Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations

The effect of sodium butyrate and cisplatin on expression of EMT markers

(2019) Alena Mrkvicova et al.   PLoS One

Comparative analyses of sperm DNA methylomes among human, mouse and cattle provide insights into epigenomic evolution and complex traits

(2019) Lingzhao Fang et al.   Epigenetics

Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits

(2018) Aline S. M. Cesar et al.   BMC GENOMICS

Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals

(2018) Aniek C. Bouwman et al.   NATURE GENETICS

Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds

(2018) Marina Naval-Sanchez et al.   Nature Communications

MicroRNA-guided prioritization of genome-wide association signals reveals the importance of microRNA-target gene networks for complex traits in cattle

(2018) Lingzhao Fang et al.   Scientific Reports

A comprehensive manually-curated compendium of bovine transcription factors

(2018) Marcela M. de Souza et al.   Scientific Reports

Infusion of sodium butyrate promotes rumen papillae growth and enhances expression of genes related to rumen epithelial VFA uptake and metabolism in neonatal twin lambs

(2018) Lixiang Liu et al.   JOURNAL OF ANIMAL SCIENCE

Harnessing genomic information for livestock improvement

(2018) Michel Georges et al.   NATURE REVIEWS GENETICS

Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap

(2018) Elisabetta Giuffra et al.   Annual Review of Animal Biosciences

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells

(2017) Juri Kazakevych et al.   NUCLEIC ACIDS RESEARCH

Multiple Trait Covariance Association Test Identifies Gene Ontology Categories Associated with Chill Coma Recovery Time in Drosophila melanogaster

(2017) Izel Fourie Sørensen et al.   Scientific Reports

A high resolution atlas of gene expression in the domestic sheep (Ovis aries)

(2017) Emily L. Clark et al.   PLoS Genetics

Deletion of the MAD2L1 spindle assembly checkpoint gene is tolerated in mouse models of acute T-cell lymphoma and hepatocellular carcinoma

(2017) Floris Foijer et al.   eLife

Genome-wide, Single-Cell DNA Methylomics Reveals Increased Non-CpG Methylation during Human Oocyte Maturation

(2017) Bo Yu et al.   Stem Cell Reports

The FANTOM5 collection, a data series underpinning mammalian transcriptome atlases in diverse cell types

(2017) Hideya Kawaji et al.   Scientific Data

Increased prediction accuracy using a genomic feature model including prior information on quantitative trait locus regions in purebred Danish Duroc pigs

(2016) Pernille Sarup et al.   BMC GENETICS

Exploiting biological priors and sequence variants enhances QTL discovery and genomic prediction of complex traits

(2016) I. M. MacLeod et al.   BMC GENOMICS

Covariance Association Test (CVAT) Identifies Genetic Markers Associated with Schizophrenia in Functionally Associated Biological Processes

(2016) Palle Duun Rohde et al.   GENETICS

Covariance Association Test (CVAT) Identifies Genetic Markers Associated with Schizophrenia in Functionally Associated Biological Processes

(2016) Palle Duun Rohde et al.   GENETICS

The role dietary of bioactive compounds on the regulation of histone acetylases and deacetylases: A review

(2015) F. Vahid et al.   GENE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Partitioning heritability by functional annotation using genome-wide association summary statistics

(2015) Hilary K Finucane et al.   NATURE GENETICS

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project

(2015) Leif Andersson et al.   GENOME BIOLOGY

MultiBLUP: improved SNP-based prediction for complex traits

(2014) Doug Speed et al.   GENOME RESEARCH

Genomic Signatures Reveal New Evidences for Selection of Important Traits in Domestic Cattle

(2014) Lingyang Xu et al.   MOLECULAR BIOLOGY AND EVOLUTION

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts

(2014) James R Wagner et al.   GENOME BIOLOGY

The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic Treg Cell Homeostasis

(2013) P. M. Smith et al.   SCIENCE

Gut–brain axis: how the microbiome influences anxiety and depression

(2013) Jane A. Foster et al.   TRENDS IN NEUROSCIENCES

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Genome-wide ChIP-seq mapping and analysis reveal butyrate-induced acetylation of H3K9 and H3K27 correlated with transcription activity in bovine cells

(2012) Joo Heon Shin et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

DNA Methylation and Its Basic Function

(2012) Lisa D Moore et al.   NEUROPSYCHOPHARMACOLOGY

Integrative annotation of chromatin elements from ENCODE data

(2012) Michael M. Hoffman et al.   NUCLEIC ACIDS RESEARCH

Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era

(2012) Zhi-Liang Hu et al.   NUCLEIC ACIDS RESEARCH

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Transcriptome Characterization by RNA-seq Unravels the Mechanisms of Butyrate-Induced Epigenomic Regulation in Bovine Cells

(2012) Sitao Wu et al.   PLoS One

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

CpG island chromatin

(2011) Neil P. Blackledge et al.   Epigenetics

Effect of method of delivery of sodium butyrate on rumen development in newborn calves

(2011) P. Górka et al.   JOURNAL OF DAIRY SCIENCE

New views of Arc, a master regulator of synaptic plasticity

(2011) Jason D Shepherd et al.   NATURE NEUROSCIENCE

Enhancer function: new insights into the regulation of tissue-specific gene expression

(2011) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

SLIM: a sliding linear model for estimating the proportion of true null hypotheses in datasets with dependence structures

(2010) Hong-Qiang Wang et al.   BIOINFORMATICS

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Histone deacetylase inhibition alters histone methylation associated with heat shock protein 70 promoter modifications in astrocytes and neurons

(2010) Zoya Marinova et al.   NEUROPHARMACOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Histone deacetylase inhibition and the regulation of cell growth with particular reference to liver pathobiology

(2009) Fraczek Joanna et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY