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Items: 1 to 20 of 270

1.

Integrating Epigenomics into the Understanding of Biomedical Insight.

Han Y, He X.

Bioinform Biol Insights. 2016 Dec 4;10:267-289. Review.

2.

Quantitative analysis of ChIP-seq data uncovers dynamic and sustained H3K4me3 and H3K27me3 modulation in cancer cells under hypoxia.

Adriaens ME, Prickaerts P, Chan-Seng-Yue M, van den Beucken T, Dahlmans VE, Eijssen LM, Beck T, Wouters BG, Voncken JW, Evelo CT.

Epigenetics Chromatin. 2016 Nov 1;9:48.

3.

Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus.

Hansen P, Hecht J, Ibn-Salem J, Menkuec BS, Roskosch S, Truss M, Robinson PN.

BMC Genomics. 2016 Nov 4;17(1):873.

5.

Deregulation of DUX4 and ERG in acute lymphoblastic leukemia.

Zhang J, McCastlain K, Yoshihara H, Xu B, Chang Y, Churchman ML, Wu G, Li Y, Wei L, Iacobucci I, Liu Y, Qu C, Wen J, Edmonson M, Payne-Turner D, Kaufmann KB, Takayanagi SI, Wienholds E, Waanders E, Ntziachristos P, Bakogianni S, Wang J, Aifantis I, Roberts KG, Ma J, Song G, Easton J, Mulder HL, Chen X, Newman S, Ma X, Rusch M, Gupta P, Boggs K, Vadodaria B, Dalton J, Liu Y, Valentine ML, Ding L, Lu C, Fulton RS, Fulton L, Tabib Y, Ochoa K, Devidas M, Pei D, Cheng C, Yang J, Evans WE, Relling MV, Pui CH, Jeha S, Harvey RC, Chen IL, Willman CL, Marcucci G, Bloomfield CD, Kohlschmidt J, Mrózek K, Paietta E, Tallman MS, Stock W, Foster MC, Racevskis J, Rowe JM, Luger S, Kornblau SM, Shurtleff SA, Raimondi SC, Mardis ER, Wilson RK, Dick JE, Hunger SP, Loh ML, Downing JR, Mullighan CG; St. Jude Children's Research Hospital–Washington University Pediatric Cancer Genome Project..

Nat Genet. 2016 Dec;48(12):1481-1489. doi: 10.1038/ng.3691.

PMID:
27776115
6.

Evidence for Direct Control of Virulence and Defense Gene Circuits by the Pseudomonas aeruginosa Quorum Sensing Regulator, MvfR.

Maura D, Hazan R, Kitao T, Ballok AE, Rahme LG.

Sci Rep. 2016 Sep 28;6:34083. doi: 10.1038/srep34083.

7.

systemPipeR: NGS workflow and report generation environment.

H Backman TW, Girke T.

BMC Bioinformatics. 2016 Sep 20;17:388. doi: 10.1186/s12859-016-1241-0.

8.

Complex Patterns of Association between Pleiotropy and Transcription Factor Evolution.

Chesmore KN, Bartlett J, Cheng C, Williams SM.

Genome Biol Evol. 2016 Oct 23;8(10):3159-3170.

9.

PAtCh-Cap: input strategy for improving analysis of ChIP-exo data sets and beyond.

Terooatea TW, Pozner A, Buck-Koehntop BA.

Nucleic Acids Res. 2016 Dec 1;44(21):e159.

10.

iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data.

Yang CC, Andrews EH, Chen MH, Wang WY, Chen JJ, Gerstein M, Liu CC, Cheng C.

BMC Genomics. 2016 Aug 12;17(1):632. doi: 10.1186/s12864-016-2963-0.

11.

Expansion of GA Dinucleotide Repeats Increases the Density of CLAMP Binding Sites on the X-Chromosome to Promote Drosophila Dosage Compensation.

Kuzu G, Kaye EG, Chery J, Siggers T, Yang L, Dobson JR, Boor S, Bliss J, Liu W, Jogl G, Rohs R, Singh ND, Bulyk ML, Tolstorukov MY, Larschan E.

PLoS Genet. 2016 Jul 14;12(7):e1006120. doi: 10.1371/journal.pgen.1006120.

12.

Regulation of WNT Signaling by VSX2 During Optic Vesicle Patterning in Human Induced Pluripotent Stem Cells.

Capowski EE, Wright LS, Liang K, Phillips MJ, Wallace K, Petelinsek A, Hagstrom A, Pinilla I, Borys K, Lien J, Min JH, Keles S, Thomson JA, Gamm DM.

Stem Cells. 2016 Jun 14. doi: 10.1002/stem.2414. [Epub ahead of print]

PMID:
27301076
13.

Identifying peaks in *-seq data using shape information.

Strino F, Lappe M.

BMC Bioinformatics. 2016 Jun 6;17 Suppl 5:206. doi: 10.1186/s12859-016-1042-5.

14.

Comprehensive analysis of promoter-proximal RNA polymerase II pausing across mammalian cell types.

Day DS, Zhang B, Stevens SM, Ferrari F, Larschan EN, Park PJ, Pu WT.

Genome Biol. 2016 Jun 3;17(1):120. doi: 10.1186/s13059-016-0984-2.

15.

The Transcriptional Activator Krüppel-like Factor-6 Is Required for CNS Myelination.

Laitman BM, Asp L, Mariani JN, Zhang J, Liu J, Sawai S, Chapouly C, Horng S, Kramer EG, Mitiku N, Loo H, Burlant N, Pedre X, Hara Y, Nudelman G, Zaslavsky E, Lee YM, Braun DA, Lu QR, Narla G, Raine CS, Friedman SL, Casaccia P, John GR.

PLoS Biol. 2016 May 23;14(5):e1002467. doi: 10.1371/journal.pbio.1002467.

16.

LOGIQA: a database dedicated to long-range genome interactions quality assessment.

Mendoza-Parra MA, Blum M, Malysheva V, Cholley PE, Gronemeyer H.

BMC Genomics. 2016 May 16;17:355. doi: 10.1186/s12864-016-2642-1.

17.

DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies.

Chabbert CD, Steinmetz LM, Klaus B.

PeerJ. 2016 Apr 26;4:e1981. doi: 10.7717/peerj.1981.

18.

The Role of Genome Accessibility in Transcription Factor Binding in Bacteria.

Gomes AL, Wang HH.

PLoS Comput Biol. 2016 Apr 22;12(4):e1004891. doi: 10.1371/journal.pcbi.1004891.

19.

Laminopathies disrupt epigenomic developmental programs and cell fate.

Perovanovic J, Dell'Orso S, Gnochi VF, Jaiswal JK, Sartorelli V, Vigouroux C, Mamchaoui K, Mouly V, Bonne G, Hoffman EP.

Sci Transl Med. 2016 Apr 20;8(335):335ra58. doi: 10.1126/scitranslmed.aad4991.

20.

Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples.

Snyder-Mackler N, Majoros WH, Yuan ML, Shaver AO, Gordon JB, Kopp GH, Schlebusch SA, Wall JD, Alberts SC, Mukherjee S, Zhou X, Tung J.

Genetics. 2016 Jun;203(2):699-714. doi: 10.1534/genetics.116.187492.

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