ATTED-II in 2014: Evaluation of Gene Coexpression in Agriculturally Important Plants

PLANEX: the plant co-expression database

(2013) Won Yim et al.   BMC PLANT BIOLOGY

Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics

(2013) Hiroaki Sakai et al.   PLANT AND CELL PHYSIOLOGY

The Relation of Codon Bias to Tissue-Specific Gene Expression in Arabidopsis thaliana

(2012) S. Camiolo et al.   GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Takeshi Obayashi et al.   NUCLEIC ACIDS RESEARCH

ArrayExpress update—trends in database growth and links to data analysis tools

(2012) Gabriella Rustici et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

BAR expressolog identification: expression profile similarity ranking of homologous genes in plant species

(2012) Rohan V. Patel et al.   PLANT JOURNAL

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

ATTED-II Updates: Condition-Specific Gene Coexpression to Extend Coexpression Analyses and Applications to a Broad Range of Flowering Plants

(2011) T. Obayashi et al.   PLANT AND CELL PHYSIOLOGY

PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species

(2011) M. Mutwil et al.   PLANT CELL

Comparative Network Analysis Reveals That Tissue Specificity and Gene Function Are Important Factors Influencing the Mode of Expression Evolution in Arabidopsis and Rice

(2011) S. Movahedi et al.   PLANT PHYSIOLOGY

CoP: a database for characterizing co-expressed gene modules with biological information in plants

(2010) Y. Ogata et al.   BIOINFORMATICS

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways

(2010) Takeshi Obayashi et al.   JOURNAL OF PLANT RESEARCH

COXPRESdb: a database to compare gene coexpression in seven model animals

(2010) T. Obayashi et al.   NUCLEIC ACIDS RESEARCH

OryzaExpress: An Integrated Database of Gene Expression Networks and Omics Annotations in Rice

(2010) Kazuki Hamada et al.   PLANT AND CELL PHYSIOLOGY

Food Security: The Challenge of Feeding 9 Billion People

(2010) H. C. J. Godfray et al.   SCIENCE

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis

(2009) Kengo Kinoshita et al.   BIOINFORMATICS

STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data

(2009) Daniel Jupiter et al.   BMC BIOINFORMATICS

Rank of Correlation Coefficient as a Comparable Measure for Biological Significance of Gene Coexpression

(2009) T. Obayashi et al.   DNA RESEARCH

Universal function-specificity of codon usage

(2009) Hamed Shateri Najafabadi et al.   NUCLEIC ACIDS RESEARCH

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

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

Conserved co-expression for candidate disease gene prioritization

(2008) Martin Oti et al.   BMC BIOINFORMATICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

GeneCAT—novel webtools that combine BLAST and co-expression analyses

(2008) Marek Mutwil et al.   NUCLEIC ACIDS RESEARCH

ATTED-II provides coexpressed gene networks for Arabidopsis

(2008) T. Obayashi et al.   NUCLEIC ACIDS RESEARCH

Synteny and Collinearity in Plant Genomes

(2008) H. Tang et al.   SCIENCE

Sequence-based prediction of protein-protein interactions by means of codon usage

(2008) Hamed Najafabadi et al.   GENOME BIOLOGY