David W. Burt

Is it chaotic? Chicken Linkage Disequilibrium and quantitative trait loci

The paper examines linkage disequilibrium patterns in chicken QTLRs for Mareks Disease, finding chaotic LD structures that challenge GWAS interpretation.

Transcript- and annotation-guided genome assembly of the European starling

The paper presents two genome assemblies for the European starling, using long-read transcript data and homology-based annotation to improve assembly quality and provide a reference for population genetics.

The swan genome and transcriptome: its not all black and white

The paper generates the first chromosome-length annotated genomes and transcriptomes of black and mute swans, revealing immune system limitations and plumage-related genetic differences.

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.

The paper identifies widespread transcription initiation at microsatellites across species and develops deep learning models to predict STR-associated transcription and its impact on disease variants.

Complex and long-range linkage disequilibrium and its relationship with QTL for Marek's Disease resistance in chicken populations

The paper studies long-range linkage disequilibrium (LRLD) and its relationship with Marek's Disease resistance QTL in chicken populations, finding complex LD structures that suggest causative mutations may lie farther from markers than previously thought.

Towards complete and error-free genome assemblies of all vertebrate species

The paper summarizes methods and lessons from assembling 16 vertebrate genomes, highlights the importance of long-read sequencing, and introduces the Vertebrate Genomes Project to generate complete reference genomes for all vertebrate species.

Genomes of Symbiodiniaceae reveal extensive sequence divergence but conserved functions at family and genus levels

The paper presents whole-genome comparisons of Symbiodiniaceae isolates, revealing extensive sequence divergence but conserved gene functions across species and genera.

Illuminating the dark side of the human transcriptome with TAMA Iso-Seq analysis

The paper uses TAMA to analyze long-read RNA sequencing data and identifies thousands of potential novel genes while highlighting challenges in RNA preparation and data processing.

Mapping QTL associated with resistance to avian oncogenic Mareks Disease Virus (MDV) reveals major candidate genes and variants

This study identifies 38 QTL regions associated with resistance to Mareks Disease Virus (MDV) in chickens, highlighting candidate genes and variants that could inform breeding, vaccine design, or gene-editing strategies.

Circadian clock mechanism driving mammalian photoperiodism

This study identifies the circadian clock mechanism in mammals that drives seasonal responses to photoperiod changes through BMAL2 and EYA3/TSH pathways.

Polarella glacialis genomes encode tandem repeats of single-exon genes with functions critical to adaptation of dinoflagellates

This study presents genome assemblies of Polarella glacialis, revealing a high proportion of single-exon genes and their role in cold adaptation.

The quail as an avian model system: its genome provides insights into social behaviour, seasonal biology and infectious disease response

The paper presents a high-quality quail genome and uses it to study social behavior, photoperiodism, and immune response to H5N1 influenza.

Structural rearrangements drive extensive genome divergence between symbiotic and free-living Symbiodinium

This study compares genome structures of symbiotic and free-living Symbiodinium species, finding extensive divergence and suggesting structural rearrangements contribute to lifestyle differences.

The Avian RNAseq Consortium: a community effort to annotate the chicken genome

The Avian RNAseq Consortium provides chicken RNAseq data to improve genome annotation, contributing to Ensembl's Galgal4 gene build and ncRNA prediction.