Chromosome Fusion Affects Genetic Diversity and Evolutionary Turnover of Functional Loci but Consistently Depends on Chromosome Size

Rampant genome-wide admixture across the Heliconius radiation

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The Dryas iulia Genome Supports Multiple Gains of a W Chromosome from a B Chromosome in Butterflies

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Selective sweeps on novel and introgressed variation shape mimicry loci in a butterfly adaptive radiation

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Speciation through chromosomal fusion and fission in Lepidoptera

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Millipede genomes reveal unique adaptations during myriapod evolution

(2020) Zhe Qu et al.   PLOS BIOLOGY

Many functionally connected loci foster adaptive diversification along a neotropical hybrid zone

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Errors in long-read assemblies can critically affect protein prediction

(2019) Mick Watson et al.   NATURE BIOTECHNOLOGY

A rigorous measure of genome-wide genetic shuffling that takes into account crossover positions and Mendel’s second law

(2019) Carl Veller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recombination rate variation shapes barriers to introgression across butterfly genomes

(2019) Simon H. Martin et al.   PLOS BIOLOGY

The Effects on Neutral Variability of Recurrent Selective Sweeps and Background Selection

(2019) José Luis Campos et al.   GENETICS

Simultaneous TE Analysis of 19 Heliconiine Butterflies Yields Novel Insights into Rapid TE-based Genome Diversification and Multiple SINE Births and Deaths

(2019) David A Ray et al.   Genome Biology and Evolution

The determinants of genetic diversity in butterflies

(2019) Alexander Mackintosh et al.   Nature Communications

Parallel evolution of ancient, pleiotropic enhancers underlies butterfly wing pattern mimicry

(2019) James J. Lewis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic architecture and introgression shape a butterfly radiation

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Dichotomy of Dosage Compensation along the Neo Z Chromosome of the Monarch Butterfly

(2019) Liuqi Gu et al.   CURRENT BIOLOGY

Interplay between Developmental Flexibility and Determinism in the Evolution of Mimetic Heliconius Wing Patterns

(2019) Carolina Concha et al.   CURRENT BIOLOGY

Minimap2: pairwise alignment for nucleotide sequences

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P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads

(2018) Bai-Han Zhu et al.   BMC GENOMICS

Genome-Wide Regulatory Adaptation Shapes Population-Level Genomic Landscapes in Heliconius

(2018) James J Lewis et al.   MOLECULAR BIOLOGY AND EVOLUTION

UniProt: a worldwide hub of protein knowledge

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The Pfam protein families database in 2019

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(2018) Gui-Cai Xu et al.   GigaScience

Efficient and accurate detection of splice junctions from RNA-seq with Portcullis

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Genome evolution, structural rearrangements and speciation

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CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features

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Coevolution between transposable elements and recombination

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Complex modular architecture around a simple toolkit of wing pattern genes

(2017) Steven M. Van Belleghem et al.   Nature Ecology & Evolution

Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene

(2016) Simon H. Martin et al.   GENETICS

ChIP-Seq-Annotated Heliconius erato Genome Highlights Patterns of cis -Regulatory Evolution in Lepidoptera

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Major Improvements to the Heliconius melpomene Genome Assembly Used to Confirm 10 Chromosome Fusion Events in 6 Million Years of Butterfly Evolution

(2016) John W. Davey et al.   G3-Genes Genomes Genetics

Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene

(2016) Simon H. Martin et al.   GENETICS

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Enhancer Evolution across 20 Mammalian Species

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Multilocus Species Trees Show the Recent Adaptive Radiation of the Mimetic Heliconius Butterflies

(2015) Krzysztof M. Kozak et al.   SYSTEMATIC BIOLOGY

Natural Selection Constrains Neutral Diversity across A Wide Range of Species

(2015) Russell B. Corbett-Detig et al.   PLOS BIOLOGY

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(2015) Haibao Tang et al.   GENOME BIOLOGY

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

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The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera

(2014) Virpi Ahola et al.   Nature Communications

The complex hybrid origins of the root knot nematodes revealed through comparative genomics

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Genomic signatures of selection at linked sites: unifying the disparity among species

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The Drosophila melanogaster Genetic Reference Panel

(2012) Trudy F. C. Mackay et al.   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

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Exonization of transposed elements: A challenge and opportunity for evolution

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A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

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The genome of Tetranychus urticae reveals herbivorous pest adaptations

(2011) Miodrag Grbić et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

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(2011) David I. Warton et al.   Methods in Ecology and Evolution

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

The role of transposable elements in the evolution of non-mammalian vertebrates and invertebrates

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

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