Jacqueline Smith

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.

The ChickenGTEx pilot analysis: a reference of regulatory variants across 28 chicken tissues

The ChickenGTEx project provides a multi-tissue reference of regulatory variants in chicken, analyzing their functional impacts and utility in genetics, genomics, and evolutionary studies.

A single-nucleus census of immune and non-immune cell types for the major immune organ systems of chicken.

The paper presents a single-nucleus atlas of immune and non-immune cell types in chicken immune organs, revealing transcriptomic diversity and intercellular communication in response to bacterial infection.

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.

A high-quality Genome and Comparison of Short versus Long Read Transcriptome of the Palaearctic duck Aythya fuligula (Tufted Duck)

The paper presents a high-quality genome and transcriptome of the tufted duck, comparing short and long-read sequencing technologies for transcriptome assembly.

A framework for defining livestock ecotypes based on ecological modelling and exploring genomic environmental adaptation: the example of Ethiopian village chicken

This study defines livestock ecotypes using ecological modeling and genomics, identifying adaptive genetic signatures in Ethiopian village chickens.

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.

Integrated environmental and genomic analysis reveals the drivers of local adaptation in African indigenous chickens

The paper identifies environmental drivers of adaptation in Ethiopian indigenous chickens and finds genomic regions associated with altitude, water scarcity, and feeding behavior.

Mining unknown porcine protein isoforms by tissue-based map of proteome enhances the pig genome annotation

The paper identifies and characterizes unknown porcine protein isoforms using tissue-based proteome maps and improves genome annotation.

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.

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.

Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

The paper integrates public and new RNA-seq data to create a chicken mRNA expression atlas, revealing tissue-specific gene clusters and developmental patterns.

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.