Avi Ma’ayan’s Publications on PubMed | Google Scholar | ResearchGate
Featured Publication
ChEA3: transcription factor enrichment analysis by orthogonal omics integration
2025
Marino GB, Evangelista JE, Clarke DJB, Ma’ayan A. L2S2: chemical perturbation and CRISPR KO LINCS L1000 signature search engine. Nucleic Acids Research gkaf373 (2025) PMID: 40308216
Marino GB, Olaiya S, Evangelista JE, Clarke DJB, Ma’ayan A. GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets. GigaScience 14:giaf025 (2025) PMID: 40208796
Clarke DJB, Evangelista JE, Xie Z, Marino GB, Byrd AI, Maurya MR, Srinivasan S, Yu K, Petrosyan V, Roth ME, Milinkov M, King CH, Vora JK, Keeney J, Nemarich C, Khan W, Lachmann A, Ahmed N, Agris A, Pan J, Ramachandran S, Fahy E, Esquivel E, Mihajlovic A, Jevtic B, Milinovic V, Kim S, McNeely P, Wang T, Wenger E, Brown MA, Sickler A, Zhu Y, Jenkins SL, Blood PD, Taylor DM, Resnick AC, Mazumder R, Milosavljevic A, Subramaniam S, Ma’ayan A. Playbook workflow builder: Interactive construction of bioinformatics workflows. PLOS Computational Biology 21(4):e1012901 (2025) PMID: 40179105
Evangelista JE, Clarke DJB, Xie Z, Olaiya S, Kim H, Marino GB, Byrd A, Srinivasan S, Srinivasan S, Maurya MR, Jenkins SL, Lutsky AD, Sasaya L, Lachmann A, Ahmed N, Diamant I, Sanchez E, Ramachandran S, Subramaniam S, Ma’ayan A. The CFDE Workbench: integrating metadata and processed data from Common Fund programs. bioRxiv 2025.02.04.636535 (2025)
Evangelista JE, Ali-Nasser T, Malek LE, Xie X, Marino GB, Bester AC, Ma’ayan A. lncRNAlyzr: Enrichment analysis for lncRNA sets. Journal of Molecular Biology 168938 (2025) PMID: 40133794
2024
Diamant I, Clarke DJB, Evangelista JE, Lingam N, Ma’ayan A. Harmonizome 3.0: integrated knowledge about genes and proteins from diverse multi-omics resources. Nucleic Acids Research gkae1080 (2024) PMID: 39565209
Marino GB, Deng EZ, Clarke DJB, Diamant I, Resnick AC, Ma W, Wang P, Ma’ayan A. Protocol for using Multiomics2Targets to identify targets and driver kinases for cancer cohorts profiled with multi-omics assays. STAR Protocols 5(4):103457 (2024) PMID: 39565691
Marino GB, Clarke DJB, Lachmann A, Deng EZ, Ma’ayan A. RummaGEO: Automatic mining of human and mouse gene sets from GEO. Patterns (10):101072 (2024) PMID: 39569206
Deng EZ, Marino GB, Clarke DJB, Diamant I, Resnick AC, Ma W, Wang P, Ma’ayan A. Multiomics2Targets identifies targets from cancer cohorts profiled with transcriptomics, proteomics, and phosphoproteomics. Cell Reports Methods 4(8):100839 (2024) PMID: 39127042
Clarke DJB, Evangelista JE et al. […] Ma’ayan A. Playbook Workflow Builder: interactive construction of bioinformatics workflows from a network of microservices. bioRxiv 2024.06.08.598037 (2024)
Clarke DJB, Marino GB, Deng EZ, Xie Z, Evangelista JE, Ma’ayan A. Rummagene: massive mining of gene sets from supporting materials of biomedical research publications. Communications Biology 7(1):482 (2024) PMID: 38643247
Vinik Y, Maimon A, Dubey V, Raj H, Abramovitch I, Malitsky S, Itkin M, Ma’ayan A, Westermann F, Gottlieb E, Ruppin E, Lev S. Programming a ferroptosis-to-apoptosis transition landscape revealed ferroptosis biomarkers and repressors for cancer therapy. Advanced Science 11(17):e2307263 (2024) PMID: 38441406
Petralia F, Ma W, Yaron TM, Caruso FP, Tignor N, Wang JM, Charytonowicz D, Johnson JL, Huntsman EM, Marino GB, Calinawan A, Evangelista JE, Selvan ME, Chowdhury S, Rykunov D, Krek A, Song X, Turhan B, Christianson KE, Lewis DA, Deng EZ, Clarke DJB, Whiteaker JR, Kennedy JJ, Zhao L, Segura RL, Batra H, Raso MG, Parra ER, Soundararajan R, Tang X, Li Y, Yi X, Satpathy S, Wang Y, Wiznerowicz M, González-Robles TJ, Iavarone A, Gosline SJC, Reva B, Robles AI, Nesvizhskii AI, Mani DR, Gillette MA, Klein RJ, Cieslik M, Zhang B, Paulovich AG, Sebra R, Gümüş ZH, Hostetter G, Fenyö D, Omenn GS, Cantley LC, Ma’ayan A, Lazar AJ, Ceccarelli M, Wang P; Clinical Proteomic Tumor Analysis Consortium. Pan-cancer proteogenomics characterization of tumor immunity. Cell 187(5):1255-1277.e27 (2024) PMID: 38359819
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(1):vbad178 (2023) PMID: 38107655
Ma’ayan A, Schlessinger A, Filizola M, Sebra R, Shi Y, Pandey G, Itan Y, Kenny EE. AI + omics are bringing the bench closer to the bedside. Frontiers of Medical Research: Artificial Intelligence (Science/AAAS Washington, DC, 2023) p. 8-10.
Xie Z, Chen C, Ma’ayan A. Dex-Benchmark: datasets and code to evaluate algorithms for transcriptomics data analysis. PeerJ 11:e16351 (2023) PMID: 37953774
Amadori L, Calcagno C, Fernandez DM, Koplev S, Fernandez N, Kaur R, Mury P, Khan NS, Sajja S, Shamailova R, Cyr Y, Jeon M, Hill CA, Chong PS, Naidu S, Sakurai K, Ghotbi AA, Soler R, Eberhardt N, Rahman A, Faries P, Moore KJ, Fayad ZA, Ma’ayan A, Giannarelli C. Systems immunology-based drug repurposing framework to target inflammation in atherosclerosis. Nature Cardiovascular Research 2(6):550-571 (2023) PMID: 37771373
Evangelista JE, Clarke DJB, Xie Z, Marino GB, Utti V, Jenkins SL, Ahooyi TM, Bologa CG, Yang JJ, Binder JL, Kumar P, Lambert CG, Grethe JS, Wenger E, Taylor D, Oprea TI, de Bono B, Ma’ayan A. Toxicology knowledge graph for structural birth defects. Communications Medicine 3(1):98 (2023) PMID: 37460679
Evangelista JE, Xie Z, Marino GB, Nguyen N, Clarke DJB, Ma’ayan A. Enrichr-KG: bridging enrichment analysis across multiple libraries. Nucleic Acids Research 51(W1):W168-W179 (2023) PMID: 37166973
Marino GB, Ngai M, Clarke DJB, Fleishman RH, Deng EZ, Xie Z, Ahmed N, Ma’ayan A. GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery. Nucleic Acids Research 51(W1):W213-W224 (2023) PMID: 37166966
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 22(6):e13809 (2023) PMID: 37082798
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 (Oxford) 2023:baad009 (2023) PMID: 36869839
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 (2023) PMID: 36874981
2022
Charbonneau AL, Brady A, Czajkowski K, Aluvathingal J, Canchi S, Carter R, Chard K, Clarke DJB, Crabtree J, Creasy HH, D’Arcy M, Felix V, Giglio M, Gingrich A, Harris RM, Hodges TK, Ifeonu O, Jeon M, Kropiwnicki E, Lim MCW, Liming RL, Lumian J, Mahurkar AA, Mandal M, Munro JB, Nadendla S, Richter R, Romano C, Rocca-Serra P, Schor M, Schuler RE, Tangmunarunkit H, Waldrop A, Williams C, Word K, Sansone SA, Ma’ayan A , Wagner R, Foster I, Kesselman C, Brown CT, White O. Making Common Fund data more findable: catalyzing a data ecosystem. Gigascience 11:giac105 (2022) PMID: 36409836
Clarke DJB, Rebman AW, Fan J, Soloski MJ, Aucott JN, Ma’ayan A. Gene set predictor for post-treatment Lyme disease. Cell Reports Medicine 3(11):100816 (2022) PMID: 36384094
Gross SM, Dane MA, Smith RL, Devlin KL, McLean IC, Derrick DS, Mills CE, Subramanian K, London AB, Torre D, Evangelista JE, Clarke DJB, Xie Z, Erdem C, Lyons N, Natoli T, Pessa S, Lu X, Mullahoo J, Li J, Adam M, Wassie B, Liu M, Kilburn DF, Liby TA, Bucher E, Sanchez-Aguila C, Daily K, Omberg L, Wang Y, Jacobson C, Yapp C, Chung M, Vidovic D, Lu Y, Schurer S, Lee A, Pillai A, Subramanian A, Papanastasiou M, Fraenkel E, Feiler HS, Mills GB, Jaffe JD, Ma’ayan A, Birtwistle MR, Sorger PK, Korkola JE, Gray JW, Heiser LM. A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses. Communications Biology 5(1):1066 (2022) PMID: 36207580
Jenkins EC, Chattopadhyay M, Gomez M, Torre D, Ma’ayan A, Torres-Martin M, Sia D, Germain D. Age alters the oncogenic trajectory toward luminal mammary tumors that activate unfolded proteins responses. Cell Aging 21(10):e13665 (2022) PMID: 36111352
Jeon M, Xie Z, Evangelista JE, Wojciechowicz ML, Clarke DJB, Ma’ayan A. Transforming L1000 profiles to RNA-seq-like profiles with deep learning. BMC Bioinformatics 23(1):74 (2022) PMID: 36100892
Pilarczyk M, Fazel-Najafabadi M, Kouril M, Shamsaei B, Vasiliauskas J, Niu W, Mahi N, Zhang L, Clark NA, Ren Y, White S, Karim R, Xu H, Biesiada J, Bennett MF, Davidson SE, Reichard JF, Roberts K, Stathias V, Koleti A, Vidovic D, Clarke DJB, Schürer SC, Ma’ayan A, Meller J, Medvedovic M. Connecting omics signatures and revealing biological mechanisms with iLINCS. Nature Communications 13(1):4678 (2022) PMID: 35945222
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(7):e487 (2022) PMID: 35876555
Evangelista JE, Clarke DJB, Xie Z, Lachmann A, Jeon M, Chen K, Jagodnik KM, Jenkins SL, Kuleshov MV, Wojciechowicz ML, Schurer SC, Medvedovic M, Ma’ayan A. SigCom LINCS: data and metadata search engine for a million gene expression signatures. Nucleic Acids Research 50(W1):W697-709 (2022) PMID: 35524556
Clarke DJB, Kuleshov MV, Xie Z, Evangelista JE, Meyers MR, Kropiwnicki E, Jenkins SL, Ma’ayan A. Gene and drug landing page aggregator. Bioinformatics Advances 2(1):vbac013 (2022) PMID: 35368424
Wickramasinghe NM, Sachs D, Shewale B, Gonzalez DM, Dhanan-Krishnan P, Torre D, LaMarca E, Raimo S, Dariolli R, Serasinghe MN, Mayourian J, Sebra R, Beaumont K, Iyengar S, French DL, Hansen A, Eschenhagen T, Chipuk JE, Sobie EA, Jacobs A, Akbarian S, Ischiropoulos H, Ma’ayan A, Houten SM, Costa K, Dubois NC. PPARdelta activation induces metabolic and contractile maturation of human pluripotent stem cell-derived cardiomyocytes. Cell Stem Cell 29(4):559-576.e7 (2022) PMID: 35325615
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(1):76 (2022) PMID: 35183110
Lachmann A, Xie Z, Ma’ayan A. blitzGSEA: Efficient computation of Gene Set Enrichment Analysis through Gamma distribution approximation. Bioinformatics btac076 (2022) PMID: 35143610
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(1):e355 (2022) PMID: 35085427
2021
Onoufriadis A, Proudfoot LE, Ainali C, Torre D, Papanikolaou M, Rayinda T, Rashidghamat E, Danarti R, Mellerio JE, Ma’ayan A, McGrath JA. Transcriptomic profiling of recessive dystrophic epidermolysis bullosa wounded skin highlights drug repurposing opportunities to improve wound healing. Experimental Dermatology (2021) PMID: 34694680
Piret SE, Attallah AA, Gu X, Guo Y, Gujarati NA, Henein J, Zollman A, Hato T, Ma’ayan A, Revelo MP, Dickman KG, Chen CH, Shun CT, Rosenquist TA, He JC, Mallipattu SK. Loss of proximal tubular transcription factor Krüppel-like factor 15 exacerbates kidney injury through loss of fatty acid oxidation. Kidney International (2021) PMID: 34634362
Bobe JR, Jutras BL, Horn EJ, Embers ME, Bailey A, Moritz RL, Zhang Y, Soloski MJ, Ostfeld RS, Marconi RT, Aucott J, Ma’ayan A, Keesing F, Lewis K, Ben Mamoun C, Rebman AW, McClune ME, Breitschwerdt EB, Reddy PJ, Maggi R, Yang F, Nemser B, Ozcan A, Garner O, Di Carlo D, Ballard Z, Joung HA, Garcia-Romeu A, Griffiths RR, Baumgarth N, Fallon BA. Recent progress in Lyme disease and remaining challenges. Frontiers in Medicine (2021) PMID: 34485323
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 49(W1):W304-W316 (2021) PMID: 34019655
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. Proc Natl Acad Sci USA 118(23) (2021) PMID: 34074766
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, Melnick A, Garcia BA, Whetton AD, MacArthur BD, Ma’ayan A, Lemischka IR. An Esrrb and Nanog cell fate regulatory module controlled by feed forward loop interactions. Frontiers in Cell and Developmental Biology 9:630067 (2021) PMID: 33816475
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 baab017 (2021) PMID: 33787872
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(3):e90 (2021) PMID: 33780170
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, Ma’ayan A. Predicting Lyme Disease from patients’ peripheral blood mononuclear cells profiled with RNA-sequencing. Frontiers in Immunology 12:636289 (2021) PMID: 33763080
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(1):7315 (2021) PMID: 33795767
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, Bhuiyan S, Cheng M, Karam J, Jagodnik KM, Shu I, Lachmann A, Ayling S, Jenkins SL, Ma’ayan A. Appyters: Turning Jupyter notebooks into data-driven web apps. Patterns 2(3):100213 (2021) PMID: 33748796
Jeon M, Jagodnik KM, Kropiwnicki E, Stein DJ, Ma’ayan A. Prioritizing pain-associated targets with machine learning. Biochemistry (2021) PMID: 33606503
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 70(2):589-602 (2021) PMID: 33067313
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 205(8):2169-2187 (2020) PMID: 32948687
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 205(8):2188-2206 (2020) PMID: 32948682
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 gene and drug set library. Patterns 1(6):100090 (2020) PMID: 32838343
Chen Z, Herting CJ, Ross JL, Gabanic B, Vallcorba MP, 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 68(10):2148-2166 (2020) PMID: 32639068
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 Technologies and Informatics 272:334-337 (2020) PMID: 32604670
Wojciechowicz ML, Ma’ayan A. GPR84: an immune response dial? Nature Reviews Drug Discovery 19(6):374 (2020) PMID: 32494048
Bartal A, Lachmann A, Clarke DJB, Seiden AH, Jagodnik KM, Ma’ayan A. EnrichrBot: Twitter bot tracking tweets about human genes. Bioinformatics 36(12):3932-3934 (2020) PMID: 32277816
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 14(4):561-574 (2020) PMID: 32243840
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 1863(6):194521 (2020) PMID: 32156561
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, Roberts AE, Newburger JW, Goldmuntz E, Brueckner M, Lifton RP, Seidman CE, Chung WK, Tristani-Firouzi M, Yost HJ, Ma’ayan A, Gelb BD. Systems analysis implicates WAVE2 complex in the pathogenesis of developmental left-sided obstructive heart defects. JACC Basic to Translational Science 5(4):376-386 (2020) PMID: 32368696
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 367(6474):161-166 (2020) PMID: 31857493
2019
Clarke DJB, Wang L, Jones A, Wojciechowicz ML, Torre D, Jagodnik KM, Jenkins SL, McQuilton P, Flamholz Z et al. […] Ma’ayan A. FAIRshake: Toolkit to evaluate the FAIRness of research digital resources. Cell Systems 9(5):417-421 (2019) PMID: 31677972
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, Becnel LB, Bridges D, Ma’ayan A, Huss JM, Stossi F, Foulds CE, Kralli A, McDonnell DP, McKenna NJ. The Signaling Pathways Project, an integrated ‘omics knowledgebase for mammalian cellular signaling pathways. Scientific Data 6(1):252 (2019) PMID: 31672983
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, Lu Q, Kamenecka TM, Ma’ayan A, O’Neill HC, Ibanez-Tallon I, Geurts AM, Kenny PJ. Habenular TCF7L2 links nicotine addiction to diabetes. Nature 574(7778):372-377 (2019) PMID: 31619789
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, Awad AJ, Moss N, Bjorkegren JLM, Kim-Schulze S, Gnjatic S, Ma’ayan A, Mocco J, Faries P, Merad M, Giannarelli C. Single-cell immune landscape of human atherosclerotic plaques. Nature Medicine (10):1576-1588 (2019) PMID: 31591603
Niepel M, Hafner M, Mills CE, Subramanian K, Williams EH, Chung M, Gaudio B, Barrette AM, Stern AD, Hu B, Korkola JE, LINCS Consortium et al. A Multi-center study on the reproducibility of drug-response assays in mammalian cell lines. Cell Systems 9(1):35-48.e5 (2019) PMID: 31302153
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 47(W1):W571-W577 (2019) PMID: 31114885
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 47(W1):W212-W224 (2019) PMID: 31114921
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 47(W1):W183-W190 (2019) PMID: 31069376
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 21(5):560-567 (2019) PMID: 30988422
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 (2019)
Tohme R, Izadmehr S, Gandhe S, Tabaro G, Vallabhaneni S, Thomas A, Vasireddi N, Dhawan NS, Ma’ayan A, Sharma N, Galsky MD, Ohlmeyer M, Sangodkar J, Narla G. Direct activation of PP2A for the treatment of tyrosine kinase inhibitor-resistant lung adenocarcinoma. JCI Insight 4(4) pii: 125693 (2019) PMID: 30830869
Ellis RJ, Wang Z, Genes N, Ma’ayan A. Predicting opioid dependence from electronic health records with machine learning. BioData Mining 12:3 (2019) PMID: 30728857
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 48(1):32-48 (2019) PMID: 30595537
Wang Z, Lachmann A, Ma’ayan A. Mining data and metadata from the gene expression omnibus. Biophysical Reviews 11(1):103-110 (2019) PMID: 30594974
2018
Torre D, Lachmann A, Ma’ayan A. BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud. Cell Systems 7(5):556-561 (2018) PMID: 30447998
Oprea TI, Jan L, Johnson GL, Roth BL, Ma’ayan A, Schurer S, Shoichet BK, Sklar LA, McManus MT. Far away from the lamppost. PLoS Biology 16(12):e3000067 (2018) PMID: 30532236
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(1):267 (2018) PMID: 30518843
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(10):2821-2835 (2018) PMID: 30517869
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 (2018) PMID: 30169739
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, Zheng B, Bernstein E. SIRT6 haploinsufficiency induces BRAFV600E melanoma cell resistance to MAPK inhibitors via IGF signalling. Nature Communications 9(1):3440 (2018) PMID: 30143629
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 America Society of Nephrology pii: ASN.2018030324(2018) PMID: 30143559
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 46(W1):W171-W179 (2018) PMID: 29800326
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 (2018) PMID: 29936335
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