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

Browne AS, Biggs PJ, Wilkinson DA, Cookson AL, Midwinter AC, Bloomfield SJ, Hranac CR, Rogers LE, Marshall JC, Benschop J, Withers H, Hathaway S, George T, Jaros P, Irshad H, Fong Y, Dufour M, Karki N, Winkleman T, French NP.

Emerg Infect Dis. 2019 Mar;25(3):489-500. doi: 10.3201/eid2503.180899.


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

Wheeler NE, Blackmore T, Reynolds AD, Midwinter AC, Marshall J, French NP, Savoian MS, Gardner PP, Biggs PJ.

Microb Genom. 2019 Feb 19. doi: 10.1099/mgen.0.000251. [Epub ahead of print]


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

Bojanić K, Midwinter AC, Marshall JC, Biggs PJ, Acke E.

J Vet Diagn Invest. 2018 Dec 21:1040638718820082. doi: 10.1177/1040638718820082. [Epub ahead of print]


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

Angelin-Bonnet O, Biggs PJ, Vignes M.

Methods Mol Biol. 2019;1883:347-383. doi: 10.1007/978-1-4939-8882-2_15.


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

Pinpimai K, Roe WD, Biggs PJ, Dittmer KE.

Microbiol Resour Announc. 2018 Nov 21;7(20). pii: e01270-18. doi: 10.1128/MRA.01270-18. eCollection 2018 Nov.


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

Pinpimai K, Roe WD, Biggs PJ, Dittmer KE, Michael SA.

Microbiol Resour Announc. 2018 Nov 21;7(20). pii: e01328-18. doi: 10.1128/MRA.01328-18. eCollection 2018 Nov.


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

Collis RM, Burgess SA, Biggs PJ, Midwinter AC, French NP, Toombs-Ruane L, Cookson AL.

Foodborne Pathog Dis. 2019 Jan;16(1):5-22. doi: 10.1089/fpd.2018.2524. Epub 2018 Nov 10.


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

Franz E, Rotariu O, Lopes BS, MacRae M, Bono JL, Laing C, Gannon V, Söderlund R, van Hoek AHAM, Friesema I, French NP, George T, Biggs PJ, Jaros P, Rivas M, Chinen I, Campos J, Jernberg C, Gobius K, Mellor GE, Chandry PS, Perez-Reche F, Forbes KJ, Strachan NJC.

Clin Infect Dis. 2018 Oct 29. doi: 10.1093/cid/ciy919. [Epub ahead of print]


Molecular Epidemiology of Shiga Toxin-Producing Escherichia coli (STEC) on New Zealand Dairy Farms: Application of a Culture-Independent Assay and Whole-Genome Sequencing.

Browne AS, Midwinter AC, Withers H, Cookson AL, Biggs PJ, Marshall JC, Benschop J, Hathaway S, Haack NA, Akhter RN, French NP.

Appl Environ Microbiol. 2018 Jul 2;84(14). pii: e00481-18. doi: 10.1128/AEM.00481-18. Print 2018 Jul 15.


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

Browne AS, Biggs PJ, Elliott A, Jaros P, French NP, Midwinter AC.

Genome Announc. 2018 Apr 19;6(16). pii: e00300-18. doi: 10.1128/genomeA.00300-18.


Updating the genomic taxonomy and epidemiology of Campylobacter hyointestinalis.

Wilkinson DA, O'Donnell AJ, Akhter RN, Fayaz A, Mack HJ, Rogers LE, Biggs PJ, French NP, Midwinter AC.

Sci Rep. 2018 Feb 5;8(1):2393. doi: 10.1038/s41598-018-20889-x.


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

Bloomfield SJ, Midwinter AC, Biggs PJ, French NP, Marshall JC, Hayman DTS, Carter PE, Thornley C, Yap R, Benschop J.

J Infect Dis. 2017 Dec 27;217(1):103-111. doi: 10.1093/infdis/jix561.


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

Bulgarella M, Biggs PJ, de Lange PJ, Shepherd LD.

Appl Plant Sci. 2017 Aug 25;5(8). pii: apps.1700041. doi: 10.3732/apps.1700041. eCollection 2017 Aug.


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

Purcell RV, Visnovska M, Biggs PJ, Schmeier S, Frizelle FA.

Sci Rep. 2017 Sep 14;7(1):11590. doi: 10.1038/s41598-017-11237-6.


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

Grinberg A, Biggs PJ, Zhang J, Ritchie S, Oneroa Z, O'Neill C, Karkaba A, Velathanthiri NS, Coombs GW.

J Infect. 2017 Oct;75(4):326-335. doi: 10.1016/j.jinf.2017.07.010. Epub 2017 Aug 4.


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

Cornelius AJ, Miller WG, Lastovica AJ, On SLW, French NP, Vandenberg O, Biggs PJ.

Genome Announc. 2017 Jul 20;5(29). pii: e00711-17. doi: 10.1128/genomeA.00711-17.


Insights into the Geobacillus stearothermophilus species based on phylogenomic principles.

Burgess SA, Flint SH, Lindsay D, Cox MP, Biggs PJ.

BMC Microbiol. 2017 Jun 26;17(1):140. doi: 10.1186/s12866-017-1047-x.


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

Slow S, Anderson T, Miller J, Singh S, Murdoch D, Biggs PJ.

Genome Announc. 2017 Jun 15;5(24). pii: e00564-17. doi: 10.1128/genomeA.00564-17.


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

Bloomfield SJ, Benschop J, Biggs PJ, Marshall JC, Hayman DTS, Carter PE, Midwinter AC, Mather AE, French NP.

Emerg Infect Dis. 2017 Jun;23(6):906-913. doi: 10.3201/eid2306.161934.


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

Cookson AL, Biggs PJ, Marshall JC, Reynolds A, Collis RM, French NP, Brightwell G.

Sci Rep. 2017 Apr 12;7(1):841. doi: 10.1038/s41598-017-00890-6.


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

Grange ZL, Biggs PJ, Rose SP, Gartrell BD, Nelson NJ, French NP.

Microb Ecol. 2017 Oct;74(3):735-744. doi: 10.1007/s00248-017-0959-1. Epub 2017 Mar 30.


Inferring Ancestral Recombination Graphs from Bacterial Genomic Data.

Vaughan TG, Welch D, Drummond AJ, Biggs PJ, George T, French NP.

Genetics. 2017 Feb;205(2):857-870. doi: 10.1534/genetics.116.193425. Epub 2016 Dec 22.


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

Bojanić K, Midwinter AC, Marshall JC, Rogers LE, Biggs PJ, Acke E.

Zoonoses Public Health. 2017 Sep;64(6):438-449. doi: 10.1111/zph.12323. Epub 2016 Nov 12.


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

Bojanić K, Midwinter AC, Marshall JC, Rogers LE, Biggs PJ, Acke E.

J Microbiol Methods. 2016 Aug;127:236-241. doi: 10.1016/j.mimet.2016.06.016. Epub 2016 Jun 15.


Sticky Genomes: Using NGS Evidence to Test Hybrid Speciation Hypotheses.

Morgan-Richards M, Hills SF, Biggs PJ, Trewick SA.

PLoS One. 2016 May 17;11(5):e0154911. doi: 10.1371/journal.pone.0154911. eCollection 2016.


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

Grange ZL, Gartrell BD, Biggs PJ, Nelson NJ, Anderson M, French NP.

Microb Ecol. 2016 May;71(4):1020-9. doi: 10.1007/s00248-015-0721-5. Epub 2015 Dec 26.


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

Burgess SA, Cox MP, Flint SH, Lindsay D, Biggs PJ.

Genome Announc. 2015 Oct 15;3(5). pii: e00939-15. doi: 10.1128/genomeA.00939-15.


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

Strachan NJ, Rotariu O, Lopes B, MacRae M, Fairley S, Laing C, Gannon V, Allison LJ, Hanson MF, Dallman T, Ashton P, Franz E, van Hoek AH, French NP, George T, Biggs PJ, Forbes KJ.

Sci Rep. 2015 Oct 7;5:14145. doi: 10.1038/srep14145.


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

Friedrich A, Marshall JC, Biggs PJ, Midwinter AC, French NP.

Epidemiol Infect. 2016 Mar;144(4):820-8. doi: 10.1017/S0950268815002009. Epub 2015 Sep 7.


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

Grange ZL, Gartrell BD, Biggs PJ, Nelson NJ, Marshall JC, Howe L, Balm MG, French NP.

Conserv Biol. 2015 Oct;29(5):1327-36. doi: 10.1111/cobi.12521. Epub 2015 May 11.


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

Gregory SJ, Anderson CW, Camps-Arbestain M, Biggs PJ, Ganley AR, O'Sullivan JM, McManus MT.

PLoS One. 2015 Apr 29;10(4):e0125393. doi: 10.1371/journal.pone.0125393. eCollection 2015.


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

Lindgreen S, Umu SU, Lai AS, Eldai H, Liu W, McGimpsey S, Wheeler NE, Biggs PJ, Thomson NR, Barquist L, Poole AM, Gardner PP.

PLoS Comput Biol. 2014 Oct 30;10(10):e1003907. doi: 10.1371/journal.pcbi.1003907. eCollection 2014 Oct.


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

Binney BM, Biggs PJ, Carter PE, Holland BR, French NP.

N Z Vet J. 2014 Nov;62(6):309-14. doi: 10.1080/00480169.2014.914861. Epub 2014 Jun 26. Erratum in: N Z Vet J. 2015 Nov;63(6):347. Holland, B M [corrected to Holland, B R].


Outcomes in a multi-institutional cohort of patients treated with intraoperative radiation therapy for advanced or recurrent renal cell carcinoma.

Paly JJ, Hallemeier CL, Biggs PJ, Niemierko A, Roeder F, Martínez-Monge R, Whitson J, Calvo FA, Fastner G, Sedlmayer F, Wong WW, Ellis RJ, Haddock MG, Choo R, Shipley WU, Zietman AL, Efstathiou JA.

Int J Radiat Oncol Biol Phys. 2014 Mar 1;88(3):618-23. doi: 10.1016/j.ijrobp.2013.11.207. Epub 2014 Jan 8.


Semi-automatic selection of summary statistics for ABC model choice.

Prangle D, Fearnhead P, Cox MP, Biggs PJ, French NP.

Stat Appl Genet Mol Biol. 2014 Feb;13(1):67-82. doi: 10.1515/sagmb-2013-0012.


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

Ahmed I, Matthews PJ, Biggs PJ, Naeem M, McLenachan PA, Lockhart PJ.

Mol Ecol Resour. 2013 Sep;13(5):929-37. doi: 10.1111/1755-0998.12128. Epub 2013 May 30.


Environmental bio-monitoring with high-throughput sequencing.

Wang J, McLenachan PA, Biggs PJ, Winder LH, Schoenfeld BI, Narayan VV, Phiri BJ, Lockhart PJ.

Brief Bioinform. 2013 Sep;14(5):575-88. doi: 10.1093/bib/bbt032. Epub 2013 May 15. Review.


Mutational dynamics of aroid chloroplast genomes.

Ahmed I, Biggs PJ, Matthews PJ, Collins LJ, Hendy MD, Lockhart PJ.

Genome Biol Evol. 2012;4(12):1316-23. doi: 10.1093/gbe/evs110.


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

Grinberg A, Biggs PJ, Dukkipati VS, George TT.

Infect Genet Evol. 2013 Apr;15:18-24. doi: 10.1016/j.meegid.2012.08.017. Epub 2012 Sep 6.


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

Miller HC, Biggs PJ, Voelckel C, Nelson NJ.

BMC Genomics. 2012 Aug 31;13:439. doi: 10.1186/1471-2164-13-439.


The evolutionary root of flowering plants.

Goremykin VV, Nikiforova SV, Biggs PJ, Zhong B, Delange P, Martin W, Woetzel S, Atherton RA, McLenachan PA, Lockhart PJ.

Syst Biol. 2013 Jan 1;62(1):50-61. doi: 10.1093/sysbio/sys070. Epub 2012 Jul 31.


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

Dunowska M, Biggs PJ, Zheng T, Perrott MR.

Vet Microbiol. 2012 May 4;156(3-4):418-24. doi: 10.1016/j.vetmic.2011.11.013. Epub 2011 Nov 25.


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

Biggs PJ, Fearnhead P, Hotter G, Mohan V, Collins-Emerson J, Kwan E, Besser TE, Cookson A, Carter PE, French NP.

PLoS One. 2011;6(11):e27121. doi: 10.1371/journal.pone.0027121. Epub 2011 Nov 11.


Systematic error in seed plant phylogenomics.

Zhong B, Deusch O, Goremykin VV, Penny D, Biggs PJ, Atherton RA, Nikiforova SV, Lockhart PJ.

Genome Biol Evol. 2011;3:1340-8. doi: 10.1093/gbe/evr105. Epub 2011 Oct 19.


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

Collins LJ, Biggs PJ.

Adv Exp Med Biol. 2011;722:221-30. doi: 10.1007/978-1-4614-0332-6_14.


RNA networks in prokaryotes I: CRISPRs and riboswitches.

Biggs PJ, Collins LJ.

Adv Exp Med Biol. 2011;722:209-20. doi: 10.1007/978-1-4614-0332-6_13.


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

Cox MP, Peterson DA, Biggs PJ.

BMC Bioinformatics. 2010 Sep 27;11:485. doi: 10.1186/1471-2105-11-485.


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

McComish BJ, Hills SF, Biggs PJ, Penny D.

Genome Biol Evol. 2010 Jul 12;2:410-24. doi: 10.1093/gbe/evq029.


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

Chen XS, Collins LJ, Biggs PJ, Penny D.

Genome Biol Evol. 2009 Jul 6;1:165-75. doi: 10.1093/gbe/evp017.


Do angles of obliquity apply to 30 degrees scattered radiation from megavoltage beams?

Biggs PJ, Styczynski JR.

Health Phys. 2008 Oct;95(4):425-32. doi: 10.1097/01.HP.0000319905.27506.88.


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