QTL mapping for maize starch content and candidate gene prediction combined with co-expression network analysis

Identifying gene coexpression networks underlying the dynamic regulation of wood-forming tissues in Populus under diverse environmental conditions

(2017) Matthew Zinkgraf et al.   NEW PHYTOLOGIST

The genetic architecture of amylose biosynthesis in maize kernel

(2017) Changsheng Li et al.   PLANT BIOTECHNOLOGY JOURNAL

Genomewide Expression and Functional Interactions of Genes under Drought Stress in Maize

(2017) Nepolean Thirunavukkarasu et al.   International Journal of Genomics

Statistical Approaches for Gene Selection, Hub Gene Identification and Module Interaction in Gene Co-Expression Network Analysis: An Application to Aluminum Stress in Soybean (Glycine max L.)

(2017) Samarendra Das et al.   PLoS One

mInDel: a high-throughput and efficient pipeline for genome-wide InDel marker development

(2016) Yuanda Lv et al.   BMC GENOMICS

Network analysis of the metabolome and transcriptome reveals novel regulation of potato pigmentation

(2016) Kyoungwon Cho et al.   JOURNAL OF EXPERIMENTAL BOTANY

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Co-expression network analysis reveals transcription factors associated to cell wall biosynthesis in sugarcane

(2016) Savio Siqueira Ferreira et al.   PLANT MOLECULAR BIOLOGY

GEM, a member of the GRAM domain family of proteins, is part of the ABA signaling pathway

(2016) Nuria Mauri et al.   Scientific Reports

Identification of Crowding Stress Tolerance Co-Expression Networks Involved in Sweet Corn Yield

(2016) Eunsoo Choe et al.   PLoS One

Genetic basis of maize kernel starch content revealed by high-density single nucleotide polymorphism markers in a recombinant inbred line population

(2015) Tingting Wang et al.   BMC PLANT BIOLOGY

Identification of quantitative trait loci underlying the protein, oil and starch contents of maize in multiple environments

(2015) Huaduo Zhang et al.   EUPHYTICA

Cross-Species Network Analysis Uncovers Conserved Nitrogen-Regulated Network Modules in Rice

(2015) Mariana Obertello et al.   PLANT PHYSIOLOGY

Regulatory motifs identified from a maize developmental coexpression network

(2014) Gregory S. Downs et al.   GENOME

Integrated Network Analysis Identifies Fight-Club Nodes as a Class of Hubs Encompassing Key Putative Switch Genes That Induce Major Transcriptome Reprogramming during Grapevine Development

(2014) Maria Concetta Palumbo et al.   PLANT CELL

GEm-Related 5 (GER5), an ABA and stress-responsive GRAM domain protein regulating seed development and inflorescence architecture

(2014) Kevin N. Baron et al.   PLANT SCIENCE

Construction and comparison of gene co-expression networks shows complex plant immune responses

(2014) Luis Guillermo Leal et al.   PeerJ

A Developmental Transcriptional Network for Maize Defines Coexpression Modules

(2013) G. S. Downs et al.   PLANT PHYSIOLOGY

Verification of QTL for Grain Starch Content and Its Genetic Correlation with Oil Content Using Two Connected RIL Populations in High-Oil Maize

(2013) Guohu Yang et al.   PLoS One

Genes and Co-Expression Modules Common to Drought and Bacterial Stress Responses in Arabidopsis and Rice

(2013) Rafi Shaik et al.   PLoS One

Biosynthesis of Antinutritional Alkaloids in Solanaceous Crops Is Mediated by Clustered Genes

(2013) M. Itkin et al.   SCIENCE

The protein expression landscape of the Arabidopsis root

(2012) J. J. Petricka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Architecture of Maize Kernel Composition in the Nested Association Mapping and Inbred Association Panels

(2011) J. P. Cook et al.   PLANT PHYSIOLOGY

Weighted Correlation Network Analysis (WGCNA) Applied to the Tomato Fruit Metabolome

(2011) Matthew V. DiLeo et al.   PLoS One

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

QTL detection for grain oil and starch content and their associations in two connected F2:3 populations in high-oil maize

(2010) Y. Z. Wang et al.   EUPHYTICA

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Arabidopsis RAP2.2: An Ethylene Response Transcription Factor That Is Important for Hypoxia Survival

(2010) M. Hinz et al.   PLANT PHYSIOLOGY

Starch biosynthesis in cereal endosperm

(2010) Jong-Seong Jeon et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Overexpression of the Rap2.4f transcriptional factor in Arabidopsis promotes leaf senescence

(2010) Heng Xu et al.   Science China-Life Sciences

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Analysis of the platypus genome suggests a transposon origin for mammalian imprinting

(2009) Andrew J Pask et al.   GENOME BIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Role of Arabidopsis RAP2.4 in Regulating Light- and Ethylene-Mediated Developmental Processes and Drought Stress Tolerance

(2007) Rong-Cheng Lin et al.   Molecular Plant