BackmEpiLab

Contact details +6469517597

Associate Professor Patrick Biggs PhD, BSc

Associate Professor in Genomics and Computational Biology

Doctoral Supervisor
School of Fundamental Sciences

Associate Professor in Computational Biology

School of Veterinary Science

Professional

Contact details

Ph: +64 6 951 7597
Location: 2.32, Hopkirk Institute
Campus: Turitea
Ph: +64 6 951 7597
Location: D5-30, Science Tower D
Campus: Turitea

Qualifications

Doctor of Philosophy - University of London (1996)
Bachelor of Science - Brunel University (1992)

Certifications and Registrations

Licence, Supervisor, Massey University

Research Expertise

Research Interests

The pathogenomics and evolution of food-borne pathogens, in particular Campylobacter spp. and Escherichia coli. Also in functional bacterial genomics and metagenomics.

Thematics

Health and Well-being

Area of Expertise

Field of research codes
Biochemistry and Cell Biology (060100): Bioinformatics (060102): Biological Sciences (060000): Evolutionary Biology (060300): Genetics (060400): Genomics (060408): Infectious Agents (060502): Microbial Ecology (060504): Microbial Genetics (060503): Microbiology (060500): Molecular Evolution (060409): Phylogeny and Comparative Analysis (060309)

Research Projects

Summary of Research Projects

Position	Current	Completed
Not Specified	0	1
Project Leader	5	10
Team Member	0	2

Research Outputs

Journal

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Browne, AS., Midwinter, AC., Withers, H., Cookson, AL., Biggs, PJ., Marshall, JC., . . . French, NP. (2021). Evaluating transmission dynamics of Shiga toxin-producing E. coli (STEC) in New Zealand cattle from farm to slaughter using PCR/MALDI-TOF and genome sequencing.. Appl Environ Microbiol.
[Journal article]Authored by: Benschop, J., Biggs, P., French, N., Marshall, J., Midwinter, A.

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Burgess, SA., Francois, M., Midwinter, AC., & Biggs, PJ. (2021). Draft Genome Sequences of Seven Extended-Spectrum β-Lactamase-Producing Escherichia coli Strains Isolated from New Zealand Waterways.. Microbiol Resour Announc. 10(11)
[Journal article]Authored by: Biggs, P., Burgess, S., Midwinter, A.

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Cornelius, AJ., Huq, M., On, SLW., French, NP., Vandenberg, O., Miller, WG., . . . Biggs, PJ. (2021). Genetic characterisation of Campylobacter concisus: Strategies for improved genomospecies discrimination. Systematic and Applied Microbiology. 44(3)
[Journal article]Authored by: Biggs, P., French, N.

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Mizzi, R., Timms, VJ., Price-Carter, ML., Gautam, M., Whittington, R., Heuer, C., . . . Plain, KM. (2021). Comparative Genomics of Mycobacterium avium Subspecies Paratuberculosis Sheep Strains. Frontiers in Veterinary Science. 8
[Journal article]Authored by: Biggs, P., Heuer, C.

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Burgess, SA., Aplin, J., Biggs, PJ., Breckell, G., Benschop, J., Fayaz, A., . . . Midwinter, AC. (2021). Characterisation of AmpC and extended-spectrum beta-lactamase producing E. coli from New Zealand dairy farms. International Dairy Journal. 117
[Journal article]Authored by: Benschop, J., Biggs, P., Burgess, S., Fayaz, A., Midwinter, A.

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Phiri, BJ., French, NP., Biggs, PJ., Stevenson, MA., Reynolds, AD., Garcia-R, JC., . . . Hayman, DTS. (2021). Microbial contamination in drinking water at public outdoor recreation facilities in New Zealand. Journal of Applied Microbiology. 130(1), 302-312
[Journal article]Authored by: Biggs, P., French, N., Garcia Ramirez, J., Hayman, D.

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van Hung Le, V., Biggs, PJ., Wheeler, D., Davies, IG., & Rakonjac, J. (2021). Novel mechanisms of TolC-independent decreased bile-salt susceptibility in Escherichia coli. FEMS Microbiology Letters. 367(10)
[Journal article]Authored by: Biggs, P., Le, V., Rakonjac, J.

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Phiri, BJ., Hayman, DTS., Biggs, PJ., French, NP., & Garcia-R, JC. (2020). Microbial diversity in water and animal faeces: a metagenomic analysis to assess public health risk. New Zealand Journal of Zoology.
[Journal article]Authored by: Biggs, P., French, N., Garcia Ramirez, J., Hayman, D.

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Glare, T., Campbell, M., Biggs, P., Winter, D., Durrant, A., McKinnon, A., . . . Cox, M. (2020). Mitochondrial evolution in the entomopathogenic fungal genus Beauveria. Archives of Insect Biochemistry and Physiology. 105(4)
[Journal article]Authored by: Biggs, P., Cox, M., Winter, D.

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Toombs-Ruane, LJ., Benschop, J., French, NP., Biggs, PJ., Midwinter, AC., Marshall, JC., . . . Burgess, SA. (2020). Carriage of Extended-Spectrum-Beta-Lactamase- and AmpC Beta-Lactamase-Producing Escherichia coli Strains from Humans and Pets in the Same Households. Applied and Environmental Microbiology. 86(24), 1-15
[Journal article]Authored by: Benschop, J., Biggs, P., Burgess, S., Douwes, J., Fayaz, A., French, N., Marshall, J., Midwinter, A., Roberts, M.

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Bojanić, K., Acke, E., Roe, WD., Marshall, JC., Cornelius, AJ., Biggs, PJ., . . . Midwinter, AC. (2020). 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. Pathogens. 9(9), 1-15
[Journal article]Authored by: Biggs, P., Marshall, J., Midwinter, A., Roe, W.

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Phiri, BJ., Pita, AB., Hayman, DTS., Biggs, PJ., Davis, MT., Fayaz, A., . . . Death, RG. (2020). Does land use affect pathogen presence in New Zealand drinking water supplies?. Water Research. 185
[Journal article]Authored by: Biggs, P., Death, R., Fayaz, A., French, N., Hayman, D.

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On, SLW., Miller, WG., Biggs, PJ., Cornelius, AJ., & Vandamme, P. (2020). A critical rebuttal of the proposed division of the genus Arcobacter into six genera using comparative genomic, phylogenetic, and phenotypic criteria. Systematic and Applied Microbiology. 43(5)
[Journal article]Authored by: Biggs, P.

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Gilpin, BJ., Walker, T., Paine, S., Sherwood, J., Mackereth, G., Wood, T., . . . Jones, N. (2020). A large scale waterborne Campylobacteriosis outbreak, Havelock North, New Zealand. Journal of Infection. 81(3), 390-395
[Journal article]Authored by: Biggs, P., French, N., Hayman, D., Midwinter, A.

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Collis, RM., Biggs, PJ., Midwinter, AC., Browne, AS., Wilkinson, DA., Irshad, H., . . . Cookson, AL. (2020). Genomic epidemiology and carbon metabolism of Escherichia coli serogroup O145 reflect contrasting phylogenies. PLoS ONE. 15(6 June)
[Journal article]Authored by: Biggs, P., French, N., Midwinter, A.

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Bloomfield, S., Wilkinson, D., Rogers, L., Biggs, P., French, N., Mohan, V., . . . Midwinter, A. (2020). Campylobacter novaezeelandiae sp. nov., isolated from birds and water in New Zealand. International Journal of Systematic and Evolutionary Microbiology. 70(6), 3775-3784
[Journal article]Authored by: Biggs, P., French, N., Midwinter, A., Savoian, M.

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Haviernik, J., Dawson, K., Anderson, T., Murdoch, D., Chambers, S., Biggs, P., . . . Slow, S. (2020). Complete genome sequence of a legionella longbeachae serogroup 2 isolate derived from a patient with Legionnaires’ disease. Microbiology Resource Announcements. 9(5)
[Journal article]Authored by: Biggs, P.

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Bojanić, K., Midwinter, AC., Acke, E., Marshall, JC., Cornelius, AJ., & Biggs, PJ. (2020). Draft genome sequences of eight strains of campylobacter helveticus isolated from cats and a dog in New Zealand. Microbiology Resource Announcements. 9(5)
[Journal article]Authored by: Biggs, P., Marshall, J., Midwinter, A.

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Angelin-Bonnet, O., Biggs, PJ., Baldwin, S., Thomson, S., & Vignes, M. (2020). Sismonr: Simulation of in silico multi-omic networks with adjustable ploidy and post-transcriptional regulation in R. Bioinformatics. 36(9), 2938-2940
[Journal article]Authored by: Biggs, P., Vignes, M.

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Taylor, MA., Robertson, AW., Biggs, PJ., Richards, KK., Jones, DF., & Parkar, SG. (2019). 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). PLoS ONE. 14(12)
[Journal article]Authored by: Biggs, P., Robertson, A.

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Wilkinson, DA., Rogers, LE., Fayaz, A., Akhter, RN., Biggs, PJ., French, NP., . . . Midwinter, AC. (2019). Draft whole-genome sequences of Campylobacter strains isolated from brushtail possums in New Zealand. Microbiology Resource Announcements. 8(47)
[Journal article]Authored by: Biggs, P., Fayaz, A., French, N., Midwinter, A.

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French, NP., Zhang, J., Carter, GP., Midwinter, AC., Biggs, PJ., Dyet, K., . . . Williamson, DA. (2019). Genomic analysis of fluoroquinolone- And tetracycline-resistant campylobacter jejuni sequence type 6964 in humans and poultry, New Zealand, 2014-2016. Emerging Infectious Diseases. 25(12), 2226-2234
[Journal article]Authored by: Biggs, P., Fayaz, A., French, N., Greening, S., Midwinter, A.

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Franz, E., Rotariu, O., Lopes, BS., Bono, JL., Laing, C., Gannon, V., . . . Strachan, NJC. (2020). Reply to baba and kanamori. Clinical Infectious Diseases. 71(5), 1353-1355
[Journal article]Authored by: Biggs, P., French, N.

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Guerrero, FD., Bendele, KG., Ghaffari, N., Guhlin, J., Gedye, KR., Lawrence, KE., . . . Tompkins, DM. (2019). The Pacific Biosciences de novo assembled genome dataset from a parthenogenetic New Zealand wild population of the longhorned tick, Haemaphysalis longicornis Neumann, 1901. Data in Brief. 27
[Journal article]Authored by: Biggs, P., Gedye, K., Lawrence, K.

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Van Hung Le, V., Davies, IG., Moon, CD., Wheeler, D., Biggs, PJ., & Rakonjac, J. (2019). Novel 5-nitrofuran-activating reductase in Escherichia coli. Antimicrobial Agents and Chemotherapy. 63(11)
[Journal article]Authored by: Biggs, P., Le, V., Rakonjac, J.

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Cookson, AL., Lacher, DW., Scheutz, F., Wilkinson, DA., Biggs, PJ., Marshall, JC., . . . Brightwell, G. (2019). GndDb, a Database of Partial gnd Sequences to Assist with Analysis of Escherichia coli Communities Using High-Throughput Sequencing. Microbiology Resource Announcements. 8(33)
[Journal article]Authored by: Biggs, P., Marshall, J.

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Bloomfield, S., Vaughan, T., Benschop, J., Marshall, J., Hayman, D., Biggs, P., . . . French, N. (2019). Investigation of the validity of two Bayesian ancestral state reconstruction models for estimating Salmonella transmission during outbreaks.
[Journal article]Authored by: Biggs, P.

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Visnovska, T., Biggs, PJ., Schmeier, S., Frizelle, FA., & Purcell, RV. (2019). Metagenomics and transcriptomics data from human colorectal cancer. Scientific Data. 6(1)
[Journal article]Authored by: Biggs, P.

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Zhang, D., Palmer, J., Teh, KH., Biggs, P., & Flint, S. (2019). 16S rDNA high-throughput sequencing and MALDI-TOF MS are complementary when studying psychrotrophic bacterial diversity of raw cows' milk. International Dairy Journal. 97, 86-91
[Journal article]Authored by: Biggs, P., Flint, S., Palmer, J.

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Wilkinson, DA., Midwinter, AC., Kwan, E., Bloomfield, SJ., French, NP., & Biggs, PJ. (2019). Draft whole-genome sequences of three isolates of a novel strain of a Campylobacter sp. Isolated from New Zealand birds and water. Microbiology Resource Announcements. 8(18)
[Journal article]Authored by: Biggs, P., French, N., Midwinter, A.

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Brauning, R., Plain, K., Gautam, M., Russell, T., Carolina Correa, C., Biggs, P., . . . Price-Carter, M. (2019). Complete genome sequence of the telford type s strain of mycobacterium avium subsp. Paratuberculosis. Microbiology Resource Announcements. 8(11)
[Journal article]Authored by: Biggs, P.

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Le, VVH., Bruce, I., Biggs, PJ., & Rakonjac, J. (2019). Draft genome sequence of a canine uropathogenic Escherichia coli strain isolated in New Zealand. Microbiology Resource Announcements. 8(10)
[Journal article]Authored by: Biggs, P., Le, V., Rakonjac, J.

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Shepherd, LD., Frericks, J., Biggs, PJ., & de Lange, PJ. (2019). Phylogeography of the endemic New Zealand tree Entelea arborescens (whau; Malvaceae). New Zealand Journal of Botany. 57(3), 154-168
[Journal article]Authored by: Biggs, P.

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Browne, AS., Biggs, PJ., Wilkinson, DA., Cookson, AL., Midwinter, AC., Bloomfield, SJ., . . . French, NP. (2019). Use of genomics to investigate historical importation of shiga toxin-producing Escherichia coli serogroup O26 and nontoxigenic variants into New Zealand. Emerging Infectious Diseases. 25(3), 489-500
[Journal article]Authored by: Benschop, J., Biggs, P., French, N., Marshall, J., Midwinter, A.

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Wheeler, NE., Blackmore, T., Reynolds, AD., Midwinter, AC., Marshall, J., French, NP., . . . Biggs, PJ. (2019). Genomic correlates of extraintestinal infection are linked with changes in cell morphology in Campylobacter jejuni. Microbial Genomics. 5(2)
[Journal article]Authored by: Biggs, P., French, N., Marshall, J., Midwinter, A., Savoian, M.

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Angelin-Bonnet, O., Biggs, PJ., & Vignes, M. (2019). Gene Regulatory Networks: A Primer in Biological Processes and Statistical Modelling. 1883, 347-383
[Journal article]Authored by: Biggs, P., Vignes, M.

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Bojanić, K., Midwinter, AC., Marshall, JC., Biggs, PJ., & Acke, E. (2019). Isolation of emerging Campylobacter species in working farm dogs and their frozen home-killed raw meat diets. Journal of Veterinary Diagnostic Investigation. 31(1), 23-32
[Journal article]Authored by: Biggs, P., Marshall, J., Midwinter, A.

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Collis, RM., Burgess, SA., Biggs, PJ., Midwinter, AC., French, NP., Toombs-Ruane, L., . . . Cookson, AL. (2019). Extended-spectrum beta-lactamase-producing enterobacteriaceae in dairy farm environments: A New Zealand perspective. Foodborne Pathogens and Disease. 16(1), 5-22
[Journal article]Authored by: Biggs, P., Burgess, S., French, N., Midwinter, A.

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Franz, E., Rotariu, O., Lopes, BS., Macrae, M., Bono, JL., Laing, C., . . . Strachan, NJC. (2019). Phylogeographic Analysis Reveals Multiple International transmission Events Have Driven the Global Emergence of Escherichia coli O157:H7. Clinical Infectious Diseases. 69(3), 428-437
[Journal article]Authored by: Biggs, P., French, N.

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Pinpimai, K., Roe, WD., Biggs, PJ., & Dittmer, KE. (2018). Draft Whole-Genome Sequences of Seven Isolates of Klebsiella pneumoniae from New Zealand Sea Lions. Microbiology Resource Announcements. 7(20)
[Journal article]Authored by: Biggs, P., Dittmer, K., Roe, W.

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Pinpimai, K., Roe, WD., Biggs, PJ., Dittmer, KE., & Michael, SA. (2018). Draft whole-genome sequences of five klebsiella pneumoniae isolates from the subantarctic islands of New Zealand. Microbiology Resource Announcements. 7(20)
[Journal article]Authored by: Biggs, P., Dittmer, K., Roe, W.

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Browne, AS., Midwinter, AC., Withers, H., Cookson, AL., Biggs, PJ., Marshall, JC., . . . French, NP. (2018). Molecular epidemiology of Shiga toxinproducing Escherichia coli (STEC) on New Zealand dairy farms: Application of a culture-independent assay and whole-genome sequencing. Applied and Environmental Microbiology. 84(14)
[Journal article]Authored by: Benschop, J., Biggs, P., French, N., Marshall, J., Midwinter, A.

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Browne, AS., Biggs, PJ., Elliott, A., Jaros, P., French, NP., & Midwintera, AC. (2018). Draft wholegenome sequences of three diarrheagenic Escherichia coli strains isolated from farmed deer in New Zealand. Genome Announcements. 6(16)
[Journal article]Authored by: Biggs, P., French, N., Midwinter, A.

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Slow, S., Anderson, T., Biggs, P., Kennedy, M., Murdoch, D., & Cree, S. (2018). Complete genome sequence of Legionella sainthelensi isolated from a patient with Legionnaires' disease. Genome Announcements. 6(5)
[Journal article]Authored by: Biggs, P.

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Bloomfeld, SJ., Midwinter, AC., Biggs, PJ., French, NP., Marshall, JC., Hayman, DTS., . . . Benschop, J. (2018). Long-term colonization by campylobacter jejuni within a human host: Evolution, antimicrobial resistance, and adaptation. Journal of Infectious Diseases. 217(1), 103-111
[Journal article]Authored by: Benschop, J., Biggs, P., French, N., Hayman, D., Marshall, J., Midwinter, A.

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Dixon, M., Flint, S., Palmer, J., Love, R., Biggs, P., & Beuger, A. (2018). Analysis of culturable and non-culturable bacteria and their potential to form biofilms in a primary treated dairy wastewater system. Environmental Technology (United Kingdom). 39(17), 2185-2192
[Journal article]Authored by: Biggs, P., Flint, S., Love, R., Palmer, J.

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Purcell, RV., Visnovska, M., Biggs, PJ., Schmeier, S., & Frizelle, FA. (2017). Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer. Scientific Reports. 7(1)
[Journal article]Authored by: Biggs, P.

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Bulgarella, M., Biggs, PJ., De Lange, PJ., & Shepherd, LD. (2017). Isolation and Characterization of Microsatellite Loci from Arthropodium cirratum (Asparagaceae). Applications in Plant Sciences. 5(8)
[Journal article]Authored by: Biggs, P.

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Yan, J., Blair, HT., Liu, M., Li, W., He, S., Chen, L., . . . Dukkipati, VSR. (2017). Genome-wide detection of autosomal copy number variants in several sheep breeds using Illumina OvineSNP50 BeadChips. Small Ruminant Research. 155, 24-32
[Journal article]Authored by: Biggs, P., Blair, H., Dittmer, K., Dukkipati, V., Garrick, D.

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Grinberg, A., Biggs, PJ., Zhang, J., Ritchie, S., Oneroa, Z., O'Neill, C., . . . Coombs, GW. (2017). Genomic epidemiology of methicillin-susceptible Staphylococcus aureus across colonisation and skin and soft tissue infection. Journal of Infection. 75(4), 326-335
[Journal article]Authored by: Biggs, P., Grinberg, A., Velathanthiri, N.

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Cornelius, AJ., Miller, WG., Lastovica, AJ., On, SLW., French, NP., Vandenberg, O., . . . Biggs, PJ. (2017). Complete genome sequence of Campylobacter concisus ATCC 33237<sup>T</sup> and draft genome sequences for an additional eight well-characterized C. concisus strains. Genome Announcements. 5(29)
[Journal article]Authored by: Biggs, P., French, N.

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Burgess, SA., Flint, SH., Lindsay, D., Cox, MP., & Biggs, PJ. (2017). Insights into the Geobacillus stearothermophilus species based on phylogenomic principles. BMC Microbiology. 17(1)
[Journal article]Authored by: Biggs, P., Burgess, S., Cox, M., Flint, S.

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Slow, S., Anderson, T., Miller, J., Singh, S., Murdoch, D., & Biggs, PJ. (2017). Complete genome sequence of a Legionella longbeachae serogroup 1 strain isolated from a patient with Legionnaires' disease. Genome Announcements. 5(24)
[Journal article]Authored by: Biggs, P.

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Bloomfield, SJ., Benschop, J., Biggs, PJ., Marshall, JC., Hayman, DTS., Carter, PE., . . . French, NP. (2017). Genomic analysis of salmonella enterica serovar Typhimurium DT160 associated with a 14-year outbreak, New Zealand, 1998–2012. Emerging Infectious Diseases. 23(6), 906-913
[Journal article]Authored by: Benschop, J., Biggs, P., French, N., Hayman, D., Marshall, J., Midwinter, A.

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Cookson, AL., Biggs, PJ., Marshall, JC., Reynolds, A., Collis, RM., French, NP., . . . Brightwell, G. (2017). Culture independent analysis using gnd as a target gene to assess Escherichia coli diversity and community structure. Scientific Reports. 7(1)
[Journal article]Authored by: Biggs, P., French, N., Marshall, J.

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Grange, ZL., Biggs, PJ., Rose, SP., Gartrell, BD., Nelson, NJ., & French, NP. (2017). Genomic Epidemiology and Management of Salmonella in Island Ecosystems Used for Takahe Conservation. Microbial Ecology. 74(3), 735-744
[Journal article]Authored by: Biggs, P., French, N., Gartrell, B.

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Vaughan, TG., Welch, D., Drummond, AJ., Biggs, PJ., George, T., & French, NP. (2017). Inferring ancestral recombination graphs from bacterial genomic data. Genetics. 205(2), 857-870
[Journal article]Authored by: Biggs, P., French, N.

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Bojanić, K., Midwinter, AC., Marshall, JC., Rogers, LE., Biggs, PJ., & Acke, E. (2017). Isolation of Campylobacter spp. from Client-Owned Dogs and Cats, and Retail Raw Meat Pet Food in the Manawatu, New Zealand. Zoonoses and Public Health. 64(6), 438-449
[Journal article]Authored by: Biggs, P., Marshall, J., Midwinter, A.

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Bojanić, K., Midwinter, AC., Marshall, JC., Rogers, LE., Biggs, PJ., & Acke, E. (2016). Variation in the limit-of-detection of the ProSpecT Campylobacter microplate enzyme immunoassay in stools spiked with emerging Campylobacter species. Journal of Microbiological Methods. 127, 236-241
[Journal article]Authored by: Biggs, P., Marshall, J., Midwinter, A.

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Morgan-Richards, M., Hills, SFK., Biggs, PJ., & Trewick, SA. (2016). Sticky genomes: Using NGS evidence to test hybrid speciation hypotheses. PLoS ONE. 11(5)
[Journal article]Authored by: Biggs, P., Hills, S., Morgan-Richards, M., Trewick, S.

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Grange, ZL., Gartrell, BD., Biggs, PJ., Nelson, NJ., Anderson, M., & French, NP. (2016). Microbial Genomics of a Host-Associated Commensal Bacterium in Fragmented Populations of Endangered Takahe. Microbial Ecology. 71(4), 1020-1029
[Journal article]Authored by: Anderson, M., Biggs, P., French, N., Gartrell, B.

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Friedrich, A., Marshall, JC., Biggs, PJ., Midwinter, AC., & French, NP. (2016). Seasonality of Campylobacter jejuni isolates associated with human campylobacteriosis in the Manawatu region, New Zealand. Epidemiology and Infection. 144(4), 820-828
[Journal article]Authored by: Biggs, P., French, N., Marshall, J., Midwinter, A.

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Strachan, NJC., Rotariu, O., Lopes, B., Macrae, M., Fairley, S., Laing, C., . . . Forbes, KJ. (2015). Whole Genome Sequencing demonstrates that Geographic Variation of Escherichia coli O157 Genotypes Dominates Host Association. Scientific Reports. 5
[Journal article]Authored by: Biggs, P., French, N.

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Burgess, SA., Cox, MP., Flint, SH., Lindsay, D., & Biggs, PJ. (2015). Draft genome sequences of three strains of Geobacillus stearothermophilus isolated from a milk powder manufacturing plant. Genome Announcements. 3(5)
[Journal article]Authored by: Biggs, P., Burgess, S., Cox, M., Flint, S.

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Fearnhead, P., Yu, S., Biggs, P., Holland, B., & French, N. (2015). Estimating the relative rate of recombination to mutation in bacteria from single-locus variants using composite likelihood methods. Annals of Applied Statistics. 9(1), 200-224
[Journal article]Authored by: Biggs, P., French, N.

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Grange, ZL., Gartrell, BD., Biggs, PJ., Nelson, NJ., Marshall, JC., Howe, L., . . . French, NP. (2015). Using a common commensal bacterium in endangered Takahe as a model to explore pathogen dynamics in isolated wildlife populations. Conservation Biology. 29(5), 1327-1336
[Journal article]Authored by: Biggs, P., French, N., Gartrell, B., Howe, L., Marshall, J.

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Gregory, SJ., Anderson, CWN., Camps-Arbestain, M., Biggs, PJ., Ganley, ARD., O'Sullivan, JM., . . . McManus, MT. (2015). Biochar in co-contaminated soil manipulates arsenic solubility and microbiological community structure, and promotes organochlorine degradation. PLoS ONE. 10(4)
[Journal article]Authored by: Anderson, C., Biggs, P., Camps Arbestain, M.

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Teh, BT., Linblad, K., Nord, B., Kytola, S., Schalling, M., Larsson, C., . . . Nicol, D. (1999). Familial testicular cancer: Lack of evidence for trinucleotide repeat expansions and association with PKD1 in one family [2]. Journal of Medical Genetics. 36(4), 348-349
[Journal article]Authored by: Biggs, P.

Wooster, R., Bignell, G., Lancaster, J., Swift, S., Seal, S., Mangion, J., . . . Arason, A. (1996). Addendum: Identification of the breast cancer susceptibility gene BRCA2 (Nature (1995) 378 (789-792)). Nature. 379(6567), 749
[Journal article]Authored by: Biggs, P.

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Altherr, MR., Auerbach, AD., Biggs, PO., Burn, TC., Breuning, MH., Peters, DJM., . . . Sood, R. (1996). Report of the fourth international workshop on human chromosome 16 mapping 1995 - Held on 12-14 November 1995 at the University of Leiden, The Netherlands. CYTOGENETICS AND CELL GENETICS. 72(4), 271-285
[Journal article]Authored by: Biggs, P.

Wooster, R., Bignell, G., Lancaster, J., Swift, S., Seal, S., Mangion, J., . . . Stratton, MR. (1996). Identification of the breast cancer susceptibility gene BRCA2 (vol 378, pg 789, 1995). NATURE. 379(6567), 749-749
[Journal article]Authored by: Biggs, P.

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Warren, W., Biggs, PJ., Ei-baz, M., Ghoneim, MA., Stratton, MR., & Venitt, S. (1995). Mutations in the p53 gene in schistosomal bladder cancer: A study of 92 tumours from egyptian patients and a comparison between mutational spectra from schistosomal and non-schistosomal urothelial tumours. Carcinogenesis. 16(5), 1181-1189
[Journal article]Authored by: Biggs, P.

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Venitt, S., & Biggs, PJ. (1994). Radon, mycotoxins, p53, and uranium mining. The Lancet. 343(8900), 795
[Journal article]Authored by: Biggs, P.

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Lindgreen, S., Umu, SU., Lai, ASW., Eldai, H., Liu, W., McGimpsey, S., . . . Gardner, PP. (2014). Robust Identification of Noncoding RNA from Transcriptomes Requires Phylogenetically-Informed Sampling. PLoS Computational Biology. 10(10)
[Journal article]Authored by: Biggs, P.

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Binney, BM., Biggs, PJ., Carter, PE., Holland, BM., & French, NP. (2014). Quantification of historical livestock importation into New Zealand 1860–1979. New Zealand Veterinary Journal. 62(6), 309-314
[Journal article]Authored by: Biggs, P., French, N.

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Prangle, D., Fearnhead, P., Cox, MP., Biggs, PJ., & French, NP. (2014). Semi-automatic selection of summary statistics for ABC model choice. Statistical Applications in Genetics and Molecular Biology. 13(1), 67-82
[Journal article]Authored by: Biggs, P., Cox, M., French, N.

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Han, J., Collins, LJ., Biggs, PJ., White, WT., & Penny, ED. (2013). Are Signature Proteins the Key to Evaluating Eukaryotic Phylogeny?. Review of bioinformatics and biometrics. 2(2), 37-44 Retrieved from http://www.seipub.org/rbb/paperInfo.aspx?ID=6248
[Journal article]Authored by: Biggs, P.

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Grinberg, A., Biggs, PJ., Dukkipati, VSR., & George, TT. (2013). Extensive intra-host genetic diversity uncovered in Cryptosporidium parvum using Next Generation Sequencing. Infection, Genetics and Evolution. 15, 18-24
[Journal article]Authored by: Biggs, P.

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Ahmed, I., Matthews, PJ., Biggs, PJ., Naeem, M., Mclenachan, PA., & Lockhart, PJ. (2013). Identification of chloroplast genome loci suitable for high-resolution phylogeographic studies of Colocasia esculenta (L.) Schott (Araceae) and closely related taxa. Molecular Ecology Resources. 13(5), 929-937
[Journal article]Authored by: Biggs, P., Lockhart, P., McLenachan, P.

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Wang, J., McLenachan, PA., Biggs, PJ., Winder, LH., Schoenfeld, BIK., Narayan, VV., . . . Lockhart, PJ. (2013). Environmental bio-monitoring with high-throughput sequencing. Briefings in Bioinformatics. 14(5), 575-588
[Journal article]Authored by: Biggs, P., Lockhart, P., McLenachan, P.

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Goremykin, VV., Nikiforova, SV., Biggs, PJ., Zhong, B., Delange, P., Martin, W., . . . Lockhart, PJ. (2013). The evolutionary root of flowering plants. Systematic Biology. 62(1), 50-61
[Journal article]Authored by: Biggs, P., Lockhart, P., McLenachan, P.

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Grinberg, A., Biggs, PJ., Dukkipati, VSR., & George, TT. (2012). Extensive intra-host genetic diversity uncovered in Cryptosporidium parvum using Next Generation Sequencing. Infection, Genetics and Evolution.
[Journal article]Authored by: Biggs, P., Dukkipati, V., Grinberg, A.

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Ahmed, I., Biggs, PJ., Matthews, PJ., Collins, LJ., Hendy, MD., & Lockhart, PJ. (2012). Mutational dynamics of aroid chloroplast genomes. Genome Biology and Evolution. 4(12), 1316-1323
[Journal article]Authored by: Biggs, P., Lockhart, P.

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Miller, HC., Biggs, PJ., Voelckel, C., & Nelson, NJ. (2012). De novo sequence assembly and characterisation of a partial transcriptome for an evolutionarily distinct reptile, the tuatara (Sphenodon punctatus). BMC Genomics. 13(1)
[Journal article]Authored by: Biggs, P.

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Voelckel, C., Gruenheit, N., Biggs, P., Deusch, O., & Lockhart, P. (2012). Chips and tags suggest plant-environment interactions differ for two alpine Pachycladon species. BMC Genomics. 13(1)
[Journal article]Authored by: Biggs, P., Lockhart, P.

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Yu, S., Fearnhead, P., Holland, BR., Biggs, P., Maiden, M., & French, N. (2012). Estimating the relative roles of recombination and point mutation in the generation of single locus variants in Campylobacter jejuni and Campylobacter coli. Journal of Molecular Evolution. 74(5-6), 273-280
[Journal article]Authored by: Biggs, P., French, N.

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Dunowska, M., Biggs, PJ., Zheng, T., & Perrott, MR. (2012). Identification of a novel nidovirus associated with a neurological disease of the Australian brushtail possum (Trichosurus vulpecula). Veterinary Microbiology. 156(3-4), 418-424
[Journal article]Authored by: Biggs, P., Dunowska, M., Perrott, M.

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Zhong, B., Deusch, O., Goremykin, VV., Penny, D., Biggs, PJ., Atherton, RA., . . . Lockhart, PJ. (2011). Systematic error in seed plant phylogenomics. Genome Biology and Evolution. 3(1), 1340-1348
[Journal article]Authored by: Biggs, P., Lockhart, P.

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Biggs, PJ., Fearnhead, P., Hotter, G., Mohan, V., Collins-Emerson, J., Kwan, E., . . . French, NP. (2011). Whole-genome comparison of two campylobacter jejuni isolates of the same sequence type reveals multiple loci of different ancestral lineage. PLoS ONE. 6(11)
[Journal article]Authored by: Biggs, P., Collins-Emerson, J., French, N.

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Skarnes, WC., Rosen, B., West, AP., Koutsourakis, M., Bushell, W., Iyer, V., . . . Bradley, A. (2011). A conditional knockout resource for the genome-wide study of mouse gene function. Nature. 474(7351), 337-344
[Journal article]Authored by: Biggs, P.

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Cox, MP., Peterson, DA., & Biggs, PJ. (2010). SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics. 11
[Journal article]Authored by: Biggs, P., Cox, M.

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820

McComish, BJ., Hills, SFK., Biggs, PJ., & Penny, D. (2010). Index-free de novo assembly and deconvolution of mixed mitochondrial genomes. Genome Biology and Evolution. 2(1), 410-424
[Journal article]Authored by: Biggs, P., Hills, S.

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Collins, LJ., Kurland, CG., Biggs, P., & Penny, D. (2009). The modern RNP world of eukaryotes. Journal of Heredity. 100(5), 597-604
[Journal article]Authored by: Biggs, P.

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Chen, XS., Collins, LJ., Biggs, PJ., & Penny, D. (2009). High Throughput Genome-Wide Survey of Small RNAs from the Parasitic Protists Giardia intestinalis and Trichomonas vaginalis. GENOME BIOLOGY AND EVOLUTION. 1, 165-175
[Journal article]Authored by: Biggs, P.

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Adams, DJ., Biggs, PJ., Cox, T., Davies, R., Van Der Weyden, L., Jonkers, J., . . . Bradley, A. (2004). Mutagenic insertion and chromosome engineering resource (MICER). Nature Genetics. 36(8), 867-871
[Journal article]Authored by: Biggs, P.

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104

Biggs, PJ., Vogel, H., Sage, M., Martin, LA., Donehower, LA., & Bradley, A. (2003). Allelic phasing of a mouse chromosome 11 deficiency influences p53 tumorigenicity. Oncogene. 22(21), 3288-3296
[Journal article]Authored by: Biggs, P.

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Takahashi, M., Rapley, E., Biggs, PJ., Lakhani, SR., Cooke, D., Hansen, J., . . . Stratton, MR. (2000). Linkage and LOH studies in 19 cylindromatosis families show no evidence of genetic heterogeneity and refine the CYLD locus on chromosome 16q12-q13. Human Genetics. 106(1), 58-65
[Journal article]Authored by: Biggs, P.

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Rapley, EA., Crockford, GP., Teare, D., Biggs, P., Seal, S., Barfoot, R., . . . Bishop, DT. (2000). Localization to Xq27 of a susceptibility gene for testicular germ-cell tumours. Nature Genetics. 24(2), 197-200
[Journal article]Authored by: Biggs, P.

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Pershouse, M., Li, J., Yang, C., Su, H., Brundage, E., Di, W., . . . Chinault, AC. (2000). BAC contig from a 3-cM region of mouse chromosome 11 surrounding Brca1. Genomics. 69(1), 139-142
[Journal article]Authored by: Biggs, P.

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Bignell, GR., Warren, W., Seal, S., Takahashi, M., Rapley, E., Barfoot, R., . . . Stratton, MR. (2000). Identification of the familial cylindromatosis tumour-suppressor gene. Nature Genetics. 25(2), 160-165
[Journal article]Authored by: Biggs, P.

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509

Eeles, RA., Durocher, F., Edwards, S., Teare, D., Badzioch, M., Hamoudi, R., . . . Foulkes, WD. (1998). Linkage analysis of chromosome 1q markers in 136 prostate cancer families. American Journal of Human Genetics. 62(3), 653-658
[Journal article]Authored by: Biggs, P.

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Bishop, DT., Rapley, E., Tucker, K., Collins, F., Donald, J., Friedlander, M., . . . Heimdal, K. (1998). Candidate regions for testicular cancer susceptibility genes: The International Testicular Cancer Linkage Consortium. APMIS. 106(1), 64-72
[Journal article]Authored by: Biggs, P.

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Biggs, PJ., & Bradley, A. (1998). A step toward genotype-based therapeutic regimens for breast cancer in patients with BRCA2 mutations?. Journal of the National Cancer Institute. 90(13), 951-953
[Journal article]Authored by: Biggs, P.

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Bignell, GR., Canzian, F., Shayeghi, M., Stark, M., Shugart, YY., Biggs, P., . . . Foulkes, WD. (1997). Familial nontoxic multinodular thyroid goiter locus maps to chromosome 14q but does not account for familial nonmedullary thyroid cancer. American Journal of Human Genetics. 61(5), 1123-1130
[Journal article]Authored by: Biggs, P.

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Biggs, PJ., Chapman, P., Lakhani, SR., Burn, J., & Stratton, MR. (1996). The cylindromatosis gene (cyld1) on chromosome 16q may be the only tumour suppressor gene involved in the development of cylindromas. Oncogene. 12(6), 1375-1377
[Journal article]Authored by: Biggs, P.

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Wooster, R., Bignell, G., Lancaster, J., Swift, S., Seal, S., Mangion, J., . . . Stratton, MR. (1995). Identification of the breast cancer susceptibility gene BRCA2. Nature. 378(6559), 789-792
[Journal article]Authored by: Biggs, P.

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Biggs, PJ., Wooster, R., Ford, D., Chapman, P., Mangion, J., Quirk, Y., . . . Stratton, MR. (1995). Familial cylindromatosis (turban tumour syndrome) gene localised to chromosome 16q12–q13: evidence for its role as a tumour suppressor gene. Nature Genetics. 11(4), 441-443
[Journal article]Authored by: Biggs, P.

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Knox, RJ., Friedlos, F., Biggs, PJ., Flitter, WD., Gaskell, M., Goddard, P., . . . Jarman, M. (1993). Identification, synthesis and properties of 5-(aziridin-1-YL)-2-nitro-4-nitrosobenzamide, A novel DNA crosslinking agent derived from CB1954. Biochemical Pharmacology. 46(5), 797-803
[Journal article]Authored by: Biggs, P.

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Biggs, PJ., Warren, W., Venitt, S., & Stratton, MR. (1993). Does a genotoxic carcinogen contribute to human breast cancer?: The value of mutational spectra in unravelling the aetiology of cancer. Mutagenesis. 8(4), 275-283
[Journal article]Authored by: Biggs, P.

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Friedlos, F., Biggs, PJ., Abrahamson, JA., & Knox, RJ. (1992). Potentiation of CB 1954 cytotoxicity by reduced pyridine nucleotides in human tumour cells by stimulation of DT diaphorase activity. Biochemical Pharmacology. 44(9), 1739-1743
[Journal article]Authored by: Biggs, P.

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Book

Biggs, PJ., & French, NP. (2014). Evolution of campylobacter species in New Zealand. In Campylobacter Ecology and Evolution. (pp. 221 - 240). : Caister Academic Press
[Chapter]Authored by: Biggs, P., French, N.

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Biggs, PJ., & French, NP. (2014). Learning about recombination in campylobacter. In SK. Sheppard, & G. Meric (Eds.) Campylobacter ecology and eveloution. (pp. 9 - 22). : Caister Academic Press
[Chapter]Authored by: Biggs, P., French, N.

Collins, LJ., & Biggs, PJ. (2011). RNA networks in prokaryotes II: TRNA processing and small RNAs. (pp. 221 - 230).
[Chapter]Authored by: Biggs, P.

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Biggs, PJ., & Collins, LJ. (2011). RNA networks in prokaryotes I: CRISPRs and riboswitches. (pp. 209 - 220).
[Chapter]Authored by: Biggs, P.

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Conference

Burgess, S., Collis, R., Biggs, P., Cookson, A., & McDougall, S. (2019, May). Antimicrobial resistant bacteria associated with dairy cattle - a New Zealand perspective. Presented at The 6th International Symposium on Dairy Cow Nutrition and Milk Quality
[Conference Oral Presentation]Authored by: Biggs, P., Burgess, S.

Guerrero, FD., Guhlin, J., Gedye, KR., Lawrence, K., Dearden, PK., Harrop, TWR., . . . Tompkins, DM. (2019). The de novo assembled and annotation genome of the New Zealand cattle tick, Haemaphysalis longicornis Neumann, 1901. , New Zealand Society for Parasitology Annual Meeting No.47
[Conference Abstract]Authored by: Biggs, P., Gedye, K., Lawrence, K.

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Coker, S., Pomroy, W., McInnes, K., Howe, L., Vallee, E., Biggs, P., . . . Morgan, K. (2019). Morphological description of coccidia in Haast tokoeka (Apteryx australis "Haast"). , New Zealand Society for Parasitology Annual Meeting No.47
[Conference Abstract]Authored by: Biggs, P., Howe, L., Morgan, K., Vallee, E.

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Taylor, MA., Robertson, A., Biggs, P., Richards, KK., & Parkar, S. (2019). The effect of carbohydrate sources: sucrose, invert sugar and components of manuka honey on bacteria within the digestive tract of honeybees. Poster session presented at the meeting of 46th Apidmondia - International Agricultural Congress. Montreal, Canada
[Conference Poster]Authored by: Biggs, P., Robertson, A.

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Angelin-Bonnet, O., Biggs, PJ., & Vignes, M.The sismonr Package: Simulation of in Silico Multi-Omic Networks in R. Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. (pp. 2729 - 2731).
[Conference]Authored by: Biggs, P., Vignes, M.

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Burgess, S., Toombs-Ruane, L., Biggs, P., Midwinter, A., & Benschop, J. (2018). Urban waterways a vehicle for the spread of antimicrobial resistant E. coli ?. Poster session presented at the meeting of NZMS-NZSBMB Joint Annual Conference 2018
[Conference Poster]Authored by: Benschop, J., Biggs, P., Burgess, S., Midwinter, A.

Heydari, A., Kim, N., Bromhead, C., Horswell, J., Gielen, G., Biggs, P., . . . Palmer, B. (2018). Heavy Metals and Antibiotic Resistance Diversity Investigation in Soil Bacteria Using 16SrDNA Sequencing and Specific PCR. Poster session presented at the meeting of Joint NZMS & NZSBMB Annual Conference. University of Otago, Dunedin, New Zealand
[Conference Poster]Authored by: Biggs, P., Bromhead, C., Kim, N., Palmer, B.

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Wilkinson, DA., O'Donnell, AJ., Akhter, RN., Fayaz, A., MacK, HJ., Rogers, LE., . . . Midwinter, AC. (2018). Updating the genomic taxonomy and epidemiology of Campylobacter hyointestinalis.
[Conference Poster]Authored by: Biggs, P., Fayaz, A., French, N., Midwinter, A.

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Flint, SH., Zhang, D., Palmer, J., Lindsay, D., Teh, K., & Biggs, P. (2017). Next Generation Sequencing reveals the seasonal variation of psychrotrophic bacteria in New Zealand raw milk. Poster session presented at the meeting of New Zealand Microbiological Society Conference
[Conference Poster]Authored by: Biggs, P., Flint, S.Contributed to by: Flint, S.

Burgess, SA., Aplin, J., Biggs, P., Benschop, J., & Midwinter, A. (2017, December). New Zealand dairy cattle – a reservoir for antimicrobial resistant Serratia spp. Presented at One Health Aotearoa 3rd Symposium. Wellington, New Zealand.
[Conference Oral Presentation]Authored by: Benschop, J., Biggs, P., Burgess, S., Midwinter, A.

Wilkinson, D., Nisa, S., Haake, N., Biggs, P., French, N., Collins-Emerson, JM., . . . Benschop, J. (2017). Scalable comparative genomics to address key questions for modern leptospirosis research in New Zealand. , 10th International Leptospirosis society conference
[Conference Abstract]Authored by: Benschop, J., Biggs, P., Collins-Emerson, J., French, N.

Bohorquez, J., McLenachan, PA., Johansen, R., Archer, R., Stephens, J., Biggs, PJ., . . . Robertson, AW. (2017, December). The root system of mānuka: a host for a richly diverse and variable mycorrhizal fungal community. Presented at 2017 New Zealand Molecular Ecology Conference. The Catlins, Suthland.
[Conference Oral Presentation]Authored by: Archer, R., Biggs, P., McLenachan, P., Millner, J., Robertson, A.

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Wheeler, N., Biggs, PJ., Blackmore, T., Reynolds, A., Midwinter, A., Marshall, J., . . . French, N. (2017). Identification of genomic changes associated with invasiveness in campylobacter jejuni. , 19th International workshop on campylobacter, Helicobacter and related organisms
[Conference Abstract]Authored by: Biggs, P., French, N., Marshall, J., Midwinter, A.

cornelius, A., Tilmanne, A., Martiny, D., On, S., French, N., Lin, S., . . . Biggs, PJ. (2017). The role of emerging epsilonproteobacteria in childhood gastroenteritis. , 19th International workshop on campylobacter, helicobacter and related organisms
[Conference Abstract]Authored by: Biggs, P., French, N.

Cornelius, A., Vandenberg, O., On, S., French, N., Wheeler, N., Lin, S., . . . Biggs, PJ. (2017). Using pan-genomes for molecular assay design: development of a multiplex ligation-dependent probe amplification (MLPA) assay for the detection of 28epsilonproteobacterial taxa. , 19th International workshop on campylobacter, helicobacter and related organisms
[Conference Abstract]Authored by: Biggs, P., French, N.

Cornelius, A., Biggs, PJ., Hayman, D., French, N., Draper, J., Wilkinson, D., . . . Gilpin, B. (2017). use of genotyping tools to characterise and investigate the New Zealand Havelock North campylobacteriosis outbreak. , 19th international workshop on campylobacter, helicobacter and related organisms
[Conference Abstract]Authored by: Biggs, P., French, N., Hayman, D., Marshall, J., Midwinter, A.

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Zhang, J., Biggs, P., Wilkinson, D., Midwinter, A., Gilpin, B., Draper, J., . . . French, N. (2017, September). Ad hoc whole-genome MLST (wgMLST) analysis reveals multiple Campylobacter jejuni clones caused a massive waterborne outbreak in New Zealand in 2016. Presented at 19th International Workshop on Campylobacter, Helicobacter and Related Organisms. Nantes, France.
[Conference Oral Presentation]Authored by: Biggs, P., French, N., Hayman, D., Midwinter, A.

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Wilkinson, DA., Zhang, J., Biggs, P., Marshall, J., & French, N. (2017). How open is the Campylobacter genome?. Poster session presented at the meeting of CHRO 2017. Nantes, France
[Conference Poster]Authored by: Biggs, P., French, N., Marshall, J.

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Gates, MC., Dwyer, C., Grinberg, A., & Biggs, P. (2017, July). Mastitis Mayhem: an on-farm exercise for integrating epidemiology into clinical skills training. Presented at ANCVS Science Week. Gold Coast Australia.
[Conference Oral Presentation]Authored by: Biggs, P., Gates, M., Grinberg, A.

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Yan, J., Dukkipati, VSR., Blair, HT., Biggs, PJ., Hamie, JC., & Greer, A. (2017). A genome-wide scan of positive selection signature using Ovine Infinium® HD SNP BeadChip in two Romney lines, selected for resistance or resilience to nematodes. Poster session presented at the meeting of 22nd Conference of the Association for the Advancement of Animal Breeding and Genetics. Townsville, QLD, Australia
[Conference Poster]Authored by: Biggs, P., Blair, H., Dukkipati, V.

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Yan, J., Dukkipati, VSR., Blair, HT., Biggs, PJ., Hamie, JC., & Greer, A. (2017). A genome-wide scan of positive selection signature using Ovine Infinium® HD SNP BeadChip in two Romney lines, selected for resistance or resilience to nematodes. Proceedings of the Association for the Advancement of Animal Breeding and Genetics. Vol. 22 (pp. 1 - 4). : 22nd Conference of the Association for the Advancement of Animal Breeding and Genetics
[Conference Paper in Published Proceedings]Authored by: Biggs, P., Blair, H., Dukkipati, V.

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Robertson, AW., Bohorquez, J., Archer, R., Stephens, J., Biggs, P., & Millner, J.Companion Biota. . Massey University, Palmerston North
[Conference Paper]Authored by: Archer, R., Biggs, P., Millner, J., Robertson, A.

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Purcell, R., Visnovska, M., Biggs, P., Schmeier, S., & Frizelle, F.(2017, June). Consensus molecular classification of colorectal cancer and association with the colonic microbiome. Diseases of the Colon and Rectum. 60 (6)(pp. E90 - E91). 0012-3706.
[Conference]Authored by: Biggs, P.

Biggs, PJ.(2017, February). eResearch 2017 conference. .
[Conference]Authored by: Biggs, P.

Wierenga, JR., Gedye, K., Kalema-Zikusoka, G., Valdivia, W., Hall, R., Biggs, PB., . . . Hayman, DTS. (2016, December). Metagenomic studies of infection transmission between multiple species in rural Uganda. Presented at One Health Ecohealth 2016 Conference. Melbourne, Australia.
[Conference Oral Presentation]Authored by: Biggs, P., Gedye, K., Hayman, D., Wierenga, J.

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Sammarro, M., Friedrich, A., Marshall, J., Biggs, P., French, N., & Vignes, MCL.Revealing the genetic basis for host-pathogen interaction using machine learning. Paper presented at the meeting of JOURNÉES OUVERTES DE BIOLOGIE INFORMATIQUE & MATHÉMATIQUES. Lyon, France
[Conference Paper]Authored by: Biggs, P., French, N., Marshall, J., Vignes, M.

Zhang, D., Palmer, J., Lindsay, D., Teh, KH., & Flint, SH.(2016, November). Isolation, identification and characterization of heat resistant enzyme producing psychrotrophs from raw milk using MALDI-TOF mass spectrometry and high-throughput 16S DNA sequencing. .
[Conference]Authored by: Biggs, P., Flint, S.

Burgess, SA., Flint, SH., Lindsay, D., & Biggs, PJ. (2016, October). Genomic insight into the adaptation of Geobacillus stearothermophilus to a milk powder. Presented at Omics Symposium V. Christchurch, New Zealand.
[Conference Oral Presentation]Authored by: Biggs, P., Burgess, S., Flint, S.

Browne, A., Midwinter, A., Withers, H., Cookson, A., Biggs, P., Marshall, J., . . . French, N. (2016). Epidemiology of shiga toxin-producing E. coli (STEC) on New Zealand dairy farms using new molecular and genomic technologies. 2016 Proceedings of Food Safety, Animal Welfare and Biosecurity Branch of the NZVA Conference. (pp. 21 - 25). Palmerston North, New Zealand: Food Safety, Animal Welfare and Biosecurity Branch of the New Zealand Veternary Animal Science Conference
[Conference Paper in Published Proceedings]Authored by: Benschop, J., Biggs, P., French, N., Marshall, J., Midwinter, A.

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Sammarro, M., Schrefheere, A., Biggs, P., marshall, J., Tate, J., Cox, M., . . . Vignes, MCL. (2016). Challenges and leads for modelling complex molecular biological systems. Poster session presented at the meeting of Complex Networks and Applications 2016 workshop. Marseilles, France
[Conference Poster]Authored by: Biggs, P., Cox, M., French, N., Marshall, J., Tate, J., Vignes, M.

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Flint, SH., Biggs, P., & Burgess, SA. (2015, November). Genomic insights into the adaptation of Geobacillus stearothermophilus to a milk powder manufacturing plant. Presented at New Zealand Microbiological Society Conference. Rotorua, New Zealand.
[Conference Oral Presentation]Authored by: Biggs, P., Burgess, S., Flint, S.

Burgess, S., Flint, SH., Lindsay, D., & Biggs, P.(2015, November). Genomic insights into the adaptation of Geobacillus stearothermophilus to a milk powder manufacturing plant. . (pp. 27 - 27).
[Conference]Authored by: Biggs, P., Flint, S.

French, NP., Biggs, R., Biggs, PJ., Bloomfield, S., Dyet, K., Gilpin, BJ., . . . Williamson, DE. (2015). Rapid emergence of tetracycline and fluoroquinolone resistant Campylobacter jejuni ST-6964 in poultry and humans in New Zealand. Campylobacter, Helicobacter & Related Organisms (CHRO) : 18th International Workshop 2015, 1-5 November 2015, Rotorua, New Zealand : delegate handbook. (pp. 109 - 109). : 18th International Conference on Campylobacter, Helicobacter, and Related Organisms
[Conference Paper in Published Proceedings]Authored by: Biggs, P., French, N., Midwinter, A.

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Bloomfield, S., Benschop, J., Midwinter, AC., Biggs, P., Marshall, J., Hayman, D., . . . French, N. (2015). Evolution of Campylobacter in a persistently infected human host. : 18th International Conference on Campylobacter, Helicobacter, and Related Organisms
[Conference Paper in Published Proceedings]Authored by: Benschop, J., Biggs, P., French, N., Hayman, D., Marshall, J., Midwinter, A.

Biggs, PJ., Blackmore, T., Reynolds, AD., Midwinter, AC., & French, NP. (2015). Comparative genomic analysis of human bacteraemic Campylobacter jejuni isolates from New Zealand. Proceedings of the 18th International workshop on Campylobacter, Helicobacter & Related Organisms - CHRO 2015. ER - .... (pp. 29 - 29). : 18th International Conference on Campylobacter, Helicobacter, and Related Organisms
[Conference Paper in Published Proceedings]Authored by: Biggs, P., French, N., Midwinter, A.

Bojanic, K., Midwinter, AC., Biggs, PJ., Marshall, JC., & Acke, E. (2015). Pathogenicity of Campylobacter jejuni, C. upsaliensis and C. helveticus in the invertebrate disease model Galleria mellonella. Proceedings of the 18th International workshop on Campylobacter, Helicobacter & Related Organisms. (pp. 38 - 38). New Zealand: 18th International Conference on Campylobacter, Helicobacter, and Related Organisms
[Conference Paper in Published Proceedings]Authored by: Biggs, P., Marshall, J., Midwinter, A.Contributed to by: Midwinter, A.

Friedrich, A., Marshall, JC., Biggs, PJ., Midwinter, AC., & French, NP. (2015). Short-term evolutionary dynamics of Campylobacter jejuni in chickens. Poster session presented at the meeting of 18th International workshop on Campylobacter, Helicobacter and Related Organisms. Rotorua, New Zealand
[Conference Poster]Authored by: Biggs, P., French, N., Marshall, J., Midwinter, A.

Collins-Emerson, JM., Biggs, P., Benschop, J., Heuer, C., & Wilson, P. (2015, October). Whole genome sequence and r MLST analysis of New Zealand strains of leptospira. Presented at 9th scientific meeting of international leptospirosis society. Semarang, Indonesia.
[Conference Oral Presentation]Authored by: Benschop, J., Biggs, P., Collins-Emerson, J., Heuer, C.

Collins-Emerson, J., Biggs, P., Benschop, J., Heuer, C., & Wilson, P. (2015). Whole genome sequence and rMLST analysis of New Zealand strains of Leptospira. (pp. 21 - 21). , 9th scientific meeting of international leptospirosis society
[Conference Abstract]Authored by: Benschop, J., Biggs, P., Collins-Emerson, J., Heuer, C.

Pinpimai, K., Roe, W., Dittmer, K., & Biggs, P. (2015, February). Klebsiella pneumoniae in New Zealand sealions. Presented at New Zealand Society for Veterinary Pathology Conference. Palmerston North, New Zealand.
[Conference Oral Presentation]Authored by: Biggs, P., Dittmer, K., Roe, W.

Biggs, PJ., Cao, M., Jauregui, R., & Elshire, R. (2015, March). QC considerations for BBS. Presented at eResearch NZ 2015. Queenstown, New Zealand.
[Conference Oral Presentation]Authored by: Biggs, P.

Biggs, PJ., Sun, D., Jones, D., Maxwell, P., & Sturrock, S. (2015, March). An example of cross-platform collaboration. Presented at eResearch NZ 2015. Queenstown, New Zealand.
[Conference Oral Presentation]Authored by: Biggs, P.

Grange, ZL., Gartrell, B., Biggs, P., Nelson, N., & French, N. (2015). Genomic analysis of enteric bacteria in isolated translocated wildlife populations. Poster session presented at the meeting of ZSL symposium: Health and disease in translocated wild animals
[Conference Poster]Authored by: Biggs, P., French, N., Gartrell, B.

Grange, Z., Gartrell, B., Biggs, P., Nelson, N., Howe, L., & French, N. (2014, May). Use of genomic sequencing of Campylobacter for population differentiation in a translocated population of takahē (Porphyrio hochstetteri). Presented at NCBID Molecular Diagnostics Workshop. Wellington, New Zealand.
[Conference Oral Presentation]Authored by: Biggs, P., French, N., Gartrell, B., Howe, L.

Grange, ZL., Gartrell, B., Biggs, P., Nelson, N., Howe, L., & French, N. (2014, July). Population management influences Campylobacter carriage in an endangered population of takahē (Porphyrio hochstetteri). Presented at 63rd Annual International Conference of the Wildlife Disease Association: One Health Transitioning from Theory to Prctice. Albuquerque, New Mexico.
[Conference Oral Presentation]Authored by: Biggs, P., French, N., Gartrell, B., Howe, L.Edited by: Biggs, P., French, N., Gartrell, B., Howe, L.

Friedrich, A., Biggs, P., Midwinter, A., & French, N. (2013, September). Use of microarrays to identify phenotypic variation in specific sequence types of Campylobacter jejuni. Presented at 17th International Workshop on Campylobacter, Helicobacter and Related Organisms. Aberdeen, Scotland.
[Conference Oral Presentation]Authored by: Biggs, P., French, N., Midwinter, A.

Bojanic, K., Midwinter, A., Marshall, J., Biggs, P., Benschop, J., & Acke, E. (2013, September). Comparison of culture methods for campylobacter spp. in working farm dogs and their home-kill meat diets. Presented at 17th International Workshop on Campylobacter, Helicobacter and related organisms. Aberdeen, United Kingdom.
[Conference Oral Presentation]Authored by: Benschop, J., Biggs, P., Marshall, J., Midwinter, A.

Binney, B., Biggs, P., Carter, P., Holland, B., Marshall, J., & French, N. (2013, September). Carbon utilisation in campylobacter jejuni is affected by temperature and host generalist or specialist lifestlye. Presented at 17th International workshop on Campylobacter, Helicobacter and related organisms. Aberdeen, Scotland.
[Conference Oral Presentation]Authored by: Biggs, P., French, N., Marshall, J.

Biggs, PJ., Collins-Emerson, J., Midwinter, A., Fearnhead, P., Jolley, K., Maiden, M., . . . French, N. (2013). The pathogenomics of campylobacter jejuni in New Zealand. (pp. 43 - 43). , 17th International workshop on Campylobacter, Helicobacter and related organisms: Society for General Microbiology
[Conference Abstract]Authored by: Biggs, P., Collins-Emerson, J., French, N., Midwinter, A.

Grange, Z., Gartrell, B., Nelson, N., Howe, L., Biggs, P., & French, N. (2013, September). The tale of takahē translocations and bacterial biogeographic prevalence. Presented at Wildlife Disease Association Australasian Annual Conference. Melbourne, Australia.
[Conference Oral Presentation]Authored by: Biggs, P., French, N., Gartrell, B., Howe, L.

Phiri, BJ., French, NP., Rainey, PB., Stevenson, MA., Prattley, DJ., & Biggs, PJ. (2012, June). Water quality, metagenomics and the microbial community in DOC campground water. Presented at Allan Wilson Centre Disease Ecology and Pathogen Evolution Workshop. Palmerston North, New Zealand.
[Conference Oral Presentation]Authored by: Biggs, P., French, N.

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Phiri, BJ., Biggs, PJ., Prattley, DJ., Stevenson, MA., Rainey, PB., & French, NP. (2012). Characterising the drinking water microbiome on campgrounds in New Zealand. Poster session presented at the meeting of The first Infectious Disease Research Centre symposium, Palmerston North. Palmerston North, New Zealand
[Conference Poster]Authored by: Biggs, P., French, N.

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Bignell, GR., Warren, W., Seal, S., Takahashi, M., Rapley, E., Barfoot, R., . . . Stratton, M.Identification and charactarisation of the familial cylindromatosis gene.. AMERICAN JOURNAL OF HUMAN GENETICS. 67 (4)(pp. 94 - 94). 0002-9297.
[Conference]Authored by: Biggs, P.

Takahashi, M., Bignell, G., Rapley, E., Seal, S., Brown, C., Biggs, P., . . . Stratton, M.Fine mapping of the gene for familial cylindromatosis.. AMERICAN JOURNAL OF HUMAN GENETICS. 65 (4)(pp. A448 - A448). 0002-9297.
[Conference]Authored by: Biggs, P.

Rapley, E., Tucker, K., Collins, F., Donald, J., Friedlander, M., Peng, HQ., . . . Consortium, ITCL.Candidate regions for testicular cancer susceptibility genes. APMIS. 106 (1)(pp. 64 - 70). 0903-4641.
[Conference]Authored by: Biggs, P.

Bishop, DT., Rapley, E., Crockford, G., Biggs, P., Leahy, M., Teare, D., . . . Stratton, M.Candidate regions for testicular cancer susceptibility genes: The results of two genomic searches.. AMERICAN JOURNAL OF HUMAN GENETICS. 61 (4)(pp. A268 - A268). 0002-9297.
[Conference]Authored by: Biggs, P.

Bignell, GR., Canzian, F., Shayeghi, M., Stark, M., Shugart, YY., Biggs, P., . . . Foulkes, WD.A familial non-toxic multinodular thyroid goiter locus maps to chromosome 14q but does not account for familial non-medullary thyroid cancer.. AMERICAN JOURNAL OF HUMAN GENETICS. 61 (4)(pp. A268 - A268). 0002-9297.
[Conference]Authored by: Biggs, P.

Biggs, PJ., Wooster, R., Chapman, P., Ford, D., Mangion, J., Quirk, Y., . . . Stratton, MR.Hereditary and sporadic cylindromas (turban tumours) result from loss of a tumour suppressor gene at 16ql2 closely linked to D16S304. CYTOGENETICS AND CELL GENETICS. 72 (4)(pp. 2 - 2). 0301-0171.
[Conference]Authored by: Biggs, P.

McLean, D., Biggs, P., Leblanc-Maridor, M., Hall, R., French, N., Pearce, N., . . . Douwes, J. (2014). 0164 Metagenomic detection of bacteria in aerosol samples in animal slaughterhouses to develop exposure profiles for an epidemiological analysis.. Occup Environ Med. Vol. 71 Suppl 1 (pp. A21).
[Conference Paper in Published Proceedings]Authored by: Biggs, P., Douwes, J., French, N.

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Dukkipati, VSR., Blair, H., Biggs, P., & Murray, A. (2014). An investigation into the association of polymorphisms at selected candidate gene loci with immune parameters in sheep infected with Mycobacterium avium subspecies paratuberculosis. In 2nd JRC Workshop on Sheep Breeding and Developmental Biology: Abstracts(pp. 36 - 36). , 2nd JRC Workshop on Sheep Breeding and Developmental Biology: Massey University, New Zealand
[Conference Abstract]Authored by: Biggs, P., Blair, H., Dukkipati, V.

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Bojanic, K., Midwinter, AC., Biggs, P., Marshall, J., Benschop, J., Cave, N., . . . Acke, E. (2013). Salmonella,E.coli and campylobacter spp. in working farm dogs in New Zealand and their home-kill diets. In P. Angus-Cook, K. Crews, N. Dymond, N. Harding, J. Hunnam, S. Marshall, . . . V. Williams (Eds.) Proceedings of the New Zealand Veterinary Association Annual Conference. (pp. 13 - 14). : New Zealand Veterinary Association Annual Conference, The Science Behind Veterinary Practice
[Conference Paper in Published Proceedings]Authored by: Benschop, J., Biggs, P., Cave, N., Marshall, J., Midwinter, A.

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Biggs, PJ., Collins-Emerson, J., Midwinter, A., Kwan, E., Fearnhead, P., & French, N. (2013). The application of ribosomal multilocus sequence typing (rMLST) in epidemiological studies. In P. Angus-Cook, K. Crews, N. Dymond, N. Harding, J. Hunnam, S. Marshall, . . . V. Williams (Eds.): New Zealand Veterinary Association Annual Conference
[Conference Paper in Published Proceedings]Authored by: Biggs, P., Collins-Emerson, J., French, N., Midwinter, A.

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Grange, Z., Gartrell, BD., Nelson, N., Howe, L., Biggs, P., & French, N. (2013). The tale of takahe translocations and bacterial biogeographic prevalence. Wildlife disease Association Australasian Section Conference. : Wildlife disease Association Australasian Section Conference Proceedings
[Conference Paper in Published Proceedings]Authored by: Biggs, P., French, N., Gartrell, B., Howe, L.Contributed to by: Gartrell, B.

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Bojanic, K., Midwinter, A., Biggs, P., Benschop, J., Cave, N., & Acke, E.(2013, February 18). Salmonella E.Coli and Campylobacter SPP. in working farm dogs in New Zealand and their home-kill diets. In 8th International Sheep Veterinary Congress: Handbook(pp. 70 - 70). , 8th International Sheep Veterinary Congress: Connecting Sheep and Science New Zealand: International Sheep Veterinary Congress
[Conference Abstract]Authored by: Benschop, J., Biggs, P., Cave, N., Midwinter, A.

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Bojanic, K., Midwinter, A., Biggs, P., Benschop, J., Cave, N., & Acke, E. (2013, February). Salmonella E.Coli and Campylobacter SPP. in working farm dogs in New Zealand and their home-kill diets. Presented at 8th International Sheep Veterinary Congress: Connecting Sheep and Science. Rotorua, New Zealand.
[Conference Oral Presentation]Authored by: Benschop, J., Biggs, P., Cave, N., Midwinter, A.

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French, N., Biggs, P., & Marshall, J. (2012). From takahe and microarrays to the Reverent Bayes - the work of the molecular epidemiology and public health laboratory(mEpiLab). In First Infectious Disease Research Centre [IDReC] Science Symposium: Delegate Handbook(pp. 18). , First Infectious Disease Research Centre [IDReC] Science Symposium New Zealand: Infectious Disease Research Centre, Massey University
[Conference Abstract]Authored by: Biggs, P., French, N., Marshall, J.

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French, N., Biggs, P., & Marshall, J. (2012, October). From takahe and microarrays to the Reverend Bayes - the work of the molecular epidemiology and public health laboratory (mEpiLab). Presented at First Infectious Disease Research Centre [IDReC] Science Symposium. Palmerston North, New Zealand.
[Conference Oral Presentation]Authored by: Biggs, P., French, N., Marshall, J.

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Vaughan, T., Cox, M., Biggs, P., Drummond, A., & French, N. (2012). Demographic histories of host-associated campylobacter populations in New Zealand. In First Infectious Disease Research Centre [IDReC] Science Symposium: Delegate Handbook(pp. 72 - 72). , First Infectious Disease Research Centre [IDReC] Science Symposium New Zealand: Infectious Disease Research Centre, Massey University
[Conference Abstract]Authored by: Biggs, P., Cox, M., French, N.

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Yu, S., Fearnhead, P., Holland, BR., Biggs, P., & French, N. (2012). Investigating the impact of geographical isolation on the evolution of campylobacter by comparing New Zealand and United Kingdom datasets. In First Infectious Disease Research Centre [IDReC] Science Symposium: Delegate Handbook(pp. 71 - 71). , First Infectious Disease Research Centre [IDReC] Science Symposium Palmerston North, New Zealand: Infectious Disease Research Centre, Massey University
[Conference Abstract]Authored by: Biggs, P., French, N.

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Phiri, BJ., Biggs, P., Prattley, D., Stevenson, MA., Rainey, PB., & French, N. (2012). Characterising the drinking water microbiome on campgrounds in New Zealand. In First Infectious Disease Research Centre [IDReC] Science Symposium: Delegate Handbook(pp. 64 - 64). , First Infectious Disease Research Centre [IDReC] Science Symposium New Zealand: Infectious Disease Research Centre, MAssey University
[Conference Abstract]Authored by: Biggs, P., French, N.

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Grinberg, A., Biggs, PJ., Dukkipati, RS., & George, TT. (2012). Are cryptosporidium parvum isolates genetic microcosms of local populations of origin?. In First Infectious Disease Research Centre [IDReC] Science Symposium: Delegate Handbook(pp. 54 - 54). , First Infectious Disease Research Centre [IDReC] Science Symposium New Zealand: Infectious Disease Research Centre, Massey University
[Conference Abstract]Authored by: Biggs, P., Dukkipati, V., Grinberg, A.

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George, T., Midwinter, AC., Biggs, P., Cookson, A., & French, N. (2012). Pheno-genotypic characterisation of New Zealand associated Escherishia coli O157:H7 isolates. In First Infectious Disease Research Centre [IDReC] Science Symposium: Delegate Handbook(pp. 51 - 51). , First Infectious Disease Research Centre [IDReC] Science Symposium New Zealand: Infectious Disease Research Centre, Massey University
[Conference Abstract]Authored by: Biggs, P., French, N., Midwinter, A.

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Bojanic, K., Midwinter, A., Rogers, LE., Biggs, P., & Acke, E. (2012). Prospect® Campylobacter microplate assay detection of C upsaliensis, C helveticus and C hyointestinalis in spiked human clinical faecal samples. In First Infectious Disease Research Centre [IDReC] Science Symposium: Delegate Handbook(pp. 44 - 44). , First Infectious Disease Research Centre [IDReC] Science Symposium New Zealand: Infectious Disease Research Centre, Massey University
[Conference Abstract]Authored by: Biggs, P., Midwinter, A.

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Binney, BM., Bigg, PJ., Carter, PE., Holland, BR., & French, N. (2012). A preliminary examination of the relationship between host-association, temperature and phentotype for genetically characterised strains of Campylobacter jejnui. In First Infectious Disease Research Centre [IDReC] Science Symposium: Delegate Handbook(pp. 42 - 42). , First Infectious Disease Research Centre [IDReC] Science Symposium New Zealand: Infectious Disease REsearch Centre, Massey University
[Conference Abstract]Authored by: Biggs, P., French, N.Edited by: Biggs, P.

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Biggs, P., Jolley, KA., Maiden, MCJ., Cody, AJ., & French, N. (2012, August). The pathogenomics of Campylobacter jejuni at the at the "micro" and "macro" scale. Presented at Queenstown Molecular Biology Meeting (QMB). Queenstown, New Zealand.
[Conference Oral Presentation]Authored by: Biggs, P., French, N.

Biggs, P. (2012, October). Genomic epidemiology and public health. Presented at The First Infectious Disease Research Centre [IDReC] Symposium. Palmerston North, New Zealand.
[Conference Oral Presentation]Authored by: Biggs, P.

Biggs, P., & Grinberg, A. (2012). An overview of next generation sequencing technologies with a focus on protist research. In 4th International Giardia and Cryptosporidium Conference: Abstracts(pp. 62 - 62). , 4th International Giardia and Cryptosporidium Conference New Zealand: Massey University
[Conference Abstract]Authored by: Biggs, P., Grinberg, A.

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Biggs, P., & Grinberg, A. (2012, January). An overview of next generation sequencing technologies with a focus on protist research. Presented at 4th International Giardia & Cryptosporidium Conference. Wellington, New Zealand.
[Conference Oral Presentation]Authored by: Biggs, P.

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Balm, M., Collins-Emerson, J., Midwinter, A., Biggs, P., & French, N. (2012). Host association and evolution of Campylobacter species in native rails: An endeavour teacher fellowship experience. Poster session presented at the meeting of First Infectious Disease Research Centre [IDReC] Science Symposium. Palmerston North, New Zealand
[Conference Poster]Authored by: Biggs, P., Collins-Emerson, J., French, N., Midwinter, A.

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Grinberg, A., Dukkipati, R., Biggs, P., & George, T. (2012, January). Are cryptosporidium parvum 'isolates' genetic microcosms?. Presented at IV International Giardia and Cryptosporidium Conference. Wellington, New Zealand.
[Conference Oral Presentation]Authored by: Biggs, P., Dukkipati, V., Grinberg, A.

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Grinberg, A., Dukkipati, R., Biggs, P., & George, T. (2012). Are cryptosporidium parvum 'isolates' genetic microcosms?. In IV International Giardia and Cryptosporidium Conference: Conference Abstracts on CD(pp. 22 - 22). , IV International Giardia and Cryptosporidium Conference New Zealand: Massey University
[Conference Abstract]Authored by: Biggs, P., Dukkipati, V., Grinberg, A.

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Dunowska, M., Biggs, PJ., Perrott, M., Giles, J., & Zheng, T. (2012). What makes the possums wobbly?. In Institute of Veterinary, Animal and Biomedical Sciences [IVABS] Research Colloquium: Programme and Abstracts(pp. 4 - 4). , Institute of Veterinary, Animal and Biomedical Sciences [IVABS] Research Colloquium New Zealand: Institute of Veterinary, Animal and Biomedical Sciences, Massey University
[Conference Abstract]Authored by: Biggs, P., Dunowska, M., Perrott, M.

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Vaughan, T., Cox, M., Biggs, P., Drummond, A., & French, N. (2012, October). Non-parametric inference of the demographic history of host-associated Campylobacter in New Zealand. Presented at Allan Wilson Centre for Molecular Ecology and Evolution Annual Meeting 2012. Palmerston North, New Zealand.
[Conference Oral Presentation]Authored by: Biggs, P., Cox, M., French, N.

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Vaughan, T., Cox, M., Biggs, P., Drummond, A., & French, N. (2012). Non-parametric inference of the demographic history of host-associated Campylobacter in New Zealand. In Allan Wilson Centre for Molecular Ecology and Evolution Annual Meeting: Abstracts of Meeting Speakers(pp. 14 - 14). , Allan Wilson Centre for Molecular Ecology and Evolution Annual Meeting 2012 New Zealand: Allan Wilson Centre, Massey University
[Conference Abstract]Authored by: Biggs, P., French, N.

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Biggs, P., Hotter, G., Mohan, V., Collins-Emerson, J., Kwan, E., Besser, TE., . . . French, N. (2012, October). The pathogenomics of Campylobacter jejuni at the 'micro' and 'macro' scale. Presented at Allan Wilson Centre for Molecular Ecology and Evolution Annual Meeting 2012. Palmerston North, New Zealand.
[Conference Oral Presentation]Authored by: Biggs, P., Collins-Emerson, J., French, N.

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Biggs, P., Hotter, G., Mohan, V., Collins-Emerson, J., Kwan, E., Besser, TE., . . . French, N. (2012). The pathogenomics of Campylobacter jejuni at the 'micro' and 'macro' scale. In Allan Wilson Centre for Molecular Ecology and Evolution Annual Meeting: Abstracts of Meeting Speakers(pp. 9 - 9). , Allan Wilson Centre for Molecular Ecology and Evolution Annual Meeting 2012 New Zealand: Allan Wilson Centre, Massey University
[Conference Abstract]Authored by: Biggs, P., Collins-Emerson, J., French, N.

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Dunowska, M., McBrearty, K., Biggs, PJ., & Murray, A. (2012). Survey of equine respiratory viruses in New Zealand. Poster session presented at the meeting of IX International Congress of Veterinary Virology and joint meeting with the European Society of Clinical Virology (ESVV 2012)- One world, One Health, One Virology. Madrid, Spain
[Conference Poster]Authored by: Biggs, P., Dunowska, M.

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Dunowska, M., Biggs, PJ., & Perrott, M. (2012, September). Genomic characterisation of a new nidovirus associated with a neurological disease of possums. Presented at IX International Congress of Veterinary Virology and joint meeting with the European Society of Clinical Virology [ESVV 2012]: One world, One Health, One Virology. Madrid, Spain.
[Conference Oral Presentation]Authored by: Biggs, P., Dunowska, M., Perrott, M.

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Dunowska, M., McBrearty, K., Biggs, PJ., & Murray, A. (2012, October). Survey of equine respiratory viruses in New Zealand. Presented at First Infectious Disease Research Centre (IDReC) Science Symposium. Palmerston North, New Zealand.
[Conference Oral Presentation]Authored by: Biggs, P., Dunowska, M.

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Dunowska, M., McBrearty, K., Biggs, PJ., & Murray, A. (2012). Survey of equine respiratory viruses in New Zealand. In First Infectious Disease Research Centre (IDReC) Science Symposium- Delegate Handbook(pp. 47 - 47). , First Infectious Disease Research Centre (IDReC) Science Symposium New Zealand: Infectious Disease Research Centre, Massey University
[Conference Abstract]Authored by: Biggs, P., Dunowska, M.

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Dunowska, M., Biggs, PJ., & Perrott, M. (2012). Genomic characterisation of a new nidovirus associated with a neurological disease of possums. In Final Program and Abstract Book- IX International Congress of Veterinary Virology and joint meeting with the European Society of Clinical Virology (ESVV 2012)(pp. 71 - 71). , IX International Congress of Veterinary Virology and joint meeting with the European Society of Clinical Virology [ESVV 2012]: One world, One Health, One Virology Spain: European Society for Veterinary Virology
[Conference Abstract]Authored by: Biggs, P., Dunowska, M., Perrott, M.

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Dunowska, M., McBrearty, K., Biggs, PJ., & Murray, A. (2012). Survey of equine respiratory viruses in New Zealand. In Final Program and Abstract Book- IX International Congress of Veterinary Virology and joint meeting with the European Society of Clinical Virology (ESVV 2012)(pp. 156 - 157). , IX International Congress of Veterinary Virology and joint meeting with the European Society of Clinical Virology (ESVV 2012)- One world, One Health, One Virology Spain: Veterinary Faculty, Complutense University of Madrid
[Conference Abstract]Authored by: Biggs, P., Dunowska, M.

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Yu, S., Fearnhead, P., Holland, BR., Biggs, P., Maiden, M., & French, N. (2012). Estimating the Relative Roles of Recombination and Point Mutation in the Generation of Single Locus Variants in Campylobacter jejuni and Campylobacter coli. In Journal of Molecular Evolution(pp. 1 - 8).
[Conference Abstract]Authored by: Biggs, P., French, N.

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Dunowska, M., Biggs, PJ., Zheng, T., & Perrott, MR. (2011). Identification of a novel nidovirus associated with a neurological disease of the Australian brushtail possum (Trichosurus vulpecula). In Veterinary Microbiology
[Conference Abstract]Authored by: Biggs, P., Dunowska, M., Perrott, M.

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French, N., Collins-Emerson, JM., Midwinter, A., Biggs, P., Mohan, V., Muellner, P., . . . Carter, P. (2011, November). The evolution, epidemiology and control of enteric zoonoses in New Zealand. Presented at New Zealand Microbiological Society Conference 2011. Palmerston North, New Zealand.
[Conference Oral Presentation]Authored by: Biggs, P., Collins-Emerson, J., French, N., Midwinter, A.

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French, N., Collins-Emerson, JM., Midwinter, A., Biggs, P., Mohan, V., Muellner, P., . . . Carter, P.(2011, November 23). The evolution, epidemiology and control of enertic zoonoses in New Zealand. (pp. 128 - 128). , New Zealand Microbiological Society Conference 2011
[Conference Abstract]Authored by: Biggs, P., Collins-Emerson, J., Midwinter, A.

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Biggs, PJ., Collins-Emerson, J., Friedrich, A., Kwan, E., Midwinter, A., & French, NP.(2011, November 23). The movement of DNA in and out of Campylobacter spp.- CRISPRs and the analysis of full length MLST genes. (pp. 96 - 96). , New Zealand Microbiological Society Conference 2011
[Conference Abstract]Authored by: Biggs, P., Collins-Emerson, J., French, N., Midwinter, A.

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Biggs, PJ., Collins-Emerson, J., Friedrich, A., Kwan, E., Midwinter, A., & French, NP. (2011, November). The movement of DNA in and out of Campylobacter spp.- CRISPRs and the analysis of full length MLST genes. Presented at New Zealand Microbiological Society Conference 2011. Palmerston North, New Zealand.
[Conference Oral Presentation]Authored by: Biggs, P., Collins-Emerson, J., French, N., Midwinter, A.

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Dunowska, M., Biggs, PJ., Zheng, T., & Perrott, MRF. (2011, December). Indentification of a novel nidovirus associated with a neurological disease of the Australian brushtail possum (Trichosurus vulpecula). Presented at 6th Australasian Virology Society Meeting. Kingscliff, New South Wales, Australia.
[Conference Oral Presentation]Authored by: Biggs, P., Dunowska, M., Perrott, M.

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Collins, DM., Kawakami, RP., Wards BJ, ., Biggs, PJ., Hotter, GS., & de Lisle, GW.(2011, September 15). Emulating mutations of a random mutant of Mycobacterium bovis with better tuberculosis vaccine efficacy than BCG. (pp. 22 - 22). , Webster Centre Symposium 2011-Webster Centre for Infectious Diseases
[Conference Abstract]Authored by: Biggs, P.

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Biggs, PJ., Collins-Emerson, J., Holland, B., Carter, P., Cookson, A., Fearnhead, P., . . . French, N. (2011, April). Campylobacter spp. in New Zealand: the evolution of an important human pathogen in an island ecosystem. Presented at Hopkirk Research Institute Seminar. Palmerston North, New Zealand.
[Conference Oral Presentation]Authored by: Biggs, P., Collins-Emerson, J., French, N.

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Biggs, PJ. (2011, August). Introduction to the main NGS platforms. Presented at Advanced Workshop 3rd Annual Next Generation Sequencing Conference. Palmerston North, New Zealand.
[Conference Oral Presentation]Authored by: Biggs, P.

Cookson, A., Biggs, PJ., Hotter, G., Fearnhead, P., Carter, P., & French, N. (2011). Recombination events associated with Campylobacter jejuni ST-474 drive clonal diversity, population structure and evolution. Poster session presented at the meeting of 16th International Workshop on Campylobacter, Helicobacter and Related Organisms. Vancouver, Canada
[Conference Poster]Authored by: Biggs, P., French, N.

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Carter, P., Collins-Emerson, JM., Midwinter, A., Cookson, A., Biggs, P., & French, N. (2011). A new campylobacter species identified in water and wild birds (Rallidae) in New Zealand. Poster session presented at the meeting of 16th International Workshop on Campylobacter, Helicobacter and Related Organisms. Vancouver, Canada
[Conference Poster]Authored by: Biggs, P., Collins-Emerson, J., French, N., Midwinter, A.

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Murray, PC., Peterson, DA., & Biggs, PJ. (2010, April). SolexaQA: At-a-glance quality assessment of Illumina second generation sequencing data. Presented at 2010 Illumina User Symposium. Napa Valley, CA, United States.
[Conference Oral Presentation]Authored by: Biggs, P.

Biggs, PJ., Hotter, G., Mohan, V., Collins-Emerson, J., Kwan, E., Besser, TE., . . . French, N.(2010, April 27). New insight gained from a whole-genome comparison of two Campylobacter jejuni isolates that were indistinguishable on the basis of multilocus genotyping. , Molecular Diagnostics Workshop: MAF Biosecurity New Zealand
[Conference Abstract]Authored by: Biggs, P., Collins-Emerson, J., French, N.

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Biggs, PJ., Hotter, G., Mohan, V., Collins-Emerson, J., Kwan, E., Besser, TE., . . . French, NP. (2010, April). New insight gained from a whole-genome comparison of two campylobacter jejuni isolates that were indistinguishable on the basis of multilocus genotyping. Presented at Molecular Diagnostics Workshop. Upper Hutt, New Zealand.
[Conference Oral Presentation]Authored by: Biggs, P., Collins-Emerson, J., French, N.

Biggs, PJ., Collins-Emerson, J., Holland, B., Carter, P., Cookson, A., Fearnhead, P., . . . French, N. (2010, August). Campylobacter spp. in New Zealand: the evolution of an important human pathogen in an island ecosystem. Presented at New Zealand Next Generation Sequencing 2010 Meeting. Dunedin, New Zealand.
[Conference Oral Presentation]Authored by: Biggs, P., Collins-Emerson, J., French, N.

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Biggs, PJ., Collins, LJ., Xiaowei Chen, S., & French, NP. (2008). Practical evolutionary genomics from short-read sequence experiments. Poster session presented at the meeting of The 19th International Conference on Genome Informatics. Surfers Paradise, Queensland, Australia
[Conference Poster]Authored by: Biggs, P., French, N.

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Collins, LJ., Biggs, PJ., Voelckel, C., & Joly, S. (2008). An approach to transcriptome analysis of non-model organisms using short-read sequences.. Genome informatics. International Conference on Genome Informatics. Vol. 21 (pp. 3 - 14).
[Conference Paper in Published Proceedings]Authored by: Biggs, P.

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106

Han, J., Collins, LJ., Biggs, PJ., & Penny, D. (2008). Eukaryotic Signature Proteins Guides to modern eukaryotic Parasites. Poster session presented at the meeting of 19th International Conference on Genome Informatics GIW 2008. Surfers Paradise, QLD, Australia
[Conference Poster]Authored by: Biggs, P.

Penny, ED., Gibb, GC., Collins, LJ., & Biggs, PJ. (2008, June). Mass generation of new sequences and analysis. Presented at Evolution 2008. Minneapolis, Minnesota, United States of America.
[Conference Oral Presentation]Authored by: Biggs, P.

Biggs, PJ., & Collins, L. (2007, November). Next generation sequencing at the Allan Wilson Centre. Presented at 3rd New Zealand Molecular Mapping Workshop 2007. Hamilton, New Zealand.
[Conference Oral Presentation]Authored by: Biggs, P.

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Other

Toombs-Ruane, L., Burgess, S., French, N., Biggs, PJ., Midwinter, A., Marshall, J., . . . Benschop, J. (2017, June). Faecal carriage of ESBL - and AmpC - producing Escherichia coli from co-habiting people and pets. In 7th symposium on antimicrobial resistance in animals and the environment. Presented at Braunschweig, germany.
[Oral Presentation]Authored by: Benschop, J., Biggs, P., Burgess, S., Douwes, J., French, N., Marshall, J., Midwinter, A., Roberts, M.

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Biggs, P., Jolley, KA., Maiden, MCJ., Cody, AJ., & French, N. (2012, June). Advances in bioinformatics for pathogens and applications for human health: rMLST and visualisation software. In Allan Wilson Centre Disease and Ecology Pathogen Evolution Workshop, Massey University, Palmerston North, New Zealand, 14-15 June 2012.
[Oral Presentation]Authored by: Biggs, P., French, N.

Biggs, P., Jolley, KA., Maiden, MCJ., Cody, AJ., & French, N. (2012, August). Advances in bioinformatics for pathogens and applications for human health: rMLST and visualisation software. In Environmental Science and Research [ESR] - Massey University Meeting, Massey University, Palmerston North, New Zealand.
[Oral Presentation]Authored by: Biggs, P., French, N.

Biggs, P., Jolley, KA., Maiden, MCJ., Collins-Emerson, J., Kwan, E., Midwinter, A., . . . French, N. (2012, December). The pathogenomics of Campylobacter jejuni at the "micro" and "macro" scale. In Seminars: Biological Sciences, University of Canterbury, Christchurch, New Zealand.
[Oral Presentation]Authored by: Biggs, P., Collins-Emerson, J., French, N., Midwinter, A.

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Biggs, P., Midwinter, A., Binney, BM., Phiri, B., Fong, R., & French, N. (2012, May). Beyond the bacterial genome: The application of metagenomics and the Omniolog™ phenotypic microarray system to food safety, animal health and water quality issues in New Zealand. In Molecular Diagnostics Workshop, National Centre for Biosecurity and Infectious Disease, Wellington, New Zealand.
[Oral Presentation]Authored by: Biggs, P., French, N., Midwinter, A.

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Biggs, P., Jolley, KA., Martin, MCJ., & French, N. (2012, May). The application of ribosomal MLST (rMLST) typing to foodborne zoonotic bacterial pathogens. In Molecular Diagnostics Workshop, National Centre for Biosecurity and Infectious Disease, Wellington, New Zealand.
[Oral Presentation]Authored by: Biggs, P., French, N.

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French, N., Biggs, PJ., & Cox, M. (2011, June). Campylobacter- background. In Allan Wilson Centre Disease Ecology and Pathogen Evolution Workshop, Palmerston North, New Zealand.
[Oral Presentation]Authored by: Biggs, P., French, N.

Biggs, PJ. (2009, August). Your data from the Illumina Genome Analyser GAII. In Next Generation Sequencing Workshop, Palmerston North, New Zealand.
[Oral Presentation]Authored by: Biggs, P.

Biggs, PJ. (2009, August). Databases and data management. In Program for Next Generation Sequencing Workshop, Palmerston North, New Zealand.
[Oral Presentation]Authored by: Biggs, P.

Biggs, PJ. (2009, August). Using velvet for de novo assembly. In Program for Next Generation Sequencing Workshop, Palmerston North, New Zealand.
[Oral Presentation]Authored by: Biggs, P.

Collins, LJ., & Biggs, PJ. (2008, April). Next generation sequencing using Solexa technology. In AgResearch, Invermay.
[Oral Presentation]Authored by: Biggs, P.

Collins, LJ., & Biggs, PJ. (2008, July). Solexa bioinformatics. In Solexa Workshop, Palmerston North, New Zealand.
[Oral Presentation]Authored by: Biggs, P.

Biggs, PJ. (2008). Next generation sequencing of plants using solexa technology. In BioCommerce Centre, Palmerston North, New Zealand.
[Oral Presentation]Authored by: Biggs, P.

Collins, L., & Biggs, PJ. (2007, October). What your results will look like, and how to work with them. In Solexa Workshop, Palmerston North, New Zealand.
[Oral Presentation]Authored by: Biggs, P.

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Thesis

Phiri, B. (2015). Estimating the public health risk associated with drinking water in New Zealand. (Doctoral Thesis)
[Doctoral Thesis]Edited by: Biggs, P., French, N.

Teaching and Supervision

Courses Coordinated

203.328 Genome Analysis

Contact Supervisor

Summary of Doctoral Supervision

Position	Current	Completed
Main Supervisor	2	1
Co-supervisor	10	20

Current Doctoral Supervision

Main Supervisor of:

Rose Collis - Doctor of Philosophy
Metagenomic analysis and.culture-based. methods to examine prevalence and distribution of antibiotic resistance genes on dairy farms

Co-supervisor of:

Leonardo Meza Joya - Doctor of Philosophy
Climate change impacts on New Zealand ecosystems; a case study in the alpine zone
Valter Dos Anjos Almeida - Doctor of Philosophy
Genetic diversity of enteric microbes and its impacts on host switching
Andrea Grana - Doctor of Philosophy
Exploring innovative ways, based on skin thickness and brown adipose tissue metabolism, for genetic improvement of new-born lamb survival
Paul Ogbuigwe - Doctor of Philosophy
The role of protozoan genetic diversity in disease in New Zealand
Olivia Angelin-Bonnet - Doctor of Philosophy
Investigation of genotype and phenotype interactions using computational statistics
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Richard Fong - Doctor of Philosophy
Evolution and Rapid Diagnosis of Mycobacterium
Jabin Vijayan Genitha Helan - Doctor of Philosophy
Studies of staphylococcus aureus mastitis in dairy cows
Sarah Coker - Doctor of Philosophy
Morphological and Molecular Characterisation of Coccidia (Eimeria spp.) in Kiwi (Apteryx spp.)
Janelle Wierenga - Doctor of Philosophy
Metagenomic evaluation of zoonotic pathogen transmission in Uganda
Helen Smith - Doctor of Philosophy
Source attribution models for whole genome sequencing data

Completed Doctoral Supervision

Main Supervisor of:

2018 - Angela Cornelius - Doctor of Philosophy
Pangenome-guided Tools for Investigating the Role of Epsilonproteobacteria in Human Gastroenteritis

Co-supervisor of:

2020 - Michelle Taylor - Doctor of Philosophy
Microbiota in the honey bee gut and their association with bee health
2019 - Van Hung Vuong Le - Doctor of Philosophy
Antibiotic Combinations to Tackle Gram-negative Bacterial Pathogens
2019 - Ngonidzashe Faya - Doctor of Philosophy
The reproductive biology and venom system of the parasitoid wasp Nasonia vitripennis
2019 - Leah Toombs-Ruane - Doctor of Philosophy
Is the family pet a risk for multidrug resistant infections?
2019 - Milan Gautam - Doctor of Philosophy
Epidemiology of Ovine Paratuberculosis in New Zealand
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2019 - Komkiew Pinpimai - Doctor of Philosophy
Klebsiella pneumoniae in New Zealand sea lions
2018 - Julia Bohorquez Rodriguez De Medina - Doctor of Philosophy
Companion biota associated with Leptospermum scoparium (mānuka; Myrtaceae)
2018 - Juncong Yan - Doctor of Philosophy
Genome-wide copy number variation in sheep: detection and utility as a genetic marker for quantitative traits, with reference to gastrointestinal nema
2018 - Andrew Springer Browne - Doctor of Philosophy
A food chain approach to control of shiga-toxin producing E. coli in New Zealand
2017 - Samuel Bloomfield - Doctor of Philosophy
Transmission and evolution of bacteria during the course of enteritis outbreaks
2017 - Krunoslav Bojanic - Doctor of Philosophy
Campylobacter species in dogs and cats and significance to public health in New Zealand
2016 - Kenneth Sugrim - Doctor of Philosophy
Commercial and Public Health Applications of DNA Monitoring
2016 - Barbara Binney - Doctor of Philosophy
The Microbial Ecology of Camplyobacter jejuni in New Zealand Within a Spatial-Temporal Framework
2016 - Rima Shrestha - Doctor of Philosophy
Molecular Epidemiology of Waterborne Zoonoses in North Island of New Zealand
2016 - Sara Burgess - Doctor of Philosophy
Characterisation of dairy strains of Geobacillus stearothermophilus and a genomics insight into its growth and survival during dairy manufacture
2015 - Zoe Grange - Doctor of Philosophy
Ecology, epidemiology and evolution of enteric microbes in fragmented populations of the endangered takahe (Porphyrio hochstetteri)
2015 - Anja Friedrich - Doctor of Philosophy
Campylobacter jejuni microevolution and phenotype: genotype relationships
2015 - Bernard Phiri - Doctor of Philosophy
Estimating the public health risk associated with drinking water in New Zealand
2013 - Shoukai Yu - Doctor of Philosophy
The Evolution of Campylobacter
2012 - Jian Han - Doctor of Philosophy
Eukaryotic Signature Proteins: Guides to pathogenic eukaryotic parasites

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Associate Professor Patrick Biggs PhD, BSc

Associate Professor in Genomics and Computational Biology

Associate Professor in Computational Biology

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Thesis

Teaching and Supervision

Courses Coordinated

Summary of Doctoral Supervision

Current Doctoral Supervision

Completed Doctoral Supervision

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