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rmRNAseq: differential expression analysis for repeated-measures RNA-seq data

Bioinformatics, 2020-08, Vol.36 (16), p.4432-4439

2020

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The Arabidopsis MicroRNA396-GRF1/GRF3 Regulatory Module Acts as a Developmental Regulator in the Reprogramming of Root Cells during Cyst Nematode Infection

Plant physiology (Bethesda), 2012-05, Vol.159 (1), p.321-335

2012

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Copy number variation detection using next generation sequencing read counts

BMC bioinformatics, 2014-04, Vol.15 (1), p.109-109, Article 109

2014

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Gene mapping via bulked segregant RNA-Seq (BSR-Seq)

PloS one, 2012-05, Vol.7 (5), p.e36406-e36406

2012

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Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution

BMC biology, 2008-04, Vol.6 (1), p.16-16

2008

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Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content

PLoS genetics, 2009-11, Vol.5 (11), p.e1000734-e1000734

2009

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Testing for the Supremacy of a Multinomial Cell Probability

Journal of the American Statistical Association, 2009-09, Vol.104 (487), p.1052-1059

Nettleton, Dan

2009

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Transcriptional responses of Pseudomonas syringae to growth in epiphytic versus apoplastic leaf sites

Proceedings of the National Academy of Sciences - PNAS, 2013-01, Vol.110 (5), p.E425-E434

2013

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Host-Induced Gene Silencing in Barley Powdery Mildew Reveals a Class of Ribonuclease-Like Effectors

Molecular plant-microbe interactions, 2013-06, Vol.26 (6), p.633-642

2013

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Root Type-Specific Reprogramming of Maize Pericycle Transcriptomes by Local High Nitrate Results in Disparate Lateral Root Branching Patterns

Plant physiology (Bethesda), 2016-03, Vol.170 (3), p.1783-1798

2016

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Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS

Genome Biology, 2017-10, Vol.18 (1), p.192-192, Article 192

2017

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A hidden Markov tree model for testing multiple hypotheses corresponding to Gene Ontology gene sets

BMC bioinformatics, 2018-03, Vol.19 (1), p.107-107, Article 107

2018

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Small RNA discovery in the interaction between barley and the powdery mildew pathogen

BMC genomics, 2019-07, Vol.20 (1), p.610-610, Article 610

2019

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Gene Expression Programs during Shoot, Root, and Callus Development in Arabidopsis Tissue Culture

Plant physiology (Bethesda), 2006-06, Vol.141 (2), p.620-637

2006

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QQS orphan gene regulates carbon and nitrogen partitioning across species via NF-YC interactions

Proceedings of the National Academy of Sciences - PNAS, 2015-11, Vol.112 (47), p.14734-14739

2015

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All possible modes of gene action are observed in a global comparison of gene expression in a maize F1 hybrid and its inbred parents

Proceedings of the National Academy of Sciences - PNAS, 2006-05, Vol.103 (18), p.6805-6810

2006

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Crowdsourcing image analysis for plant phenomics to generate ground truth data for machine learning

PLoS computational biology, 2018-07, Vol.14 (7), p.e1006337-e1006337

2018

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Code-assisted discovery of TAL effector targets in bacterial leaf streak of rice reveals contrast with bacterial blight and a novel susceptibility gene

PLoS pathogens, 2014-02, Vol.10 (2), p.e1003972-e1003972

2014

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Stress response to CO2 deprivation by Arabidopsis thaliana in plant cultures

PloS one, 2019-03, Vol.14 (3), p.e0212462-e0212462

2019

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Loss of RNA-dependent RNA polymerase 2 (RDR2) function causes widespread and unexpected changes in the expression of transposons, genes, and 24-nt small RNAs

PLoS genetics, 2009-11, Vol.5 (11), p.e1000737-e1000737

2009

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Developmental Transcript Profiling of Cyst Nematode Feeding Cells in Soybean Roots

Molecular plant-microbe interactions, 2007-05, Vol.20 (5), p.510-525

2007

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QQS orphan gene and its interactor NF‐YC4 reduce susceptibility to pathogens and pests

Plant biotechnology journal, 2019-01, Vol.17 (1), p.252-263

2019

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Agrobacterium tumefaciens-Mediated Transformation of Maize Embryos Using a Standard Binary Vector System

Plant physiology (Bethesda), 2002-05, Vol.129 (1), p.13-22

2002

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Unique genome-wide transcriptome profiles of chicken macrophages exposed to Salmonella-derived endotoxin

BMC genomics, 2010-10, Vol.11 (1), p.545-545, Article 545

2010

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Parallel genome-wide expression profiling of host and pathogen during soybean cyst nematode infection of soybean

Molecular plant-microbe interactions, 2007-03, Vol.20 (3), p.293-305

2007

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rmRNAseq: differential expression analysis for repeated-measures RNA-seq data

The Arabidopsis MicroRNA396-GRF1/GRF3 Regulatory Module Acts as a Developmental Regulator in the Reprogramming of Root Cells during Cyst Nematode Infection

Copy number variation detection using next generation sequencing read counts

Gene mapping via bulked segregant RNA-Seq (BSR-Seq)

Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution

Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content

Testing for the Supremacy of a Multinomial Cell Probability

Transcriptional responses of Pseudomonas syringae to growth in epiphytic versus apoplastic leaf sites

Host-Induced Gene Silencing in Barley Powdery Mildew Reveals a Class of Ribonuclease-Like Effectors

Root Type-Specific Reprogramming of Maize Pericycle Transcriptomes by Local High Nitrate Results in Disparate Lateral Root Branching Patterns

Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS

A hidden Markov tree model for testing multiple hypotheses corresponding to Gene Ontology gene sets

Small RNA discovery in the interaction between barley and the powdery mildew pathogen

Gene Expression Programs during Shoot, Root, and Callus Development in Arabidopsis Tissue Culture

QQS orphan gene regulates carbon and nitrogen partitioning across species via NF-YC interactions

All possible modes of gene action are observed in a global comparison of gene expression in a maize F1 hybrid and its inbred parents

Crowdsourcing image analysis for plant phenomics to generate ground truth data for machine learning

Code-assisted discovery of TAL effector targets in bacterial leaf streak of rice reveals contrast with bacterial blight and a novel susceptibility gene

Stress response to CO2 deprivation by Arabidopsis thaliana in plant cultures

Loss of RNA-dependent RNA polymerase 2 (RDR2) function causes widespread and unexpected changes in the expression of transposons, genes, and 24-nt small RNAs

Developmental Transcript Profiling of Cyst Nematode Feeding Cells in Soybean Roots

QQS orphan gene and its interactor NF‐YC4 reduce susceptibility to pathogens and pests

Agrobacterium tumefaciens-Mediated Transformation of Maize Embryos Using a Standard Binary Vector System

Unique genome-wide transcriptome profiles of chicken macrophages exposed to Salmonella-derived endotoxin

Parallel genome-wide expression profiling of host and pathogen during soybean cyst nematode infection of soybean

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