| 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 |
0.443 |
|
| 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 |
0.589 |
|
| 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 |
0.565 |
|
| 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 |
0.555 |
|
| 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 |
0.624 |
|
| 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 |
0.526 |
|
| 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 |
0.577 |
|
| 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 |
0.546 |
|
| 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 |
0.525 |
|
| 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 |
0.511 |
|
| 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 |
0.596 |
|
| 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, ... ... Lachmann A, 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 |
0.534 |
|
| 2020 |
Broyde J, Simpson DR, Murray D, Paull EO, Chu BW, Tagore S, Jones SJ, Griffin AT, Giorgi FM, Lachmann A, Jackson P, Sweet-Cordero EA, Honig B, Califano A. Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses. Nature Biotechnology. PMID 32929263 DOI: 10.1038/S41587-020-0652-7 |
0.396 |
|
| 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 |
0.53 |
|
| 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 |
0.549 |
|
| 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 |
0.532 |
|
| 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 |
0.556 |
|
| 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 |
0.576 |
|
| 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 |
0.58 |
|
| 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 |
0.611 |
|
| 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 |
0.639 |
|
| 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 |
0.629 |
|
| 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 |
0.64 |
|
| 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 |
0.521 |
|
| 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 |
0.628 |
|
| 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 |
0.539 |
|
| 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 |
0.605 |
|
| 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 |
0.643 |
|
| 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 |
0.53 |
|
| 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 |
0.635 |
|
| 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 |
0.596 |
|
| 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 |
0.543 |
|
| 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 |
0.561 |
|
| 2017 |
Shen Y, Alvarez MJ, Bisikirska B, Lachmann A, Realubit R, Pampou S, Coku J, Karan C, Califano A. Systematic, network-based characterization of therapeutic target inhibitors. Plos Computational Biology. 13: e1005599. PMID 29023443 DOI: 10.1371/Journal.Pcbi.1005599 |
0.328 |
|
| 2017 |
Broyde J, Simpson D, Murray D, Lachmann A, Giorgi FM, Honig B, Sweet-Cordero AE, Califano A. Abstract LB-289: Computational detection of oncogene‐centric pathway members Cancer Research. 77. DOI: 10.1158/1538-7445.Am2017-Lb-289 |
0.38 |
|
| 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 |
0.511 |
|
| 2016 |
Alvarez MJ, Shen Y, Giorgi FM, Lachmann A, Ding BB, Ye BH, Califano A. Functional characterization of somatic mutations in cancer using network-based inference of protein activity. Nature Genetics. PMID 27322546 DOI: 10.1038/Ng.3593 |
0.319 |
|
| 2016 |
Lachmann A, Giorgi FM, Alvarez MJ, Califano A. Detection and removal of spatial bias in multiwell assays. Bioinformatics (Oxford, England). PMID 27153732 DOI: 10.1093/Bioinformatics/Btw092 |
0.388 |
|
| 2016 |
Lachmann A, Giorgi FM, Lopez G, Califano A. ARACNe-AP: Gene Network Reverse Engineering through Adaptive Partitioning inference of Mutual Information. Bioinformatics (Oxford, England). PMID 27153652 DOI: 10.1093/Bioinformatics/Btw216 |
0.363 |
|
| 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 |
0.623 |
|
| 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 |
0.511 |
|
| 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 |
0.52 |
|
| 2015 |
Broyde J, Simpson D, Wah DA, Giorgi FM, Petrey D, Alvarez MJ, Silkov A, Lachmann A, Hill DE, Vidal M, Jackson P, Honig B, Sweet-Cordero A, Califano A. Abstract PR13: Systems and structural biology approaches to elucidate new effectors in KRAS mutant tumors Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-Pr13 |
0.388 |
|
| 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 |
0.491 |
|
| 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 |
0.489 |
|
| 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 |
0.586 |
|
| 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 |
0.508 |
|
| 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 |
0.604 |
|
| 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 |
0.518 |
|
| 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 |
0.653 |
|
| 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 |
0.562 |
|
| 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 |
0.578 |
|
| 2009 |
Lachmann A, Ma'ayan A. KEA: kinase enrichment analysis. Bioinformatics (Oxford, England). 25: 684-6. PMID 19176546 DOI: 10.1093/Bioinformatics/Btp026 |
0.564 |
|
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