A Systems-Genetics Approach and Data Mining Tool to Assist in the Discovery of Genes Underlying Complex Traits in Oryza sativa

Massive-Scale Gene Co-Expression Network Construction and Robustness Testing Using Random Matrix Theory

(2013) Scott M. Gibson et al.   PLoS One

Discriminative local subspaces in gene expression data for effective gene function prediction

(2012) Tomas Puelma et al.   BIOINFORMATICS

Utilizing RNA-Seq data for de novo coexpression network inference

(2012) Ovidiu D. Iancu et al.   BIOINFORMATICS

Ectopic Expression of RiceOsBIANK1, Encoding an Ankyrin Repeat-Containing Protein, inArabidopsisConfers Enhanced Disease Resistance toBotrytis cinereaandPseudomonas syringae

(2012) Dayong Li et al.   JOURNAL OF PHYTOPATHOLOGY

Conserved Non-Coding Regulatory Signatures in Arabidopsis Co-Expressed Gene Modules

(2012) Jacob B. Spangler et al.   PLoS One

linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type

(2011) Alex T. Kalinka et al.   BIOINFORMATICS

Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm

(2011) Xuehui Huang et al.   NATURE GENETICS

Functional Network Construction inArabidopsisUsing Rule-Based Machine Learning on Large-Scale Data Sets

(2011) George W. Bassel et al.   PLANT CELL

The Transcriptome of the Reference Potato Genome Solanum tuberosum Group Phureja Clone DM1-3 516R44

(2011) Alicia N. Massa et al.   PLoS One

Systems Genetics

(2011) J. H. Nadeau et al.   SCIENCE

Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa

(2011) Keyan Zhao et al.   Nature Communications

Tripal: a construction toolkit for online genome databases

(2011) S. P. Ficklin et al.   Database-The Journal of Biological Databases and Curation

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

(2010) Y. Ogata et al.   BIOINFORMATICS

Cytoscape Web: an interactive web-based network browser

(2010) Christian T. Lopes et al.   BIOINFORMATICS

TobEA: an atlas of tobacco gene expression from seed to senescence

(2010) Kieron D Edwards et al.   BMC GENOMICS

Link communities reveal multiscale complexity in networks

(2010) Yong-Yeol Ahn et al.   NATURE

Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana

(2010) Insuk Lee et al.   NATURE BIOTECHNOLOGY

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments

(2010) H. Parkinson et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets--10 years on

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

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

Arabidopsis gene co-expression network and its functional modules

(2009) Linyong Mao et al.   BMC BIOINFORMATICS

Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network

(2009) Osnat Atias et al.   BMC Systems Biology

Towards the Understanding of Complex Traits in Rice: Substantially or Superficially?

(2009) T. Yamamoto et al.   DNA RESEARCH

A database for poplar gene co-expression analysis for systematic understanding of biological processes, including stress responses

(2009) Yoshiyuki Ogata et al.   JOURNAL OF WOOD SCIENCE

Molecular characterization of rice OsBIANK1, encoding a plasma membrane-anchored ankyrin repeat protein, and its inducible expression in defense responses

(2009) Xinchun Zhang et al.   MOLECULAR BIOLOGY REPORTS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

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

(2009) M. Mutwil et al.   PLANT PHYSIOLOGY

RiceArrayNet: A Database for Correlating Gene Expression from Transcriptome Profiling, and Its Application to the Analysis of Coexpressed Genes in Rice

(2009) T.-H. Lee et al.   PLANT PHYSIOLOGY

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

(2009) K. Vandepoele et al.   PLANT PHYSIOLOGY

arrayQualityMetrics—a bioconductor package for quality assessment of microarray data

(2008) Audrey Kauffmann 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

Articulation of three core metabolic processes in Arabidopsis: Fatty acid biosynthesis, leucine catabolism and starch metabolism

(2008) Wieslawa I Mentzen et al.   BMC PLANT BIOLOGY

Function Annotation of an SBP-box Gene in Arabidopsis Based on Analysis of Co-expression Networks and Promoters

(2008) Yi Wang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

ATTED-II provides coexpressed gene networks for Arabidopsis

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

InterPro: the integrative protein signature database

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

Waxy gene haplotypes: Associations with apparent amylose content and the effect by the environment in an international rice germplasm collection

(2007) Ming-Hsuan Chen et al.   JOURNAL OF CEREAL SCIENCE