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Results: 1 to 20 of 86

1.

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data.

Korbel JO, Abyzov A, Mu XJ, Carriero N, Cayting P, Zhang Z, Snyder M, Gerstein MB.

Genome Biol. 2009 Feb 23;10(2):R23. doi: 10.1186/gb-2009-10-2-r23.

PMID:
19236709
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants.

Du J, Bjornson RD, Zhang ZD, Kong Y, Snyder M, Gerstein MB.

PLoS Comput Biol. 2009 Jul;5(7):e1000432. doi: 10.1371/journal.pcbi.1000432. Epub 2009 Jul 10.

PMID:
19593373
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Computational methods for discovering structural variation with next-generation sequencing.

Medvedev P, Stanciu M, Brudno M.

Nat Methods. 2009 Nov;6(11 Suppl):S13-20. doi: 10.1038/nmeth.1374. Review.

PMID:
19844226
[PubMed - indexed for MEDLINE]
4.

'PACLIMS': a component LIM system for high-throughput functional genomic analysis.

Donofrio N, Rajagopalon R, Brown D, Diener S, Windham D, Nolin S, Floyd A, Mitchell T, Galadima N, Tucker S, Orbach MJ, Patel G, Farman M, Pampanwar V, Soderlund C, Lee YH, Dean RA.

BMC Bioinformatics. 2005 Apr 12;6:94.

PMID:
15826298
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Gevab: a prototype genome variation analysis browsing server.

Kim WY, Kim SY, Kim TH, Ahn SM, Byun HN, Kim D, Kim DS, Lee YS, Ghang H, Park D, Kim BC, Kim C, Lee S, Kim SJ, Bhak J.

BMC Bioinformatics. 2009 Dec 3;10 Suppl 15:S3. doi: 10.1186/1471-2105-10-S15-S3.

PMID:
19958513
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Preparing a re-sequencing DNA library of 2 cancer candidate genes using the ligation-by-amplification protocol by two PCR reactions.

Su Y, Lin L, Tian G, Chen C, Liu T, Xu X, Qi X, Zhang X, Yang H.

Sci China C Life Sci. 2009 May;52(5):483-91. doi: 10.1007/s11427-009-0066-8. Epub 2009 May 27.

PMID:
19471873
[PubMed - indexed for MEDLINE]
7.

Protein structure computing in the genomic era.

Schwede T, Diemand A, Guex N, Peitsch MC.

Res Microbiol. 2000 Mar;151(2):107-12. Review.

PMID:
10865955
[PubMed - indexed for MEDLINE]
8.

A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case.

Yu GX, Snyder EE, Boyle SM, Crasta OR, Czar M, Mane SP, Purkayastha A, Sobral B, Setubal JC.

Nucleic Acids Res. 2007;35(12):3953-62. Epub 2007 Jun 6.

PMID:
17553834
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Automatic detection of subsystem/pathway variants in genome analysis.

Ye Y, Osterman A, Overbeek R, Godzik A.

Bioinformatics. 2005 Jun;21 Suppl 1:i478-86.

PMID:
15961494
[PubMed - indexed for MEDLINE]
Free Article
10.

PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data.

Chiu KP, Wong CH, Chen Q, Ariyaratne P, Ooi HS, Wei CL, Sung WK, Ruan Y.

BMC Bioinformatics. 2006 Aug 25;7:390.

PMID:
16934139
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

ESTPiper--a web-based analysis pipeline for expressed sequence tags.

Tang Z, Choi JH, Hemmerich C, Sarangi A, Colbourne JK, Dong Q.

BMC Genomics. 2009 Apr 21;10:174. doi: 10.1186/1471-2164-10-174.

PMID:
19383159
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Multiplex parallel pair-end-ditag sequencing approaches in system biology.

Ruan Y, Wei CL.

Wiley Interdiscip Rev Syst Biol Med. 2010 Mar-Apr;2(2):224-34. doi: 10.1002/wsbm.40. Review.

PMID:
20836024
[PubMed - indexed for MEDLINE]
13.

SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data.

Zeitouni B, Boeva V, Janoueix-Lerosey I, Loeillet S, Legoix-né P, Nicolas A, Delattre O, Barillot E.

Bioinformatics. 2010 Aug 1;26(15):1895-6. doi: 10.1093/bioinformatics/btq293.

PMID:
20639544
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

The complete genome of an individual by massively parallel DNA sequencing.

Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, Gomes X, Tartaro K, Niazi F, Turcotte CL, Irzyk GP, Lupski JR, Chinault C, Song XZ, Liu Y, Yuan Y, Nazareth L, Qin X, Muzny DM, Margulies M, Weinstock GM, Gibbs RA, Rothberg JM.

Nature. 2008 Apr 17;452(7189):872-6. doi: 10.1038/nature06884.

PMID:
18421352
[PubMed - indexed for MEDLINE]
15.

Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes.

Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC.

Genome Res. 2009 Jul;19(7):1270-8. doi: 10.1101/gr.088633.108. Epub 2009 May 15.

PMID:
19447966
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

PPD - Proteome Profile Database.

Sakharkar KR, Chow VT.

In Silico Biol. 2004;4(2):219-23.

PMID:
15107025
[PubMed - indexed for MEDLINE]
17.

mlRho - a program for estimating the population mutation and recombination rates from shotgun-sequenced diploid genomes.

Haubold B, Pfaffelhuber P, Lynch M.

Mol Ecol. 2010 Mar;19 Suppl 1:277-84. doi: 10.1111/j.1365-294X.2009.04482.x.

PMID:
20331786
[PubMed - indexed for MEDLINE]
18.

xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features.

Schlueter SD, Wilkerson MD, Dong Q, Brendel V.

Genome Biol. 2006;7(11):R111.

PMID:
17116260
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Repeat-aware modeling and correction of short read errors.

Yang X, Aluru S, Dorman KS.

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S52. doi: 10.1186/1471-2105-12-S1-S52.

PMID:
21342585
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands.

Ou HY, He X, Harrison EM, Kulasekara BR, Thani AB, Kadioglu A, Lory S, Hinton JC, Barer MR, Deng Z, Rajakumar K.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W97-W104. Epub 2007 May 30.

PMID:
17537813
[PubMed - indexed for MEDLINE]
Free PMC Article

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