Prioritization of candidate genes in QTL regions based on associations between traits and biological processes

Guilt by rewiring: gene prioritization through network rewiring in Genome Wide Association Studies

(2014) L. Hou et al.   HUMAN MOLECULAR GENETICS

The Role of Target of Rapamycin Signaling Networks in Plant Growth and Metabolism

(2014) Y. Xiong et al.   PLANT PHYSIOLOGY

Harvesting the Promising Fruits of Genomics: Applying Genome Sequencing Technologies to Crop Breeding

(2014) Rajeev K. Varshney et al.   PLOS BIOLOGY

Can a late bloomer become an early bird? Tools for flowering time adjustment

(2013) Zbyněk Milec et al.   BIOTECHNOLOGY ADVANCES

Gene, pathway and network frameworks to identify epistatic interactions of single nucleotide polymorphisms derived from GWAS data

(2013) Yu Liu et al.   BMC Systems Biology

Pathway-based analysis of genomic variation data

(2013) Nir Atias et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The spectrum of mutations controlling complex traits and the genetics of fitness in plants

(2013) K Christin Falke et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Rice breeding in the post-genomics era: from concept to practice

(2013) Zhi-Kang Li et al.   CURRENT OPINION IN PLANT BIOLOGY

Genes offering the potential for designing yield-related traits in rice

(2013) Mayuko Ikeda et al.   CURRENT OPINION IN PLANT BIOLOGY

Sequencing-based genome-wide association study in rice

(2013) Bin Han et al.   CURRENT OPINION IN PLANT BIOLOGY

eXtasy: variant prioritization by genomic data fusion

(2013) Alejandro Sifrim et al.   NATURE METHODS

A large-scale evaluation of computational protein function prediction

(2013) Predrag Radivojac et al.   NATURE METHODS

Evolution of crop species: genetics of domestication and diversification

(2013) Rachel S. Meyer et al.   NATURE REVIEWS GENETICS

PosMed: ranking genes and bioresources based on Semantic Web Association Study

(2013) Yuko Makita et al.   NUCLEIC ACIDS RESEARCH

PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors

(2013) Jinpu Jin et al.   NUCLEIC ACIDS RESEARCH

Manually curated database of rice proteins

(2013) Pratibha Gour et al.   NUCLEIC ACIDS RESEARCH

NAC Transcription Factor SPEEDY HYPONASTIC GROWTH Regulates Flooding-Induced Leaf Movement in Arabidopsis

(2013) M. Rauf et al.   PLANT CELL

A Large-Scale Identification of Direct Targets of the Tomato MADS Box Transcription Factor RIPENING INHIBITOR Reveals the Regulation of Fruit Ripening

(2013) M. Fujisawa et al.   PLANT CELL

QTL Map Meets Population Genomics: An Application to Rice

(2013) Jeffrey A. Fawcett et al.   PLoS One

Association of functional nucleotide polymorphisms at DTH2 with the northward expansion of rice cultivation in Asia

(2013) W. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype–phenotype relationships and its relevance to crop improvement

(2013) Joshua N. Cobb et al.   THEORETICAL AND APPLIED GENETICS

Molecular mechanisms involved in convergent crop domestication

(2013) Teresa Lenser et al.   TRENDS IN PLANT SCIENCE

Towards revealing the functions of all genes in plants

(2013) Seung Yon Rhee et al.   TRENDS IN PLANT SCIENCE

Applications of next-generation sequencing in plant biology

(2012) Ashley N. Egan et al.   AMERICAN JOURNAL OF BOTANY

Marker2sequence, mine your QTL regions for candidate genes

(2012) Pierre-Yves Chibon et al.   BIOINFORMATICS

An unbiased evaluation of gene prioritization tools

(2012) Daniela Börnigen et al.   BIOINFORMATICS

Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms

(2012) Marco Falda et al.   BMC BIOINFORMATICS

Integrating genome annotation and QTL position to identify candidate genes for productivity, architecture and water-use efficiency in Populus spp

(2012) Romain Monclus et al.   BMC PLANT BIOLOGY

Flowering Time in Maize: Linkage and Epistasis at a Major Effect Locus

(2012) E. Durand et al.   GENETICS

Integrated Genome-Wide Pathway Association Analysis with INTERSNP

(2012) Christine Herold et al.   HUMAN HEREDITY

Yield-related QTLs and Their Applications in Rice Genetic ImprovementF

(2012) Xufeng Bai et al.   Journal of Integrative Plant Biology

LHD1,an Allele ofDTH8/Ghd8, Controls Late Heading Date in Common Wild Rice (Oryza rufipogon)F

(2012) Xiaodong Dai et al.   Journal of Integrative Plant Biology

Control of grain size, shape and quality by OsSPL16 in rice

(2012) Shaokui Wang et al.   NATURE GENETICS

Computational tools for prioritizing candidate genes: boosting disease gene discovery

(2012) Yves Moreau et al.   NATURE REVIEWS GENETICS

Functions of rice NAC transcriptional factors, ONAC122 and ONAC131, in defense responses against Magnaporthe grisea

(2012) Lijun Sun et al.   PLANT MOLECULAR BIOLOGY

PICARA, an Analytical Pipeline Providing Probabilistic Inference about A Priori Candidates Genes Underlying Genome-Wide Association QTL in Plants

(2012) Charles Chen et al.   PLoS One

Dynamics of Brassinosteroid Response Modulated by Negative Regulator LIC in Rice

(2012) Cui Zhang et al.   PLoS Genetics

Fine mapping of stable QTLs related to eating quality in rice (Oryza sativa L.) by CSSLs harboring small target chromosomal segments

(2011) Jingjing Li et al.   BREEDING SCIENCE

Using the gene ontology to scan multilevel gene sets for associations in genome wide association studies

(2011) Daniel J. Schaid et al.   GENETIC EPIDEMIOLOGY

Genetic architecture of regulatory variation in Arabidopsis thaliana

(2011) X. Zhang et al.   GENOME RESEARCH

Prioritizing candidate disease genes by network-based boosting of genome-wide association data

(2011) I. Lee et al.   GENOME RESEARCH

Genome-wide association study of leaf architecture in the maize nested association mapping population

(2011) Feng Tian et al.   NATURE GENETICS

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

Phytozome: a comparative platform for green plant genomics

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

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

(2011) M. Mutwil et al.   PLANT CELL

Rice Ethylene-Response AP2/ERF Factor OsEATB Restricts Internode Elongation by Down-Regulating a Gibberellin Biosynthetic Gene

(2011) Weiwei Qi et al.   PLANT PHYSIOLOGY

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Adaptation to Climate Across the Arabidopsis thaliana Genome

(2011) A. M. Hancock et al.   SCIENCE

Map-based cloning proves qGC-6, a major QTL for gel consistency of japonica/indica cross, responds by Waxy in rice (Oryza sativa L.)

(2011) Yan Su et al.   THEORETICAL AND APPLIED GENETICS

Fine mapping a major QTL for flag leaf size and yield-related traits in rice

(2011) Peng Wang et al.   THEORETICAL AND APPLIED GENETICS

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

(2011) Keyan Zhao et al.   Nature Communications

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

(2010) Susanna Atwell et al.   NATURE

Genome-wide association studies of 14 agronomic traits in rice landraces

(2010) Xuehui Huang et al.   NATURE GENETICS

Analysing biological pathways in genome-wide association studies

(2010) Kai Wang et al.   NATURE REVIEWS GENETICS

Gramene database in 2010: updates and extensions

(2010) K. Youens-Clark et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Computational Function Prediction of Arabidopsis Proteins by Integration of Multiple Data Sources

(2010) Y. A. I. Kourmpetis et al.   PLANT PHYSIOLOGY

The SEPALLATA-Like Gene OsMADS34 Is Required for Rice Inflorescence and Spikelet Development

(2010) X. Gao et al.   PLANT PHYSIOLOGY

DTH8 Suppresses Flowering in Rice, Influencing Plant Height and Yield Potential Simultaneously

(2010) X. Wei et al.   PLANT PHYSIOLOGY

Bayesian Markov Random Field Analysis for Protein Function Prediction Based on Network Data

(2010) Yiannis A. I. Kourmpetis et al.   PLoS One

Gene Ontology Analysis of GWA Study Data Sets Provides Insights into the Biology of Bipolar Disorder

(2009) Peter Holmans et al.   AMERICAN JOURNAL OF HUMAN GENETICS

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

(2009) J. Chen et al.   NUCLEIC ACIDS RESEARCH

PosMed-plus: An Intelligent Search Engine that Inferentially Integrates Cross-Species Information Resources for Molecular Breeding of Plants

(2009) Yuko Makita et al.   PLANT AND CELL PHYSIOLOGY

The Ethylene Receptor ETR2 Delays Floral Transition and Affects Starch Accumulation in Rice

(2009) H. Wuriyanghan et al.   PLANT CELL

Multilevel Analysis of Primary Metabolism Provides New Insights into the Role of Potassium Nutrition for Glycolysis and Nitrogen Assimilation in Arabidopsis Roots

(2009) P. Armengaud et al.   PLANT PHYSIOLOGY

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Flowering time control and applications in plant breeding

(2009) Christian Jung et al.   TRENDS IN PLANT SCIENCE

Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies †

(2008) Daniel Shriner et al.   NUCLEIC ACIDS RESEARCH