Uncovering co-expression gene network modules regulating fruit acidity in diverse apples

A co-expression gene network associated with developmental regulation of apple fruit acidity

(2015) Yang Bai et al.   MOLECULAR GENETICS AND GENOMICS

Identification of co-expression gene networks, regulatory genes and pathways for obesity based on adipose tissue RNA Sequencing in a porcine model

(2014) Lisette J A Kogelman et al.   BMC Medical Genomics

Expression Profiling of the Wheat Pathogen Zymoseptoria tritici Reveals Genomic Patterns of Transcription and Host-Specific Regulatory Programs

(2014) Ronny Kellner et al.   Genome Biology and Evolution

Ethylene negatively regulates aluminium-induced malate efflux from wheat roots and tobacco cells transformed with TaALMT1

(2014) Qiuying Tian et al.   JOURNAL OF EXPERIMENTAL BOTANY

The role of aluminum sensing and signaling in plant aluminum resistance

(2014) Jiping Liu et al.   Journal of Integrative Plant Biology

Review on statistical methods for gene network reconstruction using expression data

(2014) Y.X. Rachel Wang et al.   JOURNAL OF THEORETICAL BIOLOGY

Towards an improved apple reference transcriptome using RNA-seq

(2014) Yang Bai et al.   MOLECULAR GENETICS AND GENOMICS

Transcriptional landscape of the prenatal human brain

(2014) Jeremy A. Miller et al.   NATURE

Floral Transcriptomes in Woodland Strawberry Uncover Developing Receptacle and Anther Gene Networks

(2014) C. A. Hollender et al.   PLANT PHYSIOLOGY

The columnar mutation (“Co gene”) of apple (Malus × domestica) is associated with an integration of a Gypsy-like retrotransposon

(2013) Dominik Otto et al.   MOLECULAR BREEDING

The Genome Database for Rosaceae (GDR): year 10 update

(2013) Sook Jung et al.   NUCLEIC ACIDS RESEARCH

An IQ Domain Mediates the Interaction with Calmodulin in a Plant Cyclic Nucleotide-Gated Channel

(2013) Cornelia Fischer et al.   PLANT AND CELL PHYSIOLOGY

Genome-Scale Transcriptomic Insights into Early-Stage Fruit Development in Woodland Strawberry Fragaria vesca

(2013) C. Kang et al.   PLANT CELL

Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data

(2013) MARC LOHSE et al.   PLANT CELL AND ENVIRONMENT

Evaluation of the hormonal state of columnar apple trees (Malus x domestica) based on high throughput gene expression studies

(2013) Clemens Krost et al.   PLANT MOLECULAR BIOLOGY

The group IV-A cyclic nucleotide-gated channels, CNGC19 and CNGC20, localize to the vacuole membrane in Arabidopsis thaliana

(2013) Christen C. Y. Yuen et al.   AoB Plants

Biomarker development for external CO2 injury prediction in apples through exploration of both transcriptome and DNA methylation changes

(2013) Nigel E. Gapper et al.   AoB Plants

Identification, characterization, and utilization of genome-wide simple sequence repeats to identify a QTL for acidity in apple

(2012) Qiong Zhang et al.   BMC GENOMICS

The transcriptomes of columnar and standard type apple trees (Malus x domestica) — A comparative study

(2012) Clemens Krost et al.   GENE

A natural mutation-led truncation in one of the two aluminum-activated malate transporter-like genes at the Ma locus is associated with low fruit acidity in apple

(2012) Yang Bai et al.   MOLECULAR GENETICS AND GENOMICS

A travel guide to Cytoscape plugins

(2012) Rintaro Saito et al.   NATURE METHODS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Characterization of Transcriptional Differences Between Columnar and Standard Apple Trees Using RNA-Seq

(2012) Yugang Zhang et al.   PLANT MOLECULAR BIOLOGY REPORTER

Genomic Selection for Fruit Quality Traits in Apple (Malus×domestica Borkh.)

(2012) Satish Kumar et al.   PLoS One

Comparative Transcriptome Profiling of the Early Response to Magnaporthe oryzae in Durable Resistant vs Susceptible Rice (Oryza sativa L.) Genotypes

(2012) Paolo Bagnaresi et al.   PLoS One

Differences in acidity of apples are probably mainly caused by a malic acid transporter gene on LG16

(2012) Sabaz Ali Khan et al.   Tree Genetics & Genomes

Transcriptional regulation of aluminium tolerance genes

(2012) Emmanuel Delhaize et al.   TRENDS IN PLANT SCIENCE

Apple miRNAs and tasiRNAs with novel regulatory networks

(2012) Rui Xia et al.   GENOME BIOLOGY

Anion Channels/Transporters in Plants: From Molecular Bases to Regulatory Networks

(2011) Hélène Barbier-Brygoo et al.   Annual Review of Plant Biology

Genetic characterization of the Ma locus with pH and titratable acidity in apple

(2011) Kenong Xu et al.   MOLECULAR BREEDING

Developmental changes of carbohydrates, organic acids, amino acids, and phenolic compounds in ‘Honeycrisp’ apple flesh

(2010) Yanzi Zhang et al.   FOOD CHEMISTRY

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

(2010) G. Zhang et al.   GENOME RESEARCH

The developmental dynamics of the maize leaf transcriptome

(2010) Pinghua Li et al.   NATURE GENETICS

Characterization of Transcriptional Complexity during Berry Development in Vitis vinifera Using RNA-Seq

(2010) S. Zenoni et al.   PLANT PHYSIOLOGY

Module networks revisited: computational assessment and prioritization of model predictions

(2009) A. Joshi et al.   BIOINFORMATICS

Ethylene signaling and response: where different regulatory modules meet

(2009) Anna N Stepanova et al.   CURRENT OPINION IN PLANT BIOLOGY

Aluminium-induced inhibition of root elongation in Arabidopsis is mediated by ethylene and auxin

(2009) P. Sun et al.   JOURNAL OF EXPERIMENTAL BOTANY

RNA-Seq—quantitative measurement of expression through massively parallel RNA-sequencing

(2009) Brian T. Wilhelm et al.   METHODS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH

Identification and stability of QTLs for fruit quality traits in apple

(2008) Katrien Kenis et al.   Tree Genetics & Genomes