Comprehensive analysis of the whole transcriptomes from two different pig breeds using RNA-Seq method

Transcriptome Changes in the Porcine Endometrium During the Preattachment Phase1

(2013) Anastazia Samborski et al.   BIOLOGY OF REPRODUCTION

Deep Sequencing of the Porcine Endometrial Transcriptome on Day 14 of Pregnancy1

(2013) Anastazia Samborski et al.   BIOLOGY OF REPRODUCTION

RNA-SeQC: RNA-seq metrics for quality control and process optimization

(2012) David S. DeLuca et al.   BIOINFORMATICS

RNA-Seq reveals differentially expressed isoforms and novel splice variants in buccal mucosal cancer

(2012) Subhash J. Jakhesara et al.   GENE

Variability of mRNA abundance of leukemia inhibitory factor gene (LIF) in porcine ovary, oviduct and uterus tissues

(2012) Katarzyna Ropka-Molik et al.   MOLECULAR BIOLOGY REPORTS

Porcine SPP1 gene polymorphism association with phenotypic traits in the Landrace × Jeju (Korea) black pig F2 population

(2012) Sang-Hyun Han et al.   MOLECULAR BIOLOGY REPORTS

Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome

(2012) Zhiyu Peng et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Genome-wide RNA-seq analysis of human and mouse platelet transcriptomes

(2011) J. W. Rowley et al.   BLOOD

Joint analysis of quantitative trait loci and major-effect causative mutations affecting meat quality and carcass composition traits in pigs

(2011) Pierre Cherel et al.   BMC GENETICS

Exploring the gonad transcriptome of two extreme male pigs with RNA-seq

(2011) Anna Esteve-Codina et al.   BMC GENOMICS

Bridging endometrial receptivity and implantation: network of hormones, cytokines, and growth factors

(2011) Mohan Singh et al.   JOURNAL OF ENDOCRINOLOGY

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

SAMStat: monitoring biases in next generation sequencing data

(2010) T. Lassmann et al.   BIOINFORMATICS

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Novel porcine housekeeping genes for real-time RT-PCR experiments normalization in adipose tissue: Assessment of leptin mRNA quantity in different pig breeds

(2010) K. Piórkowska et al.   MEAT SCIENCE

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Genome-wide allele-specific analysis: insights into regulatory variation

(2010) Tomi Pastinen   NATURE REVIEWS GENETICS

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

Modeling non-uniformity in short-read rates in RNA-Seq data

(2010) Jun Li et al.   GENOME BIOLOGY

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

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

(2009) Likun Wang et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Transcript length bias in RNA-seq data confounds systems biology

(2009) Alicia Oshlack et al.   Biology Direct

Effect of the polymorphism of RBP4 and OPN genes on litter size in Tibet pigs

(2008) S. Y. Niu et al.   ACTA AGRICULTURAE SCANDINAVICA SECTION A-ANIMAL SCIENCE

Quantitative trait loci for production traits in pigs: a combined analysis of two Meishan × Large White populations

(2008) Y.-M. Guo et al.   ANIMAL GENETICS

Transcriptome architecture across tissues in the pig

(2008) André LJ Ferraz et al.   BMC GENOMICS

Osteopontin: Role in immune regulation and stress responses

(2008) Kathryn X. Wang et al.   CYTOKINE & GROWTH FACTOR REVIEWS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Uterine Expression of Epidermal Growth Factor Family During the Course of Pregnancy in Pigs

(2008) Y-J Kim et al.   REPRODUCTION IN DOMESTIC ANIMALS