Finding the missing honey bee genes: lessons learned from a genome upgrade

Genome reannotation of the lizard Anolis carolinensis based on 14 adult and embryonic deep transcriptomes

(2013) Walter L Eckalbar et al.   BMC GENOMICS

Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality

(2013) D. F. Simola et al.   GENOME RESEARCH

Web Apollo: a web-based genomic annotation editing platform

(2013) Eduardo Lee et al.   GENOME BIOLOGY

Understanding the Relationship Between Brain Gene Expression and Social Behavior: Lessons from the Honey Bee

(2012) Amro Zayed et al.   Annual Review of Genetics

OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs

(2012) Robert M. Waterhouse et al.   NUCLEIC ACIDS RESEARCH

Ecologically Appropriate Xenobiotics Induce Cytochrome P450s in Apis mellifera

(2012) Reed M. Johnson et al.   PLoS One

Insect Pollinated Crops, Insect Pollinators and US Agriculture: Trend Analysis of Aggregate Data for the Period 1992–2009

(2012) Nicholas W. Calderone   PLoS One

Pathogen Webs in Collapsing Honey Bee Colonies

(2012) R. Scott Cornman et al.   PLoS One

Recombination is associated with the evolution of genome structure and worker behavior in honey bees

(2012) C. F. Kent et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees

(2012) S. Foret et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

A honey bee (Apis mellifera L.) PeptideAtlas crossing castes and tissues

(2011) Queenie WT Chan et al.   BMC GENOMICS

Nutrigenomics in honey bees: digital gene expression analysis of pollen's nutritive effects on healthy and varroa-parasitized bees

(2011) Cédric Alaux et al.   BMC GENOMICS

The genome of the leaf-cutting antAcromyrmex echinatiorsuggests key adaptations to advanced social life and fungus farming

(2011) Sanne Nygaard et al.   GENOME RESEARCH

Mechanisms of stable lipid loss in a social insect

(2011) S. A. Ament et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Differential Expressions of Nuclear Proteomes between Honeybee (Apis mellifera L.) Queen and Worker Larvae: A Deep Insight into Caste Pathway Decisions

(2011) Desalegn Begna et al.   JOURNAL OF PROTEOME RESEARCH

Gene Space Dynamics During the Evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor Genomes

(2011) A. N. Massa et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis

(2011) J. Lees et al.   NUCLEIC ACIDS RESEARCH

The sequence read archive: explosive growth of sequencing data

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

InterPro in 2011: new developments in the family and domain prediction database

(2011) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

SMART 7: recent updates to the protein domain annotation resource

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

Genome Assembly Has a Major Impact on Gene Content: A Comparison of Annotation in Two Bos Taurus Assemblies

(2011) Liliana Florea et al.   PLoS One

Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile)

(2011) C. D. Smith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Draft genome of the red harvester ant Pogonomyrmex barbatus

(2011) C. R. Smith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies

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

The Genome Sequence of the Leaf-Cutter Ant Atta cephalotes Reveals Insights into Its Obligate Symbiotic Lifestyle

(2011) Garret Suen et al.   PLoS Genetics

Hundreds of putatively functional small open reading frames in Drosophila

(2011) Emmanuel Ladoukakis et al.   GENOME BIOLOGY

Proteome profile and lentiviral transduction of cultured honey bee (Apis mellifera L.) cells

(2010) M. M. Y. Chan et al.   INSECT MOLECULAR BIOLOGY

The developmental transcriptome of Drosophila melanogaster

(2010) Brenton R. Graveley et al.   NATURE

Identifying compositionally homogeneous and nonhomogeneous domains within the human genome using a novel segmentation algorithm

(2010) Eran Elhaik et al.   NUCLEIC ACIDS RESEARCH

Hymenoptera Genome Database: integrated community resources for insect species of the order Hymenoptera

(2010) M. C. Munoz-Torres et al.   NUCLEIC ACIDS RESEARCH

Genomic Comparison of the Ants Camponotus floridanus and Harpegnathos saltator

(2010) R. Bonasio et al.   SCIENCE

Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species

(2010) J. H. Werren et al.   SCIENCE

Genome Sequence of the Pea Aphid Acyrthosiphon pisum

(2010)   PLOS BIOLOGY

Apollo: a community resource for genome annotation editing

(2009) E. Lee et al.   BIOINFORMATICS

The innate immune and systemic response in honey bees to a bacterial pathogen, Paenibacillus larvae

(2009) Queenie WT Chan et al.   BMC GENOMICS

Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences

(2009) Vladimir V. Kapitonov et al.   GENE

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium

(2009) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

PROSITE, a protein domain database for functional characterization and annotation

(2009) Christian J. A. Sigrist et al.   NUCLEIC ACIDS RESEARCH

Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse

(2009) Deanna M. Church et al.   PLOS BIOLOGY

Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species

(2008) Oliver Keller et al.   BMC BIOINFORMATICS

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

The complete genome of an individual by massively parallel DNA sequencing

(2008) David A. Wheeler et al.   NATURE

A universal classification of eukaryotic transposable elements implemented in Repbase

(2008) Vladimir V. Kapitonov et al.   NATURE REVIEWS GENETICS

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH

SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny

(2008) Derek Wilson et al.   NUCLEIC ACIDS RESEARCH

Changes in protein expression during honey bee larval development

(2008) Queenie WT Chan et al.   GENOME BIOLOGY