Genomic changes associated with adaptation to arid environments in cactophilic Drosophila species

Faster Evolving Primate Genes Are More Likely to Duplicate

(2017) Áine N O’Toole et al.   MOLECULAR BIOLOGY AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Early events in speciation: Cryptic species of Drosophila aldrichi

(2017) Cynthia Castro Vargas et al.   Ecology and Evolution

Genomics of parallel adaptation at two timescales in Drosophila

(2017) Li Zhao et al.   PLoS Genetics

Exploration of the Drosophila buzzatii transposable element content suggests underestimation of repeats in Drosophila genomes

(2016) Nuria Rius et al.   BMC GENOMICS

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution by gene loss

(2016) Ricard Albalat et al.   NATURE REVIEWS GENETICS

Recurrent specialization on a toxic fruit in an islandDrosophilapopulation

(2016) Amir Yassin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Are feeding preferences and insecticide resistance associated with the size of detoxifying enzyme families in insect herbivores?

(2016) Rahul V Rane et al.   Current Opinion in Insect Science

BFC: correcting Illumina sequencing errors

(2015) Heng Li   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Loss of function of the yellow-e gene causes dehydration-induced mortality of adult Tribolium castaneum

(2015) Mi Young Noh et al.   DEVELOPMENTAL BIOLOGY

Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow

(2015) Scott P. Egan et al.   ECOLOGY LETTERS

Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection

(2015) Martin D. Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transcriptional variation associated with cactus host plant adaptation inDrosophila mettleripopulations

(2015) Kim Hoang et al.   MOLECULAR ECOLOGY

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Genomics of Ecological Adaptation in Cactophilic Drosophila

(2015) Yolanda Guillén et al.   Genome Biology and Evolution

QuorUM: An Error Corrector for Illumina Reads

(2015) Guillaume Marçais et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Sensitivity to thermal extremes in AustralianDrosophilaimplies similar impacts of climate change on the distribution of widespread and tropical species

(2014) Johannes Overgaard et al.   GLOBAL CHANGE BIOLOGY

Radiation of theDrosophila nannopteraspecies group in Mexico

(2014) M. Lang et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Diversity and dynamics of the Drosophila transcriptome

(2014) James B. Brown et al.   NATURE

Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm

(2014) Alexandre Lomsadze et al.   NUCLEIC ACIDS RESEARCH

Differences in Tolerance to Host Cactus Alkaloids in Drosophila koepferae and D. buzzatii

(2014) Ignacio M. Soto et al.   PLoS One

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

Stick Insect Genomes Reveal Natural Selection's Role in Parallel Speciation

(2014) V. Soria-Carrasco et al.   SCIENCE

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

New Levels of Transcriptome Complexity at Upper Thermal Limits in Wild Drosophila Revealed by Exon Expression Analysis

(2013) Marina Telonis-Scott et al.   GENETICS

Functional genomic and phenotypic responses to desiccation in natural populations of a desert drosophilid

(2013) Subhash Rajpurohit et al.   MOLECULAR ECOLOGY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Gene amplification and microsatellite polymorphism underlie a recent insect host shift

(2013) C. Bass et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

PHYLOGENETIC CONSTRAINTS IN KEY FUNCTIONAL TRAITS BEHIND SPECIES’ CLIMATE NICHES: PATTERNS OF DESICCATION AND COLD RESISTANCE ACROSS 95DROSOPHILASPECIES

(2012) Vanessa Kellermann et al.   EVOLUTION

Estimating Divergence Dates and Substitution Rates in the Drosophila Phylogeny

(2012) Darren J. Obbard et al.   MOLECULAR BIOLOGY AND EVOLUTION

Monophyly, divergence times, and evolution of host plant use inferred from a revised phylogeny of the Drosophila repleta species group

(2012) Deodoro C.S.G. Oliveira et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential

(2012) Gengyun Zhang et al.   NATURE BIOTECHNOLOGY

Estimating divergence times in large molecular phylogenies

(2012) K. Tamura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Upper thermal limits of Drosophila are linked to species distributions and strongly constrained phylogenetically

(2012) V. Kellermann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Species of Drosophila (Diptera: Drosophilidae) attracted to dung and carrion baited pitfall traps in the Uruguayan Eastern Serranías

(2012) Beatriz Goñi et al.   Zoologia

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Dietary Protein and Sugar Differentially Affect Development and Metabolic Pools in Ecologically Diverse Drosophila

(2011) Luciano M. Matzkin et al.   JOURNAL OF NUTRITION

High Resolution Mapping of Candidate Alleles for Desiccation Resistance in Drosophila melanogaster under Selection

(2011) Marina Telonis-Scott et al.   MOLECULAR BIOLOGY AND EVOLUTION

FlyBase 101 - the basics of navigating FlyBase

(2011) P. McQuilton et al.   NUCLEIC ACIDS RESEARCH

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

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

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

The physiology of climate change: how potentials for acclimatization and genetic adaptation will determine 'winners' and 'losers'

(2010) G. N. Somero   JOURNAL OF EXPERIMENTAL BIOLOGY

DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila

(2010) Thilakam Murali et al.   NUCLEIC ACIDS RESEARCH

OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011

(2010) Robert M. Waterhouse et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Evolution of stress resistance inDrosophila: interspecific variation in tolerance to desiccation and starvation

(2009) Luciano M. Matzkin et al.   FUNCTIONAL ECOLOGY

Transcriptional Regulation of Metabolism Associated With the Increased Desiccation Resistance of the Cactophilic Drosophila mojavensis

(2009) Luciano M. Matzkin et al.   GENETICS

Fundamental Evolutionary Limits in Ecological Traits Drive Drosophila Species Distributions

(2009) V. Kellermann et al.   SCIENCE

Genetic Changes Accompanying the Evolution of Host Specialization in Drosophila sechellia

(2008) I. Dworkin et al.   GENETICS

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY