Mount Sinai Center for Bioinformatics


Avi Ma’ayan and the Mount Sinai Center for Bioinformatics have contributed significantly to the field of bioinformatics and their research has been reported in the top peer-reviewed journals of this field.

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 Mar 23.

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.

L1000FWD: Fireworks visualization of drug-induced transcriptomic signatures.
Wang Z, Lachmann A, Keenan AB, Ma'ayan A.
Bioinformatics 2018 Feb 6.

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

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 2017 Nov 24. pii: S2405-4712(17)30490-8.

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 2017 Nov 13.

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.

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 2017 Feb 15.

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.