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Items: 1 to 20 of 329

1.
2.

Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data.

Teng M, Irizarry RA.

Genome Res. 2017 Nov;27(11):1930-1938. doi: 10.1101/gr.220673.117. Epub 2017 Oct 12.

PMID:
29025895
3.

Ritornello: high fidelity control-free chromatin immunoprecipitation peak calling.

Stanton KP, Jin J, Lederman RR, Weissman SM, Kluger Y.

Nucleic Acids Res. 2017 Dec 1;45(21):e173. doi: 10.1093/nar/gkx799.

4.

Data exploration, quality control and statistical analysis of ChIP-exo/nexus experiments.

Welch R, Chung D, Grass J, Landick R, Keles S.

Nucleic Acids Res. 2017 Sep 6;45(15):e145. doi: 10.1093/nar/gkx594.

5.

FOXP3 Is a HCC suppressor gene and Acts through regulating the TGF-β/Smad2/3 signaling pathway.

Shi JY, Ma LJ, Zhang JW, Duan M, Ding ZB, Yang LX, Cao Y, Zhou J, Fan J, Zhang X, Zhao YJ, Wang XY, Gao Q.

BMC Cancer. 2017 Sep 13;17(1):648. doi: 10.1186/s12885-017-3633-6.

6.

Proteins Recognizing DNA: Structural Uniqueness and Versatility of DNA-Binding Domains in Stem Cell Transcription Factors.

Yesudhas D, Batool M, Anwar MA, Panneerselvam S, Choi S.

Genes (Basel). 2017 Aug 1;8(8). pii: E192. doi: 10.3390/genes8080192. Review.

7.

Genome-wide identification of Grainy head targets in Drosophila reveals regulatory interactions with the POU domain transcription factor Vvl.

Yao L, Wang S, Westholm JO, Dai Q, Matsuda R, Hosono C, Bray S, Lai EC, Samakovlis C.

Development. 2017 Sep 1;144(17):3145-3155. doi: 10.1242/dev.143297. Epub 2017 Jul 31.

PMID:
28760809
8.

Modeling the cis-regulatory modules of genes expressed in developmental stages of Drosophila melanogaster.

López Y, Vandenbon A, Nose A, Nakai K.

PeerJ. 2017 May 30;5:e3389. doi: 10.7717/peerj.3389. eCollection 2017.

9.

Expresso: A database and web server for exploring the interaction of transcription factors and their target genes in Arabidopsis thaliana using ChIP-Seq peak data.

Aghamirzaie D, Raja Velmurugan K, Wu S, Altarawy D, Heath LS, Grene R.

F1000Res. 2017 Mar 28;6:372. doi: 10.12688/f1000research.10041.1. eCollection 2017.

10.

Mll3 and Mll4 Facilitate Enhancer RNA Synthesis and Transcription from Promoters Independently of H3K4 Monomethylation.

Dorighi KM, Swigut T, Henriques T, Bhanu NV, Scruggs BS, Nady N, Still CD 2nd, Garcia BA, Adelman K, Wysocka J.

Mol Cell. 2017 May 18;66(4):568-576.e4. doi: 10.1016/j.molcel.2017.04.018. Epub 2017 May 5.

PMID:
28483418
11.

Unrealistic phylogenetic trees may improve phylogenetic footprinting.

Nettling M, Treutler H, Cerquides J, Grosse I.

Bioinformatics. 2017 Jun 1;33(11):1639-1646. doi: 10.1093/bioinformatics/btx033.

12.

Insights into nuclear dynamics using live-cell imaging approaches.

Bigley RB, Payumo AY, Alexander JM, Huang GN.

Wiley Interdiscip Rev Syst Biol Med. 2017 Mar;9(2). doi: 10.1002/wsbm.1372. Epub 2017 Jan 12. Review.

PMID:
28078793
13.

Induced Genome-Wide Binding of Three Arabidopsis WRKY Transcription Factors during Early MAMP-Triggered Immunity.

Birkenbihl RP, Kracher B, Somssich IE.

Plant Cell. 2017 Jan;29(1):20-38. doi: 10.1105/tpc.16.00681. Epub 2016 Dec 23. Erratum in: Plant Cell. 2017 May;29(5):1175.

14.

Integrating Epigenomics into the Understanding of Biomedical Insight.

Han Y, He X.

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

15.

The Neurospora Transcription Factor ADV-1 Transduces Light Signals and Temporal Information to Control Rhythmic Expression of Genes Involved in Cell Fusion.

Dekhang R, Wu C, Smith KM, Lamb TM, Peterson M, Bredeweg EL, Ibarra O, Emerson JM, Karunarathna N, Lyubetskaya A, Azizi E, Hurley JM, Dunlap JC, Galagan JE, Freitag M, Sachs MS, Bell-Pedersen D.

G3 (Bethesda). 2017 Jan 5;7(1):129-142. doi: 10.1534/g3.116.034298.

16.

An Emerging Regulatory Landscape for Skeletal Development.

Hojo H, McMahon AP, Ohba S.

Trends Genet. 2016 Dec;32(12):774-787. doi: 10.1016/j.tig.2016.10.001. Epub 2016 Nov 1. Review.

17.

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.

18.

Differential peak calling of ChIP-seq signals with replicates with THOR.

Allhoff M, Seré K, F Pires J, Zenke M, G Costa I.

Nucleic Acids Res. 2016 Nov 16;44(20):e153. Epub 2016 Aug 2.

19.

Conserved Noncoding Elements in the Most Distant Genera of Cephalochordates: The Goldilocks Principle.

Yue JX, Kozmikova I, Ono H, Nossa CW, Kozmik Z, Putnam NH, Yu JK, Holland LZ.

Genome Biol Evol. 2016 Aug 25;8(8):2387-405. doi: 10.1093/gbe/evw158.

20.

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.

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