Comparative study of RNA-seq- and Microarray-derived coexpression networks in Arabidopsis thaliana

Utilizing RNA-Seq data for de novo coexpression network inference

(2012) Ovidiu D. Iancu et al.   BIOINFORMATICS

Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis

(2012) Shan Wang et al.   BMC PLANT BIOLOGY

RNA-seq transcriptome analysis of male and female zebra finch cell lines

(2012) Christopher N. Balakrishnan et al.   GENOMICS

LASSO modeling of the Arabidopsis thaliana seed/seedling transcriptome: a model case for detection of novel mucilage and pectin metabolism genes

(2012) Aleksandar Vasilevski et al.   Molecular BioSystems

COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals

(2012) Takeshi Obayashi et al.   NUCLEIC ACIDS RESEARCH

Comparative co-expression analysis in plant biology

(2012) SARA MOVAHEDI et al.   PLANT CELL AND ENVIRONMENT

Arabidopsis Seed Coat Mucilage is a Specialized Cell Wall that Can be Used as a Model for Genetic Analysis of Plant Cell Wall Structure and Function

(2012) George W. Haughn et al.   Frontiers in Plant Science

The Choice between MapMan and Gene Ontology for Automated Gene Function Prediction in Plant Science

(2012) Sebastian Klie et al.   Frontiers in Genetics

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

A local average connectivity-based method for identifying essential proteins from the network level

(2011) Min Li et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions

(2011) G. W. Bassel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SLocX: predicting subcellular localization of Arabidopsis proteins leveraging gene expression data

(2011) Malgorzata Ryngajllo   Frontiers in Plant Science

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

AtPIN: Arabidopsis thaliana Protein Interaction Network

(2010) Marcelo M Brandão et al.   BMC BIOINFORMATICS

Algorithm-driven Artifacts in median polish summarization of Microarray data

(2010) Federico M Giorgi et al.   BMC BIOINFORMATICS

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments

(2010) Hugues Richard et al.   NUCLEIC ACIDS RESEARCH

AGRIS: the Arabidopsis Gene Regulatory Information Server, an update

(2010) A. Yilmaz et al.   NUCLEIC ACIDS RESEARCH

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Coexpression Analysis Identifies Rice Starch Regulator1, a Rice AP2/EREBP Family Transcription Factor, as a Novel Rice Starch Biosynthesis Regulator

(2010) F.-F. Fu et al.   PLANT PHYSIOLOGY

Robin: An Intuitive Wizard Application for R-Based Expression Microarray Quality Assessment and Analysis

(2010) M. Lohse et al.   PLANT PHYSIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human

(2009) Kun Zhang et al.   NATURE METHODS

Evolution of biomolecular networks — lessons from metabolic and protein interactions

(2009) Takuji Yamada et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

UDP-Glucose Pyrophosphorylase is not Rate Limiting, but is Essential in Arabidopsis

(2009) M. Meng et al.   PLANT AND CELL PHYSIOLOGY

Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

(2009) BJ��RN USADEL et al.   PLANT CELL AND ENVIRONMENT

Assembly of an Interactive Correlation Network for the Arabidopsis Genome Using a Novel Heuristic Clustering Algorithm

(2009) M. Mutwil et al.   PLANT PHYSIOLOGY

Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks

(2009) K. Vandepoele et al.   PLANT PHYSIOLOGY

Discerning static and causal interactions in genome-wide reverse engineering problems

(2008) Mattia Zampieri et al.   BIOINFORMATICS

Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks

(2008) Antonio Reverter et al.   BIOINFORMATICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Network Analysis Tools: from biological networks to clusters and pathways

(2008) Sylvain Brohée et al.   Nature Protocols

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Low duplicability and network fragility of cancer genes

(2008) Davide Rambaldi et al.   TRENDS IN GENETICS