Publications

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 AL2S2: chemical perturbation and CRISPR KO LINCS L1000 signature search engineNucleic Acids Research gkaf373 (2025) PMID: 40308216

Marino GB, Olaiya S, Evangelista JE, Clarke DJB, Ma’ayan AGeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene setsGigaScience 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 APlaybook workflow builder: Interactive construction of bioinformatics workflowsPLOS 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 AThe CFDE Workbench: integrating metadata and processed data from Common Fund programsbioRxiv 2025.02.04.636535 (2025)

Evangelista JE, Ali-Nasser T, Malek LE, Xie X, Marino GB, Bester AC, Ma’ayan AlncRNAlyzr: Enrichment analysis for lncRNA setsJournal of Molecular Biology 168938 (2025) PMID: 40133794

2024

Diamant I, Clarke DJB, Evangelista JE, Lingam N, Ma’ayan AHarmonizome 3.0: integrated knowledge about genes and proteins from diverse multi-omics resourcesNucleic Acids Research gkae1080 (2024) PMID: 39565209

Marino GB, Deng EZ, Clarke DJB, Diamant I, Resnick AC, Ma W, Wang P, Ma’ayan AProtocol for using Multiomics2Targets to identify targets and driver kinases for cancer cohorts profiled with multi-omics assaysSTAR Protocols 5(4):103457 (2024) PMID: 39565691

Marino GB, Clarke DJB, Lachmann A, Deng EZ, Ma’ayan ARummaGEO: Automatic mining of human and mouse gene sets from GEOPatterns (10):101072 (2024) PMID: 39569206

Deng EZ, Marino GB, Clarke DJB, Diamant I, Resnick AC, Ma W, Wang P, Ma’ayan AMultiomics2Targets identifies targets from cancer cohorts profiled with transcriptomics, proteomics, and phosphoproteomicsCell Reports Methods 4(8):100839 (2024) PMID: 39127042

Clarke DJB, Evangelista JE et al. […] Ma’ayan APlaybook Workflow Builder: interactive construction of bioinformatics workflows from a network of microservicesbioRxiv 2024.06.08.598037 (2024)

Clarke DJB, Marino GB, Deng EZ, Xie Z, Evangelista JE, Ma’ayan ARummagene: massive mining of gene sets from supporting materials of biomedical research publicationsCommunications 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 therapyAdvanced 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 immunityCell 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 AD2H2: diabetes data and hypothesis hubBioinformatics 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 ADex-Benchmark: datasets and code to evaluate algorithms for transcriptomics data analysisPeerJ 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 atherosclerosisNature 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 AToxicology knowledge graph for structural birth defectsCommunications Medicine 3(1):98 (2023) PMID: 37460679

Evangelista JE, Xie Z, Marino GB, Nguyen N, Clarke DJB, Ma’ayan AEnrichr-KG: bridging enrichment analysis across multiple librariesNucleic 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 AGeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discoveryNucleic Acids Research 51(W1):W213-W224 (2023) PMID: 37166966

Deng EZ, Fleishman RH, Xie Z, Marino GB, Clarke DJB, Ma’ayan AComputational screen to identify potential targets for immunotherapeutic identification and removal of senescence cellsAging Cell 22(6):e13809 (2023) PMID: 37082798

Marino GB, Wojciechowicz ML, Clarke DJB, Kuleshov MV, Xie Z, Jeon M, Lachmann A, Ma’ayan AlncHUB2: aggregated and inferred knowledge about human and mouse lncRNAsDatabase (Oxford) 2023:baad009 (2023) PMID: 36869839

Lachmann A, Rizzo KA, Bartal A, Jeon M, Clarke DJB, Ma’ayan APrismEXP: gene annotation prediction from stratified gene-gene co-expression matricesPeerJ 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 ecosystemGigascience 11:giac105 (2022) PMID: 36409836

Clarke DJB, Rebman AW, Fan J, Soloski MJ, Aucott JN, Ma’ayan AGene set predictor for post-treatment Lyme diseaseCell 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 responsesCommunications 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 responsesCell Aging 21(10):e13665 (2022) PMID: 36111352

Jeon M, Xie Z, Evangelista JE, Wojciechowicz ML, Clarke DJB, Ma’ayan ATransforming L1000 profiles to RNA-seq-like profiles with deep learningBMC 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 iLINCSNature 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 AGetting started with LINCS datasets and toolsCurrent 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 ASigCom LINCS: data and metadata search engine for a million gene expression signaturesNucleic 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 AGene and drug landing page aggregatorBioinformatics 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 cardiomyocytesCell Stem Cell 29(4):559-576.e7 (2022) PMID: 35325615

Kropiwnicki E, Lachmann A, Clarke DJB, Xie Z, Jagodnik KM, Ma’ayan ADrugShot: querying biomedical search terms to retrieve prioritized lists of small moleculesBMC Bioinformatics 23(1):76 (2022) PMID: 35183110

Lachmann A, Xie Z, Ma’ayan AblitzGSEA: Efficient computation of Gene Set Enrichment Analysis through Gamma distribution approximationBioinformatics 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 toolsCurrent 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 healingExperimental 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 oxidationKidney 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 challengesFrontiers in Medicine (2021) PMID: 34485323

Kuleshov MV, Xie Z, London ABK, Yang J, Evangelista JE, Lachmann A, Shu I, Torre D, Ma’ayan AKEA3: improved kinase enrichment analysis via data integrationNucleic 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 humansProc 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 interactionsFrontiers 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 ADrugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learningDatabase 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 AGene set knowledge discovery with EnrichrCurrent 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 APredicting Lyme Disease from patients’ peripheral blood mononuclear cells profiled with RNA-sequencingFrontiers 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 phototherapyScientific 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 AAppyters: Turning Jupyter notebooks into data-driven web appsPatterns 2(3):100213 (2021) PMID: 33748796

Jeon M, Jagodnik KM, Kropiwnicki E, Stein DJ, Ma’ayan APrioritizing pain-associated targets with machine learningBiochemistry (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 diseaseDiabetes 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 cellsJournal 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

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, Schurer SC. Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center. Scientific Data 5:180117 (2018) PMID: 29917015

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