Enhanced genome assembly and a new official gene set for Tribolium castaneum

Enhancer identification and activity evaluation in the red flour beetle,Tribolium castaneum

(2018) Yi-Ting Lai et al.   DEVELOPMENT

A morphological novelty evolved by co-option of a reduced gene regulatory network and gene recruitment in a beetle

(2018) Yonggang Hu et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Expanded and updated data and a query pipeline for iBeetle-Base

(2017) Jürgen Dönitz et al.   NUCLEIC ACIDS RESEARCH

The insect central complex as model for heterochronic brain development—background, concepts, and tools

(2016) Nikolaus Dieter Bernhard Koniszewski et al.   DEVELOPMENT GENES AND EVOLUTION

FlyBase at 25: looking to the future

(2016) L. Sian Gramates et al.   NUCLEIC ACIDS RESEARCH

Cuticle formation and pigmentation in beetles

(2016) Mi Young Noh et al.   Current Opinion in Insect Science

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Large scale RNAi screen in Tribolium reveals novel target genes for pest control and the proteasome as prime target

(2015) Julia Ulrich et al.   BMC GENOMICS

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

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

MicroRNA evolution, expression, and function during short germband development inTribolium castaneum

(2015) Maria Ninova et al.   GENOME RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

The iBeetle large-scale RNAi screen reveals gene functions for insect development and physiology

(2015) Christian Schmitt-Engel et al.   Nature Communications

Multiple In Vivo Biological Processes Are Mediated by Functionally Redundant Activities of Drosophila mir-279 and mir-996

(2015) Kailiang Sun et al.   PLoS Genetics

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

Tissue-specific transcriptomics, chromosomal localization, and phylogeny of chemosensory and odorant binding proteins from the red flour beetle Tribolium castaneum reveal subgroup specificities for olfaction or more general functions

(2015) Stefan Dippel et al.   BMC GENOMICS

Malpighian tubule development in the red flour beetle (Tribolium castaneum)

(2014) Benedict King et al.   ARTHROPOD STRUCTURE & DEVELOPMENT

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

(2014) Christine G Elsik et al.   BMC GENOMICS

Regulation of microRNA biogenesis

(2014) Minju Ha et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software

(2014) Evgenia V. Kriventseva et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Jürgen Dönitz et al.   NUCLEIC ACIDS RESEARCH

Tc-knirps plays different roles in the specification of antennal and mandibular parasegment boundaries and is regulated by a pair-rule gene in the beetle Tribolium castaneum

(2013) Andrew D Peel et al.   BMC DEVELOPMENTAL BIOLOGY

FlyBase 102—advanced approaches to interrogating FlyBase

(2013) Susan E. St. Pierre et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Odoriferous Defensive Stink Gland Transcriptome to Identify Novel Genes Necessary for Quinone Synthesis in the Red Flour Beetle, Tribolium castaneum

(2013) Jianwei Li et al.   PLoS Genetics

Heat shock-mediated misexpression of genes in the beetle Tribolium castaneum

(2012) Johannes Benno Schinko et al.   DEVELOPMENT GENES AND EVOLUTION

Opposing effects of Notch-signaling in maintaining the proliferative state of follicle cells in the telotrophic ovary of the beetle Tribolium

(2012) Daniel Bäumer et al.   Frontiers in Zoology

Streaming fragment assignment for real-time analysis of sequencing experiments

(2012) Adam Roberts et al.   NATURE METHODS

EvolView, an online tool for visualizing, annotating and managing phylogenetic trees

(2012) Huangkai Zhang et al.   NUCLEIC ACIDS RESEARCH

A Segmentation Clock with Two-Segment Periodicity in Insects

(2012) A. F. Sarrazin et al.   SCIENCE

Toward almost closed genomes with GapFiller

(2012) Marten Boetzer et al.   GENOME BIOLOGY

Genomic and proteomic studies on the effects of the insect growth regulator diflubenzuron in the model beetle species Tribolium castaneum

(2011) Hans Merzendorfer et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

Genetics, development and composition of the insect head – A beetle’s view

(2010) Nico Posnien et al.   ARTHROPOD STRUCTURE & DEVELOPMENT

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Functionality of the GAL4/UAS system in Tribolium requires the use of endogenous core promoters

(2010) Johannes B Schinko et al.   BMC DEVELOPMENTAL BIOLOGY

Functional Shifts in Insect microRNA Evolution

(2010) Antonio Marco et al.   Genome Biology and Evolution

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Large-scale insertional mutagenesis of a coleopteran stored grain pest, the red flour beetle Tribolium castaneum, identifies embryonic lethal mutations and enhancer traps

(2009) Jochen Trauner et al.   BMC BIOLOGY

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

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

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

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

From development to biodiversity—Tribolium castaneum, an insect model organism for short germband development

(2008) Reinhard Schröder et al.   DEVELOPMENT GENES AND EVOLUTION

The genome of the model beetle and pest Tribolium castaneum

(2008) Stephen Richards et al.   NATURE

Exploring systemic RNA interference in insects: a genome-wide survey for RNAi genes in Tribolium

(2008) Yoshinori Tomoyasu et al.   GENOME BIOLOGY

Extraembryonic development in insects and the acrobatics of blastokinesis

(2007) Kristen A. Panfilio   DEVELOPMENTAL BIOLOGY