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Results: 1 to 20 of 98

1.

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions.

Rashid NU, Giresi PG, Ibrahim JG, Sun W, Lieb JD.

Genome Biol. 2011 Jul 25;12(7):R67. doi: 10.1186/gb-2011-12-7-r67.

PMID:
21787385
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Systematic inference of copy-number genotypes from personal genome sequencing data reveals extensive olfactory receptor gene content diversity.

Waszak SM, Hasin Y, Zichner T, Olender T, Keydar I, Khen M, Stütz AM, Schlattl A, Lancet D, Korbel JO.

PLoS Comput Biol. 2010 Nov 11;6(11):e1000988. doi: 10.1371/journal.pcbi.1000988.

PMID:
21085617
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

A generalized linear model for peak calling in ChIP-Seq data.

Xu J, Zhang Y.

J Comput Biol. 2012 Jun;19(6):826-38. doi: 10.1089/cmb.2012.0023. Epub 2012 Apr 25.

PMID:
22533622
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

rSW-seq: algorithm for detection of copy number alterations in deep sequencing data.

Kim TM, Luquette LJ, Xi R, Park PJ.

BMC Bioinformatics. 2010 Aug 18;11:432. doi: 10.1186/1471-2105-11-432.

PMID:
20718989
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

OncoSNP-SEQ: a statistical approach for the identification of somatic copy number alterations from next-generation sequencing of cancer genomes.

Yau C.

Bioinformatics. 2013 Oct 1;29(19):2482-4. doi: 10.1093/bioinformatics/btt416. Epub 2013 Aug 7.

PMID:
23926227
[PubMed - indexed for MEDLINE]
6.

Multiscale representation of genomic signals.

Knijnenburg TA, Ramsey SA, Berman BP, Kennedy KA, Smit AF, Wessels LF, Laird PW, Aderem A, Shmulevich I.

Nat Methods. 2014 Jun;11(6):689-94. doi: 10.1038/nmeth.2924. Epub 2014 Apr 13.

PMID:
24727652
[PubMed - indexed for MEDLINE]
7.

Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion.

Xi R, Hadjipanayis AG, Luquette LJ, Kim TM, Lee E, Zhang J, Johnson MD, Muzny DM, Wheeler DA, Gibbs RA, Kucherlapati R, Park PJ.

Proc Natl Acad Sci U S A. 2011 Nov 15;108(46):E1128-36. doi: 10.1073/pnas.1110574108. Epub 2011 Nov 7.

PMID:
22065754
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

A comparison of peak callers used for DNase-Seq data.

Koohy H, Down TA, Spivakov M, Hubbard T.

PLoS One. 2014 May 8;9(5):e96303. doi: 10.1371/journal.pone.0096303. eCollection 2014.

PMID:
24810143
[PubMed - in process]
Free PMC Article
9.

Detection of rare genomic variants from pooled sequencing using SPLINTER.

Vallania F, Ramos E, Cresci S, Mitra RD, Druley TE.

J Vis Exp. 2012 Jun 23;(64). pii: 3943. doi: 10.3791/3943.

PMID:
22760212
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Quantifying copy number variations using a hidden Markov model with inhomogeneous emission distributions.

McCallum KJ, Wang JP.

Biostatistics. 2013 Jul;14(3):600-11. doi: 10.1093/biostatistics/kxt003. Epub 2013 Feb 20.

PMID:
23428932
[PubMed - indexed for MEDLINE]
11.

MochiView: versatile software for genome browsing and DNA motif analysis.

Homann OR, Johnson AD.

BMC Biol. 2010 Apr 21;8:49. doi: 10.1186/1741-7007-8-49.

PMID:
20409324
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

De novo detection of copy number variation by co-assembly.

Nijkamp JF, van den Broek MA, Geertman JM, Reinders MJ, Daran JM, de Ridder D.

Bioinformatics. 2012 Dec 15;28(24):3195-202. doi: 10.1093/bioinformatics/bts601. Epub 2012 Oct 9.

PMID:
23047563
[PubMed - indexed for MEDLINE]
Free Article
13.

Normalization, bias correction, and peak calling for ChIP-seq.

Diaz A, Park K, Lim DA, Song JS.

Stat Appl Genet Mol Biol. 2012 Mar 31;11(3):Article 9. doi: 10.1515/1544-6115.1750.

PMID:
22499706
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

A signal processing approach for enriched region detection in RNA polymerase II ChIP-seq data.

Han Z, Tian L, Pécot T, Huang T, Machiraju R, Huang K.

BMC Bioinformatics. 2012 Mar 13;13 Suppl 2:S2. doi: 10.1186/1471-2105-13-S2-S2.

PMID:
22536865
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions.

Muiño JM, Kaufmann K, van Ham RC, Angenent GC, Krajewski P.

Plant Methods. 2011 May 9;7:11. doi: 10.1186/1746-4811-7-11.

PMID:
21554688
[PubMed]
Free PMC Article
16.

Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods.

Stevens M, Cheng JB, Li D, Xie M, Hong C, Maire CL, Ligon KL, Hirst M, Marra MA, Costello JF, Wang T.

Genome Res. 2013 Sep;23(9):1541-53. doi: 10.1101/gr.152231.112. Epub 2013 Jun 26.

PMID:
23804401
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.

Jothi R, Cuddapah S, Barski A, Cui K, Zhao K.

Nucleic Acids Res. 2008 Sep;36(16):5221-31. doi: 10.1093/nar/gkn488. Epub 2008 Aug 6.

PMID:
18684996
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

CNV-seq, a new method to detect copy number variation using high-throughput sequencing.

Xie C, Tammi MT.

BMC Bioinformatics. 2009 Mar 6;10:80. doi: 10.1186/1471-2105-10-80.

PMID:
19267900
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Characterizing and interpreting genetic variation from personal genome sequencing.

Johansson AC, Feuk L.

Methods Mol Biol. 2012;838:343-67. doi: 10.1007/978-1-61779-507-7_17.

PMID:
22228021
[PubMed - indexed for MEDLINE]
20.

Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts.

Szalkowski AM, Schmid CD.

Brief Bioinform. 2011 Nov;12(6):626-33. doi: 10.1093/bib/bbq068. Epub 2010 Nov 8.

PMID:
21059603
[PubMed - indexed for MEDLINE]
Free Article

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