Literature DB >> 20676076

mrsFAST: a cache-oblivious algorithm for short-read mapping.

Faraz Hach, Fereydoun Hormozdiari, Can Alkan, Farhad Hormozdiari, Inanc Birol, Evan E Eichler, S Cenk Sahinalp.   

Abstract

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Year:  2010        PMID： 20676076      PMCID： PMC3115707          DOI： 10.1038/nmeth0810-576

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


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  6 in total

1.  Mapping short DNA sequencing reads and calling variants using mapping quality scores.

Authors:  Heng Li; Jue Ruan; Richard Durbin
Journal:  Genome Res       Date:  2008-08-19       Impact factor: 9.043

2.  RazerS--fast read mapping with sensitivity control.

Authors:  David Weese; Anne-Katrin Emde; Tobias Rausch; Andreas Döring; Knut Reinert
Journal:  Genome Res       Date:  2009-07-10       Impact factor: 9.043

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

Authors:  Fereydoun Hormozdiari; Can Alkan; Evan E Eichler; S Cenk Sahinalp
Journal:  Genome Res       Date:  2009-05-15       Impact factor: 9.043

4.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Authors:  Ben Langmead; Cole Trapnell; Mihai Pop; Steven L Salzberg
Journal:  Genome Biol       Date:  2009-03-04       Impact factor: 13.583

5.  Fast and accurate short read alignment with Burrows-Wheeler transform.

Authors:  Heng Li; Richard Durbin
Journal:  Bioinformatics       Date:  2009-05-18       Impact factor: 6.937

6.  Personalized copy number and segmental duplication maps using next-generation sequencing.

Authors:  Can Alkan; Jeffrey M Kidd; Tomas Marques-Bonet; Gozde Aksay; Francesca Antonacci; Fereydoun Hormozdiari; Jacob O Kitzman; Carl Baker; Maika Malig; Onur Mutlu; S Cenk Sahinalp; Richard A Gibbs; Evan E Eichler
Journal:  Nat Genet       Date:  2009-08-30       Impact factor: 38.330
  6 in total
  139 in total

1.  Simultaneous structural variation discovery among multiple paired-end sequenced genomes.

Authors:  Fereydoun Hormozdiari; Iman Hajirasouliha; Andrew McPherson; Evan E Eichler; S Cenk Sahinalp
Journal:  Genome Res       Date:  2011-11-02       Impact factor: 9.043

2.  Copy number variation of individual cattle genomes using next-generation sequencing.

Authors:  Derek M Bickhart; Yali Hou; Steven G Schroeder; Can Alkan; Maria Francesca Cardone; Lakshmi K Matukumalli; Jiuzhou Song; Robert D Schnabel; Mario Ventura; Jeremy F Taylor; Jose Fernando Garcia; Curtis P Van Tassell; Tad S Sonstegard; Evan E Eichler; George E Liu
Journal:  Genome Res       Date:  2012-02-02       Impact factor: 9.043

3.  Analysis of allele-specific expression in mouse liver by RNA-Seq: a comparison with Cis-eQTL identified using genetic linkage.

Authors:  Sandrine Lagarrigue; Lisa Martin; Farhad Hormozdiari; Pierre-François Roux; Calvin Pan; Atila van Nas; Olivier Demeure; Rita Cantor; Anatole Ghazalpour; Eleazar Eskin; Aldons J Lusis
Journal:  Genetics       Date:  2013-09-11       Impact factor: 4.562

4.  Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing.

Authors:  Cristian Coarfa; Fuli Yu; Christopher A Miller; Zuozhou Chen; R Alan Harris; Aleksandar Milosavljevic
Journal:  BMC Bioinformatics       Date:  2010-11-23       Impact factor: 3.169

5.  Compressive mapping for next-generation sequencing.

Authors:  Deniz Yorukoglu; Yun William Yu; Jian Peng; Bonnie Berger
Journal:  Nat Biotechnol       Date:  2016-04       Impact factor: 54.908

6.  The road from next-generation sequencing to personalized medicine.

Authors:  Manuel L Gonzalez-Garay
Journal:  Per Med       Date:  2014       Impact factor: 2.512

7.  Efficient algorithms for tandem copy number variation reconstruction in repeat-rich regions.

Authors:  Dan He; Farhad Hormozdiari; Nicholas Furlotte; Eleazar Eskin
Journal:  Bioinformatics       Date:  2011-04-19       Impact factor: 6.937

8.  Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives.

Authors:  Min Zhao; Qingguo Wang; Quan Wang; Peilin Jia; Zhongming Zhao
Journal:  BMC Bioinformatics       Date:  2013-09-13       Impact factor: 3.169

9.  Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs.

Authors:  Anna Esteve-Codina; Yogesh Paudel; Luca Ferretti; Emanuele Raineri; Hendrik-Jan Megens; Luis Silió; María C Rodríguez; Martein A M Groenen; Sebastian E Ramos-Onsins; Miguel Pérez-Enciso
Journal:  BMC Genomics       Date:  2013-03-05       Impact factor: 3.969

Review 10.  Clinical analysis and interpretation of cancer genome data.

Authors:  Eliezer M Van Allen; Nikhil Wagle; Mia A Levy
Journal:  J Clin Oncol       Date:  2013-04-15       Impact factor: 44.544
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