedAlertMe--standalone Windows-based PubMed SDI software application. Computers in Biology and Medicine. 38: 620-2. PMID 18402930 DOI: 10.1016/J.Compbiomed.2008.02.009  1
2008 Lipshtat A, Purushothaman SP, Iyengar R, Ma'ayan A. Functions of bifans in context of multiple regulatory motifs in signaling networks. Biophysical Journal. 94: 2566-79. PMID 18178648 DOI: 10.1529/biophysj.107.116673  1
2007 Caplan AJ, Ma'ayan A, Willis IM. Multiple kinases and system robustness: a link between Cdc37 and genome integrity. Cell Cycle (Georgetown, Tex.). 6: 3145-7. PMID 18075309 DOI: 10.4161/Cc.6.24.5147  1
2007 Berger SI, Posner JM, Ma'ayan A. Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. Bmc Bioinformatics. 8: 372. PMID 17916244 DOI: 10.1186/1471-2105-8-372  1
2007 Berger SI, Iyengar R, Ma'ayan A. AVIS: AJAX viewer of interactive signaling networks. Bioinformatics (Oxford, England). 23: 2803-5. PMID 17855420 DOI: 10.1093/Bioinformatics/Btm444  1
2007 Zaidel-Bar R, Itzkovitz S, Ma'ayan A, Iyengar R, Geiger B. Functional atlas of the integrin adhesome. Nature Cell Biology. 9: 858-67. PMID 17671451 DOI: 10.1038/Ncb0807-858  1
2007 Ma'ayan A, Jenkins SL, Goldfarb J, Iyengar R. Network analysis of FDA approved drugs and their targets. The Mount Sinai Journal of Medicine, New York. 74: 27-32. PMID 17516560 DOI: 10.1002/Msj.20002  1
2007 White AG, Ma'ayan A. Connecting seed lists of mammalian proteins using Steiner Trees Conference Record - Asilomar Conference On Signals, Systems and Computers. 155-159. DOI: 10.1038/Npre.2008.1768.1  1
2007 Ma'ayan A, Iyengar R, Sontag ED. Intracellular Regulatory Networks are close to Monotone Systems Nature Precedings. 2: 1-1. DOI: 10.1038/Npre.2007.25.1  1
2006 Ma'ayan A, Lipshtat A, Iyengar R. Topology of resultant networks shaped by evolutionary pressure. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 73: 061912. PMID 16906869 DOI: 10.1103/PhysRevE.73.061912  1
2006 Ma'ayan A, Gardiner K, Iyengar R. The cognitive phenotype of Down syndrome: insights from intracellular network analysis. Neurorx : the Journal of the American Society For Experimental Neurotherapeutics. 3: 396-406. PMID 16815222 DOI: 10.1016/J.Nurx.2006.05.036  1
2006 Ma'ayan A, Iyengar R. From components to regulatory motifs in signalling networks. Briefings in Functional Genomics & Proteomics. 5: 57-61. PMID 16769680 DOI: 10.1093/Bfgp/Ell004  1
2005 Ma'ayan A, Jenkins SL, Neves S, Hasseldine A, Grace E, Dubin-Thaler B, Eungdamrong NJ, Weng G, Ram PT, Rice JJ, Kershenbaum A, Stolovitzky GA, Blitzer RD, Iyengar R. Formation of regulatory patterns during signal propagation in a Mammalian cellular network. Science (New York, N.Y.). 309: 1078-83. PMID 16099987 DOI: 10.1126/Science.1108876  1
2005 Ma'ayan A, Blitzer RD, Iyengar R. Toward predictive models of mammalian cells. Annual Review of Biophysics and Biomolecular Structure. 34: 319-49. PMID 15869393 DOI: 10.1146/Annurev.Biophys.34.040204.144415  1
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