Next Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline Workflows

CNVAS: Copy Number Variation Analysis System — The analysis tool for genomic alteration with a powerful visualization module

(2011) Jinho Yoo et al.   BioChip Journal

Comparative analysis of algorithms for next-generation sequencing read alignment

(2011) M. Ruffalo et al.   BIOINFORMATICS

SVA: software for annotating and visualizing sequenced human genomes

(2011) Dongliang Ge et al.   BIOINFORMATICS

Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection

(2011) Michiaki Hamada et al.   BIOINFORMATICS

Applications of the pipeline environment for visual informatics and genomics computations

(2011) Ivo D Dinov et al.   BMC BIOINFORMATICS

Next generation sequencing--implications for clinical practice

(2011) E. Raffan et al.   BRITISH MEDICAL BULLETIN

A probabilistic disease-gene finder for personal genomes

(2011) M. Yandell et al.   GENOME RESEARCH

Annotating individual human genomes

(2011) Ali Torkamani et al.   GENOMICS

The impact of next-generation sequencing on genomics

(2011) Jun Zhang et al.   Journal of Genetics and Genomics

Next-generation sequencing entering the clinical arena

(2011) Jan Haas et al.   MOLECULAR AND CELLULAR PROBES

Discovery and genotyping of genome structural polymorphism by sequencing on a population scale

(2011) Robert E Handsaker et al.   NATURE GENETICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Next generation sequencing in epigenetics: Insights and challenges

(2011) Emma Meaburn et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Testing for an Unusual Distribution of Rare Variants

(2011) Benjamin M. Neale et al.   PLoS Genetics

Savant: genome browser for high-throughput sequencing data

(2010) M. Fiume et al.   BIOINFORMATICS

High quality SNP calling using Illumina data at shallow coverage

(2010) N. Malhis et al.   BIOINFORMATICS

Genome variation discovery with high-throughput sequencing data

(2010) A. V. Dalca et al.   BRIEFINGS IN BIOINFORMATICS

Detecting copy number variation with mated short reads

(2010) P. Medvedev et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Assembly algorithms for next-generation sequencing data

(2010) Jason R. Miller et al.   GENOMICS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

A picture worth 1000 Genomes

(2010) Chris Gunter   NATURE REVIEWS GENETICS

Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries

(2010) Michal Mokry et al.   NUCLEIC ACIDS RESEARCH

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Neuroimaging Study Designs, Computational Analyses and Data Provenance Using the LONI Pipeline

(2010) Ivo Dinov et al.   PLoS One

Heterogeneity of Mitochondrial Membrane Potential: A Novel Tool to Isolate and Identify Cancer Stem Cells from a Tumor Mass?

(2010) Xiao-Qun Ye et al.   Stem Cell Reviews and Reports

The $1,000 genome, the $100,000 analysis?

(2010) Elaine R Mardis   Genome Medicine

The Characterization of Twenty Sequenced Human Genomes

(2010) Kimberly Pelak et al.   PLoS Genetics

The missing graphical user interface for genomics

(2010) Michael C Schatz   GENOME BIOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds

(2009) Yangho Chen et al.   BIOINFORMATICS

A geometric approach for classification and comparison of structural variants

(2009) S. Sindi et al.   BIOINFORMATICS

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

CNV-seq, a new method to detect copy number variation using high-throughput sequencing

(2009) Chao Xie et al.   BMC BIOINFORMATICS

Exon expression in lymphoblastoid cell lines from subjects with schizophrenia before and after glucose deprivation

(2009) Maureen V Martin et al.   BMC Medical Genomics

A probabilistic approach for SNP discovery in high-throughput human resequencing data

(2009) R. Hoberman et al.   GENOME RESEARCH

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

(2009) F. Hormozdiari et al.   GENOME RESEARCH

A SNP discovery method to assess variant allele probability from next-generation resequencing data

(2009) Y. Shen et al.   GENOME RESEARCH

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions

(2009) Seunghak Lee et al.   NATURE METHODS

Sense from sequence reads: methods for alignment and assembly

(2009) Paul Flicek et al.   NATURE METHODS

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

Web API for biology with a workflow navigation system

(2009) Y. Kwon et al.   NUCLEIC ACIDS RESEARCH

Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

(2009) R. Drmanac et al.   SCIENCE

Efficient clustered server-side data analysis workflows using SWAMP

(2009) Daniel L. Wang et al.   Earth Science Informatics

SHRiMP: Accurate Mapping of Short Color-space Reads

(2009) Stephen M. Rumble et al.   PLoS Computational Biology

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data

(2009) Jan O Korbel et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Next-Generation DNA Sequencing Methods

(2008) Elaine R. Mardis   Annual Review of Genomics and Human Genetics

ZOOM! Zillions of oligos mapped

(2008) H. Lin et al.   BIOINFORMATICS

Quality scores and SNP detection in sequencing-by-synthesis systems

(2008) W. Brockman et al.   GENOME RESEARCH

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

(2008) H. Li et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

The complete genome of an individual by massively parallel DNA sequencing

(2008) David A. Wheeler et al.   NATURE

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Rare Structural Variants Disrupt Multiple Genes in Neurodevelopmental Pathways in Schizophrenia

(2008) T. Walsh et al.   SCIENCE

The impact of next-generation sequencing technology on genetics

(2008) Elaine R. Mardis   TRENDS IN GENETICS