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List of works by Paul Stothard

A 2cM genome-wide scan of European Holstein cattle affected by classical BSE.

scientific article

A first generation whole genome RH map of the river buffalo with comparison to domestic cattle

scientific article

A high resolution radiation hybrid map of bovine chromosome 14 identifies scaffold rearrangement in the latest bovine assembly

scientific article

A large and diverse collection of bovine genome sequences from the Canadian Cattle Genome Project

scientific article published on 26 October 2015

Automated bacterial genome analysis and annotation

scientific article published on 22 August 2006

BASys: a web server for automated bacterial genome annotation

scientific article

BacMap: an interactive picture atlas of annotated bacterial genomes

scientific article

BacMap: an up-to-date electronic atlas of annotated bacterial genomes

scientific article

BioSpider: a web server for automating metabolome annotations.

scientific article published on January 2007

Characterization of DC1, a Broad-Host-Range Bcep22-Like Podovirus ⬇️

scientific article published on December 2, 2011

Characterization of bovine miRNAs by sequencing and bioinformatics analysis

scientific article published in 2009

Characterization of the altered gene expression profile in early porcine embryos generated from parthenogenesis and somatic cell chromatin transfer

scientific article

Circular genome visualization and exploration using CGView

scientific article

Comparative analysis of two phenotypically-similar but genomically-distinct Burkholderia cenocepacia-specific bacteriophages ⬇️

scientific article published on June 7, 2012

Comparing thousands of circular genomes using the CGView Comparison Tool ⬇️

scientific article published on May 23, 2012

Conspecific and interspecific interactions between the FEM-2 and the FEM-3 sex-determining proteins despite rapid sequence divergence

scientific article published on 13 February 2006

Correlation of particular bacterial PCR-denaturing gradient gel electrophoresis patterns with bovine ruminal fermentation parameters and feed efficiency traits

scientific article

Differences in Whole Blood Gene Expression Associated with Infection Time-Course and Extent of Fetal Mortality in a Reproductive Model of Type 2 Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Infection

scientific article

Dominant Red Coat Color in Holstein Cattle Is Associated with a Missense Mutation in the Coatomer Protein Complex, Subunit Alpha (COPA) Gene

scientific article

Draft Genome Sequence of Pseudomonas sp. Strain B1, Isolated from a Contaminated Sediment.

scientific article

DrugBank: a comprehensive resource for in silico drug discovery and exploration

scientific article

Fast accurate missing SNP genotype local imputation

scientific article

Genome-centric evaluation of Burkholderia sp. strain SRS-W-2-2016 resistant to high concentrations of uranium and nickel isolated from the Savannah River Site (SRS), USA.

scientific article

Genome-wide association and genomic prediction of breeding values for fatty acid composition in subcutaneous adipose and longissimus lumborum muscle of beef cattle

scientific article published on 21 November 2015

Genome-wide association for milk production and female fertility traits in Canadian dairy Holstein cattle

scientific article

Genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in Holstein cattle

scientific article published on 7 November 2017

Genome-wide copy number variation in Hanwoo, Black Angus, and Holstein cattle ⬇️

scientific article published on March 30, 2013

Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars

scientific article published on 27 October 2013

Genomic analysis and relatedness of P2-like phages of the Burkholderia cepacia complex ⬇️

scientific article published on October 25, 2010

Genomic evaluation of feed efficiency component traits in Duroc pigs using 80K, 650K and whole-genome sequence variants.

scientific article

Genomic sequence and activity of KS10, a transposable phage of the Burkholderia cepacia complex

scientific article

Genotype Imputation Methods and Their Effects on Genomic Predictions in Cattle

HMDB: the Human Metabolome Database

scientific article from 2007

Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis)

scientific article published on 20 May 2015

High density linkage disequilibrium maps of chromosome 14 in Holstein and Angus cattle

scientific article

High resolution radiation hybrid maps of bovine chromosomes 19 and 29: comparison with the bovine genome sequence assembly

scientific article

Identification of novel and known oocyte-specific genes using complementary DNA subtraction and microarray analysis in three different species

scholarly article

In Sffamily Identification of Genes in Bacteriophage DNA

article

In-depth annotation of SNPs arising from resequencing projects using NGS-SNP ⬇️

scientific article published on June 22, 2011

Inactivation of Burkholderia cepacia complex phage KS9 gp41 identifies the phage repressor and generates lytic virions

scientific article published on 25 November 2009

Initial Gut Microbial Composition as a Key Factor Driving Host Response to Antibiotic Treatment, as Exemplified by the Presence or Absence of Commensal Escherichia coli

scientific article published on 30 June 2017

Interactive microbial genome visualization with GView ⬇️

scientific article published on October 17, 2010

Letter to the Editor: Complete 1H, 13C and 15N NMR assignments of MTH0776 from Methanobacterium thermoautotrophicum

Massively Parallel Sequencing of Chikso (Korean Brindle Cattle) to Discover Genome-Wide SNPs and InDels ⬇️

scientific article (publication date: September 2013)

Metabolic flexibility revealed in the genome of the cyst-forming alpha-1 proteobacterium Rhodospirillum centenum

scientific article

Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA.

scientific article

Mitochondriome and cholangiocellular carcinoma

scientific article

Most parsimonious haplotype allele sharing determination

scientific article

Novel Stenotrophomonas maltophilia temperate phage DLP4 is capable of lysogenic conversion

scholarly article by Danielle L Peters et al published 16 April 2019 in BMC Genomics

Optimizing Selection of the Reference Population for Genotype Imputation From Array to Sequence Variants.

scientific article

PROSESS: a protein structure evaluation suite and server

scientific article

Physiological and Comparative Genomic Analysis of Arthrobacter sp. SRS-W-1-2016 Provides Insights on Niche Adaptation for Survival in Uraniferous Soils

scientific article published on 11 January 2018

PlasMapper: a web server for drawing and auto-annotating plasmid maps

scientific article

PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites

scientific article published on 16 May 2008

Potential regulatory role of microRNAs in the development of bovine gastrointestinal tract during early life

scientific article

Sequence, structural and expression divergence of duplicate genes in the bovine genome

scientific article

Sex-determination gene and pathway evolution in nematodes

scientific article

Single nucleotide polymorphisms for feed efficiency and performance in crossbred beef cattle

scientific article published on 30 January 2014

Solution Structure of MTH0776 from Methanobacterium Thermoautotrophicum

The CGView Server: a comparative genomics tool for circular genomes

scientific article

The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli

scientific article

The genome of Polaromonas sp. strain JS666: insights into the evolution of a hydrocarbon- and xenobiotic-degrading bacterium, and features of relevance to biotechnology

scientific article published on 22 August 2008

The genome sequence of taurine cattle: a window to ruminant biology and evolution

scientific article

The identification of candidate genes and SNP markers for classical bovine spongiform encephalopathy susceptibility

scientific article

The isolation and characterization of Stenotrophomonas maltophilia T4-like bacteriophage DLP6.

scientific article

The isolation and characterization of two Stenotrophomonas maltophilia bacteriophages capable of cross-taxonomic order infectivity

scientific article published on 3 September 2015

Tissues, Metabolic Pathways and Genes of Key Importance in Lactating Dairy Cattle

article

Transcriptome analyses reveal reduced hepatic lipid synthesis and accumulation in more feed efficient beef cattle.

scientific article published on 8 May 2018

Transcriptome analysis reveals regional and temporal differences in mucosal immune system development in the small intestine of neonatal calves

scientific article

Transcriptome profiling of the rumen epithelium of beef cattle differing in residual feed intake

scientific article

Variance explained by whole genome sequence variants in coding and regulatory genome annotations for six dairy traits

scientific article published on 5 April 2018

Visualizing and comparing circular genomes using the CGView family of tools.

scientific article published on 26 July 2017

Whole Genome Sequence Analysis of an Alachlor and Endosulfan Degrading Micrococcus sp. strain 2385 Isolated from Ochlockonee River, Florida

scientific article published on 08 September 2016

Whole genome SNP genotype piecemeal imputation

scientific article published on 23 October 2015

Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery ⬇️

scientific article published on November 15, 2011

Whole genome sequence analysis of an Alachlor and Endosulfan degrading Pseudomonas strain W15Feb9B isolated from Ochlockonee River, Florida

scientific article published on 16 May 2016

Whole genome sequencing of Gir cattle for identifying polymorphisms and loci under selection

scientific article published on 2 August 2013

Whole-genome analyses of Korean native and Holstein cattle breeds by massively parallel sequencing

scientific article

Whole-genome resequencing of Hanwoo (Korean cattle) and insight into regions of homozygosity ⬇️

scientific article published on July 30, 2013

Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle

scientific article published on 13 July 2014

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