The Genome and Methylome of a Beetle with Complex Social Behavior,Nicrophorus vespilloides(Coleoptera: Silphidae)

DNA Methylation in Social Insects: How Epigenetics Can Control Behavior and Longevity

(2015) Hua Yan et al.   Annual Review of Entomology

Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool

(2015) Jennifer M. Shelton et al.   BMC GENOMICS

Neurogenomic mechanisms of social plasticity

(2015) S. D. Cardoso et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing

(2015) Mark A Urich et al.   Nature Protocols

Genomic signatures of evolutionary transitions from solitary to group living

(2015) K. M. Kapheim et al.   SCIENCE

Climbing the social ladder: the molecular evolution of sociality

(2015) Sandra M. Rehan et al.   TRENDS IN ECOLOGY & EVOLUTION

It's more than stamp collecting: how genome sequencing can unify biological research

(2015) Stephen Richards   TRENDS IN GENETICS

Transcriptomes of parents identify parenting strategies and sexual conflict in a subsocial beetle

(2015) Darren J. Parker et al.   Nature Communications

Genes associated with ant social behavior show distinct transcriptional and evolutionary patterns

(2015) Alexander S Mikheyev et al.   eLife

The genomes of two key bumblebee species with primitive eusocial organization

(2015) Ben M Sadd et al.   GENOME BIOLOGY

Best practices in insect genome sequencing: what works and what doesn’t

(2015) Stephen Richards et al.   Current Opinion in Insect Science

Current methods for automated annotation of protein-coding genes

(2015) KJ Hoff et al.   Current Opinion in Insect Science

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

(2014) Christine G Elsik et al.   BMC GENOMICS

The Genome of the Clonal Raider Ant Cerapachys biroi

(2014) Peter R. Oxley et al.   CURRENT BIOLOGY

Characterization of brain cell nuclei with decondensed chromatin

(2014) Ping Yu et al.   Developmental Neurobiology

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani et al.   GENOME RESEARCH

iBeetle-Base: a database for RNAi phenotypes in the red flour beetle Tribolium castaneum

(2014) Jürgen Dönitz et al.   NUCLEIC ACIDS RESEARCH

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations

(2014) G. dos Santos et al.   NUCLEIC ACIDS RESEARCH

Molecular traces of alternative social organization in a termite genome

(2014) Nicolas Terrapon et al.   Nature Communications

orthAgogue: an agile tool for the rapid prediction of orthology relations

(2013) O. K. Ekseth et al.   BIOINFORMATICS

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Nutrition during sexual maturation affects competitive ability but not reproductive productivity in burying beetles

(2013) Paul E. Hopwood et al.   FUNCTIONAL ECOLOGY

Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population

(2013) R. J. Schmitz et al.   GENOME RESEARCH

Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

(2013) Mira V. Han et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular phylogeny of the burying beetles (Coleoptera: Silphidae: Nicrophorinae)

(2013) Derek S. Sikes et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Function and Evolution of DNA Methylation in Nasonia vitripennis

(2013) Xu Wang et al.   PLoS Genetics

The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes

(2013) Sarah D Kocher et al.   GENOME BIOLOGY

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest

(2013) Christopher I Keeling 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

Genome-wide and Caste-Specific DNA Methylomes of the Ants Camponotus floridanus and Harpegnathos saltator

(2012) Roberto Bonasio et al.   CURRENT BIOLOGY

DNA Methylation as a Mechanism of Nutritional Plasticity: Limited Support From Horned Beetles

(2012) Emilie C. Snell-Rood et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Reversible switching between epigenetic states in honeybee behavioral subcastes

(2012) Brian R Herb et al.   NATURE NEUROSCIENCE

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

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

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

‘Leveling’ the playing field for analyses of single-base resolution DNA methylomes

(2012) Matthew D. Schultz et al.   TRENDS IN GENETICS

Advances in Insect Phylogeny at the Dawn of the Postgenomic Era

(2011) Michelle D. Trautwein et al.   Annual Review of Entomology

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

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

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Gene discovery in the horned beetle Onthophagus taurus

(2011) Jeong-Hyeon Choi et al.   BMC GENOMICS

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

Molecular evolutionary analyses of insect societies

(2011) B. J. Fischman 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 genomic impact of 100 million years of social evolution in seven ant species

(2011) Jürgen Gadau et al.   TRENDS IN GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

INTERACTING PHENOTYPES AND THE EVOLUTIONARY PROCESS. III. SOCIAL EVOLUTION

(2010) Joel W. McGlothlin et al.   EVOLUTION

Functional Conservation of DNA Methylation in the Pea Aphid and the Honeybee

(2010) Brendan G. Hunt et al.   Genome Biology and Evolution

Single base–resolution methylome of the silkworm reveals a sparse epigenomic map

(2010) Hui Xiang et al.   NATURE BIOTECHNOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

The Honey Bee Epigenomes: Differential Methylation of Brain DNA in Queens and Workers

(2010) Frank Lyko et al.   PLOS BIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Single-copy nuclear genes resolve the phylogeny of the holometabolous insects

(2009) Brian M Wiegmann et al.   BMC BIOLOGY

BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum

(2009) Hee Shin Kim et al.   NUCLEIC ACIDS RESEARCH

DNA methylation is widespread and associated with differential gene expression in castes of the honeybee, Apis mellifera

(2009) N. Elango et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

The genome of the model beetle and pest Tribolium castaneum

(2008) Stephen Richards et al.   NATURE

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH

InterPro: the integrative protein signature database

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

The quantitative genetics of sex differences in parenting

(2008) C. A. Walling et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Graph Clustering Via a Discrete Uncoupling Process

(2008) Stijn Van Dongen   SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS

Analysis of repetitive DNA distribution patterns in the Tribolium castaneum genome

(2008) Suzhi Wang et al.   GENOME BIOLOGY