Related references
Note: Only part of the references are listed.Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs
Marcus Kinsella et al.
BIOINFORMATICS (2011)
Efficient algorithms for tandem copy number variation reconstruction in repeat-rich regions
Dan He et al.
BIOINFORMATICS (2011)
Identification of novel transcripts in annotated genomes using RNA-Seq
Adam Roberts et al.
BIOINFORMATICS (2011)
The struggle for life of the genome's selfish architects
Aurelie Hua-Van et al.
BIOLOGY DIRECT (2011)
Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies
Joshua Wetzel et al.
BMC BIOINFORMATICS (2011)
rnaSeqMap: a Bioconductor package for RNA sequencing data exploration
Anna Lesniewska et al.
BMC BIOINFORMATICS (2011)
De Novo Assembly of Chickpea Transcriptome Using Short Reads for Gene Discovery and Marker Identification
Rohini Garg et al.
DNA RESEARCH (2011)
Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads
Gerton Lunter et al.
GENOME RESEARCH (2011)
Genome sequence and analysis of the tuber crop potato
Xun Xu et al.
NATURE (2011)
Full-length transcriptome assembly from RNA-Seq data without a reference genome
Manfred G. Grabherr et al.
NATURE BIOTECHNOLOGY (2011)
Integrative genomics viewer
James T. Robinson et al.
NATURE BIOTECHNOLOGY (2011)
A framework for variation discovery and genotyping using next-generation DNA sequencing data
Mark A. DePristo et al.
NATURE GENETICS (2011)
Limitations of next-generation genome sequence assembly
Can Alkan et al.
NATURE METHODS (2011)
Computational methods for transcriptome annotation and quantification using RNA-seq
Manuel Garber et al.
NATURE METHODS (2011)
APPLICATIONS OF NEXT-GENERATION SEQUENCING Genome structural variation discovery and genotyping
Can Alkan et al.
NATURE REVIEWS GENETICS (2011)
Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project
Xinmeng Jasmine Mu et al.
NUCLEIC ACIDS RESEARCH (2011)
High-quality draft assemblies of mammalian genomes from massively parallel sequence data
Sante Gnerre et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Demographic history and rare allele sharing among human populations
Simon Gravel et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Exome sequencing and analysis of induced pluripotent stem cells identify the cilia-related gene male germ cell-associated kinase (MAK) as a cause of retinitis pigmentosa
Budd A. Tucker et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation
David A. Rasko et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data
Dongjun Chung et al.
PLOS COMPUTATIONAL BIOLOGY (2011)
A vertebrate case study of the quality of assemblies derived from next-generation sequences
Liang Ye et al.
GENOME BIOLOGY (2011)
Sniper: improved SNP discovery by multiply mapping deep sequenced reads
Daniel F. Simola et al.
GENOME BIOLOGY (2011)
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts
Daehwan Kim et al.
GENOME BIOLOGY (2011)
RNA-Seq gene expression estimation with read mapping uncertainty
Bo Li et al.
BIOINFORMATICS (2010)
Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery
Fereydoun Hormozdiari et al.
BIOINFORMATICS (2010)
Fast and accurate long-read alignment with Burrows-Wheeler transform
Heng Li et al.
BIOINFORMATICS (2010)
A SNP discovery method to assess variant allele probability from next-generation resequencing data
Yufeng Shen et al.
GENOME RESEARCH (2010)
Assembly of large genomes using second-generation sequencing
Michael C. Schatz et al.
GENOME RESEARCH (2010)
A map of human genome variation from population-scale sequencing
David Altshuler et al.
NATURE (2010)
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
Cole Trapnell et al.
NATURE BIOTECHNOLOGY (2010)
De novo assembly and analysis of RNA-seq data
Gordon Robertson et al.
NATURE METHODS (2010)
Advances in understanding cancer genomes through second-generation sequencing
Matthew Meyerson et al.
NATURE REVIEWS GENETICS (2010)
Detection of splice junctions from paired-end RNA-seq data by SpliceMap
Kin Fai Au et al.
NUCLEIC ACIDS RESEARCH (2010)
MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery
Kai Wang et al.
NUCLEIC ACIDS RESEARCH (2010)
Transposable element insertions have strongly affected human evolution
Roy J. Britten
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding
Dominic Schmidt et al.
SCIENCE (2010)
FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data
Andrea Sboner et al.
GENOME BIOLOGY (2010)
Statistical inferences for isoform expression in RNA-Seq
Hui Jiang et al.
BIOINFORMATICS (2009)
VarScan: variant detection in massively parallel sequencing of individual and pooled samples
Daniel C. Koboldt et al.
BIOINFORMATICS (2009)
TopHat: discovering splice junctions with RNA-Seq
Cole Trapnell et al.
BIOINFORMATICS (2009)
SOAP2: an improved ultrafast tool for short read alignment
Ruiqiang Li et al.
BIOINFORMATICS (2009)
The Sequence Alignment/Map format and SAMtools
Heng Li et al.
BIOINFORMATICS (2009)
Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver
Alayne L. Brunner et al.
GENOME RESEARCH (2009)
Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes
Fereydoun Hormozdiari et al.
GENOME RESEARCH (2009)
SNP detection for massively parallel whole-genome resequencing
Ruiqiang Li et al.
GENOME RESEARCH (2009)
Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species
David Haussler et al.
JOURNAL OF HEREDITY (2009)
Personalized copy number and segmental duplication maps using next-generation sequencing
Can Alkan et al.
NATURE GENETICS (2009)
Computational methods for discovering structural variation with next-generation sequencing
Paul Medvedev et al.
NATURE METHODS (2009)
ChIP-seq: advantages and challenges of a maturing technology
Peter J. Park
NATURE REVIEWS GENETICS (2009)
Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler
Daniel R. Zerbino et al.
PLOS ONE (2009)
BFAST: An Alignment Tool for Large Scale Genome Resequencing
Nils Homer et al.
PLOS ONE (2009)
The B73 Maize Genome: Complexity, Diversity, and Dynamics
Patrick S. Schnable et al.
SCIENCE (2009)
High tandem repeat content in the genome of the short-lived annual fish Nothobranchius furzeri: a new vertebrate model for aging research
Kathrin Reichwald et al.
GENOME BIOLOGY (2009)
The 1001 Genomes Project for Arabidopsis thaliana
Detlef Weigel et al.
GENOME BIOLOGY (2009)
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Ben Langmead et al.
GENOME BIOLOGY (2009)
Aggressive assembly of pyrosequencing reads with mates
Jason R. Miller et al.
BIOINFORMATICS (2008)
Highly integrated single-base resolution maps of the epigenome in Arabidopsis
Ryan Lister et al.
CELL (2008)
Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history
Philip M. Kim et al.
GENOME RESEARCH (2008)
Mapping short DNA sequencing reads and calling variants using mapping quality scores
Heng Li et al.
GENOME RESEARCH (2008)
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
Daniel R. Zerbino et al.
GENOME RESEARCH (2008)
Stem cell transcriptome profiling via massive-scale mRNA sequencing
Nicole Cloonan et al.
NATURE METHODS (2008)
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Ali Mortazavi et al.
NATURE METHODS (2008)
The transcriptional landscape of the yeast genome defined by RNA sequencing
Ugrappa Nagalakshmi et al.
SCIENCE (2008)
Bioinformatics challenges of new sequencing technology
Mihai Pop et al.
TRENDS IN GENETICS (2008)
Genome assembly forensics: finding the elusive mis-assembly
Adam M. Phillippy et al.
GENOME BIOLOGY (2008)
Genome-wide mapping of in vivo protein-DNA interactions
David S. Johnson et al.
SCIENCE (2007)
The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host-cell interaction genes
Nam-Hyuk Cho et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Patterns of segmental duplication in the human genome
LQ Zhang et al.
MOLECULAR BIOLOGY AND EVOLUTION (2005)
Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis
TD Read et al.
SCIENCE (2002)
Alu repeats and human genomic diversity
MA Batzer et al.
NATURE REVIEWS GENETICS (2002)
An Eulerian path approach to DNA fragment assembly
PA Pevzner et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
S Kaul et al.
NATURE (2000)