Avi Ma’ayan’s Publications on PubMed  | Google Scholar | ResearchGate

Featured Publication

ChEA3: transcription factor enrichment analysis by orthogonal omics integration

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2025

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)

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

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

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(531) (2018) PMID: 29789295

Lachmann A, Torre D, Keenan AB, Jagodnik KM, Lee HJ, Wang L, Silverstein MC, Ma’ayan A. Massivc mining of publicly available RNA-sq data from human and mouse. Nature Communications 9(1):1366 (2018) PMID: 29636450

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 (2018) PMID: 29485625

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, Ma’ayan A et al. Unexplored therapeutic opportunities in the human genome. Nature Review Drug Discovery (2018) PMID: 29572638

Czarnowicki T, Dohlman AB, Malik K, Antonini D, Bissonnette R, Chan TC, Zhou L, Wen HC, Estrada Y, Xu H, Bryson C, Shen J, Lala D, Ma’ayan A, McGeehan G, Gregg R, Guttman-Yassky E. Short-term LXR activation improves epidermal barrier features in mild-to-moderate atopic dermatitis: a randomized controlled trial. Annals of Allergy, Asthma and Immunology S1081-1206(18)30211-4 (2018) PMID: 29567358

Wang Z, Lachmann A, Keenan AB, Ma’ayan A. L1000FWD: Fireworks visualization of drug-induced transcriptomic signatures. Bioinformatics 34(12)2150-2152 (2018) PMID: 29420694

Koplev S, Lin K, Dohlman AB, Ma’ayan A. Integration of pan-cancer transcriptomics with RPPA proteomics reveals mechanisms of epithelial-mesenchymal transition. PLoS Computational Biology 14(1):e1005911 (2018) PMID: 29293502

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 23:32-43 (2018) PMID: 29218867

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 et al. The Library of Integrated Network-Based Cellular Signatures NIH program: System-level cataloging of human cells response to perturbations. Cell Systems  6(1):13-24 (2018) PMID: 29199020

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, Mader C, Niu W, Fazel M, Mahi N, Pilarczyk M, Clark N, Shamsaei B, Meller J, Vasiliauskas J, Reichard J, Medvedovic M, Ma’ayan A, Pillai A, Schurer SC. 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 46(D1):D558-D566 (2018) PMID: 29140462

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 pii: S1532-0464(17)30240-X (2017) PMID: 29113935

Fu J, Wang Z, Lee K, Wei C, Liu Z, Zhang M, Zhoud 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 pii: S0085-2538(17)30671-3 (2017) PMID: 29102373

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(1):1186 (2017) PMID: 29084964

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 (2017) PMID: 28994825

Ma’ayan A. Complex systems biology. Journal of the Royal Society, Interface 14(134) pii: 20170391 (2017) PMID: 28931638

Lachmann A, Torre D, Keenan AB, Jagodnik KM, Lee HJ, Silverstein MC, Wang L, Ma’ayan A. Massive mining of publicly available RNA-seq data from human and mouse. bioRxiv 189092 (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, Borczuk AC, Gokulrangan G, Wang L, Svenson E, Farrington CC, Yuan E, Avelar RA, Stachnik A, Smith B, Gidwani V, Giannini HM, McQuaid D, McClinch K, Wang Z, Levine AC, Sears RC, Chen EY, Duan Q, Datt M, Haider S, Ma’ayan A, DiFeo A, Sharma N, Galsky MD, Brautigan DL, Ioannou YA, Xu W, Chance MR, Ohlmeyer M, Narla G. Activation of tumor suppressor protein PP2A inhibits KRAS-driven tumor growth. The Journal of Clinical Investigation pii: 89548 (2017) PMID: 28504649

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 pii: S1532-0464(17)30101-6 (2017) PMID: 28501646

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 19(3):214-22 (2017) PMID: 28218906

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 (2017) PMID: 28200013

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, Overington J, Patel J, Rouillard AD, Schürer S, Sheils T, Simeonov A, Sklar LA, Southall N, Ursu O, Vidovic D, Waller A, Yang J, Jadhav A, Oprea TI, Guha R. Pharos: Collating protein information to shed light on the druggable genome. Nucleic Acids Research 45(D1):D995-D100 (2017) PMID: 27903890

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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 (2016) PMID: 28066174

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. BMC Bioinformatics 17(1):461 (2016) PMID: 27846806

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, Woodland H, Amaral FM, Szeto GL, Fuchs O, Schüssler-Fiorenza Rose SM, Sharma S, Schwartz U, Bausela XB, Szymkiewicz M, Maroulis V, Salykin A, Barra CM, Kruth CD, Bongio NJ, Mathur V, Todoric RD, Rubin UE, Malatras A, Fulp CT, Galindo JA, Motiejunaite R, Jüschke C, Dishuck PC, Lahl K, Jafari M, Aibar S, Zaravinos A, Steenhuizen LH, Allison LR, Gamallo P, de Andres Segura F, Dae Devlin T, Pérez-García V, Ma’ayan A. Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd. Nature Communications 7:12846 (2016) PMID: 27667448

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, Ma’ayan A. L1000CDS2: LINCS L1000 characteristic direction signatures search engine. npj Systems Biology and Applications 2, 16015 (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 19(10):1321-30 (2016) PMID: 27526204

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 (Oxford) pii: baw100 (2016) PMID: 27374120

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 (2016) PMID: 27583132

Mallipattu SK, Guo Y, Revelo MP, Roa-Peña L, Miller T, Ling J, Shankland SJ, Bialkowska AB, Ly V, Estrada C, Jain MK, Lu Y, Ma’ayan A, Mehrotra A, Yacoub R, Nord EP, Woroniecki RP, Yang VW, He JC. Krüppel-Like Factor 15 Mediates Glucocorticoid-Induced Restoration of Podocyte Differentiation Markers. Journal of the American Society of Nephrology pii: ASN.2015060672 (2016) PMID: 27288011

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 (2016) PMID: 27226058

Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, Koplev S, Jenkins SL, Jagodnik KM, Lachmann A, McDermott M, Monteiro CD, Gundersen GW, Ma’ayan A. Enrichr: A Comprehensive Gene Set Enrichment Analysis Web Server 2016 Update. Nucleic Acids Research 44(W1):W90-7 (2016) PMID: 27141961

Wang Z, Clark NR, Ma’ayan A. Drug Induced Adverse Events Prediction with the LINCS L1000 Data. Bioinformatics 32(15):2338-45  (2016) PMID: 27153606

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 pii: S2211-1247(16)30213-3 (2016) PMID: 27009580

Scheckel C, Drapeau E, Frias MA, Park CY, Fak J, Zucker-Scharff I, Kou Y, Haroutunian V, Ma’ayan A, Buxbaum JD, Darnell RB. Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain. Elife pii: e10421 (2016) PMID: 26894958

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 7(10):11526-38 (2016) PMID: 26863628

Khan JA, Mendelson A, Kunisaki Y, Birbrair A, Kou Y, Arnal-Estapé A, Pinho S, Ciero P, Nakahara F, Ma’ayan A, Bergman A,