Alignment of Short Reads: A Crucial Step for Application of Next-Generation Sequencing Data in Precision Medicine

Advancing translation of biomarkers into regulatory science

(2015) Huixiao Hong et al.   Biomarkers in Medicine

Molecular regulation of miRNAs and potential biomarkers in the progression of hepatic steatosis to NASH

(2015) Yuping Wang et al.   Biomarkers in Medicine

Biomarker-based drug safety assessment in the age of systems pharmacology: from foundational to regulatory science

(2015) Chen Zhang et al.   Biomarkers in Medicine

microRNAs as pharmacogenomic biomarkers for drug efficacy and drug safety assessment

(2015) Igor Koturbash et al.   Biomarkers in Medicine

Ionotropic GABA receptor antagonism-induced adverse outcome pathways for potential neurotoxicity biomarkers

(2015) Ping Gong et al.   Biomarkers in Medicine

A New Initiative on Precision Medicine

(2015) Francis S. Collins et al.   NEW ENGLAND JOURNAL OF MEDICINE

Comparison of RNA-seq and microarray-based models for clinical endpoint prediction

(2015) Wenqian Zhang et al.   GENOME BIOLOGY

E-MEM: efficient computation of maximal exact matches for very large genomes

(2014) Nilesh Khiste et al.   BIOINFORMATICS

Emerging efforts for discovering new biomarkers of liver disease and hepatotoxicity

(2014) Huixiao Hong et al.   Biomarkers in Medicine

Whole genome sequencing of 35 individuals provides insights into the genetic architecture of Korean population

(2014) Wenqian Zhang et al.   BMC BIOINFORMATICS

Toxicogenomics and Cancer Susceptibility: Advances with Next-Generation Sequencing

(2014) Baitang Ning et al.   JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH PART C-ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS

Quality control metrics improve repeatability and reproducibility of single-nucleotide variants derived from whole-genome sequencing

(2014) W Zhang et al.   PHARMACOGENOMICS JOURNAL

CUSHAW3: Sensitive and Accurate Base-Space and Color-Space Short-Read Alignment with Hybrid Seeding

(2014) Yongchao Liu et al.   PLoS One

MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

(2014) Wan-Ping Lee et al.   PLoS One

slaMEM: efficient retrieval of maximal exact matches using a sampled LCP array

(2013) Francisco Fernandes et al.   BIOINFORMATICS

NextGenMap: fast and accurate read mapping in highly polymorphic genomes

(2013) Fritz J. Sedlazeck et al.   BIOINFORMATICS

Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms

(2013) Come Raczy et al.   BIOINFORMATICS

SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner

(2013) Ruibang Luo et al.   PLoS One

Critical role of bioinformatics in translating huge amounts of next-generation sequencing data into personalized medicine

(2013) HuiXiao Hong et al.   Science China-Life Sciences

CUSHAW2-GPU: Empowering Faster Gapped Short-Read Alignment Using GPU Computing

(2013) Yongchao Liu et al.   IEEE Design & Test

RazerS 3: Faster, fully sensitive read mapping

(2012) David Weese et al.   BIOINFORMATICS

CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows–Wheeler transform

(2012) Yongchao Liu et al.   BIOINFORMATICS

Long read alignment based on maximal exact match seeds

(2012) Yongchao Liu et al.   BIOINFORMATICS

Unipro UGENE: a unified bioinformatics toolkit

(2012) Konstantin Okonechnikov et al.   BIOINFORMATICS

SOAP3: ultra-fast GPU-based parallel alignment tool for short reads

(2012) C.-M. Liu et al.   BIOINFORMATICS

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

The GEM mapper: fast, accurate and versatile alignment by filtration

(2012) Santiago Marco-Sola et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Erratum: Repetitive DNA and next-generation sequencing: computational challenges and solutions

(2012) Todd J. Treangen et al.   NATURE REVIEWS GENETICS

Technical Reproducibility of Genotyping SNP Arrays Used in Genome-Wide Association Studies

(2012) Huixiao Hong et al.   PLoS One

Sensitive and fast mapping of di-base encoded reads

(2011) F. Hormozdiari et al.   BIOINFORMATICS

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming

(2011) Jochen Blom et al.   BIOINFORMATICS

SHRiMP2: Sensitive yet Practical Short Read Mapping

(2011) Matei David et al.   BIOINFORMATICS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Hobbes: optimized gram-based methods for efficient read alignment

(2011) Athena Ahmadi et al.   NUCLEIC ACIDS RESEARCH

An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System

(2010) Brian D. Ondov et al.   BIOINFORMATICS

GASSST: global alignment short sequence search tool

(2010) Guillaume Rizk et al.   BIOINFORMATICS

Molecular biomarkers: a US FDA effort

(2010) Huixiao Hong et al.   Biomarkers in Medicine

A survey of sequence alignment algorithms for next-generation sequencing

(2010) H. Li et al.   BRIEFINGS IN BIOINFORMATICS

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

Evaluating variations of genotype calling: a potential source of spurious associations in genome-wide association studies

(2010) Huixiao Hong et al.   JOURNAL OF GENETICS

The correlation of gene expression and co-regulated gene patterns in characteristic KEGG pathways

(2010) Lin Hua et al.   JOURNAL OF THEORETICAL BIOLOGY

International network of cancer genome projects

(2010) Thomas J. Hudson (Chairperson) et al.   NATURE

Assessment of variability in GWAS with CRLMM genotyping algorithm on WTCCC coronary artery disease

(2010) L Zhang et al.   PHARMACOGENOMICS JOURNAL

Variability in GWAS analysis: the impact of genotype calling algorithm inconsistencies

(2010) K Miclaus et al.   PHARMACOGENOMICS JOURNAL

Assessing sources of inconsistencies in genotypes and their effects on genome-wide association studies with HapMap samples

(2010) H Hong et al.   PHARMACOGENOMICS JOURNAL

Batch effects in the BRLMM genotype calling algorithm influence GWAS results for the Affymetrix 500K array

(2010) K Miclaus et al.   PHARMACOGENOMICS JOURNAL

A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data

(2010) J Luo et al.   PHARMACOGENOMICS JOURNAL

MOM: maximum oligonucleotide mapping

(2009) H. L. Eaves et al.   BIOINFORMATICS

The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing

(2009) Nathan L. Clement et al.   BIOINFORMATICS

PASS: a program to align short sequences

(2009) D. Campagna et al.   BIOINFORMATICS

A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays

(2009) Zia Khan et al.   BIOINFORMATICS

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

(2009) Yangho Chen et al.   BIOINFORMATICS

Updates to the RMAP short-read mapping software

(2009) A. D. Smith et al.   BIOINFORMATICS

CloudBurst: highly sensitive read mapping with MapReduce

(2009) M. C. Schatz   BIOINFORMATICS

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Building the sequence map of the human pan-genome

(2009) Ruiqiang Li et al.   NATURE BIOTECHNOLOGY

How to map billions of short reads onto genomes

(2009) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Sense from sequence reads: methods for alignment and assembly

(2009) Paul Flicek et al.   NATURE METHODS

BFAST: An Alignment Tool for Large Scale Genome Resequencing

(2009) Nils Homer et al.   PLoS One

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures

(2009) Steve Hoffmann et al.   PLoS Computational Biology

SHRiMP: Accurate Mapping of Short Color-space Reads

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

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Optimal spliced alignments of short sequence reads

(2008) F. De Bona et al.   BIOINFORMATICS

ZOOM! Zillions of oligos mapped

(2008) H. Lin et al.   BIOINFORMATICS

SeqMap: mapping massive amount of oligonucleotides to the genome

(2008) H. Jiang et al.   BIOINFORMATICS

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

Using quality scores and longer reads improves accuracy of Solexa read mapping

(2008) Andrew D Smith et al.   BMC BIOINFORMATICS

Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples

(2008) Huixiao Hong et al.   BMC BIOINFORMATICS

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

(2008) H. Li et al.   GENOME RESEARCH

Genomics sizes up

(2008) Jane Qiu et al.   NATURE