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Items: 1 to 20 of 213

1.

AnnTools: a comprehensive and versatile annotation toolkit for genomic variants.

Makarov V, O'Grady T, Cai G, Lihm J, Buxbaum JD, Yoon S.

Bioinformatics. 2012 Mar 1;28(5):724-5. doi: 10.1093/bioinformatics/bts032. Epub 2012 Jan 18.

2.

Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools.

San Lucas FA, Wang G, Scheet P, Peng B.

Bioinformatics. 2012 Feb 1;28(3):421-2. doi: 10.1093/bioinformatics/btr667. Epub 2011 Dec 2.

3.

CNVannotator: a comprehensive annotation server for copy number variation in the human genome.

Zhao M, Zhao Z.

PLoS One. 2013 Nov 14;8(11):e80170. doi: 10.1371/journal.pone.0080170. eCollection 2013.

4.

Impacts of variation in the human genome on gene regulation.

Haraksingh RR, Snyder MP.

J Mol Biol. 2013 Nov 1;425(21):3970-7. doi: 10.1016/j.jmb.2013.07.015. Epub 2013 Jul 16. Review.

5.

CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics.

Gai X, Perin JC, Murphy K, O'Hara R, D'arcy M, Wenocur A, Xie HM, Rappaport EF, Shaikh TH, White PS.

BMC Bioinformatics. 2010 Feb 4;11:74. doi: 10.1186/1471-2105-11-74.

6.

Copy number variations in the genome of the Qatari population.

Fakhro KA, Yousri NA, Rodriguez-Flores JL, Robay A, Staudt MR, Agosto-Perez F, Salit J, Malek JA, Suhre K, Jayyousi A, Zirie M, Stadler D, Mezey JG, Crystal RG.

BMC Genomics. 2015 Oct 22;16:834. doi: 10.1186/s12864-015-1991-5.

7.

SG-ADVISER CNV: copy-number variant annotation and interpretation.

Erikson GA, Deshpande N, Kesavan BG, Torkamani A.

Genet Med. 2015 Sep;17(9):714-8. doi: 10.1038/gim.2014.180. Epub 2014 Dec 18.

8.

SNiPA: an interactive, genetic variant-centered annotation browser.

Arnold M, Raffler J, Pfeufer A, Suhre K, Kastenmüller G.

Bioinformatics. 2015 Apr 15;31(8):1334-6. doi: 10.1093/bioinformatics/btu779. Epub 2014 Nov 26.

9.

SNPnexus: a web server for functional annotation of novel and publicly known genetic variants (2012 update).

Dayem Ullah AZ, Lemoine NR, Chelala C.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W65-70. doi: 10.1093/nar/gks364. Epub 2012 Apr 28.

10.

FEATnotator: A tool for integrated annotation of sequence features and variation, facilitating interpretation in genomics experiments.

Podicheti R, Mockaitis K.

Methods. 2015 Jun;79-80:11-7. doi: 10.1016/j.ymeth.2015.04.028. Epub 2015 Apr 29.

PMID:
25934264
11.

BIOFILTER AS A FUNCTIONAL ANNOTATION PIPELINE FOR COMMON AND RARE COPY NUMBER BURDEN.

Kim D, Lucas A, Glessner J, Verma SS, Bradford Y, Li R, Frase AT, Hakonarson H, Peissig P, Brilliant M, Ritchie MD.

Pac Symp Biocomput. 2016;21:357-68.

12.

SpeedSeq: ultra-fast personal genome analysis and interpretation.

Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, Marth GT, Quinlan AR, Hall IM.

Nat Methods. 2015 Oct;12(10):966-8. doi: 10.1038/nmeth.3505. Epub 2015 Aug 10.

13.

Genovar: a detection and visualization tool for genomic variants.

Jung KS, Moon S, Kim YJ, Kim BJ, Park K.

BMC Bioinformatics. 2012 May 8;13 Suppl 7:S12. doi: 10.1186/1471-2105-13-S7-S12.

14.

AVIA v2.0: annotation, visualization and impact analysis of genomic variants and genes.

Vuong H, Che A, Ravichandran S, Luke BT, Collins JR, Mudunuri US.

Bioinformatics. 2015 Aug 15;31(16):2748-50. doi: 10.1093/bioinformatics/btv200. Epub 2015 Apr 9.

15.

A variant by any name: quantifying annotation discordance across tools and clinical databases.

Yen JL, Garcia S, Montana A, Harris J, Chervitz S, Morra M, West J, Chen R, Church DM.

Genome Med. 2017 Jan 26;9(1):7. doi: 10.1186/s13073-016-0396-7.

16.

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.

17.

Whole-genome sequencing and genetic variant analysis of a Quarter Horse mare.

Doan R, Cohen ND, Sawyer J, Ghaffari N, Johnson CD, Dindot SV.

BMC Genomics. 2012 Feb 17;13:78. doi: 10.1186/1471-2164-13-78.

18.

The personal genome browser: visualizing functions of genetic variants.

Juan L, Teng M, Zang T, Hao Y, Wang Z, Yan C, Liu Y, Li J, Zhang T, Wang Y.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W192-7. doi: 10.1093/nar/gku361. Epub 2014 May 5.

19.

Annotation of functional variation in personal genomes using RegulomeDB.

Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, Karczewski KJ, Park J, Hitz BC, Weng S, Cherry JM, Snyder M.

Genome Res. 2012 Sep;22(9):1790-7. doi: 10.1101/gr.137323.112.

20.

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data.

Boeva V, Popova T, Bleakley K, Chiche P, Cappo J, Schleiermacher G, Janoueix-Lerosey I, Delattre O, Barillot E.

Bioinformatics. 2012 Feb 1;28(3):423-5. doi: 10.1093/bioinformatics/btr670. Epub 2011 Dec 6.

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