ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression

Guidance for RNA-seq co-expression network construction and analysis: safety in numbers

(2015) S. Ballouz et al.   BIOINFORMATICS

Comparison of Gene Coexpression Profiles and Construction of Conserved Gene Networks to Find Functional Modules

(2015) Yasunobu Okamura et al.   PLoS One

ArrayExpress update—simplifying data submissions

(2014) Nikolay Kolesnikov et al.   NUCLEIC ACIDS RESEARCH

Gene: a gene-centered information resource at NCBI

(2014) Garth R. Brown et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Takeshi Obayashi et al.   PLANT AND CELL PHYSIOLOGY

Reuse of public genome-wide gene expression data

(2012) Johan Rung et al.   NATURE REVIEWS GENETICS

DDBJ new system and service refactoring

(2012) Osamu Ogasawara et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Takeshi Obayashi et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett 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

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

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

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

(2009) Kengo Kinoshita et al.   BIOINFORMATICS

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

(2009) T. Obayashi et al.   DNA RESEARCH

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

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

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Conserved co-expression for candidate disease gene prioritization

(2008) Martin Oti et al.   BMC BIOINFORMATICS

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