Machine learning in plant science and plant breeding

Reconstruction of Networks with Direct and Indirect Genetic Effects

(2020) Willem Kruijer et al.   GENETICS

Crop Phenomics and High-Throughput Phenotyping: Past Decades, Current Challenges, and Future Perspectives

(2020) Wanneng Yang et al.   Molecular Plant

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

A CNN-RNN Framework for Crop Yield Prediction

(2020) Saeed Khaki et al.   Frontiers in Plant Science

On to the next chapter for crop breeding: Convergence with data science

(2020) Elhan S. Ersoz et al.   CROP SCIENCE

Deep learning for plant genomics and crop improvement

(2020) Hai Wang et al.   CURRENT OPINION IN PLANT BIOLOGY

Dominance Effects and Functional Enrichments Improve Prediction of Agronomic Traits in Hybrid Maize

(2020) Guillaume P. Ramstein et al.   GENETICS

Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions

(2020) Peng Zhou et al.   PLANT CELL

Regularized selection indices for breeding value prediction using hyper-spectral image data

(2020) Marco Lopez-Cruz et al.   Scientific Reports

Optimising realism of synthetic images using cycle generative adversarial networks for improved part segmentation

(2020) R. Barth et al.   COMPUTERS AND ELECTRONICS IN AGRICULTURE

Opening the Black Box: Interpretable Machine Learning for Geneticists

(2020) Christina B. Azodi et al.   TRENDS IN GENETICS

Machine learning: A powerful tool for gene function prediction in plants

(2020) Elizabeth H. Mahood et al.   Applications in Plant Sciences

Review: New sensors and data-driven approaches—A path to next generation phenomics

(2019) Thomas Roitsch et al.   PLANT SCIENCE

New Deep Learning Genomic-Based Prediction Model for Multiple Traits with Binary, Ordinal, and Continuous Phenotypes

(2019) Osval A. Montesinos-López et al.   G3-Genes Genomes Genetics

CropDeep: The Crop Vision Dataset for Deep-Learning-Based Classification and Detection in Precision Agriculture

(2019) Yang-Yang Zheng et al.   SENSORS

Evolutionarily informed deep learning methods for predicting relative transcript abundance from DNA sequence

(2019) Jacob D. Washburn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamics of gene expression in single root cells of A. thaliana

(2019) Ken Jean-Baptiste et al.   PLANT CELL

Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing

(2019) Tom Denyer et al.   DEVELOPMENTAL CELL

BrAPI - an Application Programming Interface for Plant Breeding Applications

(2019) Rafael Abbeloos et al.   BIOINFORMATICS

Genomic prediction of maize yield across European environmental conditions

(2019) Emilie J. Millet et al.   NATURE GENETICS

Crop Yield Prediction Using Deep Neural Networks

(2019) Saeed Khaki et al.   Frontiers in Plant Science

Deep learning – Method overview and review of use for fruit detection and yield estimation

(2019) Anand Koirala et al.   COMPUTERS AND ELECTRONICS IN AGRICULTURE

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

QTG-Finder: A Machine-Learning Based Algorithm To Prioritize Causal Genes of Quantitative Trait Loci in Arabidopsis and Rice

(2019) Fan Lin et al.   G3-Genes Genomes Genetics

A Guide for Using Deep Learning for Complex Trait Genomic Prediction

(2019) Pérez-Enciso et al.   Genes

Cis-regulatory code for predicting plant cell-type transcriptional response to high salinity

(2019) Sahra Uygun et al.   PLANT PHYSIOLOGY

Identification of the expressome by machine learning on omics data

(2019) Ryan C. Sartor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Benchmarking Parametric and Machine Learning Models for Genomic Prediction of Complex Traits

(2019) Christina B. Azodi et al.   G3-Genes Genomes Genetics

Crop Phenomics: Current Status and Perspectives

(2019) Chunjiang Zhao et al.   Frontiers in Plant Science

Plant-part segmentation using deep learning and multi-view vision

(2019) Weinan Shi et al.   BIOSYSTEMS ENGINEERING

Deep Learning-Based Phenotyping System With Glocal Description of Plant Anomalies and Symptoms

(2019) Alvaro Fuentes et al.   Frontiers in Plant Science

Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize

(2018) Ji Huang et al.   BMC PLANT BIOLOGY

Data synthesis methods for semantic segmentation in agriculture: A Capsicum annuum dataset

(2018) R. Barth et al.   COMPUTERS AND ELECTRONICS IN AGRICULTURE

Deep learning in agriculture: A survey

(2018) Andreas Kamilaris et al.   COMPUTERS AND ELECTRONICS IN AGRICULTURE

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

(2018) Tobias A. Schrag et al.   GENETICS

DNA sequence and shape are predictive for meiotic crossovers throughout the plant kingdom

(2018) Sevgin Demirci et al.   PLANT JOURNAL

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

(2018) Fred van Eeuwijk et al.   PLANT SCIENCE

Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants

(2018) Kranthi Varala et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient genome-wide genotyping strategies and data integration in crop plants

(2018) Davoud Torkamaneh et al.   THEORETICAL AND APPLIED GENETICS

Supervised Machine Learning for Population Genetics: A New Paradigm

(2018) Daniel R. Schrider et al.   TRENDS IN GENETICS

Translating High-Throughput Phenotyping into Genetic Gain

(2018) José Luis Araus et al.   TRENDS 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

Genome-wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon

(2018) Yann Bourgeois et al.   PLANT JOURNAL

Deep phenotyping: deep learning for temporal phenotype/genotype classification

(2018) Sarah Taghavi Namin et al.   Plant Methods

Deep Learning for Plant Stress Phenotyping: Trends and Future Perspectives

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

A primer on deep learning in genomics

(2018) James Zou et al.   NATURE GENETICS

Computer vision-based phenotyping for improvement of plant productivity: A machine learning perspective

(2018) Keiichi Mochida et al.   GigaScience

Field Scanalyzer: An automated robotic field phenotyping platform for detailed crop monitoring

(2017) Nicolas Virlet et al.   FUNCTIONAL PLANT BIOLOGY

Metabolite and transcript markers for the prediction of potato drought tolerance

(2017) Heike Sprenger et al.   PLANT BIOTECHNOLOGY JOURNAL

A computational interactome for prioritizing genes associated with complex agronomic traits in rice (Oryza sativa)

(2017) Shiwei Liu et al.   PLANT JOURNAL

Genomic Selection in Plant Breeding: Methods, Models, and Perspectives

(2017) José Crossa et al.   TRENDS IN PLANT SCIENCE

Deep Plant Phenomics: A Deep Learning Platform for Complex Plant Phenotyping Tasks

(2017) Jordan R. Ubbens et al.   Frontiers in Plant Science

Plant phenomics: an overview of image acquisition technologies and image data analysis algorithms

(2017) Fernando Perez-Sanz et al.   GigaScience

Finely-grained annotated datasets for image-based plant phenotyping

(2016) Massimo Minervini et al.   PATTERN RECOGNITION LETTERS

EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments

(2016) Olivia Wilkins et al.   PLANT CELL

Methods for causal inference from gene perturbation experiments and validation

(2016) Nicolai Meinshausen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DeepFruits: A Fruit Detection System Using Deep Neural Networks

(2016) Inkyu Sa et al.   SENSORS

Machine Learning for Plant Phenotyping Needs Image Processing

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

Machine Learning for High-Throughput Stress Phenotyping in Plants

(2016) Arti Singh et al.   TRENDS IN PLANT SCIENCE

Lights, camera, action: high-throughput plant phenotyping is ready for a close-up

(2015) Noah Fahlgren et al.   CURRENT OPINION IN PLANT BIOLOGY

Machine learning applications in genetics and genomics

(2015) Maxwell W. Libbrecht et al.   NATURE REVIEWS GENETICS

Simultaneous Discovery, Estimation and Prediction Analysis of Complex Traits Using a Bayesian Mixture Model

(2015) Gerhard Moser et al.   PLoS Genetics

Prioritization of candidate genes in QTL regions based on associations between traits and biological processes

(2014) Joachim W Bargsten et al.   BMC PLANT BIOLOGY

A Review of Imaging Techniques for Plant Phenotyping

(2014) Lei Li et al.   SENSORS

Machine learning for Big Data analytics in plants

(2014) Chuang Ma et al.   TRENDS IN PLANT SCIENCE

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

Machine Learning Approaches Distinguish Multiple Stress Conditions using Stress-Responsive Genes and Identify Candidate Genes for Broad Resistance in Rice

(2013) R. Shaik et al.   PLANT PHYSIOLOGY

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

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

Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype–phenotype relationships and its relevance to crop improvement

(2013) Joshua N. Cobb et al.   THEORETICAL AND APPLIED GENETICS

Cell to whole-plant phenotyping: the best is yet to come

(2013) Stijn Dhondt et al.   TRENDS IN PLANT SCIENCE

Machine learning and genome annotation: a match meant to be?

(2013) Kevin Y Yip et al.   GENOME BIOLOGY

SPICY: towards automated phenotyping of large pepper plants in the greenhouse

(2012) Gerie van der Heijden et al.   FUNCTIONAL PLANT BIOLOGY

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

The gradient boosting algorithm and random boosting for genome-assisted evaluation in large data sets

(2012) O. González-Recio et al.   JOURNAL OF DAIRY SCIENCE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Application of support vector regression to genome-assisted prediction of quantitative traits

(2011) Nanye Long et al.   THEORETICAL AND APPLIED GENETICS

Semi-parametric genomic-enabled prediction of genetic values using reproducing kernel Hilbert spaces methods

(2010) GUSTAVO DE LOS CAMPOS et al.   Genetics Research

Probing the Reproducibility of Leaf Growth and Molecular Phenotypes: A Comparison of Three Arabidopsis Accessions Cultivated in Ten Laboratories

(2010) C. Massonnet et al.   PLANT PHYSIOLOGY