Transcriptome analysis revealed chimeric RNAs, single nucleotide polymorphisms and allele-specific expression in porcine prenatal skeletal muscle

Dynamic transcriptome profiles of skeletal muscle tissue across 11 developmental stages for both Tongcheng and Yorkshire pigs

(2015) Yuqiang Zhao et al.   BMC GENOMICS

Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance

(2015) James J Crowley et al.   NATURE GENETICS

Integrated analysis of miRNA and mRNA paired expression profiling of prenatal skeletal muscle development in three genotype pigs

(2015) Zhonglin Tang et al.   Scientific Reports

Systematic identification and characterization of long intergenic non-coding RNAs in fetal porcine skeletal muscle development

(2015) Weimin Zhao et al.   Scientific Reports

Genome-wide association studies for hematological traits in Chinese Sutai pigs

(2014) Feng Zhang et al.   BMC GENETICS

The “Grep” Command But Not FusionMap, FusionFinder or ChimeraScan Captures the CIC-DUX4 Fusion Gene from Whole Transcriptome Sequencing Data on a Small Round Cell Tumor with t(4;19)(q35;q13)

(2014) Ioannis Panagopoulos et al.   PLoS One

Genome wide analysis reveals single nucleotide polymorphisms associated with fatness and putative novel copy number variants in three pig breeds

(2013) Katie E Fowler et al.   BMC GENOMICS

Gene-based single nucleotide polymorphism discovery in bovine muscle using next-generation transcriptomic sequencing

(2013) Anis Djari et al.   BMC GENOMICS

Identification of somatic mutations in human prostate cancer by RNA-Seq

(2013) XiaoLin Xu et al.   GENE

Whole Genome Association Studies of Residual Feed Intake and Related Traits in the Pig

(2013) Suneel K. Onteru et al.   PLoS One

Integrative Analysis of Porcine microRNAome during Skeletal Muscle Development

(2013) Lijun Qin et al.   PLoS One

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

A genome-wide association study on androstenone levels in pigs reveals a cluster of candidate genes on chromosome 6

(2012) Naomi Duijvesteijn et al.   BMC GENETICS

Identification and analysis of pig chimeric mRNAs using RNA sequencing data

(2012) Lei Ma et al.   BMC GENOMICS

Liver transcriptome profile in pigs with extreme phenotypes of intramuscular fatty acid composition

(2012) Yuliaxis Ramayo-Caldas et al.   BMC GENOMICS

Association study of molecular polymorphisms in candidate genes related to stress responses with production and meat quality traits in pigs

(2012) E. Terenina et al.   DOMESTIC ANIMAL ENDOCRINOLOGY

Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts

(2012) M. Frenkel-Morgenstern et al.   GENOME RESEARCH

Molecular characterization and expression analysis of NDUFS4 gene in m. longissimus dorsi of Laiwu pig (Sus scrofa)

(2012) Qimei Chen et al.   MOLECULAR BIOLOGY REPORTS

Analyses of pig genomes provide insight into porcine demography and evolution

(2012) Martien A. M. Groenen et al.   NATURE

ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data

(2012) Milana Frenkel-Morgenstern et al.   NUCLEIC ACIDS RESEARCH

Discovery of MicroRNAs Associated with Myogenesis by Deep Sequencing of Serial Developmental Skeletal Muscles in Pigs

(2012) Xinhua Hou et al.   PLoS One

FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution

(2011) Huanying Ge et al.   BIOINFORMATICS

ChimeraScan: a tool for identifying chimeric transcription in sequencing data

(2011) Matthew K. Iyer et al.   BIOINFORMATICS

Genome-Wide Association Study Identifies Loci for Body Composition and Structural Soundness Traits in Pigs

(2011) Bin Fan et al.   PLoS One

Comparative Analyses by Sequencing of Transcriptomes during Skeletal Muscle Development between Pig Breeds Differing in Muscle Growth Rate and Fatness

(2011) Xiao Zhao et al.   PLoS One

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing

(2011) K. Kannan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MicroRNA expression profiles of porcine skeletal muscle

(2010) B. Zhou et al.   ANIMAL GENETICS

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

A 6-bp deletion in the TYRP1 gene causes the brown colouration phenotype in Chinese indigenous pigs

(2010) J Ren et al.   HEREDITY

Analyses of porcine public SNPs in coding-gene regions by re-sequencing and phenotypic association studies

(2010) Xiaoping Li et al.   MOLECULAR BIOLOGY REPORTS

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

(2010) Tomi Pastinen   NATURE REVIEWS GENETICS

The plasticity of the mammalian transcriptome

(2009) Johan Lindberg et al.   GENOMICS

Fetal programming of skeletal muscle development in ruminant animals1

(2009) M. Du et al.   JOURNAL OF ANIMAL SCIENCE

Implications of chimaeric non-co-linear transcripts

(2009) Thomas R. Gingeras   NATURE

Global patterns of cis variation in human cells revealed by high-density allelic expression analysis

(2009) Bing Ge et al.   NATURE GENETICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

Chimeric transcript discovery by paired-end transcriptome sequencing

(2009) C. A. Maher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

A Neoplastic Gene Fusion Mimics Trans-Splicing of RNAs in Normal Human Cells

(2008) H. Li et al.   SCIENCE