Julian Catchen

Transcriptomic differences underlying fin sexual dichromatism and male color polymorphism in bluefin killifish (Lucania goodei)

This study identifies transcriptomic differences underlying color variation in bluefin killifish, revealing genes involved in pigment pathways and light-sensitive phenotypic plasticity.

Synolog: A Scalable Synteny-Based Framework for Genome Architecture Characterization

Synolog identifies orthologs, synteny clusters, and genomic features across species, demonstrating its utility in studying genome evolution and structure.

Genomic introgression between critically endangered and stable species of Darwin's tree finches on the Galapagos Islands

The paper examines genomic introgression between a critically endangered and stable Darwin's tree finch species, finding evidence of selection for hybrid alleles associated with immunity and development.

The genomic signature and transcriptional response of metal tolerance in brown trout inhabiting metal-polluted rivers

This study investigates the genomic and transcriptomic signatures of metal tolerance in brown trout from metal-polluted rivers, identifying genetic and gene expression changes associated with metal resistance.

The genome of the cryopelagic Antarctic bald notothen, Trematomus borchgrevinki

This paper presents the first high-quality long-read genome of the Antarctic bald notothen, revealing its genome structure and repetitive elements, and highlights its potential as a model for cold adaptation studies.

Klumpy: A tool to evaluate the integrity of long-read genome assemblies and illusive sequence motifs

Klumpy evaluates genome assembly integrity and identifies sequence motifs by analyzing raw reads and assemblies across multiple species.

Highly resolved genome assembly and comparative transcriptome profiling reveal genes related to developmental stages of the tapeworm Ligula intestinalis

This study presents the first genome assembly of Ligula intestinalis and identifies differentially expressed genes between adult worms and plerocercoid larvae, revealing genes related to reproductive development and immune evasion.

Single-cell dissection of a collective behaviour in honeybees

The paper uses single-cell transcriptomics to show how genetic variants influence gene regulatory networks in honeybee brains, affecting aggression-related behaviors through specific cell populations and pathways.

Chromosome-Level Genome Assembly and Circadian Gene Repertoire of the Patagonia blennie Eleginops maclovinus - the closest ancestral proxy of Antarctic cryonotothenioids

This study presents a chromosome-level genome assembly of Eleginops maclovinus and compares its circadian gene repertoire with Antarctic cryonotothenioids, finding greater conservation with the Antarctic clade.

On the causes, consequences, and avoidance of PCR duplicates: towards a theory of library complexity

The paper develops a quantitative model to understand PCR duplicate formation in sequencing datasets and shows library complexity and sequencing depth determine duplicate rates.

Genomics of secondarily temperate adaptation in the only non-Antarctic icefish

The paper studies the genetic basis of secondarily temperate adaptation in the pike icefish by comparing its genome to its Antarctic relative, identifying chromosomal rearrangements and selected pathways.

Leafy and Weedy Seadragon Genomes Connect Genic and Repetitive DNA Features to the Extravagant Biology of Syngnathid Fishes

This study presents chromosome-scale genomes for leafy and weedy seadragons, identifying genomic features linked to their unique biology and evolutionary traits.

Population genomics analysis with RAD, reprised: STACKS 2

The paper provides a detailed protocol for RAD analysis using STACKS 2, covering experimental design, parameter optimization, and analysis from de novo to reference-based approaches.

Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of genetic maps and conserved synteny

Chromonomer improves genome assemblies by integrating genetic maps and conserved synteny to correct structural errors and produce enhanced chromosome models.

Simulation with RADinitio Improves RADseq Experimental Design and Sheds Light on Sources of Missing Data

RADinitio simulates RADseq experiments to optimize protocol selection and identifies library preparation and sequencing as major sources of missing data.

Stacks 2: Analytical Methods for Paired-end Sequencing Improve RADseq-based Population Genomics

Stacks 2 improves RADseq-based population genomics by using paired-end sequencing to assemble and genotype de novo datasets with high accuracy.