Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle

GWAS and fine-mapping of livability and six disease traits in Holstein cattle

(2020) Ellen Freebern et al.   BMC GENOMICS

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

(2019) Lingzhao Fang et al.   BMC BIOLOGY

High-density genome-wide association study for residual feed intake in Holstein dairy cattle

(2019) B. Li et al.   JOURNAL OF DAIRY SCIENCE

A global overview of pleiotropy and genetic architecture in complex traits

(2019) Kyoko Watanabe et al.   NATURE GENETICS

qgg: an R package for large-scale quantitative genetic analyses

(2019) Palle Duun Rohde et al.   BIOINFORMATICS

Leveraging molecular quantitative trait loci to understand the genetic architecture of diseases and complex traits

(2018) Farhad Hormozdiari et al.   NATURE GENETICS

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types

(2018) Hilary K. Finucane et al.   NATURE GENETICS

Comparative whole genome DNA methylation profiling of cattle sperm and somatic tissues reveals striking hypomethylated patterns in sperm

(2018) Yang Zhou et al.   GigaScience

An atlas of genetic associations in UK Biobank

(2018) Oriol Canela-Xandri et al.   NATURE GENETICS

Harnessing genomic information for livestock improvement

(2018) Michel Georges et al.   NATURE REVIEWS GENETICS

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Genome editing in livestock: Are we ready for a revolution in animal breeding industry?

(2017) Jinxue Ruan et al.   TRANSGENIC 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

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Integrating Sequence-based GWAS and RNA-Seq Provides Novel Insights into the Genetic Basis of Mastitis and Milk Production in Dairy Cattle

(2017) Lingzhao Fang et al.   Scientific Reports

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

Reconstitution of the targeting of Rab6A to the Golgi apparatus in semi-intact HeLa cells: A role of BICD2 in stabilizing Rab6A on Golgi membranes and a concerted role of Rab6A/BICD2 interactions in Golgi-to-ER retrograde transport

(2015) Mariko Matsuto et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

An alternative approach to modeling genetic merit of feed efficiency in dairy cattle

(2015) Y. Lu et al.   JOURNAL OF DAIRY SCIENCE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

LD Score regression distinguishes confounding from polygenicity in genome-wide association studies

(2015) Brendan K Bulik-Sullivan et al.   NATURE GENETICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

TRIM46 Controls Neuronal Polarity and Axon Specification by Driving the Formation of Parallel Microtubule Arrays

(2015) Sam F.B. van Beuningen et al.   NEURON

Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell type-specific hypomethylation in the regulation of cell identity genes

(2015) Hongbo Liu et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Variability in hepatic expression of organic anion transporter 7/SLC22A9, a novel pravastatin uptake transporter: impact of genetic and regulatory factors

(2015) A Emami Riedmaier et al.   PHARMACOGENOMICS JOURNAL

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

(2015) Leif Andersson et al.   GENOME BIOLOGY

The Impact of Genetic Relationship and Linkage Disequilibrium on Genomic Selection

(2015) Hongjun Liu et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

CCDC88B is a novel regulator of maturation and effector functions of T cells during pathological inflammation

(2014) James M. Kennedy et al.   JOURNAL OF EXPERIMENTAL MEDICINE

DNA methylation: roles in mammalian development

(2013) Zachary D. Smith et al.   NATURE REVIEWS GENETICS

An epigenetic signature of developmental potential in neural stem cells and early neurons

(2013) Matthew J. Burney et al.   STEM CELLS

Five Years of GWAS Discovery

(2012) Peter M. Visscher et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Innate immunity in the small intestine

(2012) Rebeca Santaolalla et al.   CURRENT OPINION IN GASTROENTEROLOGY

Analysis of copy number variations in Holstein cows identify potential mechanisms contributing to differences in residual feed intake

(2012) Yali Hou et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Genome-wide association mapping including phenotypes from relatives without genotypes

(2012) H. WANG et al.   Genetics Research

Understanding and predicting complex traits: knowledge from cattle

(2012) K. E. Kemper et al.   HUMAN MOLECULAR GENETICS

Mapping cis- and trans-regulatory effects across multiple tissues in twins

(2012) Elin Grundberg et al.   NATURE GENETICS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

(2012) Huaiyu Mi 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

ZFX Controls the Self-Renewal of Human Embryonic Stem Cells

(2012) Sivan Harel et al.   PLoS One

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

(2011) Felix Krueger et al.   BIOINFORMATICS

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Rising in the East

(2010) Gregory A Petsko   GENOME BIOLOGY

Cross-regulation of Signaling Pathways by Interferon-γ: Implications for Immune Responses and Autoimmune Diseases

(2009) Xiaoyu Hu et al.   IMMUNITY

Genetic and environmental factors that affect gestation length in dairy cattle

(2009) H.D. Norman et al.   JOURNAL OF DAIRY SCIENCE

Distribution and location of genetic effects for dairy traits

(2009) J.B. Cole et al.   JOURNAL OF DAIRY SCIENCE

Mapping genes for complex traits in domestic animals and their use in breeding programmes

(2009) Michael E. Goddard et al.   NATURE REVIEWS GENETICS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Efficient Methods to Compute Genomic Predictions

(2008) P.M. VanRaden   JOURNAL OF DAIRY SCIENCE