Estimation of Complex-Trait Prediction Accuracy from the Different Holo-Omics Interaction Models

An atlas of robust microbiome associations with phenotypic traits based on large-scale cohorts from two continents

(2022) Daphna Rothschild et al.   PLoS One

Optimizing Plant Breeding Programs for Genomic Selection

(2022) Lance F. Merrick et al.   Agronomy-Basel

Comparative hologenomics of two Ixodes scapularis tick populations in New Jersey

(2021) Dana C. Price et al.   PeerJ

The Gut Microbial Architecture of Efficiency Traits in the Domestic Poultry Model Species Japanese Quail (Coturnix japonica) Assessed by Mixed Linear Models

(2020) Solveig Vollmar et al.   G3-Genes Genomes Genetics

On Hadamard and Kronecker products in covariance structures for genotype × environment interaction

(2020) Johannes W. R. Martini et al.   Plant Genome

Holo-Omics: Integrated Host-Microbiota Multi-omics for Basic and Applied Biological Research

(2020) Lasse Nyholm et al.   iScience

Microbiability of meat quality and carcass composition traits in swine

(2020) Piush Khanal et al.   JOURNAL OF ANIMAL BREEDING AND GENETICS

CORE GREML for estimating covariance between random effects in linear mixed models for complex trait analyses

(2020) Xuan Zhou et al.   Nature Communications

Applications of Support Vector Machine in Genomic Prediction in Pig and Maize Populations

(2020) Wei Zhao et al.   Frontiers in Genetics

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Machine learning to predict microbial community functions: An analysis of dissolved organic carbon from litter decomposition

(2019) Jaron Thompson et al.   PLoS One

Evolutionary Insights into the Tick Hologenome

(2019) Sandra Díaz-Sánchez et al.   TRENDS IN PARASITOLOGY

Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle

(2019) Fuyong Li et al.   Microbiome

A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions

(2019) R. John Wallace et al.   Science Advances

Identification of rumen microbial biomarkers linked to methane emission in Holstein dairy cows

(2019) Yuliaxis Ramayo‐Caldas et al.   JOURNAL OF ANIMAL BREEDING AND GENETICS

Selecting the hologenome to breed for an improved feed efficiency in pigs—A novel selection index

(2019) Ramona Weishaar et al.   JOURNAL OF ANIMAL BREEDING AND GENETICS

Current understanding of the human microbiome

(2018) Jack A Gilbert et al.   NATURE MEDICINE

Host Age Affects the Development of Southern Catfish Gut Bacterial Community Divergent From That in the Food and Rearing Water

(2018) Zhimin Zhang et al.   Frontiers in Microbiology

Environment dominates over host genetics in shaping human gut microbiota

(2018) Daphna Rothschild et al.   NATURE

Harnessing genomic information for livestock improvement

(2018) Michel Georges et al.   NATURE REVIEWS GENETICS

Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows

(2018) Gareth Frank Difford et al.   PLoS Genetics

Host Genome Influence on Gut Microbial Composition and Microbial Prediction of Complex Traits in Pigs

(2017) Amelia Camarinha-Silva et al.   GENETICS

Orthogonal Estimates of Variances for Additive, Dominance, and Epistatic Effects in Populations

(2017) Zulma G. Vitezica et al.   GENETICS

Host Genome Influence on Gut Microbial Composition and Microbial Prediction of Complex Traits in Pigs

(2017) Amelia Camarinha-Silva et al.   GENETICS

Orthogonal Estimates of Variances for Additive, Dominance, and Epistatic Effects in Populations

(2017) Zulma G. Vitezica et al.   GENETICS

Microbes Drive Evolution of Animals and Plants: the Hologenome Concept

(2016) Eugene Rosenberg et al.   mBio

A reference gene catalogue of the pig gut microbiome

(2016) Liang Xiao et al.   Nature Microbiology

Microbiota and Host Nutrition across Plant and Animal Kingdoms

(2015) Stéphane Hacquard et al.   Cell Host & Microbe

Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases

(2014) Alexander Gusev et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genome-Wide Regression and Prediction with the BGLR Statistical Package

(2014) P. Perez et al.   GENETICS

Metagenomic Predictions: From Microbiome to Complex Health and Environmental Phenotypes in Humans and Cattle

(2013) Elizabeth M. Ross et al.   PLoS One

Bayesian nonlinear regression for large p small n problems

(2012) Sounak Chakraborty et al.   JOURNAL OF MULTIVARIATE ANALYSIS

Interactions Between the Microbiota and the Immune System

(2012) L. V. Hooper et al.   SCIENCE

Using the genomic relationship matrix to predict the accuracy of genomic selection

(2011) M.E. Goddard et al.   JOURNAL OF ANIMAL BREEDING AND GENETICS

Genomic selection: prediction of accuracy and maximisation of long term response

(2008) Mike Goddard   GENETICA

Efficient Methods to Compute Genomic Predictions

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