George E. Liu
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View article: Construction of a Multitissue Cell Atlas Reveals Cell‐Type‐Specific Regulation of Molecular and Complex Phenotypes in Pigs
Construction of a Multitissue Cell Atlas Reveals Cell‐Type‐Specific Regulation of Molecular and Complex Phenotypes in Pigs Open
The systematic characterization of cellular heterogeneity among tissues and cell‐type‐specific regulation underlying complex phenotypes remains elusive in pigs. Within the Pig Genotype‐Tissue Expression (PigGTEx) project, this work present…
View article: Alteration of Biological Reaction in Aged Population Reduces Alpha-Toxin Vaccine Efficacy Against Staphylococcus Aureus Skin Infection 9098
Alteration of Biological Reaction in Aged Population Reduces Alpha-Toxin Vaccine Efficacy Against Staphylococcus Aureus Skin Infection 9098 Open
Description Staphylococcus aureus (SA) is a leading cause of severe diseases that are difficult to treat, yet no successful vaccine has been investigated. The α-toxin (HLA), a key virulence factor, has been a primary vaccine target due to …
View article: 19 The FarmGTEx Project: Building reference omics datasets for future gut stress studies.
19 The FarmGTEx Project: Building reference omics datasets for future gut stress studies. Open
The Farm Animal Genotype-Tissue Expression (FarmGTEx) project is a global collaborative effort to create a comprehensive resource for identifying tissue-specific genetic regulatory variants and predicting molecular phenotypes in farm anima…
View article: Whole-genome sequencing reveals complex structural variations at a major locus linked to pigmented spot sizes in Tianfu goats
Whole-genome sequencing reveals complex structural variations at a major locus linked to pigmented spot sizes in Tianfu goats Open
View article: A multi-tissue single-cell expression atlas in cattle
A multi-tissue single-cell expression atlas in cattle Open
View article: Oral virome metagenomic catalog links Porphyromonas gingivalis phages to obesity and type 2 diabetes
Oral virome metagenomic catalog links Porphyromonas gingivalis phages to obesity and type 2 diabetes Open
The human microbiota has a critical role in maintaining human microbiome homeostasis and health, yet the viral component of the oral microbiome remains largely unidentified. We establish the Human Oral Virome Database (HOVD) catalog, a fre…
View article: Global Pangenome Analysis Highlights the Critical Role of Structural Variants in Cattle Improvement and Identifies a Unique Event as a Novel Enhancer in <i>IGFBP7+</i> Cells
Global Pangenome Analysis Highlights the Critical Role of Structural Variants in Cattle Improvement and Identifies a Unique Event as a Novel Enhancer in <i>IGFBP7+</i> Cells Open
Based on a pangenome graph platform, we simultaneously analyzed the impacts of SNPs and SVs in the population structure and phenotypic formation of global cattle using 2,409 individuals from 82 breeds. We demonstrated that SVs, like SNPs, …
View article: Comprehensive Multi-omics Analysis of Regulatory Variants for Body Weight in Cattle
Comprehensive Multi-omics Analysis of Regulatory Variants for Body Weight in Cattle Open
Body weight is a polygenic trait with intricate inheritance patterns. Functional genomics enriched with multi-layer annotations offers essential resources for exploring the genetic architecture of complex traits. In this study, we conducte…
View article: Selection Signature Analysis of Whole-Genome Sequences to Identify Genome Differences Between Selected and Unselected Holstein Cattle
Selection Signature Analysis of Whole-Genome Sequences to Identify Genome Differences Between Selected and Unselected Holstein Cattle Open
A unique line of Holstein cattle has been maintained without selection in Minnesota since 1964. After many generations, unselected cattle produce less milk, but have better reproductive performance and health traits when compared with cont…
View article: An atlas of cell type specific regulatory effects in cattle
An atlas of cell type specific regulatory effects in cattle Open
Understanding the genetic and molecular architecture of complex traits and artificial selection is crucial for advancing sustainable precision breeding in cattle and other livestock. Yet, how genetic variation affects cellular gene express…
View article: Genetic score omics regression and multitrait meta-analysis detect widespread <i>cis</i> -regulatory effects shaping bovine complex traits
Genetic score omics regression and multitrait meta-analysis detect widespread <i>cis</i> -regulatory effects shaping bovine complex traits Open
To complete the genome-to-phenome map, transcriptome-wide association studies (TWAS) are performed to correlate genetically predicted gene expression with observed phenotypic measurements. However, the relatively small training population …
View article: An atlas of cell type specific regulatory effects in cattle
An atlas of cell type specific regulatory effects in cattle Open
Understanding the genetic and molecular architecture of complex traits and artificial selection is crucial for advancing sustainable precision breeding in cattle and other livestock. Yet, how genetic variation affects cellular gene express…
View article: Haplotype‐resolved genome and pan‐genome graphs reveal the impacts of structural variation on functional genome and feather colors in chickens
Haplotype‐resolved genome and pan‐genome graphs reveal the impacts of structural variation on functional genome and feather colors in chickens Open
Structural variation (SV) refers to a wide range of genetic variations that significantly affect genome biology and complex phenotypes. However, the population‐level SV landscape and its functional impacts on chickens are largely unknown. …
View article: Exploring Tissue- and Sex-Specific DNA Methylation in Cattle Using a Pan-Mammalian Infinium Array
Exploring Tissue- and Sex-Specific DNA Methylation in Cattle Using a Pan-Mammalian Infinium Array Open
DNA methylation is crucial in gene expression regulation and tissue differentiation in livestock. However, genome-wide methylation patterns among tissues remain underexplored in cattle, one of the world’s most important farm animals. This …
View article: Long read and preliminary pangenome analyses reveal breed-specific structural variations and novel sequences in Holstein and Jersey cattle
Long read and preliminary pangenome analyses reveal breed-specific structural variations and novel sequences in Holstein and Jersey cattle Open
View article: Transcriptional Profiling of Abomasal Mucosa from Young Calves Experimentally Infected with Ostertagia ostertagi
Transcriptional Profiling of Abomasal Mucosa from Young Calves Experimentally Infected with Ostertagia ostertagi Open
Ostertagia ostertagi, also known as the brown stomach worm, causes significant pathology in the abomasum, resulting in production and nutritional losses in cattle. Alternative control measures, such as vaccination, are urgently needed beca…
View article: Time-dependent RNA transcriptional profiling of abomasal mucosa in cattle infected with Ostertagia ostertagi
Time-dependent RNA transcriptional profiling of abomasal mucosa in cattle infected with Ostertagia ostertagi Open
In this study, we infected Holstein calves with Ostertagia ostertagi stage 3 larvae (L3) and determined gene expression profiles of abomasal fundic and pyloric mucosa by RNA sequencing (RNA-seq) at 3–5, 7–9, 10, and 21 days post-infection …
View article: Integrating large-scale meta-GWAS and PigGTEx resources to decipher the genetic basis of 232 complex traits in pigs
Integrating large-scale meta-GWAS and PigGTEx resources to decipher the genetic basis of 232 complex traits in pigs Open
Understanding the molecular and cellular mechanisms underlying complex traits in pigs is crucial for enhancing genetic gain via artificial selection and utilizing pigs as models for human disease and biology. Here, we conducted comprehensi…
View article: A Developmental Gene Expression Atlas Reveals Novel Biological Basis of Complex Phenotypes in Sheep
A Developmental Gene Expression Atlas Reveals Novel Biological Basis of Complex Phenotypes in Sheep Open
Sheep (Ovis aries) represent one of the most important livestock species for global animal protein and wool production. However, little is known about the genetic and biological basis of ovine phenotypes, particularly those with high econo…
View article: FarmGTEx TWAS-server: An Interactive Web Server for Customized TWAS Analysis
FarmGTEx TWAS-server: An Interactive Web Server for Customized TWAS Analysis Open
Transcriptome-wide association study (TWAS) is a powerful approach for investigating the molecular mechanisms linking genetic loci to complex phenotypes. However, the complexity of the TWAS analytical pipeline, including the construction o…
View article: A resource of longitudinal RNA-seq data of Holstein cow rumen, duodenum, and colon epithelial cells during the lactation cycle
A resource of longitudinal RNA-seq data of Holstein cow rumen, duodenum, and colon epithelial cells during the lactation cycle Open
Objective As one of the most important ruminant breeds, Holstein cattle supply a significant portion of milk and dairy for human consumption, playing a crucial role in agribusiness. The goal of our study was to examine the molecular adapta…
View article: Profiling Genome-Wide Methylation Patterns in Cattle Infected with Ostertagia ostertagi
Profiling Genome-Wide Methylation Patterns in Cattle Infected with Ostertagia ostertagi Open
DNA methylation (DNAm) regulates gene expression and genomic imprinting. This study aimed to investigate the effect of gastrointestinal (GI) nematode infection on host DNAm. Helminth-free Holstein steers were either infected with Ostertagi…
View article: Multiomics analysis reveals signatures of selection and loci associated with complex traits in pigs
Multiomics analysis reveals signatures of selection and loci associated with complex traits in pigs Open
The genetic basis of complex traits and phenotypic differentiation remains unclear in pigs. Using nine genomes—seven of which were newly generated, high‐quality de novo assembled genomes—and 1081 resequencing genomes, we built a pan‐genome…
View article: A multi-tissue developmental gene expression atlas towards understanding the biological basis of phenotypes in sheep
A multi-tissue developmental gene expression atlas towards understanding the biological basis of phenotypes in sheep Open
Sheep ( Ovis aries ) represents one of the most important livestock species for animal protein and wool production worldwide. However, little is known about the genetic and biological basis of ovine phenotypes, particularly for those of hi…
View article: 201 Transcriptome analysis of bovine abomasal mucosa following experimental infection with <i>Ostertagia ostertagi</i>
201 Transcriptome analysis of bovine abomasal mucosa following experimental infection with <i>Ostertagia ostertagi</i> Open
Ostertagia ostertagi is a cattle stomach nematode that causes significant disease; however, little is known about host responses to infection. Due to the emergence of drug resistance in these parasites, there is a need for alternative trea…
View article: Systemic interindividual DNA methylation variants in cattle share major hallmarks with those in humans
Systemic interindividual DNA methylation variants in cattle share major hallmarks with those in humans Open
Background We recently identified ~ 10,000 correlated regions of systemic interindividual epigenetic variation (CoRSIVs) in the human genome. These methylation variants are amenable to population studies, as DNA methylation measurements in…
View article: Cattle Cell Atlas: a multi-tissue single cell expression repository for advanced bovine genomics and comparative biology
Cattle Cell Atlas: a multi-tissue single cell expression repository for advanced bovine genomics and comparative biology Open
Systematic characterization of the molecular states of cells in livestock tissues is essential for understanding cellular and genetic mechanisms underlying economically and ecologically important physiological traits. This knowledge contri…
View article: A Pilot Detection and Associate Study of Gene Presence-Absence Variation in Holstein Cattle
A Pilot Detection and Associate Study of Gene Presence-Absence Variation in Holstein Cattle Open
Presence-absence variations (PAVs) are important structural variations, wherein a genomic segment containing one or more genes is present in some individuals but absent in others. While PAVs have been extensively studied in plants, researc…
View article: Transcriptomic profiling of gastrointestinal tracts in dairy cattle during lactation reveals molecular adaptations for milk synthesis
Transcriptomic profiling of gastrointestinal tracts in dairy cattle during lactation reveals molecular adaptations for milk synthesis Open
During lactation, dairy cattle's digestive tract requires significant adaptations to meet the increased nutrient demands for milk production. As we attempt to improve milk-related traits through selective pressure, it is crucial to underst…
View article: Structural variant landscapes reveal convergent signatures of evolution in sheep and goats
Structural variant landscapes reveal convergent signatures of evolution in sheep and goats Open