Genome-Wide DNA Methylation and Its Effect on Gene Expression During Subclinical Mastitis in Water Buffalo

Genome-wide methylation and transcriptome of blood neutrophils reveal the roles of DNA methylation in affecting transcription of protein-coding genes and miRNAs in E. coli-infected mastitis cows

(2020) Zhihua Ju et al.   BMC GENOMICS

Comparative whole genome DNA methylation profiling across cattle tissues reveals global and tissue-specific methylation patterns

(2020) Yang Zhou et al.   BMC BIOLOGY

Genome-Wide DNA Methylation Analysis of Mammary Gland Tissues From Chinese Holstein Cows With Staphylococcus aureus Induced Mastitis

(2020) Mengqi Wang et al.   Frontiers in Genetics

Bacterial Lipopolysaccharide Induced Alterations of Genome-Wide DNA Methylation and Promoter Methylation of Lactation-Related Genes in Bovine Mammary Epithelial Cells

(2019) Jingbo Chen et al.   Toxins

Complex relationship between DNA methylation and gene expression due to Lr28 in wheat-leaf rust pathosystem

(2019) Gautam Saripalli et al.   MOLECULAR BIOLOGY REPORTS

Solexa sequencing and custom microRNA chip reveal repertoire of microRNAs in mammary gland of bovine suffering from natural infectious mastitis

(2018) Zhihua Ju et al.   ANIMAL GENETICS

psRNATarget: a plant small RNA target analysis server (2017 release)

(2018) Xinbin Dai et al.   NUCLEIC ACIDS RESEARCH

Bovine mastitis: a persistent and evolving problem requiring novel approaches for its control - a review

(2018) Miroslav Benić et al.   VETERINARSKI ARHIV

A complex association between DNA methylation and gene expression in human placenta at first and third trimesters

(2017) Yen Ching Lim et al.   PLoS One

Comparative genome-wide methylation analysis of longissimus dorsi muscles between Japanese black (Wagyu) and Chinese Red Steppes cattle

(2017) Xibi Fang et al.   PLoS One

A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors

(2017) Donald M. Bryant et al.   Cell Reports

DISMISS: detection of stranded methylation in MeDIP-Seq data

(2016) Umar Niazi et al.   BMC BIOINFORMATICS

Genome-wide DNA methylation analysis identifies candidate epigenetic markers and drivers of hepatocellular carcinoma

(2016) Yongchang Zheng et al.   BRIEFINGS IN BIOINFORMATICS

One Loop to Rule Them All: The Ping-Pong Cycle and piRNA-Guided Silencing

(2016) Benjamin Czech et al.   TRENDS IN BIOCHEMICAL SCIENCES

Combined analysis of DNA methylome and transcriptome reveal novel candidate genes with susceptibility to bovine Staphylococcus aureus subclinical mastitis

(2016) Minyan Song et al.   Scientific Reports

PIWI-Interacting RNA: Its Biogenesis and Functions

(2015) Yuka W. Iwasaki et al.   Annual Review of Biochemistry

Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation

(2015) Daofeng Li et al.   METHODS

The alternative role of DNA methylation in splicing regulation

(2015) Galit Lev Maor et al.   TRENDS IN GENETICS

Epigenetic marks: regulators of livestock phenotypes and conceivable sources of missing variation in livestock improvement programs

(2015) Eveline M. Ibeagha-Awemu et al.   Frontiers in Genetics

Shifted T Helper Cell Polarization in a Murine Staphylococcus aureus Mastitis Model

(2015) Yanqing Zhao et al.   PLoS One

LncTar: a tool for predicting the RNA targets of long noncoding RNAs

(2014) Jianwei Li et al.   BRIEFINGS IN BIOINFORMATICS

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Proliferation-Stimulating Effect of Colony Stimulating Factor 2 on Porcine Trophectoderm Cells Is Mediated by Activation of Phosphatidylinositol 3-Kinase and Extracellular Signal-Regulated Kinase 1/2 Mitogen-Activated Protein Kinase

(2014) Wooyoung Jeong et al.   PLoS One

Subclinical Mastitis in Dairy Animals: Incidence, Economics, and Predisposing Factors

(2014) Mukesh Kr. Sinha et al.   TheScientificWorldJOURNAL

Different screening tests and milk somatic cell count for the prevalence of subclinical bovine mastitis in Bangladesh

(2014) Md. Nazmul Hoque et al.   TROPICAL ANIMAL HEALTH AND PRODUCTION

diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates

(2013) Li Shen et al.   PLoS One

Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression

(2012) S. A. Selamat et al.   GENOME RESEARCH

Epidemiology of coagulase-negative staphylococci intramammary infection in dairy cattle and the effect of bacteriological culture misclassification

(2012) S. Dufour et al.   JOURNAL OF DAIRY SCIENCE

Invited review: Mastitis in dairy heifers: Nature of the disease, potential impact, prevention, and control

(2012) S. De Vliegher et al.   JOURNAL OF DAIRY SCIENCE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Methylome analysis using MeDIP-seq with low DNA concentrations

(2012) Oluwatosin Taiwo et al.   Nature Protocols

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

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

Lineage-specific distribution of high levels of genomic

(2011) Alexey Ruzov et al.   CELL RESEARCH

Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors

(2011) A. Feber et al.   GENOME RESEARCH

New Concepts in the Causes and Control of Mastitis

(2011) Lorraine M. Sordillo   JOURNAL OF MAMMARY GLAND BIOLOGY AND NEOPLASIA

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Whole genome DNA methylation analysis based on high throughput sequencing technology

(2010) Ning Li et al.   METHODS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Erratum: Corrigendum: Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells

(2009) Madeleine P Ball et al.   NATURE BIOTECHNOLOGY

The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores

(2009) Rafael A Irizarry et al.   NATURE GENETICS

Characterization and distribution of retrotransposons and simple sequence repeats in the bovine genome

(2009) D. L. Adelson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

(2008) Thomas A Down et al.   NATURE BIOTECHNOLOGY

DNA methylation landscapes: provocative insights from epigenomics

(2008) Miho M. Suzuki et al.   NATURE REVIEWS GENETICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY