Machine learning bridges omics sciences and plant breeding

MODAS: exploring maize germplasm with multi-omics data association studies

(2022) Songyu Liu et al.   Science Bulletin

easyMF: A Web Platform for Matrix Factorization-Based Gene Discovery from Large-scale Transcriptome Data

(2022) Wenlong Ma et al.   Interdisciplinary Sciences-Computational Life Sciences

Predicting the suitable fertilizer for crop based on soil and environmental factors using various feature selection techniques with classifiers

(2022) Ganesan Mariammal et al.   EXPERT SYSTEMS

High-throughput soybean seeds phenotyping with convolutional neural networks and transfer learning

(2021) Si Yang et al.   Plant Methods

The Modern Plant Breeding Triangle: Optimizing the Use of Genomics, Phenomics, and Enviromics Data

(2021) Jose Crossa et al.   Frontiers in Plant Science

A Comparison for Dimensionality Reduction Methods of Single-Cell RNA-seq Data

(2021) Ruizhi Xiang et al.   Frontiers in Genetics

Tomato plant disease detection using transfer learning with C-GAN synthetic images

(2021) Amreen Abbas et al.   COMPUTERS AND ELECTRONICS IN AGRICULTURE

Prioritization of disease genes from GWAS using ensemble-based positive-unlabeled learning

(2021) Nikita Kolosov et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

A guide to machine learning for biologists

(2021) Joe G. Greener et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Crop yield prediction integrating genotype and weather variables using deep learning

(2021) Johnathon Shook et al.   PLoS One

Review: Application of Artificial Intelligence in Phenomics

(2021) Shona Nabwire et al.   SENSORS

The regulatory landscape of Arabidopsis thaliana roots at single-cell resolution

(2021) Michael W. Dorrity et al.   Nature Communications

Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought Resistance

(2021) Chirag Gupta et al.   Frontiers in Genetics

Improving Genomic Prediction Using High-Dimensional Secondary Phenotypes

(2021) Bader Arouisse et al.   Frontiers in Genetics

Next-generation deep learning based on simulators and synthetic data

(2021) Celso M. de Melo et al.   TRENDS IN COGNITIVE SCIENCES

Integrated omics networks reveal the temporal signaling events of brassinosteroid response in Arabidopsis

(2021) Natalie M. Clark et al.   Nature Communications

Prediction of Maize Phenotypic Traits With Genomic and Environmental Predictors Using Gradient Boosting Frameworks

(2021) Cathy C. Westhues et al.   Frontiers in Plant Science

5Gs for crop genetic improvement

(2020) Rajeev K Varshney et al.   CURRENT OPINION IN PLANT BIOLOGY

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

(2020) Wanneng Yang et al.   Molecular Plant

A practical view of fine-mapping and gene prioritization in the post-genome-wide association era

(2020) R. V. Broekema et al.   Open Biology

Exploring Deep Learning for Complex Trait Genomic Prediction in Polyploid Outcrossing Species

(2020) Laura M. Zingaretti et al.   Frontiers in Plant Science

Considerations in the analysis of plant chromatin accessibility data

(2020) Kerry L Bubb et al.   CURRENT OPINION IN PLANT BIOLOGY

Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions

(2020) Peng Zhou et al.   PLANT CELL

QTG-Finder2: A Generalized Machine-Learning Algorithm for Prioritizing QTL Causal Genes in Plants

(2020) Fan Lin et al.   G3-Genes Genomes Genetics

A scalable SCENIC workflow for single-cell gene regulatory network analysis

(2020) Bram Van de Sande et al.   Nature Protocols

Network‐based approaches for understanding gene regulation and function in plants

(2020) Dae Kwan Ko et al.   PLANT JOURNAL

The Wheat GENIE3 Network Provides Biologically-Relevant Information in Polyploid Wheat

(2020) Sophie A. Harrington et al.   G3-Genes Genomes Genetics

SR4R: An Integrative SNP Resource for Genomic Breeding and Population Research in Rice

(2020) Jun Yan et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

TasselGAN: An Application of the Generative Adversarial Model for Creating Field-Based Maize Tassel Data

(2020) Snehal Shete et al.   Plant Phenomics

Application of deep learning in genomics

(2020) Jianxiao Liu et al.   Science China-Life Sciences

Crop Disease Classification on Inadequate Low-Resolution Target Images

(2020) Juan Wen et al.   SENSORS

Improving Image-Based Plant Disease Classification With Generative Adversarial Network Under Limited Training Set

(2020) Luning Bi et al.   Frontiers in Plant Science

Machine learning in plant science and plant breeding

(2020) Aalt Dirk Jan van Dijk et al.   iScience

Machine learning approaches for crop improvement: Leveraging phenotypic and genotypic big data

(2020) Hao Tong et al.   JOURNAL OF PLANT PHYSIOLOGY

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

(2019) Yang-Yang Zheng et al.   SENSORS

Identification of optimal prediction models using multi-omic data for selecting hybrid rice

(2019) Shibo Wang et al.   HEREDITY

Deep learning: new computational modelling techniques for genomics

(2019) Gökcen Eraslan et al.   NATURE REVIEWS GENETICS

Hybrid Breeding of Rice via Genomic Selection

(2019) Yanru Cui et al.   PLANT BIOTECHNOLOGY JOURNAL

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

Solving Current Limitations of Deep Learning Based Approaches for Plant Disease Detection

(2019) Marko Arsenovic et al.   Symmetry-Basel

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

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

Disentangling Information in Artificial Images of Plant Seedlings Using Semi-Supervised GAN

(2019) Simon Leminen Madsen et al.   Remote Sensing

Genome Wide Association Study and Genomic Selection of Amino Acid Concentrations in Soybean Seeds

(2019) Jun Qin et al.   Frontiers in Plant Science

Visualizing structure and transitions in high-dimensional biological data

(2019) Kevin R. Moon et al.   NATURE BIOTECHNOLOGY

Genome optimization for improvement of maize breeding

(2019) Shuqin Jiang et al.   THEORETICAL AND APPLIED GENETICS

JRmGRN: joint reconstruction of multiple gene regulatory networks with common hub genes using data from multiple tissues or conditions

(2018) Wenping Deng et al.   BIOINFORMATICS

Capturing pair-wise epistatic effects associated with three agronomic traits in barley

(2018) Yi Xu et al.   GENETICA

Points of Significance: Statistics versus machine learning

(2018) Danilo Bzdok et al.   NATURE METHODS

TGMI: an efficient algorithm for identifying pathway regulators through evaluation of triple-gene mutual interaction

(2018) Chathura Gunasekara et al.   NUCLEIC ACIDS RESEARCH

iDREM: Interactive visualization of dynamic regulatory networks

(2018) Jun Ding et al.   PLoS Computational Biology

Deep learning for biology

(2018) Sarah Webb   NATURE

A deep convolutional neural network approach for predicting phenotypes from genotypes

(2018) Wenlong Ma et al.   PLANTA

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

GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks

(2018) Thomas Moerman et al.   BIOINFORMATICS

A guide to deep learning in healthcare

(2018) Andre Esteva et al.   NATURE MEDICINE

Computational prediction of gene regulatory networks in plant growth and development

(2018) Samiul Haque et al.   CURRENT OPINION IN PLANT BIOLOGY

Linear discriminant analysis reveals differences in root architecture in wheat seedlings related to nitrogen uptake efficiency

(2017) Kim Kenobi et al.   JOURNAL OF EXPERIMENTAL BOTANY

Predicting gene regulatory networks by combining spatial and temporal gene expression data inArabidopsisroot stem cells

(2017) Maria Angels de Luis Balaguer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Inference of Transcription Regulatory Network in Low Phytic Acid Soybean Seeds

(2017) Neelam Redekar et al.   Frontiers in Plant Science

ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information

(2016) Alexander Lachmann et al.   BIOINFORMATICS

Dimension reduction techniques for the integrative analysis of multi-omics data

(2016) Chen Meng et al.   BRIEFINGS IN BIOINFORMATICS

Integration of omic networks in a developmental atlas of maize

(2016) J. W. Walley et al.   SCIENCE

A Machine Learning Approach to Predict Gene Regulatory Networks in Seed Development in Arabidopsis

(2016) Ying Ni et al.   Frontiers in Plant Science

Combining tree-based and dynamical systems for the inference of gene regulatory networks

(2015) Vân Anh Huynh-Thu et al.   BIOINFORMATICS

A roadmap to multifactor dimensionality reduction methods

(2015) Damian Gola et al.   BRIEFINGS IN BIOINFORMATICS

Machine Learning-Based Differential Network Analysis: A Study of Stress-Responsive Transcriptomes in Arabidopsis

(2014) C. Ma et al.   PLANT CELL

Machine learning for Big Data analytics in plants

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

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

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

Identification of metagenes and their Interactions through Large-scale Analysis of Arabidopsis Gene Expression Data

(2012) Tyler J Wilson et al.   BMC GENOMICS