Integrating Crop Growth Models with Whole Genome Prediction through Approximate Bayesian Computation

Growing access to phenotype data

(2015)   NATURE GENETICS

Remote, aerial phenotyping of maize traits with a mobile multi-sensor approach

(2015) Frank Liebisch et al.   Plant Methods

Evaluation of Genomic Selection Training Population Designs and Genotyping Strategies in Plant Breeding Programs Using Simulation

(2014) John M. Hickey et al.   CROP SCIENCE

APSIM – Evolution towards a new generation of agricultural systems simulation

(2014) Dean P. Holzworth et al.   ENVIRONMENTAL MODELLING & SOFTWARE

Genomic prediction in biparental tropical maize populations in water-stressed and well-watered environments using low-density and GBS SNPs

(2014) X Zhang et al.   HEREDITY

Breeding drought-tolerant maize hybrids for the US corn-belt: discovery to product

(2014) Mark Cooper et al.   JOURNAL OF EXPERIMENTAL BOTANY

Nitrogen-use efficiency in maize (Zea mays L.): from 'omics' studies to metabolic modelling

(2014) M. Simons et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genomic evaluation of cattle in a multi-breed context

(2014) Mogens Sandø Lund et al.   Livestock Science

A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation

(2014) Juliane Liepe et al.   Nature Protocols

Transgenic alteration of ethylene biosynthesis increases grain yield in maize under field drought-stress conditions

(2014) Jeffrey E. Habben et al.   PLANT BIOTECHNOLOGY JOURNAL

Approximate Bayesian Computation using Markov Chain Monte Carlo simulation: DREAM(ABC)

(2014) Mojtaba Sadegh et al.   WATER RESOURCES RESEARCH

Predicting the future of plant breeding: complementing empirical evaluation with genetic prediction

(2014) Mark Cooper et al.   Crop & Pasture Science

Parametric and Nonparametric Statistical Methods for Genomic Selection of Traits with Additive and Epistatic Genetic Architectures

(2014) Réka Howard et al.   G3-Genes Genomes Genetics

Using systems modelling to explore the potential for root exudates to increase phosphorus use efficiency in cereal crops

(2013) Enli Wang et al.   ENVIRONMENTAL MODELLING & SOFTWARE

Priors in Whole-Genome Regression: The Bayesian Alphabet Returns

(2013) D. Gianola   GENETICS

Genomic BLUP Decoded: A Look into the Black Box of Genomic Prediction

(2013) D. Habier et al.   GENETICS

Post-GWAS: where next? More samples, more SNPs or more biology?

(2013) P Marjoram et al.   HEREDITY

Maize ARGOS1 (ZAR1) transgenic alleles increase hybrid maize yield

(2013) M. Guo et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genomic selection allowing for marker-by-environment interaction

(2013) Torben Schulz-Streeck et al.   PLANT BREEDING

Genomic prediction of dichotomous traits with Bayesian logistic models

(2013) Frank Technow et al.   THEORETICAL AND APPLIED GENETICS

A reaction norm model for genomic selection using high-dimensional genomic and environmental data

(2013) Diego Jarquín et al.   THEORETICAL AND APPLIED GENETICS

Integrating environmental covariates and crop modeling into the genomic selection framework to predict genotype by environment interactions

(2013) Nicolas Heslot et al.   THEORETICAL AND APPLIED GENETICS

Field high-throughput phenotyping: the new crop breeding frontier

(2013) José Luis Araus et al.   TRENDS IN PLANT SCIENCE

Genomic Prediction of Northern Corn Leaf Blight Resistance in Maize with Combined or Separated Training Sets for Heterotic Groups

(2013) Frank Technow et al.   G3-Genes Genomes Genetics

Accuracy of Genomewide Selection for Different Traits with Constant Population Size, Heritability, and Number of Markers

(2013) Emily Combs et al.   Plant Genome

Assessing the Uncertainty when Using a Model to Compare Irrigation Strategies

(2012) Daniel Wallach et al.   AGRONOMY JOURNAL

Back to Basics for Bayesian Model Building in Genomic Selection

(2012) Hanni P. Kärkkäinen et al.   GENETICS

Maximizing the Reliability of Genomic Selection by Optimizing the Calibration Set of Reference Individuals: Comparison of Methods in Two Diverse Groups of Maize Inbreds (Zea mays L.)

(2012) R. Rincent et al.   GENETICS

Improving accuracy of genomic predictions within and between dairy cattle breeds with imputed high-density single nucleotide polymorphism panels

(2012) M. Erbe et al.   JOURNAL OF DAIRY SCIENCE

Genomic and metabolic prediction of complex heterotic traits in hybrid maize

(2012) Christian Riedelsheimer et al.   NATURE GENETICS

A Gene Regulatory Network Model for Floral Transition of the Shoot Apex in Maize and Its Dynamic Modeling

(2012) Zhanshan Dong et al.   PLoS One

Nonparametric Method for Genomics-Based Prediction of Performance of Quantitative Traits Involving Epistasis in Plant Breeding

(2012) Xiaochun Sun et al.   PLoS One

Genome-wide association mapping of leaf metabolic profiles for dissecting complex traits in maize

(2012) C. Riedelsheimer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On sequential Monte Carlo, partial rejection control and approximate Bayesian computation

(2012) G. W. Peters et al.   STATISTICS AND COMPUTING

Assessing Parameter Identifiability in Phylogenetic Models Using Data Cloning

(2012) José Miguel Ponciano et al.   SYSTEMATIC BIOLOGY

Effectiveness of Genomic Prediction of Maize Hybrid Performance in Different Breeding Populations and Environments

(2012) Vanessa S. Windhausen et al.   G3-Genes Genomes Genetics

Using Whole-Genome Sequence Data to Predict Quantitative Trait Phenotypes in Drosophila melanogaster

(2012) Ulrike Ober et al.   PLoS Genetics

Ecological genetics of invasive alien species

(2011) L.-J. Lawson Handley et al.   BIOCONTROL

An in silico compartmentalized metabolic model of Brassica napus enables the systemic study of regulatory aspects of plant central metabolism

(2011) Eleftherios Pilalis et al.   BIOTECHNOLOGY AND BIOENGINEERING

Extension of the bayesian alphabet for genomic selection

(2011) David Habier et al.   BMC BIOINFORMATICS

Genomic Selection in Plant Breeding: A Comparison of Models

(2011) Nicolas Heslot et al.   CROP SCIENCE

High-throughput non-destructive biomass determination during early plant development in maize under field conditions

(2011) J.M. Montes et al.   FIELD CROPS RESEARCH

A Bayesian Antedependence Model for Whole Genome Prediction

(2011) W. Yang et al.   GENETICS

Accelerating the domestication of trees using genomic selection: accuracy of prediction models across ages and environments

(2011) M. F. R. Resende et al.   NEW PHYTOLOGIST

Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism

(2011) Rajib Saha et al.   PLoS One

Evaluation of genome-wide selection efficiency in maize nested association mapping populations

(2011) Zhigang Guo et al.   THEORETICAL AND APPLIED GENETICS

Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP

(2011) Jeffrey B. Endelman   Plant Genome

How much detail and accuracy is required in plant growth sub-models to address questions about optimal management strategies in agricultural systems?

(2011) Michael Renton   AoB Plants

ABC-SysBio--approximate Bayesian computation in Python with GPU support

(2010) J. Liepe et al.   BIOINFORMATICS

Accurate Prediction of Genetic Values for Complex Traits by Whole-Genome Resequencing

(2010) T. Meuwissen et al.   GENETICS

The Impact of Genetic Architecture on Genome-Wide Evaluation Methods

(2010) H. D. Daetwyler et al.   GENETICS

Yield–trait performance landscapes: from theory to application in breeding maize for drought tolerance

(2010) Carlos D. Messina et al.   JOURNAL OF EXPERIMENTAL BOTANY

Adapting APSIM to model the physiology and genetics of complex adaptive traits in field crops

(2010) Graeme L. Hammer et al.   JOURNAL OF EXPERIMENTAL BOTANY

Approximate Bayesian Computation (ABC) in practice

(2010) Katalin Csilléry et al.   TRENDS IN ECOLOGY & EVOLUTION

Modeling QTL for complex traits: detection and context for plant breeding

(2009) Mark Cooper et al.   CURRENT OPINION IN PLANT BIOLOGY

Genetical metabolomics: closing in on phenotypes

(2009) Joost JB Keurentjes   CURRENT OPINION IN PLANT BIOLOGY

Simulating the Yield Impacts of Organ-Level Quantitative Trait Loci Associated With Drought Response in Maize: A “Gene-to-Phenotype” Modeling Approach

(2009) Karine Chenu et al.   GENETICS

ABC: A useful Bayesian tool for the analysis of population data

(2009) J.S. Lopes et al.   INFECTION GENETICS AND EVOLUTION

Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems

(2008) T. Toni et al.   Journal of the Royal Society Interface

Personal genomes: The case of the missing heritability

(2008) Brendan Maher   NATURE

Short-term responses of leaf growth rate to water deficit scale up to whole-plant and crop levels: an integrated modelling approach in maize

(2008) KARINE CHENU et al.   PLANT CELL AND ENVIRONMENT

Metabolomics-assisted breeding: a viable option for crop improvement?

(2008) Alisdair R. Fernie et al.   TRENDS IN GENETICS