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云之南

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专业背景:计算机科学 研究方向与兴趣: JavaEE-Web软件开发, 生物信息学, 数据挖掘与机器学习, 智能信息系统 目前工作: 基因组, 转录组, NGS高通量数据分析, 生物数据挖掘, 植物系统发育和比较进化基因组学

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Next Generation Sequencing(Oxford Journal bioinformatics)  

2010-01-07 13:11:25|  分类: 生信分析软件 |  标签: |举报 |字号 订阅

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http://www.oxfordjournals.org/our_journals/bioinformatics/nextgenerationsequencing.html

 

Next Generation Sequencing

Next-generation sequencing technologies are revolutionising genomics and their effects are becoming increasingly widespread. Many tools and algorithms relevant to next-generation sequencing applications have been published in Bioinformatics, and so to celebrate this contribution we have gathered these together in this 'Bioinformatics for Next Generation Sequencing' virtual issue. This will be a living resource that we will continually update to include the very latest papers in this area to help researchers keep abreast of the latest developments.

Editorial -Bioinformatics for Next Generation Sequencing

Alex Bateman and John Quackenbush

Bioinformatics (2009) 25: 429 Full Text

A Report on the 2009 SIG on Short Read Sequencing and Algorithms (Short-SIG)

Michael Brudno et al.

Bioinformatics (2009) 25: 2863–2864 Full Text

Alignment

Optimal spliced alignments of short sequence reads

Fabio De Bona et al.

Bioinformatics (2008) 24: i174-80 Full Text

PatMaN: rapid alignment of short sequences to large databases

Kay Prüfer et al.

Bioinformatics (2008) 24: 1530-1 Full Text

SeqMap: mapping massive amount of oligonucleotides to the genome

Hui Jiang and Wing Wong

Bioinformatics (2008) 24: 2395-6 Full Text

ZOOM! Zillions of oligos mapped

Hao Lin et al.

Bioinformatics (2008) 24: 2431-7 Full Text

Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications

Brian Ondov et al.

Bioinformatics (2008) 24: 2776-7 Full Text

Slider - Maximum use of probability information for alignment of short sequence reads and SNP detection

Nawar Malhis et al.

Bioinformatics (2009) 25: 6-13 Full Text

SOAP: short oligonucleotide alignment

Ruiqiang Li et al.

Bioinformatics (2008) 24: 713-4 Full Text

Annotation of metagenome short reads using Proxygenes

Daniel Dalevi et al.

Bioinformatics (2008) 24: i7-13 Full Text

Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies

Iman Hajirasouliha

Bioinformatics (2008) 24: i32-40 Full Text

PASS: a Program to Align Short Sequences

Davide Campagna et al.

Bioinformatics (2009) 25: 967–968 Full Text

MOM: Maximum Oligonucleotide Mapping

Hugh Eaves and Yuan Gao

Bioinformatics (2009) 25: 969–970 Full Text

ProbeMatch: Rapid alignment of oligonucleotides to a genome allowing both gaps and mismatches

Jignesh Patel et al.

Advanced Access publication: 7 April 2009 Full Text

Fast and Accurate Short Read Alignment with Burrows-Wheeler Transform

Li Heng and Richard Durbin

Advanced Access publication: 18 May 2009 Full Text

CloudBurst: highly sensitive read mapping with MapReduce

Michael Schatz

Bioinformatics (2009) 25: 1363–1369 Full Text

SOAP2: an improved ultrafast tool for short read alignment

Ruiqiang Li

Advanced Access publication: 3 June 2009 Full Text

A Fast Hybrid Short Read Fragment Assembly Algorithm

Bertil Schmidt et al.

Advanced Access publication: 17 June 2009 Full Text

SNP-o-matic

Heinrich Manske and Dominic Kwiatkowski

Advanced Access publication: 2 July 2009 Full Text

VarScan: Variant detection in massively parallel

Daniel Koboldt

Advanced Access publication: 19 June 2009 Full Text

PerM: Efficient Mapping of Short Sequencing Reads with Periodic Full Sensitive Spaced Seeds

Yangho Chen et al

Advanced Access publication: 12 August 2009 Full Text

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

Jacob Degner et al.

Advanced Access publication: 6 October 2009 Full Text

Updates to the RMAP short-read mapping software

Andrew Smith et al.

Bioinformatics (2009) 25: 2841–2842 Full Text

Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite

Takehiro Hashimoto et al.

Bioinformatics (2009) 25: 2613-4 Full Text

Assembly

Aggressive Assembly of Pyrosequencing Reads with Mates

Jason Miller et al.

Bioinformatics (2008) 24: 2818-24 Full Text

Assembly reconciliation

Aleskey Zimin et al.

Bioinformatics (2008) 24: 42-5 Full Text

Consensus Generation and Variant Detection by Celera Assembler

Gennady Denisov et al.

Bioinformatics (2008) 24: 1035-40 Full Text

Assembling millions of short DNA sequences using SSAKE

Rene Warren et al.

Bioinformatics (2007) 23: 500-1 Full Text

Extending assembly of short DNA sequences to handle error

William Jeck et al.

Bioinformatics (2007) 23: 2942-4 Full Text

SCARF: Maximizing next-generation EST assemblies for evolutionary and population genomic analyses

Michael Barker et al.

Bioinformatics (2009) 25: 535-536 Full Text

Profiling model T-cell metagenomes with short reads

René Warren et al

Bioinformatics (2008) 25: 458-64 Full Text

A Consistency-based Consensus Algorithm for De Novo and Reference-guided Sequence Assembly of Short Reads.

Tobias Rausch et al.

Bioinformatics (2009) 25: 1118–1124 Full Text

HI: Haplotype Improver using paired-end short

Quan Long et al.

Advanced Access publication: 1 July 2009 Full Text

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

Kai Ye et al.

Advanced Access publication: 26 June 2009 Full Text

Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly

Bas Dutilh et al.

Advanced Access publication: 19 June 2009 Full Text

De novo Transcriptome Assembly with ABySS

Inanc Birol et al.

Advanced Access publication: 15 June 2009 Full Text

Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA

Kathryn Holt et al.

Bioinformatics (2009) 25: 2074-5 Full Text

Base Calling

SHREC: A short-read error correction method

Bertil Schmidt et al.

Advanced Access publication: 19 June 2009 Full Text

Swift: Primary Data Analysis for the Illumina

Nava Whiteford et al.

Advanced Access publication: 23 June 2009 Full Text

TagDust - A program to eliminate artifacts from next generation sequencing data

Timo Lassmann et al.

Bioinformatics (2009) 25: 2839–2840 Full Text

CDS Prediction

FrameDP: sensitive peptide detection on noisy matured sequences

Jér?me Gouzy, Sébastien Carrere and Thomas Schiex

Bioinformatics 25: 670–671 Full Text

CHIP-seq

FindPeaks 3.1: A Tool for Identifying Areas of Enrichment from Massively Parallel Short-Read Sequencing Technology

Anthony Fejes et al.

Bioinformatics (2008) 24: 1729-30 Full Text

F-Seq: A Feature Density Estimator for High-Throughput Sequence Tags

Alan Boyle et al.

Bioinformatics (2008) 24: 2537-8 Full Text

Hierarchical Hidden Markov Model with Application to Joint Analysis of ChIP-chip and ChIP-seq data

Hyungwon Choi et al.

Advanced Access publication: 14 May 2009 Ful text

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

Weiqun Peng et al.

Advanced Access publication: 8 June 2009 Full Text

Diagnosis

Statistical Model for Whole Genome Sequencing and Its Application to Minimally Invasive Diagnosis of Fetal Genetic Disease

Tianjiao Chu et al.

Bioinformatics (2009) 25: 1244–1250 Full Text

ISOLATE: A computational strategy for identifying the primary origin of cancers using high throughput sequencing

Gerald Quon and Quaid Morris

Advanced Access publication: 19 June 2009 Full Text

Mapping

The Sequence Alignment/Map (SAM) Format and SAMtools

Heng Li et al.

Advanced Access publication: 8 June 2009 Full Text

Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite

Geoffrey Faulkner et al.

Advanced Access publication: 15 July 2009 Full Text

Pipeline

PIQA: Pipeline for Illumina G1 Genome Analyzer Data Quality Assessment

Antonio Martinez-Alcantara et al.

Advanced Access publication: 14 July 2009 Full Text

ShortRead: A Bioconductor package for input, quality assessment, and exploration of high throughput sequence data

Martin Morgan et al.

Advanced Access publication: 3 August 2009 Full Text

RNA-Seq

Statistical Inferences for Isoform Expression in RNA-Seq.

Hui Jiang and Wing Wong

Bioinformatics (2009) 25: 1026–1032 Full Text

A toolkit for analysing large-scale plant small RNA datasets

Simon Moxon et al.

Bioinformatics (2008) 24: 2252-2253 Full Text

TopHat: discovering splice junctions with RNA-Seq

Cole Trapnell et al.

Bioinformatics (2009) 25: 1105–1111 Full Text

RNA-MATE: A recursive mapping strategy for high-throughput RNA-sequencing data

Nicole Cloonan et al.

Bioinformatics (2009) 25: 2615-6 Full Text

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