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Items: 1 to 20 of 56


Removing technical variability in RNA-seq data using conditional quantile normalization.

Hansen KD, Irizarry RA, Wu Z.

Biostatistics. 2012 Apr;13(2):204-16. doi: 10.1093/biostatistics/kxr054. Epub 2012 Jan 27.


Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer.

Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, Pelizzola M, Valsesia A, Ye Z, Kuan S, Edsall LE, Camargo AA, Stevenson BJ, Ecker JR, Bafna V, Strausberg RL, Simpson AJ, Ren B.

Genome Res. 2012 Feb;22(2):246-58. doi: 10.1101/gr.125872.111. Epub 2011 Dec 7.


Identification and correction of systematic error in high-throughput sequence data.

Meacham F, Boffelli D, Dhahbi J, Martin DI, Singer M, Pachter L.

BMC Bioinformatics. 2011 Nov 21;12:451. doi: 10.1186/1471-2105-12-451.


Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast.

Wilhelm BT, Marguerat S, Aligianni S, Codlin S, Watt S, Bähler J.

Genome Biol. 2011 Aug 22;12(8):R82. doi: 10.1186/gb-2011-12-8-r82.


An integrated strategy for identification of both sharp and broad peaks from next-generation sequencing data.

Peng W, Zhao K.

Genome Biol. 2011 Jul 25;12(7):120. doi: 10.1186/gb-2011-12-7-120.


Sequencing technology does not eliminate biological variability.

Hansen KD, Wu Z, Irizarry RA, Leek JT.

Nat Biotechnol. 2011 Jul 11;29(7):572-3. doi: 10.1038/nbt.1910. No abstract available.


A user's guide to the encyclopedia of DNA elements (ENCODE).

ENCODE Project Consortium.

PLoS Biol. 2011 Apr;9(4):e1001046. doi: 10.1371/journal.pbio.1001046. Epub 2011 Apr 19.


Improving RNA-Seq expression estimates by correcting for fragment bias.

Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L.

Genome Biol. 2011;12(3):R22. doi: 10.1186/gb-2011-12-3-r22. Epub 2011 Mar 16.


Identifying dispersed epigenomic domains from ChIP-Seq data.

Song Q, Smith AD.

Bioinformatics. 2011 Mar 15;27(6):870-1. doi: 10.1093/bioinformatics/btr030. Epub 2011 Feb 16.


High-resolution genome-wide mapping of the primary structure of chromatin.

Zhang Z, Pugh BF.

Cell. 2011 Jan 21;144(2):175-86. doi: 10.1016/j.cell.2011.01.003.


Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci.

Stitzel ML, Sethupathy P, Pearson DS, Chines PS, Song L, Erdos MR, Welch R, Parker SC, Boyle AP, Scott LJ; NISC Comparative Sequencing Program, Margulies EH, Boehnke M, Furey TS, Crawford GE, Collins FS.

Cell Metab. 2010 Nov 3;12(5):443-55. doi: 10.1016/j.cmet.2010.09.012. Erratum in: Cell Metab. 2010 Dec 1;12(6):683.


The NIH Roadmap Epigenomics Mapping Consortium.

Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA.

Nat Biotechnol. 2010 Oct;28(10):1045-8. doi: 10.1038/nbt1010-1045.


Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.

Goecks J, Nekrutenko A, Taylor J; Galaxy Team.

Genome Biol. 2010;11(8):R86. doi: 10.1186/gb-2010-11-8-r86. Epub 2010 Aug 25.


Evaluation of algorithm performance in ChIP-seq peak detection.

Wilbanks EG, Facciotti MT.

PLoS One. 2010 Jul 8;5(7):e11471. doi: 10.1371/journal.pone.0011471.


Transcription. Repressive transcription.

Guenther MG, Young RA.

Science. 2010 Jul 9;329(5988):150-1. doi: 10.1126/science.1193995. No abstract available.


HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data.

Qin ZS, Yu J, Shen J, Maher CA, Hu M, Kalyana-Sundaram S, Yu J, Chinnaiyan AM.

BMC Bioinformatics. 2010 Jul 2;11:369. doi: 10.1186/1471-2105-11-369.


Distinct epigenomic landscapes of pluripotent and lineage-committed human cells.

Hawkins RD, Hon GC, Lee LK, Ngo Q, Lister R, Pelizzola M, Edsall LE, Kuan S, Luu Y, Klugman S, Antosiewicz-Bourget J, Ye Z, Espinoza C, Agarwahl S, Shen L, Ruotti V, Wang W, Stewart R, Thomson JA, Ecker JR, Ren B.

Cell Stem Cell. 2010 May 7;6(5):479-91. doi: 10.1016/j.stem.2010.03.018.


Galaxy: a web-based genome analysis tool for experimentalists.

Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J.

Curr Protoc Mol Biol. 2010 Jan;Chapter 19:Unit 19.10.1-21. doi: 10.1002/0471142727.mb1910s89.


Sequencing technologies - the next generation.

Metzker ML.

Nat Rev Genet. 2010 Jan;11(1):31-46. doi: 10.1038/nrg2626. Epub 2009 Dec 8. Review.


JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles.

Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, Valen E, Yusuf D, Lenhard B, Wasserman WW, Sandelin A.

Nucleic Acids Res. 2010 Jan;38(Database issue):D105-10. doi: 10.1093/nar/gkp950. Epub 2009 Nov 11.

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