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Computational inference of gene regulatory networks: Approaches, limitations and opportunities

Biochimica et biophysica acta. Gene regulatory mechanisms, 2017-01, Vol.1860 (1), p.41-52

2017

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iTAK： A Program for Genome-wide Prediction and Classification of Plant Transcription Factors, Transcriptional Regulators, and Protein Kinases

Molecular plant, 2016-12, Vol.9 (12), p.1667-1670

2016

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Genomic Signatures of Specialized Metabolism in Plants

Science (American Association for the Advancement of Science), 2014-05, Vol.344 (6183), p.510-513

2014

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Nanotechnology to advance CRISPR-Cas genetic engineering of plants

Nature nanotechnology, 2021-03, Vol.16 (3), p.243-250

2021

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Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants

Plant physiology (Bethesda), 2017-04, Vol.173 (4), p.2041-2059

2017

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Plant Metabolic Network 15: A resource of genome‐wide metabolism databases for 126 plants and algae

Journal of integrative plant biology, 2021-11, Vol.63 (11), p.1888-1905

2021

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A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation

Cell, 2021-08, Vol.184 (16), p.4284-4298.e27

2021

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Interdependent iron and phosphorus availability controls photosynthesis through retrograde signaling

Nature communications, 2021-12, Vol.12 (1), p.7211-7211, Article 7211

2021

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METACLUSTER-an R package for context-specific expression analysis of metabolic gene clusters

Bioinformatics (Oxford, England), 2019-09, Vol.35 (17), p.3178-3180

2019

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Progress and challenges in sorghum biotechnology, a multipurpose feedstock for the bioeconomy

Journal of experimental botany, 2022-01, Vol.73 (3), p.646-664

2022

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Systems genomics approaches provide new insights into Arabidopsis thaliana root growth regulation under combinatorial mineral nutrient limitation

PLoS genetics, 2019-11, Vol.15 (11), p.e1008392-e1008392

2019

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Status of genome function annotation in model organisms and crops

Plant direct, 2023-07, Vol.7 (7), p.e499-n/a

2023

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mapman: a user‐driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes

The Plant journal : for cell and molecular biology, 2004-03, Vol.37 (6), p.914-939

2004

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

G3 : genes - genomes - genetics, 2019-10, Vol.9 (10), p.3129-3138

2019

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A high-throughput behavioral screening platform for measuring chemotaxis by C. elegans

PLoS biology, 2024-06, Vol.22 (6), p.e3002672

2024

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

G3 : genes - genomes - genetics, 2020-07, Vol.10 (7), p.2411-2421

2020

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Mineral nutrient signaling controls photosynthesis: focus on iron deficiency-induced chlorosis

Trends in plant science, 2022-05, Vol.27 (5), p.502-509

2022

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AraCyc: a biochemical pathway database for Arabidopsis

Plant physiology (Bethesda), 2003-06, Vol.132 (2), p.453-460

2003

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Molecular and cellular approaches for the detection of protein-protein interactions: latest techniques and current limitations

The Plant journal : for cell and molecular biology, 2008-02, Vol.53 (4), p.610-635

2008

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Non‐destructive, whole‐plant phenotyping reveals dynamic changes in water use efficiency, photosynthesis, and rhizosphere acidification of sorghum accessions under osmotic stress

Plant direct, 2024-03, Vol.8 (3), p.e571-n/a

2024

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Omics-guided metabolic pathway discovery in plants: Resources, approaches, and opportunities

Current opinion in plant biology, 2022-06, Vol.67 (C), p.102222-102222, Article 102222

2022

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The rules of gene expression in plants: organ identity and gene body methylation are key factors for regulation of gene expression in Arabidopsis thaliana

BMC genomics, 2008-09, Vol.9 (1), p.438-438, Article 438

2008

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Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction

BMC genomics, 2017-06, Vol.18 (1), p.480-480, Article 480

2017

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Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network

Nature protocols, 2011-09, Vol.6 (9), p.1429-1442

2011

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MetaCyc and AraCyc. Metabolic Pathway Databases for Plant Research

Plant physiology (Bethesda), 2005-05, Vol.138 (1), p.27-37

2005

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Computational inference of gene regulatory networks: Approaches, limitations and opportunities

iTAK： A Program for Genome-wide Prediction and Classification of Plant Transcription Factors, Transcriptional Regulators, and Protein Kinases

Genomic Signatures of Specialized Metabolism in Plants

Nanotechnology to advance CRISPR-Cas genetic engineering of plants

Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants

Plant Metabolic Network 15: A resource of genome‐wide metabolism databases for 126 plants and algae

A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation

Interdependent iron and phosphorus availability controls photosynthesis through retrograde signaling

METACLUSTER-an R package for context-specific expression analysis of metabolic gene clusters

Progress and challenges in sorghum biotechnology, a multipurpose feedstock for the bioeconomy

Systems genomics approaches provide new insights into Arabidopsis thaliana root growth regulation under combinatorial mineral nutrient limitation

Status of genome function annotation in model organisms and crops

mapman: a user‐driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes

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

A high-throughput behavioral screening platform for measuring chemotaxis by C. elegans

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

Mineral nutrient signaling controls photosynthesis: focus on iron deficiency-induced chlorosis

AraCyc: a biochemical pathway database for Arabidopsis

Molecular and cellular approaches for the detection of protein-protein interactions: latest techniques and current limitations

Non‐destructive, whole‐plant phenotyping reveals dynamic changes in water use efficiency, photosynthesis, and rhizosphere acidification of sorghum accessions under osmotic stress

Omics-guided metabolic pathway discovery in plants: Resources, approaches, and opportunities

The rules of gene expression in plants: organ identity and gene body methylation are key factors for regulation of gene expression in Arabidopsis thaliana

Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction

Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network

MetaCyc and AraCyc. Metabolic Pathway Databases for Plant Research

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