COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems

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

(2013) Federico M. Giorgi et al.   BIOINFORMATICS

SRAdb: query and use public next-generation sequencing data from within R

(2013) Yuelin Zhu et al.   BMC BIOINFORMATICS

Database resources of the National Center for Biotechnology Information

(2013)   NUCLEIC ACIDS RESEARCH

Canonical correlation analysis for RNA-seq co-expression networks

(2013) Shengjun Hong et al.   NUCLEIC ACIDS RESEARCH

GeneMANIA Prediction Server 2013 Update

(2013) Khalid Zuberi et al.   NUCLEIC ACIDS RESEARCH

FunCoup 3.0: database of genome-wide functional coupling networks

(2013) Thomas Schmitt et al.   NUCLEIC ACIDS RESEARCH

RefSeq: an update on mammalian reference sequences

(2013) Kim D. Pruitt 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

GeneFriends: An online co-expression analysis tool to identify novel gene targets for aging and complex diseases

(2012) Sipko van Dam et al.   BMC GENOMICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Reuse of public genome-wide gene expression data

(2012) Johan Rung et al.   NATURE REVIEWS GENETICS

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

IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks

(2012) Aaron K. Wong et al.   NUCLEIC ACIDS RESEARCH

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

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

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

Web-Queryable Large-Scale Data Sets for Hypothesis Generation in Plant Biology

(2009) S. M. Brady et al.   PLANT CELL

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

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

Decoding genes with coexpression networks and metabolomics – ‘majority report by precogs’

(2007) Kazuki Saito et al.   TRENDS IN PLANT SCIENCE