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Opening the Black Box: Interpretable Machine Learning for Geneticists

Trends in genetics, 2020-06, Vol.36 (6), p.442-455

2020

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Assessing the evolution of research topics in a biological field using plant science as an example

PLoS biology, 2024-05, Vol.22 (5), p.e3002612-e3002612

2024

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Diversity, classification and function of the plant protein kinase superfamily

Philosophical transactions of the Royal Society of London. Series B. Biological sciences, 2012-09, Vol.367 (1602), p.2619

2012

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Transcriptome-Based Prediction of Complex Traits in Maize

The Plant cell, 2020, Vol.32 (1), p.139-151

2020

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Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution

The Plant journal : for cell and molecular biology, 2012-08, Vol.71 (3), p.492-502

2012

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High‐throughput measurement of plant fitness traits with an object detection method using Faster R‐CNN

The New phytologist, 2022-05, Vol.234 (4), p.1521-1533

2022

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Importance of Lineage-Specific Expansion of Plant Tandem Duplicates in the Adaptive Response to Environmental Stimuli

Plant physiology (Bethesda), 2008-10, Vol.148 (2), p.993-1003

2008

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The causes and molecular consequences of polyploidy in flowering plants

Annals of the New York Academy of Sciences, 2014-07, Vol.1320 (1), p.16-34

2014

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Evolutionary History and Stress Regulation of Plant Receptor-Like Kinase/Pelle Genes

Plant physiology (Bethesda), 2009-05, Vol.150 (1), p.12-26

2009

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Diversity, expansion, and evolutionary novelty of plant DNA-binding transcription factor families

Biochimica et biophysica acta. Gene regulatory mechanisms, 2017-01, Vol.1860 (1), p.3-20

2017

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COST1 regulates autophagy to control plant drought tolerance

Proceedings of the National Academy of Sciences - PNAS, 2020-03, Vol.117 (13), p.7482-7493

2020

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

G3 : genes - genomes - genetics, 2019-11, Vol.9 (11), p.3691-3702

2019

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Putative cis-Regulatory Elements Predict Iron Deficiency Responses in Arabidopsis Roots

Plant physiology (Bethesda), 2020-03, Vol.182 (3), p.1420-1439

2020

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Robust predictions of specialized metabolism genes through machine learning

Proceedings of the National Academy of Sciences - PNAS, 2019-02, Vol.116 (6), p.2344-2353

2019

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Optimising the use of gene expression data to predict plant metabolic pathway memberships

The New phytologist, 2021-07, Vol.231 (1), p.475-489

2021

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MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

Plant physiology (Bethesda), 2014-02, Vol.164 (2), p.513-524

2014

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Phylogenetic comparison of F-Box (FBX) gene superfamily within the plant kingdom reveals divergent evolutionary histories indicative of genomic drift

PloS one, 2011-01, Vol.6 (1), p.e16219-e16219

2011

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The Impact of the Branched-Chain Ketoacid Dehydrogenase Complex on Amino Acid Homeostasis in Arabidopsis

Plant physiology (Bethesda), 2015-11, Vol.169 (3), p.1807-1820

2015

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Impact of short-read sequencing on the misassembly of a plant genome

BMC genomics, 2021-02, Vol.22 (1), p.99-99, Article 99

2021

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A G-Box-Like Motif Is Necessary for Transcriptional Regulation by Circadian Pseudo-Response Regulators in Arabidopsis

Plant physiology (Bethesda), 2016-01, Vol.170 (1), p.528-539

2016

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Evolution of Gene Duplication in Plants

Plant physiology (Bethesda), 2016-08, Vol.171 (4), p.2294-2316

2016

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Evolution of a plant gene cluster in Solanaceae and emergence of metabolic diversity

eLife, 2020-07, Vol.9

2020

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Changes in Transcript Abundance in Chlamydomonas reinhardtii following Nitrogen Deprivation Predict Diversion of Metabolism

Plant physiology (Bethesda), 2010-12, Vol.154 (4), p.1737-1752

2010

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Transcriptional coordination of physiological responses in Nannochloropsis oceanica CCMP1779 under light/dark cycles

The Plant journal : for cell and molecular biology, 2015-09, Vol.83 (6), p.1097-1113

2015

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Comparative analysis of the receptor-like kinase family in Arabidopsis and rice

The Plant cell, 2004-05, Vol.16 (5), p.1220-1234

2004

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Opening the Black Box: Interpretable Machine Learning for Geneticists

Assessing the evolution of research topics in a biological field using plant science as an example

Diversity, classification and function of the plant protein kinase superfamily

Transcriptome-Based Prediction of Complex Traits in Maize

Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution

High‐throughput measurement of plant fitness traits with an object detection method using Faster R‐CNN

Importance of Lineage-Specific Expansion of Plant Tandem Duplicates in the Adaptive Response to Environmental Stimuli

The causes and molecular consequences of polyploidy in flowering plants

Evolutionary History and Stress Regulation of Plant Receptor-Like Kinase/Pelle Genes

Diversity, expansion, and evolutionary novelty of plant DNA-binding transcription factor families

COST1 regulates autophagy to control plant drought tolerance

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

Putative cis-Regulatory Elements Predict Iron Deficiency Responses in Arabidopsis Roots

Robust predictions of specialized metabolism genes through machine learning

Optimising the use of gene expression data to predict plant metabolic pathway memberships

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

Phylogenetic comparison of F-Box (FBX) gene superfamily within the plant kingdom reveals divergent evolutionary histories indicative of genomic drift

The Impact of the Branched-Chain Ketoacid Dehydrogenase Complex on Amino Acid Homeostasis in Arabidopsis

Impact of short-read sequencing on the misassembly of a plant genome

A G-Box-Like Motif Is Necessary for Transcriptional Regulation by Circadian Pseudo-Response Regulators in Arabidopsis

Evolution of Gene Duplication in Plants

Evolution of a plant gene cluster in Solanaceae and emergence of metabolic diversity

Changes in Transcript Abundance in Chlamydomonas reinhardtii following Nitrogen Deprivation Predict Diversion of Metabolism

Transcriptional coordination of physiological responses in Nannochloropsis oceanica CCMP1779 under light/dark cycles

Comparative analysis of the receptor-like kinase family in Arabidopsis and rice

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