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Items: 1 to 20 of 72

1.

NSeq: a multithreaded Java application for finding positioned nucleosomes from sequencing data.

Nellore A, Bobkov K, Howe E, Pankov A, Diaz A, Song JS.

Front Genet. 2013 Jan 11;3:320. doi: 10.3389/fgene.2012.00320. eCollection 2012.

2.

CloudDOE: a user-friendly tool for deploying Hadoop clouds and analyzing high-throughput sequencing data with MapReduce.

Chung WC, Chen CC, Ho JM, Lin CY, Hsu WL, Wang YC, Lee DT, Lai F, Huang CW, Chang YJ.

PLoS One. 2014 Jun 4;9(6):e98146. doi: 10.1371/journal.pone.0098146. eCollection 2014.

3.

PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data.

Woo S, Zhang X, Sauteraud R, Robert F, Gottardo R.

Bioinformatics. 2013 Aug 15;29(16):2049-50. doi: 10.1093/bioinformatics/btt348. Epub 2013 Jun 20.

4.

Modeling nucleosome position distributions from experimental nucleosome positioning maps.

Schöpflin R, Teif VB, Müller O, Weinberg C, Rippe K, Wedemann G.

Bioinformatics. 2013 Oct 1;29(19):2380-6. doi: 10.1093/bioinformatics/btt404. Epub 2013 Jul 11.

PMID:
23846748
5.

DNA structural patterns and nucleosome positioning.

Staffelbach H, Koller T, Burks C.

J Biomol Struct Dyn. 1994 Oct;12(2):301-25.

PMID:
7702771
6.

Improved nucleosome-positioning algorithm iNPS for accurate nucleosome positioning from sequencing data.

Chen W, Liu Y, Zhu S, Green CD, Wei G, Han JD.

Nat Commun. 2014 Sep 18;5:4909. doi: 10.1038/ncomms5909.

PMID:
25233085
7.

Archaeal nucleosome positioning in vivo and in vitro is directed by primary sequence motifs.

Nalabothula N, Xi L, Bhattacharyya S, Widom J, Wang JP, Reeve JN, Santangelo TJ, Fondufe-Mittendorf YN.

BMC Genomics. 2013 Jun 10;14:391. doi: 10.1186/1471-2164-14-391.

8.

Fuento: functional enrichment for bioinformatics.

Weichselbaum D, Zagrovic B, Polyansky AA.

Bioinformatics. 2017 Aug 15;33(16):2604-2606. doi: 10.1093/bioinformatics/btx179.

PMID:
28379299
9.

DiNuP: a systematic approach to identify regions of differential nucleosome positioning.

Fu K, Tang Q, Feng J, Liu XS, Zhang Y.

Bioinformatics. 2012 Aug 1;28(15):1965-71. doi: 10.1093/bioinformatics/bts329. Epub 2012 Jun 4.

10.

Realtime analysis and visualization of MinION sequencing data with npReader.

Cao MD, Ganesamoorthy D, Cooper MA, Coin LJ.

Bioinformatics. 2016 Mar 1;32(5):764-6. doi: 10.1093/bioinformatics/btv658. Epub 2015 Nov 10.

PMID:
26556383
11.

DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra.

Muth T, Weilnböck L, Rapp E, Huber CG, Martens L, Vaudel M, Barsnes H.

J Proteome Res. 2014 Feb 7;13(2):1143-6. doi: 10.1021/pr4008078. Epub 2014 Jan 7.

12.

SDAR: a practical tool for graphical analysis of two-dimensional data.

Weeratunga S, Hu NJ, Simon A, Hofmann A.

BMC Bioinformatics. 2012 Aug 14;13:201. doi: 10.1186/1471-2105-13-201.

13.

CODOC: efficient access, analysis and compression of depth of coverage signals.

Popitsch N.

Bioinformatics. 2014 Sep 15;30(18):2676-7. doi: 10.1093/bioinformatics/btu362. Epub 2014 May 28.

PMID:
24872424
14.

Jannovar: a java library for exome annotation.

Jäger M, Wang K, Bauer S, Smedley D, Krawitz P, Robinson PN.

Hum Mutat. 2014 May;35(5):548-55. doi: 10.1002/humu.22531. Epub 2014 Apr 9.

PMID:
24677618
15.

Brain: biomedical knowledge manipulation.

Croset S, Overington JP, Rebholz-Schuhmann D.

Bioinformatics. 2013 May 1;29(9):1238-9. doi: 10.1093/bioinformatics/btt109. Epub 2013 Mar 16.

16.

NucleoFinder: a statistical approach for the detection of nucleosome positions.

Becker J, Yau C, Hancock JM, Holmes CC.

Bioinformatics. 2013 Mar 15;29(6):711-6. doi: 10.1093/bioinformatics/bts719. Epub 2013 Jan 6.

17.

StreamingTrim 1.0: a Java software for dynamic trimming of 16S rRNA sequence data from metagenetic studies.

Bacci G, Bazzicalupo M, Benedetti A, Mengoni A.

Mol Ecol Resour. 2014 Mar;14(2):426-34. doi: 10.1111/1755-0998.12187. Epub 2013 Nov 16.

PMID:
24128146
18.

nuScore: a web-interface for nucleosome positioning predictions.

Tolstorukov MY, Choudhary V, Olson WK, Zhurkin VB, Park PJ.

Bioinformatics. 2008 Jun 15;24(12):1456-8. doi: 10.1093/bioinformatics/btn212. Epub 2008 Apr 29.

19.

Combined micrococcal nuclease and exonuclease III digestion reveals precise positions of the nucleosome core/linker junctions: implications for high-resolution nucleosome mapping.

Nikitina T, Wang D, Gomberg M, Grigoryev SA, Zhurkin VB.

J Mol Biol. 2013 Jun 12;425(11):1946-60. doi: 10.1016/j.jmb.2013.02.026. Epub 2013 Feb 28.

PMID:
23458408
20.

Nucleosome positioning in relation to nucleosome spacing and DNA sequence-specific binding of a protein.

Pusarla RH, Vinayachandran V, Bhargava P.

FEBS J. 2007 May;274(9):2396-410. Epub 2007 Apr 5.

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