Breaking the curse of dimensionality to identify causal variants in Breeding 4

Leveraging biological insight and environmental variation to improve phenotypic prediction: Integrating crop growth models (CGM) with whole genome prediction (WGP)

(2018) C.D. Messina et al.   EUROPEAN JOURNAL OF AGRONOMY

Beyond Genomic Prediction: Combining Different Types ofomicsData Can Improve Prediction of Hybrid Performance in Maize

(2018) Tobias A. Schrag et al.   GENETICS

Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk

(2018) Jian Zhou et al.   NATURE GENETICS

Modelling strategies for assessing and increasing the effectiveness of new phenotyping techniques in plant breeding

(2018) Fred van Eeuwijk et al.   PLANT SCIENCE

Deep Learning: Individual Maize Segmentation From Terrestrial Lidar Data Using Faster R-CNN and Regional Growth Algorithms

(2018) Shichao Jin et al.   Frontiers in Plant Science

Beyond Genomic Prediction: Combining Different Types ofomicsData Can Improve Prediction of Hybrid Performance in Maize

(2018) Tobias A. Schrag et al.   GENETICS

Functional Genetic Variants Revealed by Massively Parallel Precise Genome Editing

(2018) Eilon Sharon et al.   CELL

Dysregulation of expression correlates with rare-allele burden and fitness loss in maize

(2018) Karl A. G. Kremling et al.   NATURE

Maize domestication and gene interaction

(2018) Michelle C. Stitzer et al.   NEW PHYTOLOGIST

Pheno-Deep Counter: a unified and versatile deep learning architecture for leaf counting

(2018) Mario Valerio Giuffrida et al.   PLANT JOURNAL

Deep Learning for Plant Stress Phenotyping: Trends and Future Perspectives

(2018) Asheesh Kumar Singh et al.   TRENDS IN PLANT SCIENCE

On the Road to Breeding 4.0: Unraveling the Good, the Bad, and the Boring of Crop Quantitative Genomics

(2018) Jason G. Wallace et al.   Annual Review of Genetics

Genomic innovation for crop improvement

(2017) Michael W. Bevan et al.   NATURE

Graphtyper enables population-scale genotyping using pangenome graphs

(2017) Hannes P Eggertsson et al.   NATURE GENETICS

Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation

(2017) Punna Ramu et al.   NATURE GENETICS

Automated Identification of Northern Leaf Blight-Infected Maize Plants from Field Imagery Using Deep Learning

(2017) Chad DeChant et al.   PHYTOPATHOLOGY

Commentary: Fisher’s infinitesimal model: A story for the ages

(2017) Michael Turelli   THEORETICAL POPULATION BIOLOGY

Multitrait, Random Regression, or Simple Repeatability Model in High-Throughput Phenotyping Data Improve Genomic Prediction for Wheat Grain Yield

(2017) Jin Sun et al.   Plant Genome

Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize

(2017) Jinliang Yang et al.   PLoS Genetics

Deep learning for computational biology

(2016) Christof Angermueller et al.   Molecular Systems Biology

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

ARGOS8 variants generated by CRISPR-Cas9 improve maize grain yield under field drought stress conditions

(2016) Jinrui Shi et al.   PLANT BIOTECHNOLOGY JOURNAL

Morphogenic Regulators Baby boom and Wuschel Improve Monocot Transformation

(2016) Keith Lowe et al.   PLANT CELL

Metabolomic prediction of yield in hybrid rice

(2016) Shizhong Xu et al.   PLANT JOURNAL

Open chromatin reveals the functional maize genome

(2016) Eli Rodgers-Melnick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Machine Learning for Plant Phenotyping Needs Image Processing

(2016) Sotirios A. Tsaftaris et al.   TRENDS IN PLANT SCIENCE

Using Deep Learning for Image-Based Plant Disease Detection

(2016) Sharada P. Mohanty et al.   Frontiers in Plant Science

Unmanned Aerial Vehicles for High-Throughput Phenotyping and Agronomic Research

(2016) Yeyin Shi et al.   PLoS One

Perspectives for Genomic Selection Applications and Research in Plants

(2015) Nicolas Heslot et al.   CROP SCIENCE

Deep learning

(2015) Yann LeCun et al.   NATURE

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

Natural Variations and Genome-Wide Association Studies in Crop Plants

(2013) Xuehui Huang et al.   Annual Review of Plant Biology

Image analysis is driving a renaissance in growth measurement

(2013) Edgar P Spalding et al.   CURRENT OPINION IN PLANT BIOLOGY

Development and evaluation of a field-based high-throughput phenotyping platform

(2013) Pedro Andrade-Sanchez et al.   FUNCTIONAL PLANT BIOLOGY

Priors in Whole-Genome Regression: The Bayesian Alphabet Returns

(2013) D. Gianola   GENETICS

Impact of Marker Ascertainment Bias on Genomic Selection Accuracy and Estimates of Genetic Diversity

(2013) Nicolas Heslot et al.   PLoS One

Supermodels: sorghum and maize provide mutual insight into the genetics of flowering time

(2013) E. S. Mace 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

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

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

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

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

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

Support Vector Machines and Kernels for Computational Biology

(2008) Asa Ben-Hur et al.   PLoS Computational Biology