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

    Article • August 2024, Cold Spring Harbor Laboratory Press

    Dr Jacqueline Smith

  2. Multiscale 3D genome organization underlies duck fatty liver with no adipose inflammation or serious injury

    Article • International Journal of Biological Macromolecules, June 2024, Elsevier

    Dr Jacqueline Smith

  3. Genetic variance components of the growth curve for Isfahan indigenous chicken

    Article • Veterinary Medicine and Science, February 2024, Wiley

    Dr Jacqueline Smith

  4. A new chromosome-scale duck genome shows a major histocompatibility complex with several expanded multigene families

    Article • BMC Biology, February 2024, Springer Science + Business Media

    Dr Jacqueline Smith

  5. Genomic analysis of Nigerian indigenous chickens reveals their genetic diversity and adaptation to heat-stress

    Article • Scientific Reports, January 2024, Springer Science + Business Media

    Dr Jacqueline Smith

  6. A chromosome-level genome assembly of a free-living white-crowned sparrow (Zonotrichia leucophrys gambelii)

    Article • Scientific Data, January 2024, Springer Science + Business Media

    Dr Jacqueline Smith

  7. Selection on the promoter regions plays an important role in complex traits during duck domestication

    Article • BMC Biology, December 2023, Springer Science + Business Media

    Dr Jacqueline Smith

  8. A chromosome-level genome assembly for the Silkie chicken resolves complete sequences for key chicken metabolic, reproductive, and immunity genes

    Article • Communications Biology, December 2023, Springer Science + Business Media

    Dr Jacqueline Smith

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

    Article • June 2023, Cold Spring Harbor Laboratory Press

    Dr Jacqueline Smith

  10. The Transcriptome of Chicken Migratory Primordial Germ Cells Reveals Intrinsic Sex Differences and Expression of Hallmark Germ Cell Genes

    Article • Cells, April 2023, MDPI AG

    Dr Jacqueline Smith

  11. RNA-Seq Profiling between Commercial and Indigenous Iranian Chickens Highlights Differences in Innate Immune Gene Expression

    Article • Genes, March 2023, MDPI AG

    Dr Jacqueline Smith

  12. nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing

    Article • Bioinformatics, March 2023, Oxford University Press (OUP)

    Dr Jacqueline Smith

  13. Genomics of Dwarfism in Italian Local Chicken Breeds

    Article • Genes, March 2023, MDPI AG

    Dr Jacqueline Smith

  14. Identification of alternative splicing events related to fatty liver formation in duck using full-length transcripts

    Article • BMC Genomics, March 2023, Springer Science + Business Media

    Dr Jacqueline Smith

  15. The molecular basis of differential host responses to avian influenza viruses in avian species with differing susceptibility

    Article • Frontiers in Cellular and Infection Microbiology, February 2023, Frontiers

    Dr Jacqueline Smith

  16. Comparative Analysis of Different Inbred Chicken Lines Highlights How a Hereditary Inflammatory State Affects Susceptibility to Avian Influenza Virus

    Article • Viruses, February 2023, MDPI AG

    Dr Jacqueline Smith

  17. RNAseq reveals modulation of genes involved in fatty acid biosynthesis in chicken liver according to genetic background, sex, and diet

    Article • Animal Genetics, February 2023, Wiley

    Dr Jacqueline Smith

  18. The swan genome and transcriptome, it is not all black and white

    Article • January 2023, Springer Science + Business Media

    Dr Jacqueline Smith

  19. In silico investigation of uncoupling protein function in avian genomes

    Article • Frontiers in Veterinary Science, January 2023, Frontiers

    Dr Jacqueline Smith

  20. Estimation of genetic parameters for production, reproduction, and growth curve of Fars indigenous chicken

    Article • Animal Science Journal, January 2023, Wiley

    Dr Jacqueline Smith

  21. Sex Differences in Response to Marek’s Disease: Mapping Quantitative Trait Loci Regions (QTLRs) to the Z Chromosome

    Article • Genes, December 2022, MDPI AG

    Dr Jacqueline Smith

  22. Sex Differences in Response to Marek’s Disease: Mapping Quantitative Trait Loci Regions (QTLRs) to the Z Chromosome

    Article • December 2022, MDPI AG

    Dr Jacqueline Smith

  23. The Role of Dendritic Cells in the Host Response to Marek’s Disease Virus (MDV) as Shown by Transcriptomic Analysis of Susceptible and Resistant Birds

    Article • Pathogens, November 2022, MDPI AG

    Dr Jacqueline Smith

  24. An Integrated Bioinformatics Approach to Identify Network-Derived Hub Genes in Starving Zebrafish

    Article • Animals, October 2022, MDPI AG

    Dr Jacqueline Smith

  25. Genetic variation in chicken interferon signalling pathway genes in research lines showing differential viral resistance

    Article • Animal Genetics, June 2022, Wiley

    Dr Jacqueline Smith

  26. Constraint-Based, Score-Based and Hybrid Algorithms to Construct Bayesian Gene Networks in the Bovine Transcriptome

    Article • Animals, May 2022, MDPI AG

    Dr Jacqueline Smith

  27. Network Meta-Analysis of Chicken Microarray Data following Avian Influenza Challenge—A Comparison of Highly and Lowly Pathogenic Strains

    Article • Genes, February 2022, MDPI AG

    Dr Jacqueline Smith

  28. Whole genome sequences of 234 indigenous African chickens from Ethiopia

    Article • Scientific Data, February 2022, Springer Science + Business Media

    Dr Jacqueline Smith

  29. Fourth Report on Chicken Genes and Chromosomes 2022

    Article • Cytogenetic and Genome Research, January 2022, Karger Publishers

    Dr Jacqueline Smith, Dr Heath Blackmon

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

    Article • December 2021, Cold Spring Harbor Laboratory Press

    Dr Jacqueline Smith

  31. Heterogeneity of Early Host Response to Infection with Four Low-Pathogenic H7 Viruses with a Different Evolutionary History in the Field

    Article • Viruses, November 2021, MDPI AG

    Dr Jacqueline Smith

  32. Parental methyl-enhanced diet and in ovo corticosterone affect first generation Japanese quail (Coturnix japonica) development, behaviour and stress response

    Article • Scientific Reports, October 2021, Springer Science + Business Media

    Dr Jacqueline Smith

  33. Following the Trace of HVS II Mitochondrial Region Within the Nine Iranian Ethnic Groups Based on Genetic Population Analysis

    Article • Biochemical Genetics, October 2021, Springer Science + Business Media

    Dr Jacqueline Smith

  34. Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication

    Article • Nature Communications, October 2021, Springer Science + Business Media

    Dr Jacqueline Smith

  35. Transcriptomic analysis of caecal tissue in inbred chicken lines that exhibit heritable differences in resistance to Campylobacter jejuni

    Article • BMC Genomics, June 2021, Springer Science + Business Media

    Dr Jacqueline Smith

  36. Integrated Environmental and Genomic Analysis Reveals the Drivers of Local Adaptation in African Indigenous Chickens

    Article • Molecular Biology and Evolution, May 2021, Oxford University Press (OUP)

    Dr Jacqueline Smith

  37. Avian Immunome DB: an example of a user-friendly interface for extracting genetic information

    Article • BMC Bioinformatics, November 2020, Springer Science + Business Media

    Dr Jacqueline Smith

  38. Illuminating the dark side of the human transcriptome with long read transcript sequencing

    Article • September 2020, Research Square

    Dr Jacqueline Smith

  39. Mapping QTL Associated with Resistance to Avian Oncogenic Marek’s Disease Virus (MDV) Reveals Major Candidate Genes and Variants

    Article • Genes, August 2020, MDPI AG

    Dr Jacqueline Smith

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

    Article • August 2020, Cold Spring Harbor Laboratory Press

    Dr Jacqueline Smith

  41. Illuminating the dark side of the human transcriptome with long read transcript sequencing

    Article • July 2020, Research Square

    Dr Jacqueline Smith

  42. Mapping QTL associated with resistance to avian oncogenic Marek’s Disease Virus (MDV) reveals major candidate genes and variants

    Article • July 2020, Cold Spring Harbor Laboratory Press

    Dr Jacqueline Smith

  43. Erratum: Chakraborty, P. et al. Macrophages from Susceptible and Resistant Chicken Lines have Different Transcriptomes following Marek’s Disease Virus Infection. Genes 2019, 10, 74

    Article • Genes, July 2020, MDPI AG

    Dr Jacqueline Smith

  44. Diversity of endogenous avian leukosis virus subgroup E (ALVE) insertions in indigenous chickens

    Article • Génétique Sélection Évolution, June 2020, Springer Science + Business Media

    Dr Jacqueline Smith

  45. Endogenous avian leukosis virus subgroup E elements of the chicken reference genome

    Article • Poultry Science, June 2020, Elsevier

    Dr Jacqueline Smith

  46. Illuminating the dark side of the human transcriptome with long read transcript sequencing

    Article • April 2020, Research Square

    Dr Jacqueline Smith

  47. The quail genome: insights into social behaviour, seasonal biology and infectious disease response

    Article • BMC Biology, February 2020, Springer Science + Business Media

    Dr Jacqueline Smith

  48. The wild species genome ancestry of domestic chickens

    Article • BMC Biology, February 2020, Springer Science + Business Media

    Dr Jacqueline Smith

  49. Full-length transcriptome sequencing from multiple tissues of duck, Anas platyrhynchos

    Article • Scientific Data, November 2019, Springer Science + Business Media

    Dr Jacqueline Smith

  50. Reviving rare chicken breeds using genetically engineered sterility in surrogate host birds

    Article • Proceedings of the National Academy of Sciences, October 2019, Proceedings of the National Academy of Sciences

    Dr Jacqueline Smith

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

    Article • September 2019, Cold Spring Harbor Laboratory Press

    Dr Jacqueline Smith

  52. Functional evolution of the colony‐stimulating factor 1 receptor (CSF1R) and its ligands in birds

    Article • Journal of Leukocyte Biology, September 2019, Wiley

    Dr Jacqueline Smith

  53. The wild species genome ancestry of domestic chickens

    Article • July 2019, Cold Spring Harbor Laboratory Press

    Dr Jacqueline Smith

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

    Article • March 2019, Cold Spring Harbor Laboratory Press

    Dr Jacqueline Smith

  55. Computational analysis of the evolutionarily conserved Missing In Metastasis/Metastasis Suppressor 1 gene predicts novel interactions, regulatory regions and transcriptional control

    Article • Scientific Reports, March 2019, Springer Science + Business Media

    Dr Jacqueline Smith

  56. Macrophages from Susceptible and Resistant Chicken Lines have Different Transcriptomes following Marek’s Disease Virus Infection

    Article • Genes, January 2019, MDPI AG

    Dr Jacqueline Smith

  57. Revisiting avian ‘missing’ genes from de novo assembled transcripts

    Article • BMC Genomics, January 2019, Springer Science + Business Media

    Dr Jacqueline Smith

  58. Origin and development of oligoadenylate synthetase immune system

    Article • BMC Evolutionary Biology, December 2018, Springer Science + Business Media

    Dr Jacqueline Smith

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

    Article • August 2018, Cold Spring Harbor Laboratory Press

    Dr Jacqueline Smith

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

    Article • BMC Genomics, August 2018, Springer Science + Business Media

    Dr Jacqueline Smith

  61. Molecular Mechanisms for the Adaptive Switching Between the OAS/RNase L and OASL/RIG-I Pathways in Birds and Mammals

    Article • Frontiers in Immunology, June 2018, Frontiers

    Dr Jacqueline Smith

  62. The genomic architecture of mastitis resistance in dairy sheep

    Article • BMC Genomics, August 2017, Springer Science + Business Media

    Dr Jacqueline Smith

  63. The genomic architecture of resistance to Campylobacter jejuni intestinal colonisation in chickens

    Article • BMC Genomics, April 2016, Springer Science + Business Media

    Dr Jacqueline Smith

  64. Animal genomics and infectious disease resistance in poultry

    Article • Revue Scientifique et Technique de l OIE, April 2016, O.I.E (World Organisation for Animal Health)

    Dr Jacqueline Smith

  65. The early immune response to infection of chickens with Infectious Bronchitis Virus (IBV) in susceptible and resistant birds

    Article • BMC Veterinary Research, October 2015, Springer Science + Business Media

    Dr Jacqueline Smith

  66. A comparative analysis of host responses to avian influenza infection in ducks and chickens highlights a role for the interferon-induced transmembrane proteins in viral resistance

    Article • BMC Genomics, August 2015, Springer Science + Business Media

    Dr Jacqueline Smith

  67. Chicken Genes and Chromosomes 2015

    Article • June 2015, Karger Publishers

    Dr Jacqueline Smith

  68. Characterization of the Avian Trojan Gene Family Reveals Contrasting Evolutionary Constraints

    Article • PLoS ONE, March 2015, PLOS

    Dr Jacqueline Smith

  69. The development and maintenance of the mononuclear phagocyte system of the chick is controlled by signals from the macrophage colony-stimulating factor receptor

    Article • BMC Biology, February 2015, Springer Science + Business Media

    Dr Jacqueline Smith

  70. Third Report on Chicken Genes and Chromosomes 2015

    Article • Cytogenetic and Genome Research, January 2015, Karger Publishers

    Dr Jacqueline Smith, Mr Takele Taye Desta

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

    Article • December 2014, Cold Spring Harbor Laboratory Press

    Dr Jacqueline Smith

  72. Comparative genomics reveals insights into avian genome evolution and adaptation

    Article • Science, December 2014, American Association for the Advancement of Science

    Cai Li, Edward L Braun, Dr Jacqueline Smith

  73. Analysis of the Early Immune Response to Infection by Infectious Bursal Disease Virus in Chickens Differing in Their Resistance to the Disease

    Article • Journal of Virology, December 2014, ASM Journals

    Dr Jacqueline Smith

  74. The duck genome and transcriptome provide insight into an avian influenza virus reservoir species

    Article • Nature Genetics, June 2013, Springer Science + Business Media

    Hualan Chen, Dr Jacqueline Smith

  75. Systems Analysis of Immune Responses in Marek's Disease Virus-Infected Chickens Identifies a Gene Involved in Susceptibility and Highlights a Possible Novel Pathogenicity Mechanism

    Article • Journal of Virology, August 2011, ASM Journals

    Dr Jacqueline Smith

  76. Molecular evolution of the vertebrate TLR1 gene family - a complex history of gene duplication, gene conversion, positive selection and co-evolution

    Article • BMC Evolutionary Biology, May 2011, Springer Science + Business Media

    Dr Jacqueline Smith

  77. Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis

    Article • PLoS Biology, September 2010, PLOS

    Dr Jacqueline Smith

  78. Pivotal Advance: Avian colony-stimulating factor 1 (CSF-1), interleukin-34 (IL-34), and CSF-1 receptor genes and gene products

    Article • Journal of Leukocyte Biology, January 2010, Society for Leukocyte Biology

    Dr Jacqueline Smith

  79. Molecular immunophenotyping of lungs in naïve and vaccinated chickens early after pulmonary avian influenza A (H9N2) virus infection

    Article • Veterinary Immunology and Immunopathology, March 2009, Elsevier

    Dr Jacqueline Smith

  80. Integrated Immunogenomics in the Chicken: Deciphering the Immune Response to Identify Disease Resistance Genes

    Article • January 2008, Karger Publishers

    Dr Jacqueline Smith

  81. Molecular immunophenotyping of lungs and spleens in naive and vaccinated chickens early after pulmonary avian influenza A (H9N2) virus infection

    Article • Vaccine, August 2006, Elsevier

    Dr Jacqueline Smith

  82. Development of a chicken 5 K microarray targeted towards immune function

    Article • BMC Genomics, March 2006, Springer Science + Business Media

    Dr Jacqueline Smith

  83. Second report on chicken genes and chromosomes 2005

    Article • Cytogenetic and Genome Research, January 2005, Karger Publishers

    Dr Jacqueline Smith

  84. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

    Article • Nature, December 2004, Springer Science + Business Media

    Dr Jacqueline Smith

  85. In-silico identification of chicken immune-related genes

    Article • Immunogenetics, May 2004, Springer Science + Business Media

    Dr Jacqueline Smith

  86. Molecular Cytogenetic Definition of the Chicken Genome: The First Complete Avian Karyotype

    Article • Genetics, March 2004, Genetics Society of America

    Dr Jacqueline Smith

  87. Isolation and mapping the chicken zona pellucida genes: An insight into the evolution of orthologous genes in different species

    Article • Molecular Reproduction and Development, January 2004, Wiley

    Dr Jacqueline Smith, Dr David C Hughes

  88. Preliminary linkage map of the Turkey ( Meleagris gallopavo ) based on microsatellite markers

    Article • Animal Genetics, December 2003, Wiley

    Dr Jacqueline Smith

  89. Mapping the ABCA4 , IMPDH2 and TIMP3 genes in chicken

    Article • Animal Genetics, September 2003, Wiley

    Dr Jacqueline Smith

  90. Chicken syndecan-4 (SDC4) maps to linkage group E32E47W24

    Article • Animal Genetics, June 2003, Wiley

    Dr Jacqueline Smith

  91. Molecular characterization of chicken syndecan-2 proteoglycan

    Article • Biochemical Journal, September 2002, Portland Press Ltd.

    Dr Jacqueline Smith

  92. Comparative mapping of human Chromosome 19 with the chicken shows conserved synteny and gives an insight into chromosomal evolution

    Article • Mammalian Genome, June 2002, Springer Science + Business Media

    Dr Jacqueline Smith

  93. Human Chromosomes 3 and 21 are the products of an ancestral gene arrangement that is at least 300 million years old

    Article • Mammalian Genome, September 2000, Springer Science + Business Media

    Dr Jacqueline Smith

  94. Mapping the RAIDD gene of chicken (Gallus gallus): identification of a region homologous to the mouse high-growth region

    Article • Mammalian Genome, August 2000, Springer Science + Business Media

    Dr Jacqueline Smith

  95. Differences in gene density on chicken macrochromosomes and microchromosomes

    Article • Animal Genetics, March 2000, Wiley

    Dr Jacqueline Smith

  96. Integration of the genetic and physical maps of the chicken macrochromosomes

    Article • Animal Genetics, January 2000, Wiley

    Dr Jacqueline Smith

  97. First report on chicken genes and chromosomes 2000

    Article • Cytogenetic and Genome Research, January 2000, Karger Publishers

    Dr Jacqueline Smith

  98. The dynamics of chromosome evolution in birds and mammals

    Article • Nature, November 1999, Springer Science + Business Media

    Dr Jacqueline Smith

  99. Micro- and macrochromosome paints generated by flow cytometry and microdissection: tools for mapping the chicken genome

    Article • Cytogenetic and Genome Research, January 1999, Karger Publishers

    Dr Jacqueline Smith

  100. Parameters of the chicken genome (Gallus gallus )

    Article • Animal Genetics, August 1998, Wiley

    Dr Jacqueline Smith