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Results: 1 to 20 of 105

Similar articles for PubMed (Select 21856738)

1.

Detecting biological network organization and functional gene orthologs.

Cui J, DeLuca TF, Jung JY, Wall DP.

Bioinformatics. 2011 Oct 15;27(20):2919-20. doi: 10.1093/bioinformatics/btr485. Epub 2011 Aug 19.

2.

PAGER: constructing PAGs and new PAG-PAG relationships for network biology.

Yue Z, Kshirsagar MM, Nguyen T, Suphavilai C, Neylon MT, Zhu L, Ratliff T, Chen JY.

Bioinformatics. 2015 Jun 15;31(12):i250-i257. doi: 10.1093/bioinformatics/btv265.

3.

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.

Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM.

Bioinformatics. 2015 Jun 9. pii: btv351. [Epub ahead of print]

PMID:
26059717
4.

DSigDB: drug signatures database for gene set analysis.

Yoo M, Shin J, Kim J, Ryall KA, Lee K, Lee S, Jeon M, Kang J, Tan AC.

Bioinformatics. 2015 May 19. pii: btv313. [Epub ahead of print]

PMID:
25990557
5.

EW_dmGWAS: edge-weighted dense module search for genome-wide association studies and gene expression profiles.

Wang Q, Yu H, Zhao Z, Jia P.

Bioinformatics. 2015 Mar 24. pii: btv150. [Epub ahead of print]

PMID:
25805723
6.

iTagPlot: an accurate computation and interactive drawing tool for tag density plot.

Kim SH, Ezenwoye O, Cho HG, Robertson KD, Choi JH.

Bioinformatics. 2015 Mar 19. pii: btv166. [Epub ahead of print]

PMID:
25792550
7.

An event-driven approach for studying gene block evolution in bacteria.

Ream DC, Bankapur AR, Friedberg I.

Bioinformatics. 2015 Jul 1;31(13):2075-83. doi: 10.1093/bioinformatics/btv128. Epub 2015 Feb 25.

8.

Detection of significant protein coevolution.

Ochoa D, Juan D, Valencia A, Pazos F.

Bioinformatics. 2015 Jul 1;31(13):2166-73. doi: 10.1093/bioinformatics/btv102. Epub 2015 Feb 24.

PMID:
25717190
9.

HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements.

Hwang YC, Lin CF, Valladares O, Malamon J, Kuksa PP, Zheng Q, Gregory BD, Wang LS.

Bioinformatics. 2015 Apr 15;31(8):1290-2. doi: 10.1093/bioinformatics/btu801. Epub 2014 Dec 4.

PMID:
25480377
10.

OrthoInspector 2.0: Software and database updates.

Linard B, Allot A, Schneider R, Morel C, Ripp R, Bigler M, Thompson JD, Poch O, Lecompte O.

Bioinformatics. 2015 Feb 1;31(3):447-8. doi: 10.1093/bioinformatics/btu642. Epub 2014 Oct 1.

PMID:
25273105
11.

COSMOS: Python library for massively parallel workflows.

Gafni E, Luquette LJ, Lancaster AK, Hawkins JB, Jung JY, Souilmi Y, Wall DP, Tonellato PJ.

Bioinformatics. 2014 Oct 15;30(20):2956-8. doi: 10.1093/bioinformatics/btu385. Epub 2014 Jun 30.

12.

Mobyle SNAP Workbench: a web-based analysis portal for population genetics and evolutionary genomics.

Monacell JT, Carbone I.

Bioinformatics. 2014 May 15;30(10):1488-90. doi: 10.1093/bioinformatics/btu055. Epub 2014 Jan 30.

13.

ClockstaR: choosing the number of relaxed-clock models in molecular phylogenetic analysis.

Duchêne S, Molak M, Ho SY.

Bioinformatics. 2014 Apr 1;30(7):1017-9. doi: 10.1093/bioinformatics/btt665. Epub 2013 Nov 14.

14.

Bayesian Network Webserver: a comprehensive tool for biological network modeling.

Ziebarth JD, Bhattacharya A, Cui Y.

Bioinformatics. 2013 Nov 1;29(21):2801-3. doi: 10.1093/bioinformatics/btt472. Epub 2013 Aug 21.

15.

CoreGenes3.5: a webserver for the determination of core genes from sets of viral and small bacterial genomes.

Turner D, Reynolds D, Seto D, Mahadevan P.

BMC Res Notes. 2013 Apr 8;6:140. doi: 10.1186/1756-0500-6-140.

16.

MCScanX-transposed: detecting transposed gene duplications based on multiple colinearity scans.

Wang Y, Li J, Paterson AH.

Bioinformatics. 2013 Jun 1;29(11):1458-60. doi: 10.1093/bioinformatics/btt150. Epub 2013 Mar 28.

17.

HAL: a hierarchical format for storing and analyzing multiple genome alignments.

Hickey G, Paten B, Earl D, Zerbino D, Haussler D.

Bioinformatics. 2013 May 15;29(10):1341-2. doi: 10.1093/bioinformatics/btt128. Epub 2013 Mar 16.

18.

Tracking recent adaptive evolution in microbial species using TimeZone.

Chattopadhyay S, Paul S, Dykhuizen DE, Sokurenko EV.

Nat Protoc. 2013 Apr;8(4):652-65. doi: 10.1038/nprot.2013.031. Epub 2013 Mar 7.

PMID:
23471110
19.

MetaMicrobesOnline: phylogenomic analysis of microbial communities.

Chivian D, Dehal PS, Keller K, Arkin AP.

Nucleic Acids Res. 2013 Jan;41(Database issue):D648-54. doi: 10.1093/nar/gks1202. Epub 2012 Nov 30.

20.

OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis.

Whiteside MD, Winsor GL, Laird MR, Brinkman FS.

Nucleic Acids Res. 2013 Jan;41(Database issue):D366-76. doi: 10.1093/nar/gks1241. Epub 2012 Nov 29.

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