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List of works by Patrick Biggs

0164 Metagenomic detection of bacteria in aerosol samples in animal slaughterhouses to develop exposure profiles for an epidemiological analysis

article

A Large Scale Waterborne Campylobacteriosis Outbreak, Havelock North, New Zealand

scientific article published on 28 June 2020

A conditional knockout resource for the genome-wide study of mouse gene function

scientific article

A critical rebuttal of the proposed division of the genus Arcobacter into six genera using comparative genomic, phylogenetic, and phenotypic criteria

scientific article published on 30 June 2020

A large chromosomal inversion affects antimicrobial sensitivity of Escherichia coli to sodium deoxycholate

scientific article published in 2022

A step toward genotype-based therapeutic regimens for breast cancer in patients with BRCA2 mutations?

scientific article

Allelic phasing of a mouse chromosome 11 deficiency influences p53 tumorigenicity

scientific article published on 01 May 2003

An approach to transcriptome analysis of non-model organisms using short-read sequences

scientific article published in January 2008

Analysis of culturable and non-culturable bacteria and their potential to form biofilms in a primary treated dairy wastewater system

scientific article published on 6 July 2017

Aristaeella hokkaidonensis gen. nov. sp. nov. and Aristaeella lactis sp. nov., two rumen bacterial species of a novel proposed family, Aristaeellaceae fam. nov.

scientific article published in 2023

BAC contig from a 3-cM region of mouse chromosome 11 surrounding Brca1

scientific article published on 01 October 2000

Biochar in co-contaminated soil manipulates arsenic solubility and microbiological community structure, and promotes organochlorine degradation.

scientific article published on 29 April 2015

Campylobacter novaezeelandiae sp. nov., isolated from birds and water in New Zealand

scientific article published on 05 June 2020

Carriage of extended-spectrum beta-lactamase-and AmpC beta-lactamase-producing Escherichia coli from humans and pets in the same households

scientific article published on 09 October 2020

Chips and tags suggest plant-environment interactions differ for two alpine Pachycladon species

scientific article

Comparative Genomics of Mycobacterium avium Subspecies Paratuberculosis Sheep Strains

scientific article published on 15 February 2021

Comparison of the Pathogenic Potential of Campylobacter jejuni, C. upsaliensis and C. helveticus and Limitations of Using Larvae of Galleria mellonella as an Infection Model

scientific article published on 29 August 2020

Complete Genome Sequence of Campylobacter concisus ATCC 33237T and Draft Genome Sequences for an Additional Eight Well-Characterized C. concisus Strains.

scientific article published on 20 July 2017

Complete Genome Sequence of Legionella sainthelensi Isolated from a Patient with Legionnaires' Disease

scientific article published in February 2018

Complete Genome Sequence of a Legionella longbeachae Serogroup 1 Strain Isolated from a Patient with Legionnaires' Disease

scientific article published on 15 June 2017

Complete Genome Sequence of a Legionella longbeachae Serogroup 2 Isolate Derived from a Patient with Legionnaires' Disease

scientific article published on 30 January 2020

Complete Genome Sequence of the Telford Type S Strain of Mycobacterium avium subsp. paratuberculosis

scientific article published on 14 March 2019

Culture independent analysis using gnd as a target gene to assess Escherichia coli diversity and community structure

scientific article

De novo sequence assembly and characterisation of a partial transcriptome for an evolutionarily distinct reptile, the tuatara (Sphenodon punctatus)

scientific article (publication date: 31 August 2012)

Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer

scientific article

Does a genotoxic carcinogen contribute to human breast cancer? The value of mutational spectra in unravelling the aetiology of cancer.

scientific article

Does land use affect pathogen presence in New Zealand drinking water supplies?

scientific article published on 27 July 2020

Draft Genome Sequence of a Canine Uropathogenic Escherichia coli Strain Isolated in New Zealand

article

Draft Genome Sequences of Eight Strains of Campylobacter helveticus Isolated from Cats and a Dog in New Zealand

scientific article published on 30 January 2020

Draft Genome Sequences of Seven Extended-Spectrum β-Lactamase-Producing Escherichia coli Strains Isolated from New Zealand Waterways

scientific article published in 2021

Draft Genome Sequences of Three Strains of Geobacillus stearothermophilus Isolated from a Milk Powder Manufacturing Plant

scientific article published on 15 October 2015

Draft Whole-Genome Sequences of Campylobacter Strains Isolated from Brushtail Possums in New Zealand

scientific article published on 21 November 2019

Draft Whole-Genome Sequences of Five Klebsiella pneumoniae Isolates from the Subantarctic Islands of New Zealand

article

Draft Whole-Genome Sequences of Seven Isolates of Klebsiella pneumoniae from New Zealand Sea Lions

article

Draft Whole-Genome Sequences of Three Diarrheagenic Escherichia coli Strains Isolated from Farmed Deer in New Zealand.

scientific article published on 19 April 2018

Draft Whole-Genome Sequences of Three Isolates of a Novel Strain of a sp. Isolated from New Zealand Birds and Water

article

Environmental bio-monitoring with high-throughput sequencing.

scientific article published on 15 May 2013

Erratum: Identification of the breast cancer susceptibility gene BRCA2

scientific article published in Nature

Estimating the relative rate of recombination to mutation in bacteria from single-locus variants using composite likelihood methods ⬇️

article

Estimating the relative roles of recombination and point mutation in the generation of single locus variants in Campylobacter jejuni and Campylobacter coli

scientific article published on June 2012

Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae in Dairy Farm Environments: A New Zealand Perspective

scientific article published on 10 November 2018

Extensive epigenetic modification with large-scale chromosomal and plasmid recombination characterise the Legionella longbeachae serogroup 1 genome

scientific article published on 06 April 2022

Extensive intra-host genetic diversity uncovered in Cryptosporidium parvum using Next Generation Sequencing.

scientific article published on 6 September 2012

Gene Regulatory Networks: A Primer in Biological Processes and Statistical Modelling

scientific article published on 01 January 2019

Genetic characterization of hypervirulent Klebsiella pneumoniae responsible for acute death in captive marmosets

Genome Sequences for Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Strains Isolated from Different Water Sources

scientific article published in 2021

Genomic Analysis of Fluoroquinolone- and Tetracycline-Resistant Campylobacter jejuni Sequence Type 6964 in Humans and Poultry, New Zealand, 2014-2016

scientific article published on 01 December 2019

Genomic Analysis of Salmonella enterica Serovar Typhimurium DT160 Associated with a 14-Year Outbreak, New Zealand, 1998-2012.

scientific article published on June 2017

Genomic Epidemiology and Management of Salmonella in Island Ecosystems Used for Takahe Conservation

scientific article published on 30 March 2017

Genomic correlates of extraintestinal infection are linked with changes in cell morphology in Campylobacter jejuni

article

Genomic epidemiology and carbon metabolism of Escherichia coli serogroup O145 reflect contrasting phylogenies

scientific article published on 25 June 2020

Genomic epidemiology of methicillin-susceptible Staphylococcus aureus across colonisation and skin and soft tissue infection

scientific article published on 3 August 2017

High throughput genome-wide survey of small RNAs from the parasitic protists Giardia intestinalis and Trichomonas vaginalis

scientific article

Identification of a novel nidovirus associated with a neurological disease of the Australian brushtail possum (Trichosurus vulpecula) ⬇️

scientific article published on November 25, 2011

Identification of a novel polyomavirus from a marsupial host

scientific article published in 2022

Identification of chloroplast genome loci suitable for high-resolution phylogeographic studies of Colocasia esculenta (L.) Schott (Araceae) and closely related taxa.

scientific article published on 30 May 2013

Identification of the familial cylindromatosis tumour-suppressor gene

scientific article (publication date: June 2000)

Identification, synthesis and properties of 5-(aziridin-1-yl)-2-nitro-4-nitrosobenzamide, a novel DNA crosslinking agent derived from CB1954.

scientific article published on September 1993

Index-free de novo assembly and deconvolution of mixed mitochondrial genomes.

scientific article

Inferring Ancestral Recombination Graphs from Bacterial Genomic Data.

scientific article published on 22 December 2016

Insights into the Geobacillus stearothermophilus species based on phylogenomic principles

scientific article

Investigation of the validity of two Bayesian ancestral state reconstruction models for estimating Salmonella transmission during outbreaks

scientific article published on 22 July 2019

Isolation and characterization of microsatellite loci from Arthropodium cirratum (Asparagaceae)

scientific article

Isolation of Campylobacter spp. from Client-Owned Dogs and Cats, and Retail Raw Meat Pet Food in the Manawatu, New Zealand

scientific article published on 12 November 2016

Isolation of emerging Campylobacter species in working farm dogs and their frozen home-killed raw meat diets

scientific article published on 21 December 2018

Linkage analysis of chromosome 1q markers in 136 prostate cancer families. The Cancer Research Campaign/British Prostate Group U.K. Familial Prostate Cancer Study Collaborators

scientific article

Linkage and LOH studies in 19 cylindromatosis families show no evidence of genetic heterogeneity and refine the CYLD locus on chromosome 16q12-q13

article

Localization to Xq27 of a susceptibility gene for testicular germ-cell tumours

scientific article

Long-term Colonization by Campylobacter jejuni Within a Human Host: Evolution, Antimicrobial Resistance, and Adaptation

scientific article published in November 2017

Metagenomics and transcriptomics data from human colorectal cancer

scientific article published on 05 July 2019

Microbial Genomics of a Host-Associated Commensal Bacterium in Fragmented Populations of Endangered Takahe.

scientific article published on 26 December 2015

Microbial contamination in drinking water at public outdoor recreation facilities in New Zealand

scientific article published on 08 July 2020

Microbial diversity and ecology of geothermal springs in the high-grade metamorphic terrain of Sri Lanka

scientific article published in 2022

Mitochondrial evolution in the entomopathogenic fungal genus Beauveria

scientific article published on 30 October 2020

Molecular epidemiology of Shiga toxin-producing Escherichia coli (STEC) on New Zealand dairy farms: application of a culture-independent assay and whole genome sequencing.

scientific article published on 2 July 2018

Mutagenic insertion and chromosome engineering resource (MICER).

scientific article published on 4 July 2004

Mutational dynamics of aroid chloroplast genomes

scientific article published on January 2012

Novel 5-Nitrofuran-Activating Reductase in Escherichia coli

scientific article published on 22 October 2019

Novel mechanisms of TolC-independent decreased bile-salt susceptibility in Escherichia coli

scientific article published on 14 May 2020

Phylogeographic analysis reveals multiple international transmission events have driven the global emergence of Escherichia coli O157:H7

article

Phylogeography of the endemic New Zealand tree Entelea arborescens (whau; Malvaceae)

scientific article published 2019

Potentiation of CB 1954 cytotoxicity by reduced pyridine nucleotides in human tumour cells by stimulation of DT diaphorase activity

scientific article published on 01 November 1992

Quantification of historical livestock importation into New Zealand 1860-1979.

scientific article published on 26 June 2014

RNA networks in prokaryotes I: CRISPRs and riboswitches

scientific article published on January 2011

RNA networks in prokaryotes II: tRNA processing and small RNAs.

scientific article published on January 2011

Radon, mycotoxins, p53, and uranium mining

scientific article published on 01 March 1994

Reply to Baba and Kanamori

scientific article published on 11 November 2019

Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling ⬇️

scientific article

Seasonality of Campylobacter jejuni isolates associated with human campylobacteriosis in the Manawatu region, New Zealand.

scientific article published on 7 September 2015

Semi-automatic selection of summary statistics for ABC model choice

scientific article

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data ⬇️

scientific article published on September 27, 2010

Sticky Genomes: Using NGS Evidence to Test Hybrid Speciation Hypotheses

scientific article (publication date: 2016)

Systematic error in seed plant phylogenomics

scientific article

The effect of carbohydrate sources: Sucrose, invert sugar and components of mānuka honey, on core bacteria in the digestive tract of adult honey bees (Apis mellifera)

scientific article published on 04 December 2019

The evolutionary root of flowering plants

scientific article published on 31 July 2012

The modern RNP world of eukaryotes

scientific article published on 30 July 2009

Transmission Dynamics of Shiga Toxin-Producing Escherichia coli in New Zealand Cattle from Farm to Slaughter

scientific article published in 2021

Updating the genomic taxonomy and epidemiology of Campylobacter hyointestinalis.

scientific article

Use of Genomics to Investigate Historical Importation of Shiga Toxin-Producing Escherichia coli Serogroup O26 and Nontoxigenic Variants into New Zealand

article

Using a common commensal bacterium in endangered Takahe as a model to explore pathogen dynamics in isolated wildlife populations

scientific article published on 11 May 2015

Variation in the limit-of-detection of the ProSpecT Campylobacter microplate enzyme immunoassay in stools spiked with emerging Campylobacter species.

scientific article published on 15 June 2016

Whole Genome Sequencing demonstrates that Geographic Variation of Escherichia coli O157 Genotypes Dominates Host Association

scientific article

Whole-Genome Sequencing and Virulome Analysis of Escherichia coli Isolated from New Zealand Environments of Contrasting Observed Land Use

scientific article published on 20 April 2022

Whole-genome comparison of two Campylobacter jejuni isolates of the same sequence type reveals multiple loci of different ancestral lineage

scientific article

gndDb, a Database of Partial gnd Sequences To Assist with Analysis of Escherichia coli Communities Using High-Throughput Sequencing

scientific article published on 15 August 2019

sismonr: Simulation of In Silico Multi-Omic Networks with adjustable ploidy and post-transcriptional regulation in R

scientific article published on 21 January 2020

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