Single-cell transcriptomic analyses of dairy cattle ruminal epithelial cells during weaning

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

(2020) Ellen Freebern et al.   BMC GENOMICS

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

(2020) Lingzhao Fang et al.   GENOME RESEARCH

Construction of a human cell landscape at single-cell level

(2020) Xiaoping Han et al.   NATURE

Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human

(2020) Shuli Liu et al.   BMC BIOLOGY

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

Protein profiles of enzymatically isolated rumen epithelium in sheep fed a fibrous diet

(2019) J. J. Bond et al.   Journal of Animal Science and Biotechnology

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Ruminal microbiome-host crosstalk stimulates the development of the ruminal epithelium in a lamb model

(2019) Limei Lin et al.   Microbiome

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

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

(2019) Palle Duun Rohde et al.   BIOINFORMATICS

Changes in meta-transcriptome of rumen epimural microbial community and liver transcriptome in young calves with feed induced acidosis

(2019) Wenli Li et al.   Scientific Reports

Tracing the temporal-spatial transcriptome landscapes of the human fetal digestive tract using single-cell RNA-sequencing

(2018) Shuai Gao et al.   NATURE CELL BIOLOGY

Evolution of pallium, hippocampus, and cortical cell types revealed by single-cell transcriptomics in reptiles

(2018) Maria Antonietta Tosches et al.   SCIENCE

A single-cell survey of the small intestinal epithelium

(2017) Adam L. Haber et al.   NATURE

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Rumen Function and Development

(2017) Ransom L. Baldwin et al.   VETERINARY CLINICS OF NORTH AMERICA-FOOD ANIMAL PRACTICE

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

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

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

The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery

(2016) Hendrik G. Stunnenberg et al.   CELL

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

(2016) Palle Duun Rohde et al.   GENETICS

Keratins: Biomarkers and modulators of apoptotic and necrotic cell death in the liver

(2016) Nam-On Ku et al.   HEPATOLOGY

Tracing haematopoietic stem cell formation at single-cell resolution

(2016) Fan Zhou et al.   NATURE

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

(2016) Palle Duun Rohde et al.   GENETICS

Gene network analysis identifies rumen epithelial cell proliferation, differentiation and metabolic pathways perturbed by diet and correlated with methane production

(2016) Ruidong Xiang et al.   Scientific Reports

The transcriptional landscape of age in human peripheral blood

(2015) Marjolein J. Peters et al.   Nature Communications

Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation

(2015) Hannah Dueck et al.   GENOME BIOLOGY

Single Cell Transcriptomics: Methods and Applications

(2015) Itamar Kanter et al.   Frontiers in Oncology

Transcriptional regulators transforming growth factor-β1 and estrogen-related receptor-α identified as putative mediators of calf rumen epithelial tissue development and function during weaning1

(2014) E.E. Connor et al.   JOURNAL OF DAIRY SCIENCE

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

(2014) Alex K. Shalek et al.   NATURE

Glomerular development – Shaping the multi-cellular filtration unit

(2014) C. Schell et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Ruminal epithelium transcriptome dynamics in response to plane of nutrition and age in young Holstein calves

(2013) Aisha Naeem et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

BLUEPRINT: mapping human blood cell epigenomes

(2013) J. H. A. Martens et al.   HAEMATOLOGICA

Loss of Epithelial Hypoxia-Inducible Factor Prolyl Hydroxylase 2 Accelerates Skin Wound Healing in Mice

(2013) Joanna Kalucka et al.   MOLECULAR AND CELLULAR BIOLOGY

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

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

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

(2009) Gabriela Bindea et al.   BIOINFORMATICS

APE1/Ref-1 Interacts with NPM1 within Nucleoli and Plays a Role in the rRNA Quality Control Process

(2009) C. Vascotto et al.   MOLECULAR AND CELLULAR BIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

MT1-MMP releases latent TGF-β1 from endothelial cell extracellular matrix via proteolytic processing of LTBP-1

(2008) O TATTI et al.   EXPERIMENTAL CELL RESEARCH