RummaGEO: automatic mining of human and mouse gene sets from GEO.
Marino GB, Clarke DJB, Lachmann A, Deng EZ, Ma'ayan A.
Patterns 2024 Oct 11 101072.

Multiomics2Targets identifies targets from cancer cohorts profiled with transcriptomics, proteomics, and phosphoproteomic.
Deng EZ, Marino GB, Clarke DJB, Diamant I, Resnick AC, Ma W, Wang P, Ma'ayan A.
Cell Reports Methods 2024 Aug 19;4(8):100839.

Rummagene: massive mining of gene sets from supporting materials of biomedical research publications.
Clarke DJB, Marino GB, Deng EZ, Xie Z, Evangelista JE, Ma'ayan A.
Communications Biology 2024 Apr 20;7(1):482.

Pan-cancer proteogenomics characterization of tumor immunity.
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.
Cell 2024 Feb 12:S0092-8674(24)00064-3.

D2H2: diabetes data and hypothesis hub.
Marino GB, Ahmed N, Xie Z, Jagodnik KM, Han J, Clarke DJB, Lachmann A, Keller MP, Attie AD, Ma'ayan A.
Bioinformatics Advances 2023 Dec 4;3(1):vbad178.

Toxicology knowledge graph for structural birth defects.
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.
Communications Medicine 2023 Jul 17;3(1):98.

Enrichr-KG: bridging enrichment analysis across multiple libraries.
Evangelista JE, Xie Z, Marino GB, Nguyen N, Clarke DJB, Ma'ayan A.
Nucleic Acids Research 2023 Jul 5;51(W1):W168-W179.

GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery.
Marino GB, Ngai M, Clarke DJB, Fleishman RH, Deng EZ, Xie Z, Ahmed N, Ma'ayan A.
Nucleic Acids Research 2023 Jul 5;51(W1):W213-W224.

Computational screen to identify potential targets for immunotherapeutic identification and removal of senescence cells.
Deng EZ, Fleishman RH, Xie Z, Marino GB, Clarke DJB, Ma'ayan A.
Aging Cell 2023 Jun;22(6):e13809.

lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs.
Marino GB, Wojciechowicz ML, Clarke DJB, Kuleshov MV, Xie Z, Jeon M, Lachmann A, Ma'ayan A.
Database (Oxford) 2023 Mar 4;2023:baad009.

PrismEXP: gene annotation prediction from stratified gene-gene co-expression matrices.
Lachmann A, Rizzo KA, Bartal A, Jeon M, Clarke DJB, Ma'ayan A.
PeerJ 2023 Feb 27;11:e14927.

Gene set predictor for post-treatment Lyme disease.
Clarke DJB, Rebman AW, Fan J, Soloski MJ, Aucott JN, Ma'ayan A.
Cell Reports Medicine 2022 Nov 15;3(11):100816.

A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses.
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.
Communications Biology 2022 Oct;5(1):1066.

Getting started with LINCS datasets and tools.
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.
Current Protocols 2022 Jul;2(7):e487.

SigCom LINCS: data and metadata search engine for a million gene expression signatures.
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.
Nucleic Acids Research 2022 May 7;gkac328.

PPARdelta activation induces metabolic and contractile maturation of human pluripotent stem cell-derived cardiomyocytes.
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.
Cell Stem Cell 2022 Apr 7;29(4):559-576.e7.

Transcriptomic profiling of recessive dystrophic epidermolysis bullosa wounded skin highlights drug repurposing opportunities to improve wound healing.
Onoufriadis A, Proudfoot LE, Ainali C, Torre D, Papanikolaou M, Rayinda T, Rashidghamat E, Danarti R, Mellerio JE, Ma'ayan A, McGrath JA.
Experimental Biology 2022 Mar;31(3):420-426..

DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules.
Kropiwnicki E, Lachmann A, Clarke DJB, Xie Z, Jagodnik KM, Ma'ayan A.
BMC Bioinformatics 2022 Feb 19;23(1):76.

blitzGSEA: Efficient computation of Gene Set Enrichment Analysis through Gamma distribution approximation.
Lachmann A, Xie Z, Ma'ayan A.
Bioinformatics 2022 Feb 10:btac076.

Getting started with the IDG KMC datasets and tools.
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.
Current Protocols 2022 Jan;2(1):e355.

Loss of proximal tubular transcription factor Krüppel-like factor 15 exacerbates kidney injury through loss of fatty acid oxidation.
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.
Kidney International 2021 Dec;100(6):1250-1267.

Recent progress in Lyme Disease and remaining challenges.
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.
Frontiers in Medicine 2021 Aug 18;8:666554.

KEA3: improved kinase enrichment analysis via data integration.
Kuleshov MV, Xie Z, London ABK, Yang J, Evangelista JE, Lachmann A, Shu I, Torre D, Ma'ayan A.
Nucleic Acids Research 2021 Jul 2;49(W1):W304-W316.

Krüppel-like factor 6-mediated loss of BCAA catabolism contributes to kidney injury in mice and humans.
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.
Proc Natl Acad Sci U S A. 2021 Jun 8;118(23):e2024414118.

Prioritizing pain-associated targets with machine learning.
Jeon M, Jagodnik KM, Kropiwnicki E, Stein DJ, Ma'ayan A.
Biochemistry 2021 May 11;60(18):1430-1446..

Transcriptome analysis of human dermal fibroblasts following red light phototherapy.
Austin E, Koo E, Merleev A, Torre D, Marusina A, Luxardi G, Mamalis A, Isseroff RR, Ma'ayan A, Maverakis E, Jagdeo J.
Scientific Reports 2021 Apr 1;11(1):7315.

Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning.
Kropiwnicki E, Evangelista JE, Stein DJ, Clarke DJB, Lachmann A, Kuleshov MV, Jeon M, Jagodnik KM, Ma'ayan A.
Database (Oxford) 2021 Mar 31;2021:baab017.

An Esrrb and Nanog cell fate regulatory module controlled by feed forward loop interactions.
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.
Frontiers in Cell and Developmental Biology 2021 Mar 19;9:630067.

Predicting Lyme Disease from patients' peripheral blood mononuclear cells profiled with RNA-sequencing.
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.
Frontiers in Immunology 2021 Mar 8;12:636289.

Appyters: Turning Jupyter Notebooks into data-driven web apps.
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.
Patterns 2021 Mar 4;2(3):100213.

Gene set knowledge discovery with Enrichr.
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.
Current Protocols 2021 Mar;1(3):e90.

Connectivity mapping identifies BI-2536 as a potential drug to treat diabetic kidney disease.
Zhang L, Wang Z, Liu R, Li Z, Lin J, Wojciechowicz ML, Huang J, Lee K, Ma'ayan A, He JC.
Diabetes 2020 Oct 16:db200580.

Chemokine signatures of pathogen-specific T cells I: Effector T cells.
Eberlein J, Davenport B, Nguyen TT, Victorino F, Jhun K, van der Heide V, Kuleshov M, Ma'ayan A, Kedl R, Homann D.
Journal of Immunology 2020 Oct 15;205(8):2169-2187.

Chemokine signatures of pathogen-specific T cells II: Memory T cells in acute and chronic infection.
Davenport B, Eberlein J, Nguyen TT, Victorino F, van der Heide V, Kuleshov M, Ma'ayan A, Kedl R, Homann D.
Journal of Immunology 2020 Oct 15;205(8):2188-2206.

Genetic driver mutations introduced in identical cell-of-origin in murine glioblastoma reveal distinct immune landscapes but similar response to checkpoint blockade.
Chen Z, Herting CJ, Ross JL, Gabanic B, Puigdelloses Vallcorba M, Szulzewsky F, Wojciechowicz ML, Cimino PJ, Ezhilarasan R, Sulman EP, Ying M, Ma'ayan A, Read RD, Hambardzumyan D.
Glia 2020 Oct;68(10):2148-2166.

The COVID-19 drug and gene set library.
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.
Patterns (N Y). 2020 Sep 11;1(6):100090.

GPR84: an immune response dial?
Wojciechowicz ML, Ma'ayan A.
Nature Reviews Drug Discovery 2020 Jun;19(6):374.

Towards intelligent integration and sharing of stem cell research data.
Borziak K, Qi T, Evangelista JE, Clarke DJB, Ma'ayan A, Finkelstein J.
Studies in Health Technology and Informatics 2020 Jun 26;272:334-337.

EnrichrBot: Twitter bot tracking tweets about human genes.
Bartal A, Lachmann A, Clarke DJB, Seiden AH, Jagodnik KM, Ma'ayan A.
Bioinformatics. 2020 Jun 1;36(12):3932-3934.

Interoperable RNA-Seq analysis in the cloud.
Lachmann A, Clarke DJB, Torre D, Xie Z, Ma'ayan A.
Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 2020 Jun 863(6):194521.

Memory of divisional history directs the continuous process of primitive hematopoietic lineage commitment.
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.
Stem Cell Reports. 2020 Apr 14;14(4):561-574.

Systems analysis implicates WAVE2 complex in the pathogenesis of developmental left-sided obstructive heart defect.
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.
JACC Basic to Translational Science 2020 Apr 8;5(4):376-386.

Dermal sheath contraction powers stem cell niche relocation during hair cycle regression.
Heitman N, Sennett R, Mok KW, Saxena N, Srivastava D, Martino P, Grisanti L, Wang Z, Ma'ayan A, Rompolas P, Rendl M.
Science 2020 Jan 10;367(6474):161-166.

FAIRshake: Toolkit to evaluate the FAIRness of research digital resources.
Clarke DJB, Wang L, Jones A, Wojciechowicz ML, Torre D, Jagodnik KM, Jenkins SL, McQuilton P, Flamholz Z, Silverstein MC, Schilder BM, Robasky K, Castillo C, Idaszak R, Ahalt SC, Williams J, Schurer S, Cooper DJ, de Miranda Azevedo R, Klenk JA, Haendel MA, Nedzel J, Avillach P, Shimoyama ME, Harris RM, Gamble M, Poten R, Charbonneau AL, Larkin J, Brown CT, Bonazzi VR, Dumontier MJ, Sansone SA, Ma'ayan A.
Cell Systems 2019 Nov 27;9(5):417-421.

Habenular TCF7L2 links nicotine addiction to diabetes.
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.
Nature 2019 Oct;574(7778):372-377.

Single-cell immune landscape of human atherosclerotic plaques.
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.
Nature Medicine 2019 Oct.

A multi-center study on the reproducibility of drug-response assays in mammalian cell lines.
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.
Cell Systems 2019 Jul 24;9(1):35-48.e5.

ChEA3: transcription factor enrichment analysis by orthogonal omics integration.
Keenan AB, Torre D, Lachmann A, Leong AK, Wojciechowicz ML, Utti V, Jagodnik KM, Kropiwnicki E, Wang Z, Ma'ayan A.
Nucleic Acids Research 2019 Jul 2;47(W1):W212-W224.

Geneshot: search engine for ranking genes from arbitrary text queries.
Lachmann A, Schilder BM, Wojciechowicz ML, Torre D, Kuleshov MV, Keenan AB, Ma'ayan A
Nucleic Acids Research 2019 Jul 2;47(W1):W571-W577.

modEnrichr: a suite of gene set enrichment analysis tools for model organisms.
Kuleshov MV, Diaz JEL, Flamholz ZN, Keenan AB, Lachmann A, Wojciechowicz ML, Cagan RL, Ma'ayan A.
Nucleic Acids Research 2019 Jul 2;47(W1):W183-W190.

Engineering a haematopoietic stem cell niche by revitalizing mesenchymal stromal cells.
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.
Nature Cell Biology 2019 May;21(5):560-567.

Drug Gene Budger (DGB): An application for ranking drugs to modulate a specific gene based on transcriptomic signatures.
Wang Z, He E, Sani K, Jagodnik KM, Silverstein M, Ma'ayan A.
Bioinformatics 2019 Apr 1;35(7):1247-1248.

Direct activation of PP2A for the treatment of tyrosine kinase inhibitor-resistant lung adenocarcinoma.
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.
JCI Insight 2019 Feb 21;4(4).

Mining data and metadata from the gene expression omnibus.
Wang Z, Lachmann A, Ma'ayan A.
Biophysical Reviews 2019 Feb;11(1):103-110.

Predicting opioid dependence from electronic health records with machine learning.
Ellis RJ, Wang Z, Genes N, Ma'ayan A.
BioData Mining 2019 Jan 29;12:3.

Dermal condensate niche fate specification occurs prior to formation and is placode progenitor dependent.
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.
Developmental Cell 2019 Jan 7;48(1):32-48.e5.

Far away from the lamppost.
Oprea TI, Jan L, Johnson GL, Roth BL, Ma'ayan A, Schurer S, Shoichet BK, Sklar LA, McManus MT.
PLoS Biology 2018 Dec 11;16(12):e3000067.

Temporal proteomic profiling of postnatal human cortical development.
Breen MS, Ozcan S, Ramsey JM, Wang Z, Ma'ayan A, Rustogi N, Gottschalk MG, Webster MJ, Weickert CS, Buxbaum JD, Bahn S.
Translational Psychiatry 2018 Dec 5;8(1):267.

Cooperative transcription factor induction mediates hemogenic reprogramming.
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.
Cell Reports 2018 Dec 4;25(10):2821-2835.

BioJupies: Automated generation of interactive notebooks for RNA-seq data analysis in the Cloud.
Torre D, Lachmann A, Ma'ayan A.
Cell Systems 2018 Nov 28;7(5):556-561.

SIRT6 haploinsufficiency induces BRAFV600E melanoma cell resistance to MAPK inhibitors via IGF signalling.
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.
Nature Communications 2018 Aug 24;9(1):3440.

Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning.
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.
Briefings in Bioinformatics 2018 Jul 20;19(4):656-678.

Endothelial cells instruct liver specification of embryonic stem cell-derived endoderm through endothelial VEGFR2 signaling and endoderm epigenetic modifications.
Han S, Tan C, Ding J, Wang J, Ma'ayan A, Gouon-Evans V.
Stem Cell Research 2018 Jul;30:163-170.

eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks.
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.
Nucleic Acids Research 2018 Jul 2;46(W1):W171-W179.

L1000FWD: Fireworks visualization of drug-induced transcriptomic signatures.
Wang Z, Lachmann A, Keenan AB, Ma'ayan A.
Bioinformatics 2018 Jun 15;34(12):2150-2152.

Integration of protein phosphorylation, acetylation, and methylation data sets to outline lung cancer signaling networks.
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.
Science Signaling 2018 May 22;11(531).

Unexplored therapeutic opportunities in the human genome.
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.
Nature Review Drug Discovery 2018 May;17(5):317-332.

Massive mining of publicly available RNA-seq data from human and mouse.
Lachmann A, Torre D, Keenan AB, Jagodnik KM, Lee HJ, Wang L, Silverstein MC, Ma'ayan A.
Nature Communications 2018 Apr 10;9(1):1366.

Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses.
Torre D, Krawczuk P, Jagodnik KM, Lachmann A, Wang Z, Wang L, Kuleshov MV, Ma'ayan A.
Scientific Data 2018 Feb 27;5:180023.

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

Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data.
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.
Nucleic Acids Research 2018 Jan 4;46(D1):D558-D566.

Integration of pan-cancer transcriptomics with RPPA proteomics reveals mechanisms of epithelial-mesenchymal transition.
Koplev S, Lin K, Dohlman AB, Ma'ayan A.
PLoS Computational Biology 2018 Jan 2;14(1):e1005911.

Predicting age by mining electronic medical records with deep learning characterizes differences between chronological and physiological age.
Wang Z, Li L, Glicksberg BS, Israel A, Dudley JT, Ma'ayan A.
Journal of Biomedical Informatics 2017 Nov 4. pii: S1532-0464(17)30240.

Transcriptomic analysis uncovers novel synergistic mechanisms in combination therapy for lupus nephritis.
Fu J, Wang Z, Lee K, Wei C, Liu Z, Zhang M, Zhou M, Cai M, Zhang W, Chuang PY, Ma'ayan A, He JC, Liu Z.
Kidney International 2017 Nov 1. pii: S0085-2538(17)30671-3.

Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling.
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.
Nature Communications 2017 Oct 30;8(1):1186.

Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data.
Fernandez NF, Gundersen GW, Rahman A, Grimes ML, Rikova K, Hornbeck P, Ma'ayan A.
Scientific Data 2017 Oct 10;4:170151.

Complex systems biology.
Ma'ayan A.
Journal of the Royal Society, Interface 2017 Sep;14(134).

Activation of tumor suppressor protein PP2A inhibits KRAS-driven tumor growth.
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.
Journal of Clinical Investigation 2017 Jun 1;127(6):2081-2090.

Developing a framework for digital objects in the Big Data to Knowledge (BD2K) Commons: Report from the Commons Framework Pilots Workshop.
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.
Journal of Biomedical Informatics 2017 May 10. pii: S1532-0464(17)30101-6.

Differential cytokine contributions of perivascular haematopoietic stem cell niches.
Asada N, Kunisaki Y, Pierce H, Wang Z, Fernandez NF, Birbrair A, Ma'ayan A, Frenette PS.
Nature Cell Biology 2017 Mar;19(3):214-223.

Pharos: Collating protein information to shed light on the druggable genome.
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, Schurer S, Sheils T, Simeonov A, Sklar LA, Southall N, Ursu O, Vidovic D, Waller A, Yang J, Jadhav A, Oprea TI, Guha R.
Nucleic Acids Research 2017 Jan 4;45(D1):D995-D1002.

Integrative Analysis of Sex-Specific microRNA Networks Following Stress in Mouse Nucleus Accumbens.
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.
Frontiers in  Molecular Neuroscience 2016 Dec 23;9:144.

GEN3VA: aggregation and analysis of gene expression signatures from related studies.
Gundersen GW, Jagodnik KM, Woodland H, Fernandez NF, Sani K, Dohlman AB, Ung PM, Monteiro CD, Schlessinger A, Ma'ayan A.
BMC Bioinformatics 2016 Nov 15;17(1):461. 

Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration.
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.
Nature Neuroscience 2016 Oct;19(10):1321-30.

Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd.
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, et al [...] Ma'ayan A.
Nature Communications 2016 Sep 26;7:12846.

L1000CDS2: LINCS L1000 characteristic direction signatures search engine.
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.
npj Systems Biology and Applications 2, 16015 (2016).

An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.
Wang Z, Ma'ayan A.
F1000Research 2016 Jul 5;5:1574.

The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins.
Rouillard AD, Gundersen GW, Fernandez NF, Wang Z, Monteiro CD, McDermott MG, Ma'ayan A.
Database (Oxford) 2016 Jul 3 pii: baw100.

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update.
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.
Nucleic Acids Research 2016 Jul 8;44(W1):W90-7.

Drug induced adverse events prediction with the LINCS L1000 data.
Wang Z, Clark NR, Ma'ayan A.
Bioinformatics 2016 Aug 1;32(15):2338-45.

Signaling networks among stem cell precursors, transit-amplifying progenitors, and their niche in developing hair follicles.
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.
Cell Reports 2016 Mar 18;5 pii: S2211-1247(16)30213-3.

Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain.
Scheckel C, Drapeau E, Frias MA, Park CY, Fak J, Zucker-Scharff I, Kou Y, Haroutunian V, Ma'ayan A, Buxbaum JD, Darnell RB.
eLife 2016 Feb 19;5 pii: e10421.

Integrative radiogenomic analysis for multicentric radiophenotype in glioblastoma.
Kong DS, Kim J, Lee IH, Kim ST, Seol HJ, Lee JI, Park WY, Ryu G, Wang Z, Ma'ayan A, Nam DH.
Oncotarget 2016 Mar 8;7(10):11526-38.

Fetal liver hematopoietic stem cell niches associate with portal vessels.
Khan JA, Mendelson A, Kunisaki Y, Birbrair A, Kou Y, Arnal-Estape A, Pinho S, Ciero P, Nakahara F, Ma'ayan A, Bergman A, Merad M, Frenette PS.
Science 2016 Jan 8;351(6269):176-80.

Principal Angle Enrichment Analysis (PAEA): Dimensionally reduced multivariate gene set enrichment analysis tool.
Clark NR, Szymkiewicz M, Wang Z, Monteiro CD, Jones MR, Ma'ayan A.
Proceedings (IEEE Int Conf Bioinformatics Biomed) 2015 Nov;2015:256-262.

A systems approach identifies essential FOXO3 functions at key steps of terminal erythropoiesis.
Liang R, Camprecios G, Kou Y, McGrath K, Nowak R, Catherman S, Bigarella CL, Rimmele P, Zhang X, Gnanapragasam MN, Bieker JJ, Papatsenko D, Ma'ayan A, Bresnick E, Fowler V, Palis J, Ghaffari S.
PLoS Genetics 2015 Oct 9;11(10):e1005526.

Morphine regulated synaptic networks revealed by integrated proteomics and network analysis.
Stockton SD Jr, Gomes I, Liu T, Moraje C, Hipolito L, Jones MR, Ma'ayan A, Moron JA, Li H, Devi LA.
Molecular and Cellular Proteomics 2015 Oct;14(10):2564-76.

GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions.
Gundersen GW, Jones MR, Rouillard AD, Kou Y, Monteiro CD, Feldmann AS, Hu KS, Ma'ayan A.
Bioinformatics 2015 Sep 15;31(18):3060-2.

An integrated transcriptome atlas of embryonic hair follicle progenitors, their niche, and the developing skin.
Sennett R, Wang Z, Rezza A, Grisanti L, Roitershtein N, Sicchio C, Mok KW, Heitman NJ, Clavel C, Ma'ayan A, Rendl M.
Developmental Cell 2015 Sep 14;34(5):577-91.

Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction.
Rouillard AD, Wang Z, Ma'ayan A.
Computational Biology and Chemistry 2015 Aug 18;pii: S1476-9271(15)00083-3.

Dynamics of the discovery process of protein-protein interactions from low content studies.
Wang Z, Clark NR, Ma'ayan A.
BMC Systems Biology 2015 Jun;9(1):26.

Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets.
Duan Q, Wang Z, Fernandez NF, Rouillard AD, Tan CM, Benes CH, Ma'ayan A.
Bioinformatics 2014 Nov 15;30(22):3289-90.

Histone H3.3 and its proteolytically processed form drive a cellular senescence programme.
Duarte LF, Young AR, Wang Z, Wu HA, Panda T, Kou Y, Kapoor A, Hasson D, Mills NR, Ma'ayan A, Narita M, Bernstein E.
Nature Communications 2014 Nov 14;5:5210.

A blueprint of cell identity.
Ma'ayan A, Duan Q.
Nature Biotechnology 2014 Oct;32(10):1007-8.

Lean big data integration in systems biology and systems pharmacology.
Ma'ayan A, Rouillard AD, Clark NR, Wang Z, Duan Q, Kou Y.
Trends Pharmacological Sciences 2014 Sep;35(9):450-60.

LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures.
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.
Nucleic Acids Research 2014 Jul;42:W449-60.

The characteristic direction: a geometrical approach to identify differentially expressed genes.
Clark NR, Hu KS, Feldmann AS, Kou Y, Chen EY, Duan Q, Ma'ayan A.
BMC Bioinformatics. 2014 Mar 21;15:79.