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Items: 1 to 20 of 240

1.

A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE).

Wu TJ, Shamsaddini A, Pan Y, Smith K, Crichton DJ, Simonyan V, Mazumder R.

Database (Oxford). 2014 Mar 25;2014:bau022. doi: 10.1093/database/bau022. Print 2014.

2.

Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data.

Cole C, Krampis K, Karagiannis K, Almeida JS, Faison WJ, Motwani M, Wan Q, Golikov A, Pan Y, Simonyan V, Mazumder R.

BMC Bioinformatics. 2014 Jan 27;15:28. doi: 10.1186/1471-2105-15-28.

3.

SNVDis: a proteome-wide analysis service for evaluating nsSNVs in protein functional sites and pathways.

Karagiannis K, Simonyan V, Mazumder R.

Genomics Proteomics Bioinformatics. 2013 Apr;11(2):122-6. doi: 10.1016/j.gpb.2012.10.003. Epub 2012 Dec 5.

4.

High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis.

Simonyan V, Chumakov K, Dingerdissen H, Faison W, Goldweber S, Golikov A, Gulzar N, Karagiannis K, Vinh Nguyen Lam P, Maudru T, Muravitskaja O, Osipova E, Pan Y, Pschenichnov A, Rostovtsev A, Santana-Quintero L, Smith K, Thompson EE, Tkachenko V, Torcivia-Rodriguez J, Voskanian A, Wan Q, Wang J, Wu TJ, Wilson C, Mazumder R.

Database (Oxford). 2016 Mar 17;2016. pii: baw022. doi: 10.1093/database/baw022. Print 2016.

5.

CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences.

Chen X, Laudeman TW, Rushton PJ, Spraggins TA, Timko MP.

BMC Bioinformatics. 2007 Apr 19;8:129.

6.

Genetic variations and diseases in UniProtKB/Swiss-Prot: the ins and outs of expert manual curation.

Famiglietti ML, Estreicher A, Gos A, Bolleman J, Géhant S, Breuza L, Bridge A, Poux S, Redaschi N, Bougueleret L, Xenarios I; UniProt Consortium.

Hum Mutat. 2014 Aug;35(8):927-35. doi: 10.1002/humu.22594. Epub 2014 Jun 24. Review.

7.

High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis.

Simonyan V, Mazumder R.

Genes (Basel). 2014 Sep 30;5(4):957-81. doi: 10.3390/genes5040957.

8.

CRCDA--Comprehensive resources for cancer NGS data analysis.

Thangam M, Gopal RK.

Database (Oxford). 2015 Oct 8;2015. pii: bav092. doi: 10.1093/database/bav092. Print 2015.

9.

VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing.

Medina I, De Maria A, Bleda M, Salavert F, Alonso R, Gonzalez CY, Dopazo J.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W54-8. doi: 10.1093/nar/gks572. Epub 2012 Jun 11.

10.

NGS catalog: A database of next generation sequencing studies in humans.

Xia J, Wang Q, Jia P, Wang B, Pao W, Zhao Z.

Hum Mutat. 2012 Jun;33(6):E2341-55. doi: 10.1002/humu.22096. Epub 2012 Apr 19.

11.

TIARA: a database for accurate analysis of multiple personal genomes based on cross-technology.

Hong D, Park SS, Ju YS, Kim S, Shin JY, Kim S, Yu SB, Lee WC, Lee S, Park H, Kim JI, Seo JS.

Nucleic Acids Res. 2011 Jan;39(Database issue):D883-8. doi: 10.1093/nar/gkq1101. Epub 2010 Nov 4.

12.

CanProVar: a human cancer proteome variation database.

Li J, Duncan DT, Zhang B.

Hum Mutat. 2010 Mar;31(3):219-28. doi: 10.1002/humu.21176.

13.

MutAid: Sanger and NGS Based Integrated Pipeline for Mutation Identification, Validation and Annotation in Human Molecular Genetics.

Pandey RV, Pabinger S, Kriegner A, Weinhäusel A.

PLoS One. 2016 Feb 3;11(2):e0147697. doi: 10.1371/journal.pone.0147697. eCollection 2016.

14.

GrabBlur--a framework to facilitate the secure exchange of whole-exome and -genome SNV data using VCF files.

Stade B, Seelow D, Thomsen I, Krawczak M, Franke A.

BMC Genomics. 2014;15 Suppl 4:S8. doi: 10.1186/1471-2164-15-S4-S8. Epub 2014 May 20.

15.

Census-based rapid and accurate metagenome taxonomic profiling.

Shamsaddini A, Pan Y, Johnson WE, Krampis K, Shcheglovitova M, Simonyan V, Zanne A, Mazumder R.

BMC Genomics. 2014 Oct 21;15:918. doi: 10.1186/1471-2164-15-918.

16.

BamView: visualizing and interpretation of next-generation sequencing read alignments.

Carver T, Harris SR, Otto TD, Berriman M, Parkhill J, McQuillan JA.

Brief Bioinform. 2013 Mar;14(2):203-12. doi: 10.1093/bib/bbr073. Epub 2012 Jan 16.

17.

PGen: large-scale genomic variations analysis workflow and browser in SoyKB.

Liu Y, Khan SM, Wang J, Rynge M, Zhang Y, Zeng S, Chen S, Maldonado Dos Santos JV, Valliyodan B, Calyam PP, Merchant N, Nguyen HT, Xu D, Joshi T.

BMC Bioinformatics. 2016 Oct 6;17(Suppl 13):337.

18.

HIVE-hexagon: high-performance, parallelized sequence alignment for next-generation sequencing data analysis.

Santana-Quintero L, Dingerdissen H, Thierry-Mieg J, Mazumder R, Simonyan V.

PLoS One. 2014 Jun 11;9(6):e99033. doi: 10.1371/journal.pone.0099033. eCollection 2014.

19.

Structure-PPi: a module for the annotation of cancer-related single-nucleotide variants at protein-protein interfaces.

Vázquez M, Valencia A, Pons T.

Bioinformatics. 2015 Jul 15;31(14):2397-9. doi: 10.1093/bioinformatics/btv142. Epub 2015 Mar 11.

20.

ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using next generation sequence.

Blanca JM, Pascual L, Ziarsolo P, Nuez F, Cañizares J.

BMC Genomics. 2011 Jun 2;12:285. doi: 10.1186/1471-2164-12-285.

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