| Year |
Citation |
Score |
| 2023 |
Marino GB, Ahmed N, Xie Z, Jagodnik KM, Han J, Clarke DJB, Lachmann A, Keller MP, Attie AD, Ma'ayan A. D2H2: diabetes data and hypothesis hub. Bioinformatics Advances. 3: vbad178. PMID 38107655 DOI: 10.1093/bioadv/vbad178 |
0.608 |
|
| 2023 |
Evangelista JE, Xie Z, Marino GB, Nguyen N, Clarke DJB, Ma'ayan A. Enrichr-KG: bridging enrichment analysis across multiple libraries. Nucleic Acids Research. PMID 37166973 DOI: 10.1093/nar/gkad393 |
0.331 |
|
| 2023 |
Deng EZ, Fleishman RH, Xie Z, Marino GB, Clarke DJB, Ma'ayan A. Computational screen to identify potential targets for immunotherapeutic identification and removal of senescence cells. Aging Cell. e13809. PMID 37082798 DOI: 10.1111/acel.13809 |
0.324 |
|
| 2023 |
Lachmann A, Rizzo KA, Bartal A, Jeon M, Clarke DJB, Ma'ayan A. PrismEXP: gene annotation prediction from stratified gene-gene co-expression matrices. Peerj. 11: e14927. PMID 36874981 DOI: 10.7717/peerj.14927 |
0.701 |
|
| 2023 |
Marino GB, Wojciechowicz ML, Clarke DJB, Kuleshov MV, Xie Z, Jeon M, Lachmann A, Ma'ayan A. lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs. Database : the Journal of Biological Databases and Curation. 2023. PMID 36869839 DOI: 10.1093/database/baad009 |
0.688 |
|
| 2022 |
Xie Z, Kropiwnicki E, Wojciechowicz ML, Jagodnik KM, Shu I, Bailey A, Clarke DJB, Jeon M, Evangelista JE, V Kuleshov M, Lachmann A, Parigi AA, Sanchez JM, Jenkins SL, Ma'ayan A. Getting Started with LINCS Datasets and Tools. Current Protocols. 2: e487. PMID 35876555 DOI: 10.1002/cpz1.487 |
0.677 |
|
| 2022 |
Evangelista JE, Clarke DJB, Xie Z, Lachmann A, Jeon M, Chen K, Jagodnik KM, Jenkins SL, Kuleshov MV, Wojciechowicz ML, Schürer SC, Medvedovic M, Ma'ayan A. SigCom LINCS: data and metadata search engine for a million gene expression signatures. Nucleic Acids Research. PMID 35524556 DOI: 10.1093/nar/gkac328 |
0.72 |
|
| 2022 |
Kropiwnicki E, Lachmann A, Clarke DJB, Xie Z, Jagodnik KM, Ma'ayan A. DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules. Bmc Bioinformatics. 23: 76. PMID 35183110 DOI: 10.1186/s12859-022-04590-5 |
0.674 |
|
| 2022 |
Lachmann A, Xie Z, Ma'ayan A. blitzGSEA: Efficient computation of Gene Set Enrichment Analysis through Gamma distribution approximation. Bioinformatics (Oxford, England). PMID 35143610 DOI: 10.1093/bioinformatics/btac076 |
0.693 |
|
| 2022 |
Kropiwnicki E, Binder JL, Yang JJ, Holmes J, Lachmann A, Clarke DJB, Sheils T, Kelleher KJ, Metzger VT, Bologa CG, Oprea TI, Ma'ayan A. Getting Started with the IDG KMC Datasets and Tools. Current Protocols. 2: e355. PMID 35085427 DOI: 10.1002/cpz1.355 |
0.67 |
|
| 2021 |
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. Publisher Correction: A systems approach identifies HIPK2 as a key regulator of kidney fibrosis. Nature Medicine. PMID 34285421 DOI: 10.1038/s41591-021-01427-1 |
0.657 |
|
| 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 |
0.659 |
|
| 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 |
0.78 |
|
| 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 |
0.665 |
|
| 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 |
0.697 |
|
| 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 |
0.65 |
|
| 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 |
0.537 |
|
| 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 |
0.674 |
|
| 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 |
0.687 |
|
| 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 |
0.309 |
|
| 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 |
0.714 |
|
| 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 |
0.639 |
|
| 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 |
0.702 |
|
| 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 |
0.681 |
|
| 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 |
0.472 |
|
| 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 |
0.678 |
|
| 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 |
0.535 |
|
| 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 |
0.488 |
|
| 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 |
0.513 |
|
| 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 |
0.767 |
|
| 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 |
0.691 |
|
| 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 |
0.704 |
|
| 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 |
0.496 |
|
| 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 |
0.423 |
|
| 2019 |
Nakahara F, Pinho S, Borger DK, Wei Q, Maryanovich M, Zahalka AH, Suzuki M, Cruz C, Wang Z, Xu C, Boulais P, Ma'ayan A, Greally JM, Frenette PS. Engineering a Hematopoietic Stem Cell Niche By Revitalizing Mesenchymal Stem Cells with Five Transcription Factors Blood. 134: 5004-5004. DOI: 10.1182/Blood-2019-125045 |
0.576 |
|
| 2019 |
Keenan AB, Wojciechowicz ML, Wang Z, Jagodnik KM, Jenkins SL, Lachmann A, Ma'ayan A. Connectivity Mapping: Methods and Applications Annual Review of Biomedical Data Science. 2: 69-92. DOI: 10.1146/ANNUREV-BIODATASCI-072018-021211 |
0.664 |
|
| 2019 |
Nakahara F, Borger D, Wei Q, Pinho S, Maryanovich M, Zahalka A, Suzuki M, Cruz C, Wang Z, Xu C, Boulais P, Ma'ayan A, Greally J, Frenette P. 2011 - ENGINEERING A HEMATOPOIETIC STEM CELL NICHE BY REVITALIZING MESENCHYMAL STEM CELLS Experimental Hematology. 76: S45. DOI: 10.1016/J.Exphem.2019.06.285 |
0.558 |
|
| 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 |
0.498 |
|
| 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 |
0.758 |
|
| 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 |
0.53 |
|
| 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 |
0.748 |
|
| 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 |
0.664 |
|
| 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 |
0.629 |
|
| 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 |
0.485 |
|
| 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 |
0.442 |
|
| 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 |
0.332 |
|
| 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 |
0.78 |
|
| 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 |
0.78 |
|
| 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 |
0.694 |
|
| 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 |
0.731 |
|
| 2018 |
Oprea TI, Bologa CG, Brunak S, Campbell A, Gan GN, Gaulton A, Gomez SM, Guha R, Hersey A, Holmes J, Jadhav A, Jensen LJ, Johnson GL, Karlson A, Leach AR, et al. Unexplored therapeutic opportunities in the human genome. Nature Reviews. Drug Discovery. PMID 29472638 DOI: 10.1038/Nrd.2018.14 |
0.322 |
|
| 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 |
0.731 |
|
| 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 |
0.801 |
|
| 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 |
0.795 |
|
| 2018 |
Mok K, Wang Z, Sennett R, Rezza A, Heitman N, Ma'ayan A, Rendl M. 1387 Identifying the key niche signals for hair follicle formation Journal of Investigative Dermatology. 138: S235. DOI: 10.1016/J.Jid.2018.03.1404 |
0.515 |
|
| 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 |
0.365 |
|
| 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 |
0.503 |
|
| 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 |
0.46 |
|
| 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 |
0.802 |
|
| 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 |
0.362 |
|
| 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 |
0.721 |
|
| 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 |
0.312 |
|
| 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 |
0.489 |
|
| 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 |
0.329 |
|
| 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 |
0.759 |
|
| 2017 |
Heitman N, Sennett R, Wang Z, Rezza A, Mok K, Ma'ayan A, Rendl M. 862 Defining the molecular signature of the hair follicle dermal sheath and its functional requirement for hair cycle progression during catagen Journal of Investigative Dermatology. 137: S148. DOI: 10.1016/J.Jid.2017.02.888 |
0.51 |
|
| 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 |
0.797 |
|
| 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 |
0.512 |
|
| 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 |
0.324 |
|
| 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 |
0.813 |
|
| 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 |
0.593 |
|
| 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 |
0.72 |
|
| 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 |
0.642 |
|
| 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 |
0.763 |
|
| 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 |
0.774 |
|
| 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 |
0.803 |
|
| 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 |
0.53 |
|
| 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 |
0.535 |
|
| 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 |
0.76 |
|
| 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 |
0.351 |
|
| 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 |
0.632 |
|
| 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 |
0.503 |
|
| 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 |
0.721 |
|
| 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 |
0.791 |
|
| 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 |
0.563 |
|
| 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 |
0.544 |
|
| 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 |
0.334 |
|
| 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 |
0.482 |
|
| 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 |
0.78 |
|
| 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 |
0.761 |
|
| 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 |
0.433 |
|
| 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 |
0.403 |
|
| 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 |
0.492 |
|
| 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 |
0.764 |
|
| 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 |
0.452 |
|
| 2014 |
Ma'ayan A, Duan Q. A blueprint of cell identity. Nature Biotechnology. 32: 1007-8. PMID 25299921 DOI: 10.1038/Nbt.3035 |
0.756 |
|
| 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 |
0.575 |
|
| 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 |
0.811 |
|
| 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 |
0.773 |
|
| 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 |
0.72 |
|
| 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 |
0.777 |
|
| 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 |
0.806 |
|
| 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 |
0.728 |
|
| 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 |
0.808 |
|
| 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 |
0.321 |
|
| 2014 |
Liang R, Campreciós G, Kou Y, McGrath KE, Novak R, Catherman SC, Rimmele P, Bigarella CL, Bresnick EH, Papatsenko D, Ma'ayan A, Fowler VM, Palis J, Ghaffari S. A Systems Approach Identifies Essential FOXO3 Functions in Erythroblast Enucleation Process Blood. 124: 445-445. DOI: 10.1182/Blood.V124.21.445.445 |
0.324 |
|
| 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 |
0.337 |
|
| 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 |
0.711 |
|
| 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 |
0.733 |
|
| 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 |
0.57 |
|
| 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 |
0.744 |
|
| 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 |
0.735 |
|
| 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 |
0.715 |
|
| 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 |
0.813 |
|
| 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 |
0.736 |
|
| 2013 |
Campreciós G, Zhang X, Kou Y, Ma'ayan A, Ghaffari S. RNA Sequencing Of Adult Bone Marrow Erythroid Populations Reveals Significant Transcriptional Deregulation In Foxo3-/- Mutant Cells Blood. 122: 3416-3416. DOI: 10.1182/Blood.V122.21.3416.3416 |
0.432 |
|
| 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 |
0.405 |
|
| 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 |
0.817 |
|
| 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 |
0.704 |
|
| 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 |
0.35 |
|
| 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 |
0.722 |
|
| 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 |
0.726 |
|
| 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 |
0.336 |
|
| 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 |
0.738 |
|
| 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 |
0.776 |
|
| 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 |
0.567 |
|
| 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 |
0.319 |
|
| 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 |
0.697 |
|
| 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 |
0.764 |
|
| 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 |
0.538 |
|
| 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 |
0.595 |
|
| 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 |
0.517 |
|
| 2012 |
Baron MH, Vacaru A, Isern J, Hadjantonakis A, Papatsenko D, Ma'ayan A. Regulation of Primitive Erythroid Progenitor Development Blood. 120: 1211-1211. DOI: 10.1182/Blood.V120.21.1211.1211 |
0.41 |
|
| 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 |
0.68 |
|
| 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 |
0.476 |
|
| 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 |
0.772 |
|
| 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 |
0.306 |
|
| 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 |
0.742 |
|
| 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 |
0.699 |
|
| 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 |
0.394 |
|
| 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 |
0.7 |
|
| 2011 |
Baron MH, Isern J, Fraser ST, He Z, Ma'ayan A, Schulz VP, Tuck D, Gallagher PG. Primitive Erythroid Progenitors Are Regulated by Hypoxia and Display An Aerobic Glycolytic Metabolic Profile, Blood. 118: 3159-3159. DOI: 10.1182/Blood.V118.21.3159.3159 |
0.408 |
|
| 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 |
0.432 |
|
| 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 |
0.707 |
|
| 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 |
0.572 |
|
| 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 |
0.558 |
|
| 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 |
0.801 |
|
| 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 |
0.661 |
|
| 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 |
0.446 |
|
| 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 |
0.7 |
|
| 2010 |
Berger SI, Ma'ayan A, Iyengar R. Systems pharmacology of arrhythmias. Science Signaling. 3: ra30. PMID 20407125 DOI: 10.1126/Scisignal.2000723 |
0.706 |
|
| 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 |
0.732 |
|
| 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 |
0.683 |
|
| 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 |
0.688 |
|
| 2009 |
Macarthur BD, Ma'ayan A, Lemischka IR. Systems biology of stem cell fate and cellular reprogramming. Nature Reviews. Molecular Cell Biology. 10: 672-81. PMID 19738627 DOI: 10.1038/Nrm2766 |
0.38 |
|
| 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 |
0.409 |
|
| 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 |
0.531 |
|
| 2009 |
Lachmann A, Ma'ayan A. KEA: kinase enrichment analysis. Bioinformatics (Oxford, England). 25: 684-6. PMID 19176546 DOI: 10.1093/Bioinformatics/Btp026 |
0.682 |
|
| 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 |
0.496 |
|
| 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 |
0.727 |
|
| 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 |
0.334 |
|
| 2009 |
Méndez-Ferrer S, Michurina TV, Ferraro F, Mazloom A, MacArthur B, Lira S, Scadden DT, Ma'ayan A, Enikolopov GN, Frenette PS. Coordinated Regulation of Hematopoietic and Mesenchymal Stem Cells in a Bone Marrow Niche. Blood. 114: 2-2. DOI: 10.1182/Blood.V114.22.2.2 |
0.707 |
|
| 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 |
0.506 |
|
| 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 |
0.371 |
|
| 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 |
0.505 |
|
| 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 |
0.495 |
|
| 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 |
0.76 |
|
| 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 |
0.466 |
|
| 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 |
0.382 |
|
| 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 |
0.7 |
|
| 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 |
0.704 |
|
| 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 |
0.519 |
|
| 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 |
0.526 |
|
| 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 |
0.498 |
|
| 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 |
0.431 |
|
| 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 |
0.46 |
|
| 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 |
0.527 |
|
| 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 |
0.747 |
|
| 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 |
0.529 |
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