Bulk segregant RNA-seq reveals expression and positional candidate genes and allele-specific expression for disease resistance against enteric septicemia of catfish

RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome

(2013) Katie L Ayers et al.   GENOME BIOLOGY

Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat

(2012) Martin Trick et al.   BMC PLANT BIOLOGY

Apolipoprotein B100 is a suppressor of Staphylococcus aureus-induced innate immune responses in humans and mice

(2012) Stefanie Sigel et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus

(2012) Chao Li et al.   FISH & SHELLFISH IMMUNOLOGY

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Gene Mapping via Bulked Segregant RNA-Seq (BSR-Seq)

(2012) Sanzhen Liu et al.   PLoS One

Second-Generation Genetic Linkage Map of Catfish and Its Integration with the BAC-Based Physical Map

(2012) Parichart Ninwichian et al.   G3-Genes Genomes Genetics

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

(2011) R. Kofler et al.   BIOINFORMATICS

Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array

(2011) Shikai Liu et al.   BMC GENOMICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Bulk Segregant Analysis Using Single Nucleotide Polymorphism Microarrays

(2011) Anthony Becker et al.   PLoS One

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

Bulk Segregant Analysis by High-Throughput Sequencing Reveals a Novel Xylose Utilization Gene from Saccharomyces cerevisiae

(2010) Jared W. Wenger et al.   PLoS Genetics

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genetic and epigenetic regulations of prostate cancer by genistein

(2009) B. Molinié et al.   DRUG NEWS & PERSPECTIVES

Construction of Genetic Linkage Maps and Comparative Genome Analysis of Catfish Using Gene-Associated Markers

(2009) H. Kucuktas et al.   GENETICS

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

Advances in the identification and analysis of allele-specific expression

(2009) Christopher G Bell et al.   Genome Medicine

Apolipoprotein B Is an Innate Barrier against Invasive Staphylococcus aureus Infection

(2008) M. Michal Peterson et al.   Cell Host & Microbe

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

(2008) W. Brockman et al.   GENOME RESEARCH

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Transcriptional and epigenetic regulations of embryonic stem cells

(2008) Jia-Hui Ng et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One

Microarray analysis of gene expression in the blue catfish liver reveals early activation of the MHC class I pathway after infection with Edwardsiella ictaluri

(2007) Eric Peatman et al.   MOLECULAR IMMUNOLOGY