{"id":32,"date":"2014-10-08T20:14:30","date_gmt":"2014-10-08T20:14:30","guid":{"rendered":"http:\/\/labs.icahn.mssm.edu\/maayanlab\/?page_id=32"},"modified":"2026-02-26T18:44:57","modified_gmt":"2026-02-26T18:44:57","slug":"publications","status":"publish","type":"page","link":"https:\/\/labs.icahn.mssm.edu\/maayanlab\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"

Avi Ma’ayan’s Publications on PubMed<\/a>\u00a0 |\u00a0Google Scholar<\/a>\u00a0|\u00a0ResearchGate<\/a><\/p>\n

Featured Publication<\/h2>\n

ChEA3: transcription factor enrichment analysis by orthogonal omics integration<\/strong><\/a><\/p>\n

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2026<\/h2>\n

Lachmann A, Amadori L, Nicoletti P, Crane HM, Giannarelli C, Ma’ayan A<\/strong>, Peter I.\u00a0Transcriptional response to combination antiretroviral therapy predicts side effects and novel targets<\/strong>.\u00a0Frontiers in Pharmacology<\/em> 16:1743543 (2026) PMID: 41646932<\/a><\/p>\n

Evangelista JE, Clarke DJB, Byrd AI, Srinivasan S, Srinivasan S, Maurya MR, Jenkins SL, Diamant I, Sanchez E, Xie Z, Olaiya S, Kim H, Marino GB, Ahmed N, Ramachandran S, Subramaniam S, Ma’ayan A<\/strong>.\u00a0The CFDE Workbench: Integrating metadata and processed data from Common Fund Programs<\/strong>.\u00a0Journal of Molecular Biology<\/em> 169631 (2026) PMID: 41506317<\/a><\/p>\n

2025<\/h2>\n

Marino GB, Byrd AI, Ahmed N, Clarke DJB, Ma’ayan A<\/strong>.\u00a0sc2DAT: Workflow for targeting tumor subpopulations of single cells<\/strong>.\u00a0Bioinformatics Advances<\/em> 5(1):vbaf237 (2025) PMID: 41079221<\/a><\/p>\n

Evangelista JE, Lutsky AD, Byrd AI, Clarke DJB, Prabhakaran A, Jenkins SL, Ma’ayan A<\/strong>.\u00a0Creating an interactive web interface for networks stored in knowledge graph databases<\/strong>.\u00a0Current Protocols<\/em> 5(9):e70200 (2025) PMID: 40956607<\/a><\/p>\n

Byrd AI, Evangelista JE, Lachmann A, Chung HY, Jenkins SL, Ma’ayan A<\/strong>.\u00a0ChEA-KG: Human transcription factor regulatory network with a knowledge graph interactive user interface<\/strong>.\u00a0bioRxiv<\/em> 2025.08.09.669505 (2025) PMID: 40832173<\/a><\/p>\n

Satpathy S, […], Ma’ayan A<\/strong>, Getz GA, Dhanasekaran SM, Robles AI, Chang GC, Yang PC, Yu SL, Chen HY, Nesvizhskii AI, Carr SA, Mani DR, Cieslik MP, Chen YJ, Gillette MA; Taiwan Cancer Moonshot Program; Clinical Proteomic Tumor Analysis Consortium.\u00a0Integrative analysis of lung adenocarcinoma across diverse ethnicities and exposures<\/strong>. Cancer Cell<\/em> 43(9):1731-1757.e17 (2025) PMID: 40749670<\/a><\/p>\n

Clarke DJB, Marinp GB, Ma’ayan A<\/strong>.\u00a0A gene set foundation model pre-trained on a massive collection of diverse gene sets<\/strong>.\u00a0bioRxiv<\/em> 2025.05.30.657124 (2025) PMID: 0501705<\/a><\/p>\n

Marino GB, Evangelista JE, Clarke DJB, Ma’ayan A<\/strong>.\u00a0L2S2: chemical perturbation and CRISPR KO LINCS L1000 signature search engine<\/strong>.\u00a0Nucleic Acids Research<\/em> gkaf373 (2025) PMID: 40308216<\/a><\/p>\n

Marino GB, Olaiya S, Evangelista JE, Clarke DJB, Ma’ayan A<\/strong>.\u00a0GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets<\/strong>.\u00a0GigaScience<\/em> 14:giaf025 (2025) PMID: 40208796<\/a><\/p>\n

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<\/strong>.\u00a0Playbook workflow builder: Interactive construction of bioinformatics workflows<\/strong>.\u00a0PLOS Computational Biology<\/em> 21(4):e1012901 (2025) PMID: 40179105<\/a><\/p>\n

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<\/strong>.\u00a0The CFDE Workbench: integrating metadata and processed data from Common Fund programs<\/strong>.\u00a0bioRxiv<\/em> 2025.02.04.636535 (2025)<\/a><\/p>\n

Evangelista JE, Ali-Nasser T, Malek LE, Xie X, Marino GB, Bester AC, Ma’ayan A<\/strong>.\u00a0lncRNAlyzr: Enrichment analysis for lncRNA sets<\/strong>.\u00a0Journal of Molecular Biology<\/em> 168938 (2025) PMID: 40133794<\/a><\/p>\n

2024<\/h2>\n

Diamant I, Clarke DJB, Evangelista JE, Lingam N, Ma’ayan A<\/strong>.\u00a0Harmonizome 3.0: integrated knowledge about genes and proteins from diverse multi-omics resources<\/strong>.\u00a0Nucleic Acids Research<\/em> gkae1080 (2024) PMID: 39565209<\/a><\/p>\n

Marino GB, Deng EZ, Clarke DJB, Diamant I, Resnick AC, Ma W, Wang P, Ma’ayan A<\/strong>.\u00a0Protocol for using Multiomics2Targets to identify targets and driver kinases for cancer cohorts profiled with multi-omics assays<\/strong>.\u00a0STAR Protocols<\/em> 5(4):103457 (2024) PMID: 39565691<\/a><\/p>\n

Marino GB, Clarke DJB, Lachmann A, Deng EZ, Ma’ayan A<\/strong>.\u00a0RummaGEO: Automatic mining of human and mouse gene sets from GEO<\/strong>.\u00a0Patterns<\/em> (10):101072 (2024) PMID: 39569206<\/a><\/p>\n

Deng EZ, Marino GB, Clarke DJB, Diamant I, Resnick AC, Ma W, Wang P, Ma’ayan A<\/strong>.\u00a0Multiomics2Targets identifies targets from cancer cohorts profiled with transcriptomics, proteomics, and phosphoproteomics<\/strong>.\u00a0Cell Reports Methods<\/em> 4(8):100839 (2024) PMID: 39127042<\/a><\/p>\n

Clarke DJB, Evangelista JE, […], Ma’ayan A<\/strong>.\u00a0Playbook Workflow Builder: interactive construction of bioinformatics workflows from a network of microservices<\/strong>.\u00a0bioRxiv<\/em> 2024.06.08.598037 (2024)<\/a><\/p>\n

Clarke DJB, Marino GB, Deng EZ, Xie Z, Evangelista JE, Ma’ayan A<\/strong>.\u00a0Rummagene: massive mining of gene sets from supporting materials of biomedical research publications<\/strong>.\u00a0Communications Biology<\/em> 7(1):482 (2024) PMID: 38643247<\/a><\/p>\n

Vinik Y, Maimon A, Dubey V, Raj H, Abramovitch I, Malitsky S, Itkin M, Ma’ayan A<\/strong>, Westermann F, Gottlieb E, Ruppin E, Lev S.\u00a0Programming a ferroptosis-to-apoptosis transition landscape revealed ferroptosis biomarkers and repressors for cancer therapy<\/strong>.\u00a0Advanced Science<\/em> 11(17):e2307263 (2024) PMID: 38441406<\/a><\/p>\n

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, Gonz\u00e1lez-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, G\u00fcm\u00fc\u015f ZH, Hostetter G, Feny\u00f6 D, Omenn GS, Cantley LC, Ma’ayan A<\/strong>, Lazar AJ, Ceccarelli M, Wang P; Clinical Proteomic Tumor Analysis Consortium.\u00a0Pan-cancer proteogenomics characterization of tumor immunity<\/strong>.\u00a0Cell<\/em> 187(5):1255-1277.e27 (2024) PMID: 38359819<\/a><\/p>\n

2023<\/h2>\n

Marino GB, Ahmed N, Xie Z, Jagodnik KM, Han J, Clarke DJB, Lachmann A, Keller MP, Attie AD, Ma’ayan A<\/strong>.\u00a0D2H2: diabetes data and hypothesis hub<\/strong>.\u00a0Bioinformatics Advances<\/em> 3(1):vbad178 (2023) PMID: 38107655<\/a><\/p>\n

Ma’ayan A<\/strong>, Schlessinger A, Filizola M, Sebra R, Shi Y, Pandey G, Itan Y, Kenny EE.\u00a0AI + omics are bringing the bench closer to the bedside<\/strong>. Frontiers of Medical Research: Artificial Intelligence <\/em>(Science\/AAAS Washington, DC, 2023) p. 8-10.<\/a><\/p>\n

Xie Z, Chen C, Ma’ayan A<\/strong>.\u00a0Dex-Benchmark: datasets and code to evaluate algorithms for transcriptomics data analysis<\/strong>.\u00a0PeerJ<\/em> 11:e16351 (2023) PMID: 37953774<\/a><\/p>\n

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<\/strong>, Giannarelli C.\u00a0Systems immunology-based drug repurposing framework to target inflammation in atherosclerosis<\/strong>.\u00a0Nature Cardiovascular Research<\/em> 2(6):550-571 (2023) PMID: 37771373<\/a><\/p>\n

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<\/strong>.\u00a0Toxicology knowledge graph for structural birth defects<\/strong>.\u00a0Communications Medicine<\/em> 3(1):98 (2023) PMID: 37460679<\/a><\/p>\n

Evangelista JE, Xie Z, Marino GB, Nguyen N, Clarke DJB, Ma’ayan A<\/strong>.\u00a0Enrichr-KG: bridging enrichment analysis across multiple libraries<\/strong>.\u00a0Nucleic Acids Research<\/em> 51(W1):W168-W179 (2023) PMID: 37166973<\/a><\/p>\n

Marino GB, Ngai M, Clarke DJB, Fleishman RH, Deng EZ, Xie Z, Ahmed N, Ma’ayan A<\/strong>.\u00a0GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery<\/strong>.\u00a0Nucleic Acids Research<\/em> 51(W1):W213-W224 (2023) PMID: 37166966<\/a><\/p>\n

Deng EZ, Fleishman RH, Xie Z, Marino GB, Clarke DJB, Ma’ayan A<\/strong>.\u00a0Computational screen to identify potential targets for immunotherapeutic identification and removal of senescence cells<\/strong>.\u00a0Aging Cell<\/em> 22(6):e13809 (2023) PMID: 37082798<\/a><\/p>\n

Marino GB, Wojciechowicz ML, Clarke DJB, Kuleshov MV, Xie Z, Jeon M, Lachmann A, Ma’ayan A<\/strong>.\u00a0lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs<\/strong>.\u00a0Database (Oxford)<\/em> 2023:baad009 (2023) PMID: 36869839<\/a><\/p>\n

Lachmann A, Rizzo KA, Bartal A, Jeon M, Clarke DJB, Ma’ayan A<\/strong>.\u00a0PrismEXP: gene annotation prediction from stratified gene-gene co-expression matrices<\/strong>.\u00a0PeerJ<\/em> 11:e14927 (2023) PMID: 36874981<\/a><\/p>\n

2022<\/h2>\n

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 <\/strong>, Wagner R, Foster I, Kesselman C, Brown CT, White O.\u00a0Making Common Fund data more findable: catalyzing a data ecosystem<\/strong>.\u00a0Gigascience<\/em> 11:giac105 (2022) PMID: 36409836<\/a><\/p>\n

Clarke DJB, Rebman AW, Fan J, Soloski MJ, Aucott JN, Ma’ayan A<\/strong>.\u00a0Gene set predictor for post-treatment Lyme disease<\/strong>.\u00a0Cell Reports Medicine<\/em> 3(11):100816 (2022) PMID: 36384094<\/a><\/p>\n

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<\/strong>, Birtwistle MR, Sorger PK, Korkola JE, Gray JW, Heiser LM.\u00a0A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses<\/strong>.\u00a0Communications Biology<\/em> 5(1):1066 (2022) PMID: 36207580<\/a><\/p>\n

Jenkins EC, Chattopadhyay M, Gomez M, Torre D, Ma’ayan A<\/strong>, Torres-Martin M, Sia D, Germain D.\u00a0Age alters the oncogenic trajectory toward luminal mammary tumors that activate unfolded proteins responses<\/strong>.\u00a0Cell Aging<\/em> 21(10):e13665 (2022) PMID: 36111352<\/a><\/p>\n

Jeon M, Xie Z, Evangelista JE, Wojciechowicz ML, Clarke DJB, Ma’ayan A<\/strong>.\u00a0Transforming L1000 profiles to RNA-seq-like profiles with deep learning<\/strong>.\u00a0BMC Bioinformatics<\/em> 23(1):74 (2022) PMID: 36100892<\/a><\/p>\n

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, Sch\u00fcrer SC, Ma’ayan A<\/strong>, Meller J, Medvedovic M.\u00a0Connecting omics signatures and revealing biological mechanisms with iLINCS<\/strong>.\u00a0Nature Communications<\/em> 13(1):4678 (2022) PMID: 35945222<\/a><\/p>\n

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<\/strong>.\u00a0Getting started with LINCS datasets and tools<\/strong>.\u00a0Current Protocols<\/em> 2(7):e487 (2022) PMID: 35876555<\/a><\/p>\n

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<\/strong>.\u00a0SigCom LINCS: data and metadata search engine for a million gene expression signatures<\/strong>.\u00a0Nucleic Acids Research<\/em> 50(W1):W697-709 (2022) PMID: 35524556<\/a><\/p>\n

Clarke DJB, Kuleshov MV, Xie Z, Evangelista JE, Meyers MR, Kropiwnicki E, Jenkins SL, Ma’ayan A<\/strong>.\u00a0Gene and drug landing page aggregator<\/strong>.\u00a0Bioinformatics Advances<\/em> 2(1):vbac013 (2022) PMID: 35368424<\/a><\/p>\n

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<\/strong>, Houten SM, Costa K, Dubois NC.\u00a0PPARdelta activation induces metabolic and contractile maturation of human pluripotent stem cell-derived cardiomyocytes<\/strong>.\u00a0Cell Stem Cell<\/em> 29(4):559-576.e7 (2022) PMID: 35325615<\/a><\/p>\n

Kropiwnicki E, Lachmann A, Clarke DJB, Xie Z, Jagodnik KM, Ma’ayan A<\/strong>.\u00a0DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules<\/strong>.\u00a0BMC Bioinformatics<\/em> 23(1):76 (2022) PMID: 35183110<\/a><\/p>\n

Lachmann A, Xie Z, Ma’ayan A<\/strong>.\u00a0blitzGSEA: Efficient computation of Gene Set Enrichment Analysis through Gamma distribution approximation<\/strong>.\u00a0Bioinformatics<\/em> btac076 (2022) PMID: 35143610<\/a><\/p>\n

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<\/strong>. Getting started with the IDG KMC datasets and tools<\/strong>.\u00a0Current Protocols<\/em> 2(1):e355 (2022) PMID: 35085427<\/a><\/p>\n

2021<\/h2>\n

Onoufriadis A, Proudfoot LE, Ainali C, Torre D, Papanikolaou M, Rayinda T, Rashidghamat E, Danarti R, Mellerio JE, Ma’ayan A<\/strong>, McGrath JA.\u00a0Transcriptomic profiling of recessive dystrophic epidermolysis bullosa wounded skin highlights drug repurposing opportunities to improve wound healing<\/strong>.\u00a0Experimental Dermatology<\/em> (2021) PMID: 34694680<\/a><\/p>\n

Piret SE, Attallah AA, Gu X, Guo Y, Gujarati NA, Henein J, Zollman A, Hato T, Ma’ayan A<\/strong>, Revelo MP, Dickman KG, Chen CH, Shun CT, Rosenquist TA, He JC, Mallipattu SK.\u00a0Loss of proximal tubular transcription factor Kr\u00fcppel-like factor 15 exacerbates kidney injury through loss of fatty acid oxidation<\/strong>.\u00a0Kidney International<\/em> (2021) PMID: 34634362<\/a><\/p>\n

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<\/strong>, 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.\u00a0Recent progress in Lyme disease and remaining challenges<\/strong>.\u00a0Frontiers in Medicine<\/em> (2021) PMID: 34485323<\/a><\/p>\n

Kuleshov MV, Xie Z, London ABK, Yang J, Evangelista JE, Lachmann A, Shu I, Torre D, Ma’ayan A<\/strong>.\u00a0KEA3: improved kinase enrichment analysis via data integration<\/strong>.\u00a0Nucleic Acids Research<\/em> 49(W1):W304-W316 (2021) PMID: 34019655<\/a><\/p>\n

Piret SE, Guo Y, Attallah AA, Horne SJ, Zollman A, Owusu D, Henein J, Sidorenko VS, Revelo MP, Hato T, Ma’ayan A<\/strong>, He JC, Mallipattu SK.\u00a0Kr\u00fcppel-like factor 6-mediated loss of BCAA catabolism contributes to kidney injury in mice and humans<\/strong>.\u00a0Proc Natl Acad Sci USA<\/em> 118(23) (2021) PMID: 34074766<\/a><\/p>\n

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<\/strong>, Lemischka IR.\u00a0An Esrrb and Nanog cell fate regulatory module controlled by feed forward loop interactions<\/strong>.\u00a0Frontiers in Cell and Developmental Biology<\/em> 9:630067 (2021) PMID: 33816475<\/a><\/p>\n

Kropiwnicki E, Evangelista JE, Stein DJ, Clarke DJB, Lachmann A, Kuleshov MV, Jeon M, Jagodnik KM, Ma’ayan A<\/strong>.\u00a0Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning<\/strong>.\u00a0Database<\/em> baab017 (2021) PMID: 33787872<\/a><\/p>\n

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<\/strong>.\u00a0Gene set knowledge discovery with Enrichr<\/strong>.\u00a0Current Protocols<\/em> 1(3):e90 (2021) PMID: 33780170<\/a><\/p>\n

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<\/strong>.\u00a0Predicting Lyme Disease from patients’ peripheral blood mononuclear cells profiled with RNA-sequencing<\/strong>.\u00a0Frontiers in Immunology<\/em> 12:636289 (2021) PMID: 33763080<\/a><\/p>\n

Austin E, Koo E, Merleev A, Torre D, Marusina A, Luxardi G, Mamalis A, Isseroff RR, Ma’ayan A<\/strong>, Maverakis E, Jagdeo J.\u00a0Transcriptome analysis of human dermal fibroblasts following red light phototherapy<\/strong>.\u00a0Scientific Reports<\/em> 11(1):7315 (2021) PMID: 33795767<\/a><\/p>\n

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<\/strong>.\u00a0Appyters: Turning Jupyter notebooks into data-driven web apps<\/strong>.\u00a0Patterns<\/em> 2(3):100213 (2021) PMID: 33748796<\/a><\/p>\n

Jeon M, Jagodnik KM, Kropiwnicki E, Stein DJ, Ma’ayan A<\/strong>.\u00a0Prioritizing pain-associated targets with machine learning<\/strong>.\u00a0Biochemistry<\/em> (2021) PMID: 33606503<\/a><\/p>\n

Zhang L, Wang Z, Liu R, Li Z, Lin J, Wojciechowicz ML, Huang J, Lee K, Ma’ayan A<\/strong>, He JC.\u00a0Connectivity mapping identifies BI-2536 as a potential drug to treat diabetic kidney disease<\/strong>.\u00a0Diabetes<\/em> 70(2):589-602 (2021) PMID: 33067313<\/a><\/p>\n

2020<\/h2>\n

Eberlein J, Davenport B, Nguyen TT, Victorino F, Jhun K, van der Heide V, Kuleshov M, Ma’ayan A<\/strong>, Kedl R, Homann D.\u00a0Chemokine signatures of pathogen-specific T cells I: Effector T cells<\/strong>.\u00a0Journal of Immunology<\/em> 205(8):2169-2187 (2020) PMID: 32948687<\/a><\/p>\n

Davenport B, Eberlein J, Nguyen TT, Victorino F, van der Heide V, Kuleshov M, Ma’ayan A<\/strong>, Kedl R, Homann D. Chemokine signatures of pathogen-specific T cells II: Memory T cells in acute and chronic infection<\/strong>. Journal of Immunology<\/em> 205(8):2188-2206 (2020) PMID: 32948682<\/a><\/p>\n

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<\/strong>. The COVID-19 gene and drug set library<\/strong>. Patterns<\/em> 1(6):100090 (2020) PMID: 32838343<\/a><\/p>\n

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<\/strong>, 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<\/strong>. Glia<\/em> 68(10):2148-2166 (2020) PMID: 32639068<\/a><\/p>\n

Borziak K, Qi T, Evangelista JE, Clarke DJB, Ma’ayan A<\/strong>, Finkelstein J. Towards intelligent integration and sharing of stem cell research data<\/strong>. Studies in Health Technologies and Informatics<\/em> 272:334-337 (2020) PMID: 32604670<\/a><\/p>\n

Wojciechowicz ML, Ma’ayan A<\/strong>. GPR84: an immune response dial<\/strong>? Nature Reviews Drug Discovery<\/em> 19(6):374 (2020) PMID: 32494048<\/a><\/p>\n

Bartal A, Lachmann A, Clarke DJB, Seiden AH, Jagodnik KM, Ma’ayan A<\/strong>. EnrichrBot: Twitter bot tracking tweets about human genes<\/strong>. Bioinformatics<\/em> 36(12):3932-3934 (2020) PMID: 32277816<\/a><\/p>\n

Bernitz JM, Rapp K, Daniel MG, Shcherbinin D, Yuan Y, Gomes A, Waghray A, Brosh R, Lachmann A, Ma’ayan A<\/strong>, Papatsenko D, Moore KA. Memory of divisional history directs the continuous process of primitive hematopoietic lineage commitment<\/strong>. Stem Cell Reports<\/em> 14(4):561-574 (2020) PMID: 32243840<\/a><\/p>\n

Lachmann A, Clarke DJB, Torre D, Xie Z, Ma’ayan A<\/strong>. Interoperable RNA-seq analysis in the cloud<\/strong>. Biochimica et Biophysica Acta Gene Regulatory Mechanisms<\/em> 1863(6):194521 (2020) PMID: 32156561<\/a><\/p>\n

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<\/strong>, Gelb BD. Systems analysis implicates WAVE2 complex in the pathogenesis of developmental left-sided obstructive heart defects<\/strong>. JACC Basic to Translational Science<\/em> 5(4):376-386 (2020) PMID: 32368696<\/a><\/p>\n

Heitman N, Sennett R, Mok KW, Saxena N, Srivastava D, Martino P, Grisanti L, Wang Z, Ma’ayan A<\/strong>, Rompolas P, Rendl M. Dermal sheath contraction powers stem cell niche relocation during hair cycle regression<\/strong>. Science<\/em> 367(6474):161-166 (2020) PMID: 31857493<\/a><\/p>\n

2019<\/h2>\n

Clarke DJB, Wang L, Jones A, Wojciechowicz ML, Torre D, Jagodnik KM, Jenkins SL, McQuilton P, Flamholz z, […], Ma’ayan A<\/strong>. FAIRshake: Toolkit to evaluate the FAIRness of research digital resources<\/strong>. Cell Systems<\/em> 9(5):417-421 (2019) PMID: 31677972<\/a><\/p>\n

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<\/strong>, 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<\/strong>. Scientific Data<\/em> 6(1):252 (2019) PMID: 31672983<\/a><\/p>\n

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<\/strong>, O’Neill HC, Ibanez-Tallon I, Geurts AM, Kenny PJ. Habenular TCF7L2 links nicotine addiction to diabetes<\/strong>. Nature<\/em> 574(7778):372-377 (2019) PMID: 31619789<\/a><\/p>\n

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<\/strong>, Mocco J, Faries P, Merad M, Giannarelli C. Single-cell immune landscape of human atherosclerotic plaques<\/strong>. Nature Medicine<\/em> (10):1576-1588 (2019) PMID: 31591603<\/a><\/p>\n

Niepel M, Hafner M, Mills CE, Subramanian K, Williams EH, Chung M, Gaudio B, Barrette AM, Stern AD, Hu B, Korkola JE, LINCS Consortium<\/strong> et al. A Multi-center study on the reproducibility of drug-response assays in mammalian cell lines<\/strong>. Cell Systems<\/em> 9(1):35-48.e5 (2019) PMID: 31302153<\/a><\/p>\n

Lachmann A, Schilder BM, Wojciechowicz ML, Torre D, Kuleshov MV, Keenan AB, Ma’ayan A<\/strong>. Geneshot: search engine for ranking genes from arbitrary text queries<\/strong>. Nucleic Acids Research<\/em> 47(W1):W571-W577 (2019) PMID: 31114885<\/a><\/p>\n

Keenan AB, Torre D, Lachmann A, Leong AK, Wojciechowicz ML, Utti V, Jagodnik KM, Kropiwnicki E, Wang Z, Ma’ayan A<\/strong>. ChEA3: transcription factor enrichment analysis by orthogonal omics integration<\/strong>. Nucleic Acids Research<\/em> 47(W1):W212-W224 (2019) PMID: 31114921<\/a><\/p>\n

Kuleshov MV, Diaz JEL, Flamholz ZN, Keenan AB, Lachmann A, Wojciechowicz ML, Cagan RL, Ma’ayan A<\/strong>. modEnrichr: a suite of gene set enrichment analysis tools for model organisms<\/strong>. Nucleic Acids Research<\/em> 47(W1):W183-W190 (2019) PMID: 31069376<\/a><\/p>\n

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<\/strong>, Greally JM, Frenette PS. Engineering a haematopoietic stem cell niche by revitalizing mesenchymal stromal cells<\/strong>. Nature Cell Biology<\/em> 21(5):560-567 (2019) PMID: 30988422<\/a><\/p>\n

Keenan AB, Wojciechowicz ML, Wang Z, Jagodnik KM, Jenkins SL, Lachmann A, Ma’ayan A<\/strong>. Connectivity mapping: methods and applications<\/strong>. Annual Review of Biomedical Data Science<\/em> 2:69-92 (2019)<\/a><\/p>\n

Tohme R, Izadmehr S, Gandhe S, Tabaro G, Vallabhaneni S, Thomas A, Vasireddi N, Dhawan NS, Ma’ayan A<\/strong>, Sharma N, Galsky MD, Ohlmeyer M, Sangodkar J, Narla G. Direct activation of PP2A for the treatment of tyrosine kinase inhibitor-resistant lung adenocarcinoma<\/strong>. JCI Insight<\/em> 4(4) pii: 125693 (2019) PMID: 30830869<\/a><\/p>\n

Ellis RJ, Wang Z, Genes N, Ma’ayan A<\/strong>. Predicting opioid dependence from electronic health records with machine learning<\/strong>. BioData Mining<\/em> 12:3 (2019) PMID: 30728857<\/a><\/p>\n

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<\/strong>, Ornitz DM, Kasper M, Rendl M. Dermal condensate niche fate specification occurs prior to formation and is placode progenitor dependent<\/strong>. Developmental Cell<\/em> 48(1):32-48 (2019) PMID: 30595537<\/a><\/p>\n

Wang Z, Lachmann A, Ma’ayan A<\/strong>. Mining data and metadata from the gene expression omnibus<\/strong>. Biophysical Reviews<\/em> 11(1):103-110 (2019) PMID: 30594974<\/a><\/p>\n

2018<\/h2>\n

Torre D, Lachmann A, Ma’ayan A<\/strong>. BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud<\/strong>. Cell Systems<\/em> 7(5):556-561 (2018) PMID: 30447998<\/a><\/p>\n

Oprea TI, Jan L, Johnson GL, Roth BL, Ma’ayan A<\/strong>, Schurer S, Shoichet BK, Sklar LA, McManus MT. Far away from the lamppost<\/strong>. PLoS Biology<\/em> 16(12):e3000067 (2018) PMID: 30532236<\/a><\/p>\n

Breen MS, Ozcan S, Ramsey JM, Wang Z, Ma’ayan A<\/strong>, Rustogi N, Gottschalk MG, Webster MJ, Weickert CS, Buxbaum JD, Bahn S. Temporal proteomic profiling of postnatal human cortical development<\/strong>. Translational Psychiatry<\/em> 8(1):267 (2018) PMID: 30518843<\/a><\/p>\n

Gomes AM, Kurochkin I, Chang B, Daniel M, Law K, Satija N, Lachmann A, Wang Z, Ferreira L, Ma’ayan A<\/strong>, Chen BK, Papatsenko D, Lemischka IR, Moore KA, Pereira CF. Cooperative Transcription Factor Induction Mediates Hemogenic Reprogramming<\/strong>. Cell Reports<\/em> 25(10):2821-2835 (2018) PMID: 30517869<\/a><\/p>\n

Wang Z, He E, Sani K, Jagodnik KM, Silverstein M, Ma’ayan A<\/strong>. Drug Gene Budger (DGB): An application for ranking drugs to modulate a specific gene based on transcriptomic signatures<\/strong>. Bioinformatics<\/em> (2018) PMID: 30169739<\/a><\/p>\n

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<\/strong>, Long GV, Scolyer RA, Brown B, Zheng B, Bernstein E. SIRT6 haploinsufficiency induces BRAFV600E melanoma cell resistance to MAPK inhibitors via IGF signalling<\/strong>. Nature Communications<\/em> 9(1):3440 (2018) PMID: 30143629<\/a><\/p>\n

Guo Y, Pace J, Li Z, Ma’ayan A<\/strong>, Wang Z, Revelo MP, Chen E, Gu X, Attalah A, Yang Y, Estrada C, Yang VW, He JC, Mallipattu SK. Podocyte-specific induction of Kr\u00fcppel-Like Factor 15 restores differentiation markers and attenuates kidney injury in proteinuric kidney disease.<\/strong>. Journal of the America Society of Nephrology<\/em> pii: ASN.2018030324(2018) PMID: 30143559<\/a><\/p>\n

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<\/strong>. eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks<\/strong>. Nucleic Acids Research<\/em> 46(W1):W171-W179 (2018) PMID: 29800326<\/a><\/p>\n

Han S, Tan C, Ding J, Wang J, Ma’ayan A<\/strong>, Gouon-Evans V. Endothelial cells instruct liver specification of embryonic stem cell-derived endoderm through endothelial VEGFR2 signaling and endoderm epigenetic modifications<\/strong>. Stem Cell Research<\/em> 30:163-170 (2018) PMID: 29936335<\/a><\/p>\n

Stathias V, Koleti A, Vidovi\u0107 D, Cooper DJ, Jagodnik KM, Terryn R, Forlin M, Chung C, Torre D, Ayad N, Medvedovic M, Ma’ayan A<\/strong>, Pillai A, Schurer SC. Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center<\/strong>. Scientific Data<\/em> 5:180117 (2018) PMID: 29917015<\/a><\/p>\n

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<\/strong>, Comb M. Integration of protein phosphorylation, acetylation, and methylation data sets to outline lung cancer signaling networks<\/strong>. Science Signaling<\/em> 11(531) (2018) PMID: 29789295<\/a><\/p>\n

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

Torre D, Krawczuk P, Jagodnik KM, Lachmann A, Wang Z, Wang L, Kuleshov MV, Ma’ayan A<\/strong>. Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses<\/strong>. Scientific Data<\/em> 5, 180023 (2018) PMID: 29485625<\/a><\/p>\n

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 <\/strong>et al. Unexplored therapeutic opportunities in the human genome<\/strong>. Nature Review Drug Discovery<\/em> (2018) PMID: 29572638<\/a><\/p>\n

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<\/strong>, 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<\/strong>. Annals of Allergy, Asthma and Immunology<\/em> S1081-1206(18)30211-4 (2018) PMID: 29567358<\/a><\/p>\n

Wang Z, Lachmann A, Keenan AB, Ma’ayan A<\/strong>. L1000FWD: Fireworks visualization of drug-induced transcriptomic signatures<\/strong>. Bioinformatics<\/em> 34(12)2150-2152 (2018) PMID: 29420694<\/a><\/p>\n

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

Hodos R, Zhang P, Lee HC, Duan Q, Wang Z, Clark NR, Ma’ayan A<\/strong>, Wang F, Kidd B, Hu J, Sontag D, Dudley J. Cell-specific prediction and application of drug-induced gene expression profiles<\/strong>. Pacific Symposium on Biocomputing<\/em> 23:32-43 (2018) PMID: 29218867<\/a><\/p>\n

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<\/strong> et al. The Library of Integrated Network-Based Cellular Signatures NIH program: System-level cataloging of human cells response to perturbations<\/strong>. Cell Systems<\/em>\u00a0 6(1):13-24 (2018) PMID: 29199020<\/a><\/p>\n

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<\/strong>, 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<\/strong>. Nucleic Acids Research<\/em> 46(D1):D558-D566 (2018) PMID: 29140462<\/a><\/p>\n

2017<\/h2>\n

Wang Z, Li L, Glicksberg BS, Israel A, Dudley JT, Ma’ayan A<\/strong>. Predicting age by mining electronic medical records with deep learning characterizes differences between chronological and physiological age<\/strong>. Journal of Biomedical Informatics<\/em> pii: S1532-0464(17)30240-X (2017) PMID: 29113935<\/a><\/p>\n

Fu J, Wang Z, Lee K, Wei C, Liu Z, Zhang M, Zhoud M, Cai M, Zhang W, Chuang PY, Ma’ayan A<\/strong>, He JC, Liu Z. Transcriptomic analysis uncovers novel synergistic mechanisms in combination therapy for lupus nephritis<\/strong>. Kidney International<\/em> pii: S0085-2538(17)30671-3 (2017) PMID: 29102373<\/a><\/p>\n

Niepel M, Hafner M, Duan Q, Wang Z, Paull EO, Chung M, Lu X, Stuart JM, Golub TR, Subramanian A, Ma’ayan A<\/strong>, Sorger PK. Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling<\/strong>. Nature Communications<\/em> 8(1):1186 (2017) PMID: 29084964<\/a><\/p>\n

Fernandez NF, Gundersen GW, Rahman A, Grimes ML, Rikova K, Hornbeck P,\u00a0Ma’ayan A<\/strong>. Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data<\/strong>. Scientific Data<\/em> 4:170151 (2017) PMID: 28994825<\/a><\/p>\n

Ma’ayan A<\/strong>. Complex systems biology<\/strong>. Journal of the Royal Society, Interface<\/em> 14(134) pii: 20170391 (2017) PMID: 28931638<\/a><\/p>\n

Lachmann A, Torre D, Keenan AB, Jagodnik KM, Lee HJ, Silverstein MC, Wang L, Ma’ayan A<\/strong>. Massive mining of publicly available RNA-seq data from human and mouse<\/strong>. bioRxiv<\/em> 189092 (2017)<\/a><\/p>\n

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<\/strong>, DiFeo A, Sharma N, Galsky MD, Brautigan DL, Ioannou YA, Xu W, Chance MR, Ohlmeyer M, Narla G.\u00a0Activation of tumor suppressor protein PP2A inhibits KRAS-driven tumor growth<\/strong>. The Journal of Clinical Investigation<\/em>\u00a0pii: 89548 (2017)\u00a0PMID: 28504649<\/a><\/p>\n

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<\/strong>.\u00a0Developing a Framework for Digital Objects in the Big Data to Knowledge (BD2K) Commons: Report from the Commons Framework Pilots Workshop<\/strong>. Journal of Biomedical Informatics<\/em>\u00a0pii: S1532-0464(17)30101-6 (2017) PMID:\u00a028501646<\/a><\/p>\n

Asada N, Kunisaki Y, Pierce H, Wang Z, Fernandez NF, Birbrair A, Ma’ayan A<\/strong>, Frenette PS.\u00a0Differential cytokine contributions of perivascular haematopoietic stem cell niches<\/strong>. Nature Cell Biology<\/em>\u00a019(3):214-22 (2017)\u00a0PMID: 28218906<\/a><\/p>\n

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<\/strong>, Dudley JT.\u00a0Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning<\/strong>. Briefings in Bioinformatics<\/em> (2017) PMID:\u00a028200013<\/a><\/p>\n

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<\/strong>, Mandava G, Mani S, Mehta S, Overington J, Patel J, Rouillard AD, Sch\u00fcrer S, Sheils T, Simeonov A, Sklar LA, Southall N, Ursu O, Vidovic D, Waller A, Yang J, Jadhav A, Oprea TI, Guha R.\u00a0Pharos: Collating protein information to shed light on the druggable genome<\/strong>.\u00a0Nucleic Acids Research<\/em>\u00a045(D1):D995-D100 (2017)\u00a0PMID: 27903890<\/a><\/p>\n

\n

2016<\/h2>\n

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<\/strong>, Shen L, Hodes GE, Russo SJ.\u00a0Integrative Analysis of Sex-Specific microRNA Networks Following Stress in Mouse Nucleus Accumbens<\/strong>. Frontiers in Molecular Neuroscience<\/em>\u00a09:144 (2016)\u00a0PMID: 28066174<\/a><\/p>\n

Gundersen GW, Jagodnik KM, Woodland H, Fernandez NF, Sani K, Dohlman AB, Ung PM, Monteiro CD, Schlessinger A, Ma’ayan A<\/strong>.\u00a0GEN3VA: aggregation and analysis of gene expression signatures from related studies<\/strong>.\u00a0BMC Bioinformatics<\/em> 17(1):461 (2016)\u00a0PMID: 27846806<\/a><\/p>\n

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, Sch\u00fcssler-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, J\u00fcschke C, Dishuck PC, Lahl K, Jafari M, Aibar S, Zaravinos A, Steenhuizen LH, Allison LR, Gamallo P, de Andres Segura F, Dae Devlin T, P\u00e9rez-Garc\u00eda V, Ma’ayan A<\/strong>.\u00a0Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd<\/strong>. Nature Communications<\/em> 7:12846\u00a0(2016)\u00a0PMID: 27667448<\/a><\/p>\n

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<\/strong>.\u00a0L1000CDS2: LINCS L1000 characteristic direction signatures search engine<\/strong>.\u00a0npj Systems Biology and Applications<\/em> 2, 16015 (2016)<\/a><\/p>\n

von Schimmelmann M, Feinberg PA, Sullivan JM, Ku SM, Badimon A, Duff MK, Wang Z, Lachmann A, Dewell S, Ma’ayan A<\/strong>, Han MH, Tarakhovsky A, Schaefer A.\u00a0Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration<\/strong>. Nature Neuroscience<\/em> 19(10):1321-30 (2016)\u00a0PMID: 27526204<\/a><\/p>\n

Rouillard AD, Gundersen GW, Fernandez NF, Wang Z, Monteiro CD, McDermott MG, Ma’ayan A<\/strong>.\u00a0The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins<\/strong>.\u00a0Database (Oxford)<\/em>\u00a0pii: baw100 (2016)\u00a0PMID: 27374120<\/a><\/p>\n

Wang Z, Ma’ayan A<\/strong>. An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study<\/strong>.\u00a0F1000Research<\/em>\u00a05:1574 (2016)\u00a0PMID: 27583132<\/a><\/p>\n

Mallipattu SK, Guo Y, Revelo MP, Roa-Pe\u00f1a L, Miller T, Ling J, Shankland SJ, Bialkowska AB, Ly V, Estrada C, Jain MK, Lu Y, Ma’ayan A<\/strong>, Mehrotra A, Yacoub R, Nord EP, Woroniecki RP, Yang VW, He JC.\u00a0Kr\u00fcppel-Like Factor 15 Mediates Glucocorticoid-Induced Restoration of Podocyte Differentiation Markers<\/strong>. Journal of the American Society of Nephrology<\/em>\u00a0pii: ASN.2015060672 (2016)\u00a0PMID: 27288011<\/a><\/p>\n

Morgan DJ, Poolman TM, Williamson AJ, Wang Z, Clark NR, Ma’ayan A<\/strong>, Whetton AD, Brass A, Matthews LC, Ray DW. Glucocorticoid receptor isoforms direct distinct mitochondrial programs to regulate ATP production<\/strong>. Scientific Reports<\/i> 6:26419 (2016) PMID: 27226058<\/a><\/p>\n

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<\/strong>. Enrichr: A Comprehensive Gene Set Enrichment Analysis Web Server 2016 Update<\/strong>. Nucleic Acids Research 44(W1):W90-7\u00a0<\/i>(2016) PMID: 27141961<\/a><\/p>\n

Wang Z, Clark NR, Ma’ayan A<\/strong>. Drug\u00a0Induced Adverse Events Prediction with the LINCS L1000 Data<\/strong>. Bioinformatics 32(15):2338-45<\/i>\u00a0 (2016) PMID: 27153606<\/a><\/p>\n

Rezza A, Wang Z, Sennett R, Qiao W, Wang D, Heitman N, Mok KW, Clavel C, Yi R, Zandstra P, Ma’ayan A<\/strong>, Rendl M. Signaling Networks among Stem Cell Precursors, Transit-Amplifying Progenitors, and their Niche in Developing Hair Follicles<\/strong>. Cell Reports<\/i> pii: S2211-1247(16)30213-3 (2016) PMID: 27009580<\/a><\/p>\n

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

Kong DS, Kim J, Lee IH, Kim ST, Seol HJ, Lee JI, Park WY, Ryu G, Wang Z, Ma’ayan A<\/strong>, Nam DH. Integrative radiogenomic analysis for multicentric radiophenotype in glioblastoma<\/strong>. Oncotarget<\/i> 7(10):11526-38 (2016) PMID: 26863628<\/a><\/p>\n

Khan JA, Mendelson A, Kunisaki Y, Birbrair A, Kou Y, Arnal-Estap\u00e9 A, Pinho S, Ciero P, Nakahara F, Ma’ayan A<\/strong>, Bergman A, Merad M, Frenette PS. Fetal liver hematopoietic stem cell niches associate with portal vessels<\/strong>. Science<\/i>\u00a0351(6269):176-80 (2016) PMID: 26634440<\/a><\/p>\n

\n

2015<\/h2>\n

Clark NR, Szymkiewicz M, Wang Z, Monteiro CD, Jones MR, Ma’ayan A<\/strong>. Principal Angle Enrichment Analysis (PAEA): Dimensionally reduced multivariate gene set enrichment analysis tool<\/strong>. Proceedings (IEEE Int Conf Bioinformatics Biomed)<\/i> (2015) PMID: 26848405<\/a><\/p>\n

Liang R, Campreci\u00f3s G, Kou Y, McGrath K, Nowak R, Catherman S, Bigarella CL, Rimmele P, Zhang X, Gnanapragasam MN, Bieker JJ, Papatsenko D, Ma’ayan A<\/strong>, Bresnick E, Fowler V, Palis J, Ghaffari S. A Systems Approach Identifies Essential FOXO3 Functions at Key Steps of Terminal Erythropoiesis<\/strong>. PLoS Genetics<\/i>\u00a011(10):e1005526 (2015) PMID: 26452208<\/a><\/p>\n

Sennett R, Wang Z, Rezza A, Grisanti L, Roitershtein N, Sicchio C, Mok KW, Heitman NJ, Clavel C, Ma’ayan A<\/strong>, Rendl M. An Integrated Transcriptome Atlas of Embryonic Hair Follicle Progenitors, Their Niche, and the Developing Skin<\/strong>. Developmental Cell<\/i> 34(5):577-91 (2015) PMID:26256211<\/a><\/p>\n

Stockton SD Jr, Gomes I, Liu T, Moraje C, Hip\u00f3lito L, Jones MR, Ma’ayan A<\/strong>, Mor\u00f3n JA, Li H, Devi LA. Morphine regulated synaptic networks revealed by integrated proteomics and network analysis<\/strong>. Molecular and Cellular Proteomics<\/i> pii: mcp.M115.047977 (2015) PMID: 26149443<\/a><\/p>\n

Rouillard AD, Wang Z, Ma’ayan A<\/strong>. Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction<\/strong>. Computational Biology and Chemistry<\/i> pii: S1476-9271(15)00083-3 (2015) PMID: 26297300<\/a><\/p>\n

Wang Z, Clark NR, Ma’ayan A<\/strong>. Dynamics of the discovery process of protein-protein interactions from low content studies<\/strong>. BMC Systems Biology<\/i> 9(1):26 (2015) PMID: 26048415<\/a><\/p>\n

Gundersen GW, Jones MR, Rouillard AD, Kou Y, Monteiro CD, Feldmann AS, Hu KS, Ma’ayan A<\/strong>. GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions<\/strong>. Bioinformatics<\/i> pii: btv297 (2015) PMID: 25971742<\/a><\/p>\n

Mallipattu SK, Horne SJ, D’Agati V, Narla G, Liu R, Frohman MA, Dickman K, Chen EY, Ma’ayan A<\/strong>, Bialkowska AB, Ghaleb AM, Nandan MO, Jain MK, Daehn I, Chuang PY, Yang VW, He JC. Kruppel-like factor 6 regulates mitochondrial function in the kidney<\/strong>. Journal of Clinical Investigation<\/i> 215(3):1347-61 (2015) PMID: 25689250<\/a><\/p>\n

\n

2014<\/h2>\n

Duarte LF, Young AR, Wang Z, Wu HA, Panda T, Kou Y, Kapoor A, Hasson D, Mills NR, Ma’ayan A<\/strong>, Narita M, Bernstein E. Histone H3.3 and its proteolytically processed form drive a cellular senescence programme<\/strong>. Nature Communications<\/i> 5:5210 (2014) PMID: 25394905<\/a><\/p>\n

De Rubeis S, He X, Goldberg AP, Poultney CS, Samocha K, Ercument Cicek A, Kou Y, Liu L, Fromer M, Walker S, Singh T, Klei L, Kosmicki J, Fu SC, Aleksic B, Biscaldi M, Bolton PF, Brownfeld JM, Cai J, Campbell NG, Carracedo A, Chahrour MH, Chiocchetti AG, Coon H, Crawford EL, Crooks L, Curran SR, Dawson G, Duketis E, Fernandez BA, Gallagher L, Geller E, Guter SJ, Sean Hill R, Ionita-Laza I, Jimenez Gonzalez P, Kilpinen H, Klauck SM, Kolevzon A, Lee I, Lei J, Lehtimaki T, Lin CF, Ma’ayan A<\/strong>, Marshall CR, McInnes AL, Neale B, Owen MJ, Ozaki N, Parellada M, Parr JR et al<\/i>. Synaptic, transcriptional and chromatin genes disrupted in autism<\/strong>. Nature <\/i>515(7526):209-15 (2014) PMID: 25363760<\/a><\/p>\n

Ma’ayan A<\/strong>, Duan Q. A blueprint of cell identity<\/strong>. Nature Biotechnology<\/i> 32(10):1007-1008 (2014) PMID: 25299921<\/a><\/p>\n

Xu H, Ang YS, Sevilla A, Lemischka IR, Ma’ayan A<\/strong>. Construction and validation of a regulatory network for pluripotency and self-renewal of mouse embryonic stem cells<\/strong>. PLoS Computational Biology<\/i> 10(8):e1003777 (2014) PMID: 25122140<\/a><\/p>\n

Ma’ayan A<\/strong>, Rouillard AD, Clark NR, Wang Z, Duan Q, Kou Y. Lean Big Data integration in systems biology and systems pharmacology<\/strong>. Trends in Pharmacological Sciences<\/i> 35(9):450-460 (2014) PMID: 25109570<\/a><\/p>\n

Duan Q, Wang Z, Fernandez NF, Rouillard AD, Tan CM, Benes CH, Ma’ayan A<\/strong>. Drug\/Cell-line Browser (DCB): Interactive Canvas Visualization of Cancer Drug\/Cell-Line Viability Assay Datasets<\/strong>. Bioinformatics<\/i> pii: btu526 (2014) PMID: 25100688<\/a><\/p>\n

Hays T, Ma’ayan A<\/strong>, Clark NR, Tan CM, Teixeira A, Teixeira A, Choi JW, Burdis N, Jung SY, Bajaj AO, O’Malley BW, He JC, Hyink DP, Klotman PE. Proteomics Analysis of the Non-Muscle Myosin Heavy Chain IIa-Enriched Actin-Myosin Complex Reveals Multiple Functions within the Podocyte<\/strong>. PLoS One<\/i> 9(6):e100660 (2014) PMID: 24949636<\/a><\/p>\n

Duan Q, Flynn C, Niepel M, Hafner M, Muhlich JL, Fernandez NF, Rouillard AD, Tan CM, Chen EY, Golub TR, Sorger PK, Subramanian A, Ma’ayan A<\/strong>. LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures<\/strong>. Nucleic Acids Research<\/i> pii: gku476 (2014) PMID: 24906883<\/a><\/p>\n

Clark NR, Hu KS, Feldmann AS, Kou Y, Chen EY, Duan Q, Ma’ayan A<\/strong>. The characteristic direction: a geometrical approach to identify differentially expressed genes<\/strong>. BMC Bioinformatics <\/i>15:79 (2014) PMID: 24650281<\/a><\/p>\n

Liu L, Lei J, Sanders SJ, Willsey AJ, Kou Y, Cicek AE, Klei L, Lu C, He X, Li M, Muhle RA, Ma’ayan A<\/strong>, Noonan JP, Sestan N, McFadden KA, State MW, Buxbaum JD, Devlin B, Roeder K. DAWN: A framework to identify autism genes and subnetworks using gene expression and genetics<\/strong>. Molecular Autism<\/i> 5(1):22 (2014) PMID: 24602502<\/a><\/p>\n

Baker SJ, Ma’ayan A<\/strong>, Lieu YK, John P, Reddy MV, Chen EY, Duan Q, Snoeck HW, Reddy EP. B-myb is an essential regulator of hematopoietic stem cell and myeloid progenitor cell development<\/strong>. Proc Natl Acad Sci U S A <\/i>111(8):3122-7 (2014) PMID: 24516162<\/a><\/p>\n

Azeloglu EU, Hardy SV, Eungdamrong NJ, Chen Y, Jayaraman G, Chuang PY, Fang W, Xiong H, Neves SR, Jain MR, Li H, Ma’ayan A<\/strong>, Gordon RE, He JC, Iyengar R. Interconnected network motifs control podocyte morphology and kidney function<\/strong>. Science Signaling<\/i> 7(311):ra12 (2014) PMID: 24497609<\/a><\/p>\n

Kleensang A, Maertens A, Rosenberg M, Fitzpatrick S, Lamb J, Auerbach S, Brennan R, Crofton KM, Gordon B, Fornace Jr AJ, Gaido K, Gerhold D, Haw R, Henney A, Ma’ayan A<\/strong>, McBride M, Monti S, Ochs MF, Pandey A, Sharan R, Stierum R, Tugendreich S, Willett C, Wittwehr C, Xia J, Patton GW, Arvidson K, Bouhifd M, Hogberg HT, Luechtefeld T, Smirnova L, Zhao L, Adeleye Y, Kanehisa M, Carmichael P, Andersen ME, Hartung T. t4 Workshop Report: Pathways of Toxicity<\/strong>. ALTEX<\/i> \u00a031(1):53-61 (2014) PMID: 24127042<\/a><\/p>\n

\n

2013<\/h2>\n

Poultney CS, Goldberg AP, Drapeau E, Kou Y, Harony-Nicolas H, Kajiwara Y, De Rubeis S, Durand S, Stevens C, Rehnstr\u00f6m K, Palotie A, Daly MJ, Ma’ayan A<\/strong>, Fromer M, Buxbaum JD. Identification of Small Exonic CNV from Whole-Exome Sequence Data and Application to Autism Spectrum Disorder<\/strong>. American Journal of Human Genetics<\/i> 93(4):607-619 (2013) PMID: 24094742<\/a><\/p>\n

Jakubzick C, Gautier EL, Gibbings SL, Sojka DK, Schlitzer A, Johnson TE, Ivanov S, Duan Q, Bala S, Condon T, van Rooijen N, Grainger JR, Belkaid Y, Ma’ayan A<\/strong>, Riches DW, Yokoyama WM, Ginhoux F, Henson PM, Randolph GJ.\u00a0Minimal differentiation of classical monocytes as they survey steady-state tissues and transport antigen to lymph nodes<\/strong>. Immunity<\/i> 39(3):599-610 (2013) PMID: 24012416<\/a><\/p>\n

Xu H, Baroukh C, Dannenfelser R, Chen EY, Tan CM, Kou Y, Kim YE, Lemischka IR, Ma’ayan A<\/strong>. ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells<\/strong>. Database (Oxford)<\/i> bat045 (2013) PMID: 23794736<\/a><\/p>\n

Pereira CF, Chang B, Qiu J, Niu X, Papatsenko D, Hendry CE, Clark NR, Nomura-Kitabayashi A, Kovacic JC, Ma’ayan A<\/strong>, Schaniel C, Lemischka IR, Moore K. Induction of a Hemogenic Program in Mouse Fibroblasts<\/strong>. Cell Stem Cell <\/i>13(2):205-18 (2013) PMID: 23770078<\/a><\/p>\n

Tan CM, \u00a0Chen EY, Dannenfelser R, Clark NR, Ma’ayan A<\/strong>. Network2Canvas: network visualization on a canvas with enrichment analysis<\/strong>. Bioinformatics<\/i> 29(15):1872-8 (2013) PMID: 23749960<\/a><\/p>\n

Sillivan SE, Whittard JD, Jacobs MM, Ren Y, Mazloom AR, Caputi FF, Horvath M, Keller E, Ma’ayan A<\/strong>, Pan YX, Chiang LW, Hurd YL.\u00a0ELK1 Transcription Factor Linked to Dysregulated Striatal Mu Opioid Receptor Signaling Network and OPRM1 Polymorphism in Human Heroin Abusers<\/strong>. Biological Psychiatry <\/i>74(7):511-9 (2013) PMID: 23702428<\/a><\/p>\n

Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, Clark NR, Ma’ayan \u00a0A<\/strong>. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool<\/strong>. BMC Bioinformatics<\/i> 14:128 (2013) PMID: 23586463<\/a><\/p>\n

Zhong Y, Chen EY, Liu R, Chuang PY, Mallipattu SK, Tan CM, Clark NR, Deng Y, Klotman PE, Ma’ayan A<\/strong>, He JC. Renoprotective Effect of Combined Inhibition of Angiotensin-Converting Enzyme and Histone Deacetylase<\/strong>. Journal of the American Society of Nephrology<\/i> 24(5):801-11(2013) PMID: 23559582<\/a><\/p>\n

Duan Q, Kou Y, Clark NR, Gordonov S, Ma’ayan A<\/strong>. Metasignatures identify two major subtypes of breast cancer<\/strong>. CPT: Pharmacometrics & Systems Pharmacology <\/i>2:e35 (2013) PMID: 23836026<\/a><\/p>\n

Jenkins SL, Ma’ayan A<\/strong>. Systems pharmacology meets predictive, preventive, personalized and participatory medicine<\/strong>. Pharmacogenomics<\/i> 14(2):119-22 (2013) PMID: 23327571<\/a><\/p>\n

Mallipattu SK, Liu R, Zhong Y, Chen EY, D’Agati V, Kaufman L, Ma’ayan A<\/strong>, Klotman PE, Chuang PY, He JC. Expression of HIV transgene aggravates kidney injury in diabetic mice<\/strong>. Kidney International<\/i> 83(4):626-34 (2013) PMID: 23325078<\/a><\/p>\n

\n

2012<\/h2>\n

Ma’ayan A<\/strong>. Colliding dynamical complex network models: Biological attractors versus attractors from material physics<\/strong>. Biophysical Journal<\/i> 103(9):1816-1817 (2012) PMID: 23199907<\/a><\/p>\n

Rabinowitz KM, Wang Y, Chen E, Hovhannisyan Z, Chiang D, Berin MC, Dahan S, Chaussabel D, Ma’ayan A<\/strong>, Mayer L. Transforming Growth Factor-b Signaling Controls Activities of Human Intestinal CD8 T Suppressor Cells<\/strong>. Gastroenterology<\/i> pii: S0016-5085(12)01744-1 (2012) PMID: 23232296<\/a><\/p>\n

Clavel C, Grisanti L, Zemla R, Rezza A, Barros R, Sennett R, Mazloom AR, Chung CY, Cai X, Cai CL, Pevny L, Nicolis S, Ma’ayan A<\/strong>, Rendl M. Sox2 in the Dermal Papilla Niche Controls Hair Growth by Fine-Tuning BMP Signaling in Differentiating Hair Shaft Progenitors<\/strong>. Developmental Cell<\/i> 23(5):981-94 (2012) PMID: 23153495<\/a><\/p>\n

Macarthur BD, Sevilla A, Lenz M, M\u00fcller FJ, Schuldt BM, Schuppert AA, Ridden SJ, Stumpf PS, Fidalgo M, Ma’ayan A<\/strong>, Wang J, Lemischka IR. Nanog-dependent feedback loops regulate murine embryonic stem cell heterogeneity<\/strong>. Nature Cell Biology <\/i>14(11):1139-47 (2012) PMID: 23103910<\/a><\/p>\n

Gautier EL, Shay T, Miller J, Greter M, Jakubzick C, Ivanov S, Helft J, Chow A, Elpek KG, Gordonov S, Mazloom AR, Ma’ayan A<\/strong>, Chua WJ, Hansen TH, Turley SJ, Merad M, Randolph GJ; the Immunological Genome Consortium. Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages<\/strong>. Nature Immunology<\/i> 13(11):1118-1128 (2012) PMID: 23023392<\/a><\/p>\n

Clark NR, Dannenfelser R, Tan CM, Komosinski ME, Ma’ayan A<\/strong>. Sets2Networks: network inference from repeated observations of sets<\/strong>. BMC Systems Biology<\/i> 6(1):89 (2012)\u00a0PMID 22824380<\/a><\/p>\n

Zhou Q, Lv H, Mazloom AR, Xu H, Ma’ayan A<\/strong>, Gallo JM. Activation of Alternate Pro-Survival Pathways Accounts for Acquired Sunitinib Resistance in U87MG Glioma Xenografts<\/strong>. Journal of Pharmacology and Experimental Therapeutics <\/i>343(2):509-19 (2012) PMID: 22869928<\/a><\/p>\n

Lee DF, Su J, Ang YS, Carvajal-Vergara X, Mulero-Navarro S, Pereira CF, Gingold J, Wang HL, Zhao R, Sevilla A, Darr H, Williamson AJ, Chang B, Niu X, Aguilo F, Flores ER, Sher YP, Hung MC, Whetton AD, Gelb BD, Moore KA, Snoeck HW, Ma’ayan A<\/strong>, Schaniel C, Lemischka IR. Regulation of Embryonic and Induced Pluripotency by Aurora Kinase-p53 Signaling<\/strong>. Cell Stem Cell <\/i>11(2):179-94 (2012) PMID: 22862944<\/a><\/p>\n

Dannenfelser R, Clark NR, Ma’ayan A<\/strong>. Genes2FANs: connecting genes through functional association networks<\/strong>. BMC Bioinformatics <\/i>2;13(1):156 (2012) PMID: 22748121<\/a><\/p>\n

Kou Y, Betancur C, Xu H, Buxbaum JD, Ma’ayan A<\/strong>. Network- and attribute-based classifiers can prioritize genes and pathways for autism spectrum disorders and intellectual disability<\/strong>. American Journal of \u00a0Medical Genetics Part C: Seminars in Medical Genetics <\/i>160C(2):130-42 <\/i>(2012) PMID: 22499558<\/a><\/p>\n

Neale BM, Kou Y, Liu L, Ma\u2019ayan A<\/strong>, Samocha KE et al<\/i>. Patterns and rates of exonic de novo mutations in autism spectrum disorders<\/strong>. Nature <\/i>485(7397):242-5 <\/i>(2012) PMID: 22495311<\/a><\/p>\n

Mallipattu SK, Liu R, Zheng F, Narla G, Ma’ayan A<\/strong>, Dikman S, Jain MK, Saleem M, D’Agati V, Klotman P, Chuang PY, He JC. Kruppel-Like factor 15 (KLF15) is a key regulator of podocyte differentiation<\/strong>. Journal of Biological Chemistry <\/i>287(23):19122-35 (2012) PMID: 22493483<\/a><\/p>\n

Jin Y, Ratnam K, Chuang PY, Fan Y, Zhong Y, Dai Y, Mazloom AR, Chen EY, D’Agati V, Xiong H, Ross MJ, Chen N, Ma’ayan A<\/strong>, He JC. A systems approach identifies HIPK2 as a key regulator of kidney fibrosis<\/strong>. Nature Medicine<\/i> 18(4):580-8 (2012) PMID: 22406746<\/a><\/p>\n

Rozenfeld R, Bushlin I, Gomes I, Tzavaras N, Gupta A, Neves S, Battini L, Gusella GL, Lachmann A, Ma’ayan A<\/strong>, Blitzer RD, Devi LA. Receptor heteromerization expands the repertoire of cannabinoid signaling in rodent neurons<\/strong>. PLoS One<\/i> 7(1):e29239 (2012) PMID: 22235275<\/a><\/p>\n

Chen EY, Xu H, Gordonov S, Lim MP, Perkins MH, Ma\u2019ayan A<\/strong>. Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers<\/strong>. Bioinformatics <\/i>28(1):105-11 (2012) PMID: 22080467<\/a><\/p>\n

He JC, Chuang PY, Ma’ayan A<\/strong>, Iyengar R. Systems biology of kidney diseases<\/strong>. Kidney International <\/i>81(1):22-39 (2012) PMID: 21881558<\/a><\/p>\n

Ding J, Xu H, Faiola F, Ma’ayan A<\/strong>, Wang J. Oct4 links multiple epigenetic pathways to the pluripotency network<\/strong>. Cell Research<\/i> 22(1):155-67 (2012) PMID: 22083510<\/a><\/p>\n

\n

2011<\/h2>\n

Mazloom AR, Dannenfelser R, Clark NR, Grigoryan AV, Linder KM, Cardozo TJ, Bond JC, Boran ADW, Iyengar R, Malovannaya A, Lanz RB, Ma’ayan A<\/strong>. Recovering protein-protein and domain-domain interactions from aggregation of IP-MS proteomics of coregulator complexes<\/strong>. PLoS Computational Biology<\/i> 7(12):e1002319 (2011) PMID: 22219718<\/a><\/p>\n

Xu H, Ma’ayan A<\/strong>. Visualization of Patient Samples by Dimensionality Reduction of Genome-Wide Measurements<\/strong>. Lecture Notes Computer Science<\/i> 7058:15-22 (2011)<\/a><\/p>\n

Abul-Husn NS, Annangudi SP, Ma’ayan A<\/strong>, Ramos-Ortolaza DL, Stockton SD Jr, Gomes I, Sweedler JV, Devi LA. Chronic morphine alters the presynaptic protein profile: identification of novel molecular targets using proteomics and network analysis<\/strong>. PLoS One<\/i> 6(10):e25535 (2011) PMID: 22043286<\/a><\/p>\n

Baroukh C, Jenkins SL, Dannenfelser R, Ma’ayan A<\/strong>. Genes2WordCloud: a quick way to identify biological themes from gene lists and free text<\/strong>. Source Code for Biology and Medicine<\/i> 6(1):15 (2011) PMID: \u00a021995939<\/a><\/p>\n

Ma’ayan A<\/strong>. Introduction to network analysis in systems biology<\/strong>. Science Signaling<\/i> 4(190):tr5 (2011) PMID: 21917719<\/a><\/p>\n

Clark NR, Ma’ayan A<\/strong>. Introduction to statistical methods for analyzing large data sets: gene-set enrichment analysis<\/strong>. Science Signaling<\/i> 4(190):tr4 (2011) PMID: 21917718<\/a><\/p>\n

Clark NR, Ma’ayan A<\/strong>. Introduction to statistical methods to analyze large data sets: principal components analysis<\/strong>. Science Signaling<\/i> 4(190):tr3 (2011) PMID: 21917717<\/a><\/p>\n

Dannenfelser R, Lachmann A, Szenk M, Ma’ayan A<\/strong>. FNV: Light-weight Flash-based network and pathway viewer<\/strong>. Bioinformatics<\/i> 27(8):1181-2 (2011) PMID: 21349871<\/a><\/p>\n

Webb RL, Ma’ayan A<\/strong>. Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format<\/strong>. Source Code for Biology and Medicine<\/i> 6:5 (2011) PMID: 21418653<\/a><\/p>\n

\n

2010<\/h2>\n

Xu H, Lemischka IR, Ma\u2019ayan A<\/strong>. SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells<\/strong>. BMC Systems Biology<\/i> 4(1):173 (2010) PMID: 21176149<\/a><\/p>\n

Carcea I, Ma’ayan A<\/strong>, Mesias R, Sepulveda B, Salton SR, Benson DL. Flotillin-mediated endocytic events dictate cell type-specific responses to Semaphorin 3A<\/strong>. Journal of Neuroscience<\/i> 30(45):15317-29 (2010) PMID: 21068336<\/a><\/p>\n

Lachmann A, Xu H, Krishnan J, Berger SI, Mazloom AR, Ma’ayan A<\/strong>. ChEA: Transcription factor regulation inferred from integrating genome-wide ChIP-X experiments<\/strong>. Bioinformatics<\/i> 26(19):2438-44 (2010) PMID: 20709693<\/a><\/p>\n

M\u00e9ndez-Ferrer S, Michurina TV, Ferraro F, Mazloom AR, Macarthur BD, Lira SA, Scadden DT, Ma’ayan A<\/strong>, Enikolopov GN, Frenette PS. Mesenchymal and haematopoietic stem cells form a unique bone marrow niche<\/strong>. Nature<\/i> 466(7308):829-34 (2010) PMID: 20703299<\/a><\/p>\n

Xiao K, Sun J, Kim J, Rajagopal S, Zhai B, Vill\u00e9n J, Haas W, Kovacs JJ, Shukla AK, Hara MR, Hernandez M, Lachmann A, Zhao S, Lin Y, Cheng Y, Mizuno K, Ma’ayan A<\/strong>, Gygi SP, Lefkowitz RJ. Global phosphorylation analysis of {beta}-arrestin-mediated signaling downstream of a seven transmembrane receptor (7TMR)<\/strong>. Proc Natl Acad Sci U S A<\/i> 107(34):15299-304 (2010) PMID: 20686112<\/a><\/p>\n

Ma’ayan A<\/strong>, He JC. Protein kinase target discovery from genome-wide messenger RNA expression profiling<\/strong>. Mount Sinai Journal of Medicine<\/i> 77(4):345-9 (2010) PMID: 20687179<\/a><\/p>\n

MacArthur BD, Sanchez-Garcia RJ, Ma’ayan A<\/strong>. Microdynamics and criticality of adaptive regulatory networks<\/strong>. Physical Review Letters<\/i> 104(16):168701 (2010) PMID: 20482087<\/a><\/p>\n

Berger SI, Ma’ayan A<\/strong>, Iyengar R. Systems pharmacology of arrhythmias<\/strong>. Science Signaling<\/i> 3(118):ra30 (2010)\u00a0PMID:20407125<\/a><\/p>\n

Hernandez M, Lachmann A, Zhao S, Xiao K, Ma\u2019ayan A<\/strong>. Inferring the sign of kinase-substrate interactions by combining SILAC phosphoproteomics with a literature-based mammalian kinome network<\/strong>. 10th IEEE International Conference on Bioinformatics and BioEngineering (<\/i>2010) BIBE.<\/a><\/p>\n

Xu H, Schaniel C, Lemischka IR, Ma\u2019ayan A<\/strong>. Toward a complete in-silico, multi-layered embryonic stem cell regulatory network<\/strong>. Wiley Interdisciplinary Reviews: Systems Biology and Medicine<\/i> 2(6):708-33 (2010) PMID 20890967<\/a><\/p>\n

Lachmann A, Ma\u2019ayan A<\/strong>. Lists2Networks: Integrated analysis of gene\/protein lists<\/strong>. BMC Bioinformatics<\/i> 11:87 (2010) PMID: 20152038<\/a><\/p>\n

MacArthur BD, Lachmann A, Lemischka IR, Ma\u2019ayan A<\/strong>. GATE: Software for the analysis and visualization of high-dimensional time-series expression data<\/strong>. Bioinformatics<\/i> 26(1) 143-144 (2010) PMID: 19892805<\/a><\/p>\n

\n

2009<\/h2>\n

Lu R, Markowetz F, Unwin RD, Leek JT, Airoldi EM, MacArthur BD, Lachmann A, Rozov R, Ma\u2019ayan A<\/strong>, Boyer LA, Troyanskaya OG, Whetton AD, Lemischka IR. Systems-level dynamic analyses of fate change in murine embryonic stem cells<\/strong>. Nature<\/i> 462(7271) 358-362 (2009) PMID: 19924215<\/a><\/p>\n

Cordeddu V, Di Schiavi E, Pennacchio LA, Ma’ayan A<\/strong>, Sarkozy A, Fodale V, Cecchetti S, Cardinale A, et al<\/i>. Mutation of SHOC2 promotes aberrant protein N-myristoylation and causes Noonan-like syndrome with loose anagen hair<\/strong>. Nature Genetics<\/i>. 41(9) 1022-6 (2009) PMID: 19684605<\/a><\/p>\n

MacArthur BD, Ma’ayan A<\/strong>, Lemischka IR. Systems biology of stem cell fate and cellular reprogramming<\/strong>. Nature Reviews: Molecular Cell Biology<\/i> (10) 672-81 (2009) PMID: 19738627<\/a><\/p>\n

Abul-Husn NS, Bushlin I, Mor\u00f3n JA, Jenkins SL, Dolios G, Wang R, Iyengar R, Ma\u2019ayan A<\/strong>, Devi LA. Systems approach to explore components and interactions in the presynapse<\/strong>. Proteomics<\/i> 9(12):3303-15 (2009) PMID: 19562802<\/a><\/p>\n

Lachmann A, Ma\u2019ayan A<\/strong>. KEA: Kinase enrichment analysis<\/strong>. Bioinformatics<\/i> 25(5) 684-6 (2009) PMID: 19176546<\/a><\/p>\n

Ma’ayan A<\/strong>, Jenkins SL, Barash A, Iyengar R. Neuro2A differentiation by Galphai\/o pathway<\/strong>. Science Signaling<\/i> 2(54):cm1 (2009) PMID: 19155528<\/a><\/p>\n

Ma\u2019ayan A<\/strong>, Jenkins SL, Webb RL, Berger SI, Purushothaman SP, Abul-Husn N, Posner JM, Flores T, Iyengar R. SNAVI: Desktop Application for Analysis and Visualization of Large-Scale Signaling Networks<\/strong>. BMC Systems Biology<\/i> 3;10 (2009) PMID: 19154595<\/a><\/p>\n

Ma\u2019ayan A<\/strong>. Insights into the organization of biochemical regulatory networks using graph theory analyses<\/strong>. Journal of Biological Chemistry<\/i> 284(9) 5451-5 (2009) PMID: 18940806<\/a><\/p>\n

\n

2008<\/h2>\n

Ma\u2019ayan A<\/strong>, Cecchi GA, Wagner J, Rao AR, Iyengar R, Stolovitzky G. Ordered Cyclic Motifs Contributes to Dynamic Stability in Biological and Engineered Networks<\/strong>. Proc Natl Acad Sci U\u00a0S A<\/i> 105(49) 19235-40 (2008) PMID: 19033453<\/a><\/p>\n

MacArthur BD, Ma’ayan A<\/strong>, Lemischka IR. Toward stem cell systems biology: from molecules to networks and landscapes<\/strong>. Cold Spring Harbor Symposium on Quantitative Biology<\/i> 73;211-5 (2008) PMID: 19329576<\/a><\/p>\n

Ma\u2019ayan A<\/strong>. Network integration and graph analysis in mammalian molecular systems biology.<\/strong> IET<\/i> Systems Biology<\/i> 2(5) 206-21 (2008) PMID: 19045817<\/a><\/p>\n

Lu TC, Wang Z, Feng X, Chuang P, Fang W, Chen Y, Neves S, Ma\u2019ayan A<\/strong>, Xiong H, Liu Y, Iyengar R, Klotman PE, He JC. Retinoic acid utilizes CREB and USF-1 in a transcriptional feed-forward loop in order to stimulate MKP1 expression in HIV-infected podocytes<\/strong>. Molecular and Cellular Biology <\/i>28(18) 5785-94 (2008) PMID: 18625721<\/a><\/p>\n

Bromberg KD, Ma\u2019ayan A<\/strong>, Neves SR, Iyengar R. Design of a CB1 receptor signaling network to trigger neurite outgrowth<\/strong>. Science<\/i> 320, 903-909 (2008) PMID: 18487186<\/a><\/p>\n

Ma\u2019ayan A<\/strong>, Lipshtat A, Iyengar R, Sontag ED. Proximity of Intracellular Regulatory Networks to Monotone Systems<\/strong>. IET Systems Biology<\/i> 2, 103-112 (2008) PMID: 18537452<\/a><\/p>\n

Ma’ayan A<\/strong>. PubMedAlertMe – Standalone Windows-based PubMed SDI Software<\/strong>. Computers in Biology and Medicine<\/i> 38:620-622 (2008) PMID: 18402930<\/a><\/p>\n

Lipshtat A, Purushothaman SP, Iyengar R, Ma’ayan A<\/strong>. Functions of bifans in context of multiple regulatory motifs in signaling network<\/strong>. Biophysical Journal<\/i> 94, 2566-2579 (2008) PMID: 18178648<\/a><\/p>\n

\n

2007<\/h2>\n

White AG, Ma’ayan A<\/b>. Connecting seed lists of mammalian proteins using steiner trees<\/b>. ACSSC 2007. Conference Record of the Forty-First Asilomar Conference on Signals, Systems and Computers, 2007. 4-7 Nov. 2007 page(s): 155-159 Pacific Grove, CA, USA<\/i><\/p>\n

Caplan AJ, Ma’ayan A<\/strong>, Willis IM. Multiple kinases and system robustness: A link between Cdc37 and genome integrity<\/strong>. Cell Cycle<\/i> 6:3145 (2007) PMID: 18075309<\/a><\/p>\n

Berger SI, Posner JM, Ma\u2019ayan A<\/strong>. Genes2Networks: connecting lists of proteins by using background literature-based mammalian networks<\/strong>. BMC Bioinformatics<\/i> 8:372 (2007) PMID: 17916244<\/a><\/p>\n

Berger SI, Iyengar R, Ma\u2019ayan A<\/strong>. AVIS: AJAX Viewer of Interactive Signaling Networks<\/strong>. Bioinformatics<\/i> 23, 2803-5 (2007) PMID: 17855420<\/a><\/p>\n

Zaidel-Bar R, Itzkovitz S, Ma\u2019ayan A<\/strong>, Iyengar R, Geiger B. Functional Atlas of the Integrin Adhesome<\/strong>. Nature Cell Biology<\/i> 9, 858 (2007) PMID: 17671451<\/a><\/p>\n

Ma\u2019ayan A<\/strong>, Jenkins SL, Goldfarb J, Iyengar R. Network analysis of FDA approved drugs and their targets<\/strong>. Mount Sinai Journal of Medicine<\/i> 74, 27 (2007) PMID: 17516560<\/a><\/p>\n

Hasseldine A, Lipshtat A, Iyengar R, Ma\u2019ayan A<\/b>. (2007) Modeling Cell Signaling Networks<\/b>. In \u201cBioinformatics \u2013 From Genomes to Therapies” Vol. 2 Edited by Thomas Lengauer. Pages 829- 860 (WILEY-VCH, Weinheim, Germany)<\/p>\n

\n

2006<\/h2>\n

Ma\u2019ayan A<\/strong>, Gardiner K, Iyengar R. The cognitive phenotype of Down syndrome: Insights from intracellular network analysis<\/strong>.\u00a0NeuroRx<\/i> 3, 396 (2006) PMID: 16815222<\/a><\/p>\n

Ma\u2019ayan A<\/strong>, Lipshtat A, Iyengar R. Topology of resultant signaling network shaped by evolutionary pressure<\/strong>.\u00a0Physical Review: E, Statistical, Nonlinear and Soft Matter Physics<\/i> 73, 061912 (2006) PMID: 16906869<\/a><\/p>\n

Ma\u2019ayan A<\/strong>, Iyengar R. From components to regulatory network motifs in signaling networks<\/strong>. Briefings in Functional Genomics and Proteomics <\/i>5, 57 (2006) PMID: 16769680<\/a><\/p>\n

\n

2005<\/h2>\n

Ma’ayan A<\/strong>, Blitzer RD, Iyengar R. Toward predictive models of mammalian cells<\/strong>. Annual Review of Biophysics and Biomolecular Structure <\/i>34, 319 (2005) PMID: 15869393<\/a><\/p>\n

Ma’ayan A<\/strong>, Jenkins SL, Neves S, Hasseldine A, Grace E, Dubin-Thaler B, Eungdamrong NJ, Weng G, Ram PT, Rice JJ, Kershenbaum A, Stolovitzky GA, Blitzer RD, Iyengar R. Formation of regulatory patterns during signal propagation in a Mammalian cellular network<\/strong>. Science<\/i> 309 (5737)1078 (2005) PMID: 16099987<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

Avi Ma’ayan’s Publications on PubMed\u00a0 |\u00a0Google Scholar\u00a0|\u00a0ResearchGate Featured Publication ChEA3: transcription factor enrichment analysis by orthogonal omics integration 2026 Lachmann A, Amadori L, Nicoletti P, Crane HM, Giannarelli C, Ma’ayan A, Peter I.\u00a0Transcriptional response to combination antiretroviral therapy predicts side effects and novel targets.\u00a0Frontiers in Pharmacology 16:1743543 (2026) PMID: 41646932 Evangelista JE, Clarke DJB, Byrd […]<\/p>\n","protected":false},"author":51,"featured_media":0,"parent":0,"menu_order":3,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-32","page","type-page","status-publish","hentry"],"aioseo_notices":[],"_links":{"self":[{"href":"https:\/\/labs.icahn.mssm.edu\/maayanlab\/wp-json\/wp\/v2\/pages\/32","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/labs.icahn.mssm.edu\/maayanlab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/labs.icahn.mssm.edu\/maayanlab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/maayanlab\/wp-json\/wp\/v2\/users\/51"}],"replies":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/maayanlab\/wp-json\/wp\/v2\/comments?post=32"}],"version-history":[{"count":212,"href":"https:\/\/labs.icahn.mssm.edu\/maayanlab\/wp-json\/wp\/v2\/pages\/32\/revisions"}],"predecessor-version":[{"id":3135,"href":"https:\/\/labs.icahn.mssm.edu\/maayanlab\/wp-json\/wp\/v2\/pages\/32\/revisions\/3135"}],"wp:attachment":[{"href":"https:\/\/labs.icahn.mssm.edu\/maayanlab\/wp-json\/wp\/v2\/media?parent=32"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}