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Items: 1 to 20 of 105

1.

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;2016. pii: baw100. doi: 10.1093/database/baw100. Print 2016.

2.

Krüppel-Like Factor 15 Mediates Glucocorticoid-Induced Restoration of Podocyte Differentiation Markers.

Mallipattu SK, Guo Y, Revelo MP, Roa-Peña L, Miller T, Ling J, Shankland SJ, Bialkowska AB, Ly V, Estrada C, Jain MK, Lu Y, Ma'ayan A, Mehrotra A, Yacoub R, Nord EP, Woroniecki RP, Yang VW, He JC.

J Am Soc Nephrol. 2016 Jun 10. pii: ASN.2015060672. [Epub ahead of print]

PMID:
27288011
3.

Glucocorticoid receptor isoforms direct distinct mitochondrial programs to regulate ATP production.

Morgan DJ, Poolman TM, Williamson AJ, Wang Z, Clark NR, Ma'ayan A, Whetton AD, Brass A, Matthews LC, Ray DW.

Sci Rep. 2016 May 26;6:26419. doi: 10.1038/srep26419.

4.

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

Wang Z, Clark NR, Ma'ayan A.

Bioinformatics. 2016 Apr 1. pii: btw168. [Epub ahead of print]

PMID:
27153606
5.

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.

Nucleic Acids Res. 2016 Jul 8;44(W1):W90-7. doi: 10.1093/nar/gkw377. Epub 2016 May 3.

6.

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 Rep. 2016 Mar 29;14(12):3001-18. doi: 10.1016/j.celrep.2016.02.078. Epub 2016 Mar 19.

7.

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. doi: 10.7554/eLife.10421.

8.

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. doi: 10.18632/oncotarget.7115.

9.

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.

10.

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.

Science. 2016 Jan 8;351(6269):176-80. doi: 10.1126/science.aad0084. Epub 2015 Dec 3.

11.

A Systems Approach Identifies Essential FOXO3 Functions at Key Steps of Terminal Erythropoiesis.

Liang R, Campreciós G, Kou Y, McGrath K, Nowak R, Catherman S, Bigarella CL, Rimmelé P, Zhang X, Gnanapragasam MN, Bieker JJ, Papatsenko D, Ma'ayan A, Bresnick E, Fowler V, Palis J, Ghaffari S.

PLoS Genet. 2015 Oct 9;11(10):e1005526. doi: 10.1371/journal.pgen.1005526. eCollection 2015 Oct.

12.

Reprint of "Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction".

Rouillard AD, Wang Z, Ma'ayan A.

Comput Biol Chem. 2015 Dec;59 Pt B:123-38. doi: 10.1016/j.compbiolchem.2015.08.005. Epub 2015 Aug 18. Review.

PMID:
26297300
13.

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.

Dev Cell. 2015 Sep 14;34(5):577-91. doi: 10.1016/j.devcel.2015.06.023. Epub 2015 Aug 6.

PMID:
26256211
14.

Morphine Regulated Synaptic Networks Revealed by Integrated Proteomics and Network Analysis.

Stockton SD Jr, Gomes I, Liu T, Moraje C, Hipólito L, Jones MR, Ma'ayan A, Morón JA, Li H, Devi LA.

Mol Cell Proteomics. 2015 Oct;14(10):2564-76. doi: 10.1074/mcp.M115.047977. Epub 2015 Jul 6.

PMID:
26149443
15.
16.

Dynamics of the discovery process of protein-protein interactions from low content studies.

Wang Z, Clark NR, Ma'ayan A.

BMC Syst Biol. 2015 Jun 6;9:26. doi: 10.1186/s12918-015-0173-z.

17.

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. doi: 10.1093/bioinformatics/btv297. Epub 2015 May 13.

PMID:
25971742
18.

Krüppel-like factor 6 regulates mitochondrial function in the kidney.

Mallipattu SK, Horne SJ, D'Agati V, Narla G, Liu R, Frohman MA, Dickman K, Chen EY, Ma'ayan A, Bialkowska AB, Ghaleb AM, Nandan MO, Jain MK, Daehn I, Chuang PY, Yang VW, He JC.

J Clin Invest. 2015 Mar 2;125(3):1347-61. doi: 10.1172/JCI77084. Epub 2015 Feb 17.

19.

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.

Nat Commun. 2014 Nov 14;5:5210. doi: 10.1038/ncomms6210.

20.

Synaptic, transcriptional and chromatin genes disrupted in autism.

De Rubeis S, He X, Goldberg AP, Poultney CS, Samocha K, Cicek AE, Kou Y, Liu L, Fromer M, Walker S, Singh T, Klei L, Kosmicki J, Shih-Chen F, Aleksic B, Biscaldi M, Bolton PF, Brownfeld JM, Cai J, Campbell NG, Carracedo A, Chahrour MH, Chiocchetti AG, Coon H, Crawford EL, Curran SR, Dawson G, Duketis E, Fernandez BA, Gallagher L, Geller E, Guter SJ, Hill RS, Ionita-Laza J, Jimenz Gonzalez P, Kilpinen H, Klauck SM, Kolevzon A, Lee I, Lei I, Lei J, Lehtimäki T, Lin CF, Ma'ayan A, Marshall CR, McInnes AL, Neale B, Owen MJ, Ozaki N, Parellada M, Parr JR, Purcell S, Puura K, Rajagopalan D, Rehnström K, Reichenberg A, Sabo A, Sachse M, Sanders SJ, Schafer C, Schulte-Rüther M, Skuse D, Stevens C, Szatmari P, Tammimies K, Valladares O, Voran A, Li-San W, Weiss LA, Willsey AJ, Yu TW, Yuen RK; DDD Study; Homozygosity Mapping Collaborative for Autism; UK10K Consortium, Cook EH, Freitag CM, Gill M, Hultman CM, Lehner T, Palotie A, Schellenberg GD, Sklar P, State MW, Sutcliffe JS, Walsh CA, Scherer SW, Zwick ME, Barett JC, Cutler DJ, Roeder K, Devlin B, Daly MJ, Buxbaum JD.

Nature. 2014 Nov 13;515(7526):209-15. doi: 10.1038/nature13772. Epub 2014 Oct 29.

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