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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 MG, Monteiro CD, Gundersen GW, Ma'ayan A. Kuleshov MV, et al. Nucleic Acids Res. 2016 Jul 8;44(W1):W90-7. doi: 10.1093/nar/gkw377. Epub 2016 May 3. Nucleic Acids Res. 2016. PMID: 27141961 Free PMC article.

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Complex systems biology.

Ma'ayan A. Ma'ayan A. J R Soc Interface. 2017 Sep;14(134):20170391. doi: 10.1098/rsif.2017.0391. J R Soc Interface. 2017. PMID: 28931638 Free PMC article. Review.

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Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages.

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, Chua WJ, Hansen TH, Turley SJ, Merad M, Randolph GJ; Immunological Genome Consortium. Gautier EL, et al. Nat Immunol. 2012 Nov;13(11):1118-28. doi: 10.1038/ni.2419. Epub 2012 Sep 30. Nat Immunol. 2012. PMID: 23023392 Free PMC article.

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Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool.

Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, Clark NR, Ma'ayan A. Chen EY, et al. BMC Bioinformatics. 2013 Apr 15;14:128. doi: 10.1186/1471-2105-14-128. BMC Bioinformatics. 2013. PMID: 23586463 Free PMC article.

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Drug-induced adverse events prediction with the LINCS L1000 data.

Wang Z, Clark NR, Ma'ayan A. Wang Z, et al. Bioinformatics. 2016 Aug 1;32(15):2338-45. doi: 10.1093/bioinformatics/btw168. Epub 2016 Apr 1. Bioinformatics. 2016. PMID: 27153606 Free PMC article.

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Fetal liver hematopoietic stem cell niches associate with portal vessels.

Khan JA, Mendelson A, Kunisaki Y, Birbrair A, Kou Y, Arnal-Estapé A, Pinho S, Ciero P, Nakahara F, Ma'ayan A, Bergman A, Merad M, Frenette PS. Khan JA, et al. Science. 2016 Jan 8;351(6269):176-80. doi: 10.1126/science.aad0084. Epub 2015 Dec 3. Science. 2016. PMID: 26634440 Free PMC article.

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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. von Schimmelmann M, et al. Nat Neurosci. 2016 Oct;19(10):1321-30. doi: 10.1038/nn.4360. Epub 2016 Aug 15. Nat Neurosci. 2016. PMID: 27526204 Free PMC article.

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Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers.

Chen EY, Xu H, Gordonov S, Lim MP, Perkins MH, Ma'ayan A. Chen EY, et al. Bioinformatics. 2012 Jan 1;28(1):105-11. doi: 10.1093/bioinformatics/btr625. Epub 2011 Nov 10. Bioinformatics. 2012. PMID: 22080467 Free PMC article.

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Minimal differentiation of classical monocytes as they survey steady-state tissues and transport antigen to lymph nodes.

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, Riches DW, Yokoyama WM, Ginhoux F, Henson PM, Randolph GJ. Jakubzick C, et al. Immunity. 2013 Sep 19;39(3):599-610. doi: 10.1016/j.immuni.2013.08.007. Epub 2013 Sep 5. Immunity. 2013. PMID: 24012416 Free PMC article.

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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. Rouillard AD, et al. Database (Oxford). 2016 Jul 3;2016:baw100. doi: 10.1093/database/baw100. Print 2016. Database (Oxford). 2016. PMID: 27374120 Free PMC article.

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