Annotated genes and nonannotated genomes: cross-species use of Gene Ontology in ecology and evolution research

A transcriptomic investigation of handicap models in sexual selection

(2012) Marius A. Wenzel et al.   BEHAVIORAL ECOLOGY AND SOCIOBIOLOGY

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

(2012) Marco Falda et al.   BMC BIOINFORMATICS

Genes under positive selection in a model plant pathogenic fungus, Botrytis

(2012) Gabriela Aguileta et al.   INFECTION GENETICS AND EVOLUTION

Environmental Adaptation Contributes to Gene Polymorphism across the Arabidopsis thaliana Genome

(2012) Cheng-Ruei Lee et al.   MOLECULAR BIOLOGY AND EVOLUTION

The proteomics of feather development in pied flycatchers (Ficedula hypoleuca) with different plumage coloration

(2012) Paula K. Leskinen et al.   MOLECULAR ECOLOGY

Molecular evolutionary and population genomic analysis of the nine-spined stickleback using a modified restriction-site-associated DNA tag approach

(2012) Matthieu Bruneaux et al.   MOLECULAR ECOLOGY

A proteomics approach reveals divergent molecular responses to salinity in populations of European whitefish (Coregonus lavaretus)

(2012) SPIROS PAPAKOSTAS et al.   MOLECULAR ECOLOGY

SNP-array reveals genome-wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar)

(2012) Vincent Bourret et al.   MOLECULAR ECOLOGY

Proteomics in evolutionary ecology: linking the genotype with the phenotype

(2012) ANGEL P. DIZ et al.   MOLECULAR ECOLOGY

The simple fool's guide to population genomics via RNA-Seq: an introduction to high-throughput sequencing data analysis

(2012) Pierre De Wit et al.   Molecular Ecology Resources

A beginner's guide to eukaryotic genome annotation

(2012) Mark Yandell et al.   NATURE REVIEWS GENETICS

Structural Variants in the Soybean Genome Localize to Clusters of Biotic Stress-Response Genes

(2012) L. K. McHale et al.   PLANT PHYSIOLOGY

Characterization of Common Carp Transcriptome: Sequencing, De Novo Assembly, Annotation and Comparative Genomics

(2012) Peifeng Ji et al.   PLoS One

What is needed for next-generation ecological and evolutionary genomics?

(2012) Scott A. Pavey et al.   TRENDS IN ECOLOGY & EVOLUTION

Genome-Wide Analysis of the World's Sheep Breeds Reveals High Levels of Historic Mixture and Strong Recent Selection

(2012) James W. Kijas et al.   PLOS BIOLOGY

Quality of Computationally Inferred Gene Ontology Annotations

(2012) Nives Škunca et al.   PLoS Computational Biology

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs

(2012) Adrian M. Altenhoff et al.   PLoS Computational Biology

Orthology prediction methods: A quality assessment using curated protein families

(2011) Kalliopi Trachana et al.   BIOESSAYS

RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis

(2011) Barry R Zeeberg et al.   BMC BIOINFORMATICS

Back to the sea twice: identifying candidate plant genes for molecular evolution to marine life

(2011) Lothar Wissler et al.   BMC EVOLUTIONARY BIOLOGY

Gene expression analyses of immune responses in Atlantic salmon during early stages of infection by salmon louse (Lepeophtheirus salmonis) revealed bi-phasic responses coinciding with the copepod-chalimus transition

(2011) Tariku Markos Tadiso et al.   BMC GENOMICS

Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees

(2011) B. Boeckmann et al.   BRIEFINGS IN BIOINFORMATICS

The what, where, how and why of gene ontology--a primer for bioinformaticians

(2011) L. du Plessis et al.   BRIEFINGS IN BIOINFORMATICS

Computational methods for Gene Orthology inference

(2011) D. M. Kristensen et al.   BRIEFINGS IN BIOINFORMATICS

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium

(2011) P. Gaudet et al.   BRIEFINGS IN BIOINFORMATICS

Transcriptome profiles link environmental variation and physiological response ofMytilus californianusbetween Pacific tides

(2011) Sean P. Place et al.   FUNCTIONAL ECOLOGY

Green systems biology — From single genomes, proteomes and metabolomes to ecosystems research and biotechnology

(2011) Wolfram Weckwerth   Journal of Proteomics

Transcriptional plasticity of a soil arthropod across different ecological conditions

(2011) TJALF E. DE BOER et al.   MOLECULAR ECOLOGY

Comparative and demographic analysis of orang-utan genomes

(2011) Devin P. Locke et al.   NATURE

The genome sequence of Atlantic cod reveals a unique immune system

(2011) Bastiaan Star et al.   NATURE

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

The genome of the fire ant Solenopsis invicta

(2011) Y. Wurm et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Ecoresponsive Genome of Daphnia pulex

(2011) J. K. Colbourne et al.   SCIENCE

Three Periods of Regulatory Innovation During Vertebrate Evolution

(2011) C. B. Lowe et al.   SCIENCE

Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals

(2011) Nathan L. Nehrt et al.   PLoS Computational Biology

A Functional Phylogenomic View of the Seed Plants

(2011) Ernest K. Lee et al.   PLoS Genetics

Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development

(2010) Jennifer I Deegan (née Clark) et al.   BMC BIOINFORMATICS

Automatic, context-specific generation of Gene Ontology slims

(2010) Melissa J Davis et al.   BMC BIOINFORMATICS

Sequencing, de novo annotation and analysis of the first Anguilla anguilla transcriptome: EeelBase opens new perspectives for the study of the critically endangered european eel

(2010) Alessandro Coppe et al.   BMC GENOMICS

Natural Variation, Functional Pleiotropy and Transcriptional Contexts of Odorant Binding Protein Genes in Drosophila melanogaster

(2010) G. H. Arya et al.   GENETICS

Gene Duplication and Environmental Adaptation within Yeast Populations

(2010) Ryan M. Ames et al.   Genome Biology and Evolution

Transcriptome-wide signature of hybrid breakdown associated with intrinsic reproductive isolation in lake whitefish species pairs (Coregonus spp. Salmonidae)

(2010) S Renaut et al.   HEREDITY

Proteomic Profiling of Early Life Stages of European Grayling (Thymallus thymallus)

(2010) Spiros Papakostas et al.   JOURNAL OF PROTEOME RESEARCH

Emergence and Evolution of Modern Molecular Functions Inferred from Phylogenomic Analysis of Ontological Data

(2010) K. M. Kim et al.   MOLECULAR BIOLOGY AND EVOLUTION

Female-Biased Expression on the X Chromosome as a Key Step in Sex Chromosome Evolution in Threespine Sticklebacks

(2010) Erica H. Leder et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sperm Proteomics Reveals Intensified Selection on Mouse Sperm Membrane and Acrosome Genes

(2010) Steve Dorus et al.   MOLECULAR BIOLOGY AND EVOLUTION

Six quantitative trait loci influence task thresholds for hygienic behaviour in honeybees (Apis mellifera)

(2010) PETER R. OXLEY et al.   MOLECULAR ECOLOGY

Changes in reproductive roles are associated with changes in gene expression in fire ant queens

(2010) YANNICK WURM et al.   MOLECULAR ECOLOGY

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions

(2010) J. Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

The use of gene ontology evidence codes in preventing classifier assessment bias

(2009) Mark F. Rogers et al.   BIOINFORMATICS

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

(2009) Gabriela Bindea et al.   BIOINFORMATICS

QuickGO: a web-based tool for Gene Ontology searching

(2009) D. Binns et al.   BIOINFORMATICS

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Population-specific gene expression responses to hybridization between farm and wild Atlantic salmon

(2009) Eric Normandeau et al.   Evolutionary Applications

Variation in gene expression ofAndropogon gerardiiin response to altered environmental conditions associated with climate change

(2009) Steven E. Travers et al.   JOURNAL OF ECOLOGY

Pathway databases and tools for their exploitation: benefits, current limitations and challenges

(2009) Anna Bauer-Mehren et al.   Molecular Systems Biology

The Schistosoma japonicum genome reveals features of host–parasite interplay

(2009)   NATURE

Database resources of the National Center for Biotechnology Information

(2009) Eric W. Sayers et al.   NUCLEIC ACIDS RESEARCH

G-SESAME: web tools for GO-term-based gene similarity analysis and knowledge discovery

(2009) Z. Du et al.   NUCLEIC ACIDS RESEARCH

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

(2009) G. Ostlund et al.   NUCLEIC ACIDS RESEARCH

A Statistical Model of Protein Sequence Similarity and Function Similarity Reveals Overly-Specific Function Predictions

(2009) Brenton Louie et al.   PLoS One

Towards the mammalian interactome: Inference of a core mammalian interaction set in mouse

(2009) Chang Jin Shin et al.   PROTEOMICS

Fish proteome analysis: Model organisms and non-sequenced species

(2009) Ignasi Forné et al.   PROTEOMICS

Ecological Genomics Gets Down to Genes--and Function

(2009) E. Pennisi   SCIENCE

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

(2009) Y. F. Chan et al.   SCIENCE

Semantic Similarity in Biomedical Ontologies

(2009) Catia Pesquita et al.   PLoS Computational Biology

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

(2009) Adrian M. Altenhoff et al.   PLoS Computational Biology

The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species

(2009)   PLoS Computational Biology

A transcriptional network associated with natural variation in Drosophila aggressive behavior

(2009) Alexis C Edwards et al.   GENOME BIOLOGY

Domain-Based and Family-Specific Sequence Identity Thresholds Increase the Levels of Reliable Protein Function Transfer

(2008) Sarah Addou et al.   JOURNAL OF MOLECULAR BIOLOGY

The Preferential Retention of Starch Synthesis Genes Reveals the Impact of Whole-Genome Duplication on Grass Evolution

(2008) Y. Wu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Population transcriptomics of life-history variation in the genusSalmo

(2008) THOMAS GIGER et al.   MOLECULAR ECOLOGY

Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing

(2008) J. CRISTOBAL VERA et al.   MOLECULAR ECOLOGY

Integrated network analysis platform for protein-protein interactions

(2008) Jianmin Wu et al.   NATURE METHODS

Use and misuse of the gene ontology annotations

(2008) Seung Yon Rhee et al.   NATURE REVIEWS GENETICS

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Taxonomy-based partitioning of the Gene Ontology

(2007) Wacław Kuśnierczyk   JOURNAL OF BIOMEDICAL INFORMATICS