| Enrichr: a comprehensive gene set enrichment analysis web server 2016 update MV Kuleshov, MR Jones, AD Rouillard, NF Fernandez, Q Duan, Z Wang, ... Nucleic acids research 44 (W1), W90-W97, 2016 | 9151 | 2016 |
| Gene set knowledge discovery with Enrichr Z Xie, A Bailey, MV Kuleshov, DJB Clarke, JE Evangelista, SL Jenkins, ... Current protocols 1 (3), e90, 2021 | 2404 | 2021 |
| ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments A Lachmann, H Xu, J Krishnan, SI Berger, AR Mazloom, A Ma'ayan Bioinformatics 26 (19), 2438-2444, 2010 | 1037 | 2010 |
| Functional characterization of somatic mutations in cancer using network-based inference of protein activity MJ Alvarez, Y Shen, FM Giorgi, A Lachmann, BB Ding, BH Ye, A Califano Nature genetics 48 (8), 838-847, 2016 | 831 | 2016 |
| ChEA3: transcription factor enrichment analysis by orthogonal omics integration AB Keenan, D Torre, A Lachmann, AK Leong, ML Wojciechowicz, V Utti, ... Nucleic acids research 47 (W1), W212-W224, 2019 | 760 | 2019 |
| Massive mining of publicly available RNA-seq data from human and mouse A Lachmann, D Torre, AB Keenan, KM Jagodnik, HJ Lee, L Wang, ... Nature communications 9 (1), 1366, 2018 | 711 | 2018 |
| The library of integrated network-based cellular signatures NIH program: system-level cataloging of human cells response to perturbations AB Keenan, SL Jenkins, KM Jagodnik, S Koplev, E He, D Torre, Z Wang, ... Cell systems 6 (1), 13-24, 2018 | 435 | 2018 |
| Systems-level dynamic analyses of fate change in murine embryonic stem cells R Lu, F Markowetz, RD Unwin, JT Leek, EM Airoldi, BD MacArthur, ... Nature 462 (7271), 358-362, 2009 | 339 | 2009 |
| ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information A Lachmann, FM Giorgi, G Lopez, A Califano Bioinformatics 32 (14), 2233-2235, 2016 | 336 | 2016 |
| BioJupies: automated generation of interactive notebooks for RNA-Seq data analysis in the cloud D Torre, A Lachmann, A Ma’ayan Cell systems 7 (5), 556-561. e3, 2018 | 282 | 2018 |
| KEA: kinase enrichment analysis A Lachmann, A Ma'ayan Bioinformatics 25 (5), 684-686, 2009 | 253 | 2009 |
| Global phosphorylation analysis of β-arrestin–mediated signaling downstream of a seven transmembrane receptor (7TMR) K Xiao, J Sun, J Kim, S Rajagopal, B Zhai, J Villén, W Haas, JJ Kovacs, ... Proceedings of the National Academy of Sciences 107 (34), 15299-15304, 2010 | 234 | 2010 |
| Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration M von Schimmelmann, PA Feinberg, JM Sullivan, SM Ku, A Badimon, ... Nature neuroscience 19 (10), 1321-1330, 2016 | 226 | 2016 |
| eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks DJB Clarke, MV Kuleshov, BM Schilder, D Torre, ME Duffy, AB Keenan, ... Nucleic acids research 46 (W1), W171-W179, 2018 | 190 | 2018 |
| LINCS Data Portal 2.0: next generation access point for perturbation-response signatures V Stathias, J Turner, A Koleti, D Vidovic, D Cooper, M Fazel-Najafabadi, ... Nucleic acids research 48 (D1), D431-D439, 2020 | 151 | 2020 |
| L1000FWD: fireworks visualization of drug-induced transcriptomic signatures Z Wang, A Lachmann, AB Keenan, A Ma’Ayan Bioinformatics 34 (12), 2150-2152, 2018 | 145 | 2018 |
| Correcting under-reported COVID-19 case numbers: estimating the true scale of the pandemic KM Jagodnik, F Ray, FM Giorgi, A Lachmann medRxiv, 2020.03. 14.20036178, 2020 | 126* | 2020 |
| KEA3: improved kinase enrichment analysis via data integration MV Kuleshov, Z Xie, ABK London, J Yang, JE Evangelista, A Lachmann, ... Nucleic acids research 49 (W1), W304-W316, 2021 | 106 | 2021 |
| Receptor heteromerization expands the repertoire of cannabinoid signaling in rodent neurons R Rozenfeld, I Bushlin, I Gomes, N Tzavaras, A Gupta, S Neves, L Battini, ... PLoS One 7 (1), e29239, 2012 | 100 | 2012 |
| Appyters: Turning Jupyter Notebooks into data-driven web apps DJB Clarke, M Jeon, DJ Stein, N Moiseyev, E Kropiwnicki, C Dai, Z Xie, ... Patterns 2 (3), 2021 | 99 | 2021 |
Avi Ma'ayanProfessor, Icahn School of Medicine at Mount Sinai, New York, NYVerified email at mssm.edu