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Results: 1 to 20 of 101

1.

A standard variation file format for human genome sequences.

Reese MG, Moore B, Batchelor C, Salas F, Cunningham F, Marth GT, Stein L, Flicek P, Yandell M, Eilbeck K.

Genome Biol. 2010;11(8):R88. doi: 10.1186/gb-2010-11-8-r88. Epub 2010 Aug 26.

PMID:
20796305
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

ORFer--retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files.

Büssow K, Hoffmann S, Sievert V.

BMC Bioinformatics. 2002 Dec 19;3:40. Epub 2002 Dec 19.

PMID:
12493080
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources.

Fredman D, Siegfried M, Yuan YP, Bork P, Lehväslaiho H, Brookes AJ.

Nucleic Acids Res. 2002 Jan 1;30(1):387-91.

PMID:
11752345
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

CloudMap: a cloud-based pipeline for analysis of mutant genome sequences.

Minevich G, Park DS, Blankenberg D, Poole RJ, Hobert O.

Genetics. 2012 Dec;192(4):1249-69. doi: 10.1534/genetics.112.144204. Epub 2012 Oct 10.

PMID:
23051646
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

The variant call format and VCFtools.

Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R; 1000 Genomes Project Analysis Group.

Bioinformatics. 2011 Aug 1;27(15):2156-8. doi: 10.1093/bioinformatics/btr330. Epub 2011 Jun 7.

PMID:
21653522
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment.

Habegger L, Balasubramanian S, Chen DZ, Khurana E, Sboner A, Harmanci A, Rozowsky J, Clarke D, Snyder M, Gerstein M.

Bioinformatics. 2012 Sep 1;28(17):2267-9. Epub 2012 Jun 28.

PMID:
22743228
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Ensembl 2006.

Birney E, Andrews D, Caccamo M, Chen Y, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Flicek P, Gräf S, Hammond M, Herrero J, Howe K, Iyer V, Jekosch K, Kähäri A, Kasprzyk A, Keefe D, Kokocinski F, Kulesha E, London D, Longden I, Melsopp C, Meidl P, Overduin B, Parker A, Proctor G, Prlic A, Rae M, Rios D, Redmond S, Schuster M, Sealy I, Searle S, Severin J, Slater G, Smedley D, Smith J, Stabenau A, Stalker J, Trevanion S, Ureta-Vidal A, Vogel J, White S, Woodwark C, Hubbard TJ.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D556-61.

PMID:
16381931
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

XEMBL: distributing EMBL data in XML format.

Wang L, Riethoven JJ, Robinson A.

Bioinformatics. 2002 Aug;18(8):1147-8.

PMID:
12176844
[PubMed - indexed for MEDLINE]
Free Article
9.

Interpretation errors related to the GO annotation file format.

Moreira DA, Shah NH, Musen MA.

AMIA Annu Symp Proc. 2007 Oct 11:538-42.

PMID:
18693894
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

gSearch: a fast and flexible general search tool for whole-genome sequencing.

Song T, Hwang KB, Hsing M, Lee K, Bohn J, Kong SW.

Bioinformatics. 2012 Aug 15;28(16):2176-7. doi: 10.1093/bioinformatics/bts358. Epub 2012 Jun 23.

PMID:
22730434
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

The UCSC Genome Browser Database.

Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, Weber RJ, Haussler D, Kent WJ; University of California Santa Cruz.

Nucleic Acids Res. 2003 Jan 1;31(1):51-4.

PMID:
12519945
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Human mutation databases.

Horaitis O, Cotton RG.

Curr Protoc Bioinformatics. 2005 Apr;Chapter 1:Unit 1.10. doi: 10.1002/0471250953.bi0110s9. Review.

PMID:
18428740
[PubMed - indexed for MEDLINE]
13.

Go!Poly: A gene-oriented polymorphism database.

Zhang G, Zhang S, Chen W, Qiu W, Wu H, Wang J, Luo J, Gu X, Cotton RG.

Hum Mutat. 2001 Nov;18(5):382-7.

PMID:
11668631
[PubMed - indexed for MEDLINE]
14.

Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases.

Sanderson LA, Ficklin SP, Cheng CH, Jung S, Feltus FA, Bett KE, Main D.

Database (Oxford). 2013 Oct 25;2013:bat075. doi: 10.1093/database/bat075. Print 2013.

PMID:
24163125
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Exploiting parallel R in the cloud with SPRINT.

Piotrowski M, McGilvary GA, Sloan TM, Mewissen M, Lloyd AD, Forster T, Mitchell L, Ghazal P, Hill J.

Methods Inf Med. 2013;52(1):80-90. doi: 10.3414/ME11-02-0039. Epub 2012 Dec 7.

PMID:
23223611
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

SNPper: retrieval and analysis of human SNPs.

Riva A, Kohane IS.

Bioinformatics. 2002 Dec;18(12):1681-5.

PMID:
12490454
[PubMed - indexed for MEDLINE]
Free Article
17.

EMBL-Align: a new public nucleotide and amino acid multiple sequence alignment database.

Lombard V, Camon EB, Parkinson HE, Hingamp P, Stoesser G, Redaschi N.

Bioinformatics. 2002 May;18(5):763-4.

PMID:
12050074
[PubMed - indexed for MEDLINE]
Free Article
18.

ClinVar: public archive of relationships among sequence variation and human phenotype.

Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, Maglott DR.

Nucleic Acids Res. 2014 Jan;42(Database issue):D980-5. doi: 10.1093/nar/gkt1113. Epub 2013 Nov 14.

PMID:
24234437
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server.

Ebhardt HA, Wiese KC, Unrau PJ.

BMC Bioinformatics. 2006 Apr 3;7:185.

PMID:
16584563
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Scientific LogAnalyzer: a web-based tool for analyses of server log files in psychological research.

Reips UD, Stieger S.

Behav Res Methods Instrum Comput. 2004 May;36(2):304-11.

PMID:
15354696
[PubMed - indexed for MEDLINE]

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