Publications

Our publications are listed here by project.

We also publish Genomics Aotearoa blogs.

Environmental metagenomics

Strategies for successful cyanobacterial proliferation in freshwater
S Wood, HS Tee, KM Handley
Nature Research Microbiology Community, May 2020

Tools for successful proliferation: Diverse strategies of nutrient acquisition by a benthic cyanobacterium
HS Tee, D Waite, L Payne, M Middleditch, S Wood, KM Handley
The ISME Journal, 14, 2020, https://doi.org/10.1038/s41396-020-0676-5

Determining microbial roles in ecosystem function: Redefining microbial food webs and transcending kingdom barriers
KM Handley
mSystems 4(3), e00153-19, 2019, doi:10.1128/mSystems.00153-19

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High quality genomes

Genome architecture facilitates phenotypic plasticity in the honeybee (Apis mellifera)
EJ Duncan, MP Leask, PK Dearden
Molecular Biology and Evolution, 37(7), 1964-1978, 2020, https://doi.org/10.1093/molbev/msaa057

Sawfly genomes reveal evolutionary acquisitions that fostered the mega-radiation of Parasitoid and Eusocial Hymenoptera
JP Oeyen et al.
Genome Biology and Evolution, 12(7), 1099–1188, 2020, https://doi.org/10.1093/gbe/evaa106

Genetic diversity in invasive populations of Argentine stem weevil associated with adaptation to biocontrol
TWR Harrop et al.
Insects, 11(7), 441, 2020, https://doi.org/10.3390/insects11070441

Opportunities for modern genetic technologies to maintain and enhance Aotearoa New Zealand’s bioheritage
SN Inwood, GM McLaughlin, TR Buckley, MP Cox, KA Handley, TE Steeves, TJ Strabala, R McDougal, PK Dearden
New Zealand Journal of Ecology, 44(2), 2020, https://www.jstor.org/stable/26931313

Genotyping-by-sequencing of pooled drone DNA for the management of living honeybee (Apis mellifera) queens in commercial beekeeping operations in New Zealand
GEL Petersen, PF Fenessy, TC Van Stijn, S Clarke, KG Dodds, PK Dearden
Apidologie, 51, 545–556, 2020, https://doi.org/10.1007/s13592-020-00741-w

Phylogenetic determinants of toxin gene distribution in genomes of Brevibacillus laterosporus
TR Glare, A Durrant, C Berry, L Palma, MM Ormskirk, MP Cox
Genomics, 112(1), 1042-1053, 2020, doi.org/10.1016/j.ygeno.2019.06.020

Designing and implementing a genetic improvement program in commercial beekeeping operations
GEL Petersen, PF Fennessy, PR Amer, PK Dearden
Journal of Apicultural Research, 59(4), 2020, https://doi.org/10.1080/00218839.2020.1715583

The Pacific Biosciences de novo assembled genome dataset from a parthenogenetic New Zealand wild population of the longhorned tick, Haemaphysalis longicornis Neumann, 1901
FD Guerrero et al.
Data in Brief, 27, 2019, https://doi.org/10.1016/j.dib.2019.104602

Pseudo-chromosome-length genome assembly of a double haploid “Bartlett” pear (Pyrus communis L.)
G Linsmith et al.
GigaScience, 8(12), 2019, https://doi.org/10.1093/gigascience/giz138

Ancestral hymenopteran queen pheromones do not share the broad phylogenetic repressive effects of honeybee queen mandibular pheromone
 MR Lovegrove, PK Dearden, EJ Duncan
Journal of Insect Physiology, 119, 2019, https://doi.org/10.1016/j.jinsphys.2019.103968

TCR- or cytokine-activated CD8+ mucosal-associated invariant T cells are rapid polyfunctional effectors that can coordinate immune responses
R Lamichhane et al.
Cell Reports, 28(12), 3061-3076, 2019, https://doi.org/10.1016/j.celrep.2019.08.054

Invasive insects: Management methods explored
G McLaughlin, PK Dearden
Journal of Insect Science, 19(5), 17, 2019, https://doi.org/10.1093/jisesa/iez085

Comparative transcriptomic analysis of a wing-dimorphic stonefly reveals candidate wing loss genes
G McCulloch, A Oliphant, PK Dearden, AJ Veale, CW Ellen, JM Waters
Evo Devo, 10(21), 2019, https://doi.org/10.1186/s13227-019-0135-4

The torso-like gene functions to maintain the structure of the vitelline membrane in Nasonia vitripennis, implying its co-option into Drosophila axis formation
SE Taylor, J Tuffery, D Bakopoulos, S Lequeux, C Warr, TK Johnson, PK Dearden
Biology Open, 8: 2019, doi:10.1242/bio.046284

Ecological gradients drive insect wing loss and speciation: The role of the alpine treeline
G McCulloch, B Foster, L Dutoit, T Ingram, E Hay, A Veale, PK Dearden, J Waters
Molecular Ecology, 28(13), 3141-3150, 2019, https://doi.org/10.1111/mec.15114

The complete mitogenome sequence of the agricultural pest, clover root weevil: The key to its own demise?
RA Al-Jiab, J Gillum, A Alexander, DM Tompkins, CB Phillips, PK Dearden, NJ Gemmell
Mitochondrial DNA Part B, 4(1), 878-879, 2019, https://doi.org/10.1080/23802359.2018.1561218

First complete mitochondrial genome of a Gripopterygid stonefly from the sub-order Antarctoperlaria: Zelandoperla fenestrate
AJ Veale, PK Dearden, JM Waters
Mitochondrial DNA Part B, 4(1), 886-888, 2019, https://doi.org/10.1080/23802359.2018.1546130

Science at the intersection of cultures – Māori, Pākehā and mānuka
ER Morgan, NB Perry, D Chagné
NZ Journal of Crop & Horticultural Science, 47(4), 2019, https://doi.org/10.1080/01140671.2019.1691610

Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome
KA Panfilio et al.
Genome Biology, 20(1), 64, 2019, https://doi.org/10.1186/s13059-019-1660-0

Evolution of the Torso activation cassette, a pathway required for terminal patterning and moulting
J Skelly, C Pushparajan, EJ Duncan, PK Dearden
Insect Molecular Biology, 28(3), 2019, doi.org/10.1111/imb.12560

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Te nohonga kaitiaki

Entwined processes: Rescripting consent and strengthening governance in genomics research with Indigenous communities
N Garrison, SR Carroll, M Hudson
Journal of Law, Medicine and Ethics, 48(1), 2020, https://doi.org/10.1177/1073110520917020

Rights, interests and expectations: Indigenous perspectives on unrestricted access to genomic data
M Hudson et al.
Nature Reviews Genetics, 21, 377–384, 2020, https://doi.org/10.1038/s41576-020-0228-x

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Aotearoa New Zealand genomic variome

Indigenous genomic databases: Pragmatic considerations and cultural contexts
NR Caron, M Chongo, M Hudson, L Arbour, WW Wasserman, S Robertson, S Correard, P Wilcox
Frontiers in Public Health, 8, 111, 2020, https://doi.org/10.3389/fpubh.2020.00111

Genomic medicine must reduce, not compound, health inequities: The case for hauora-enhancing genomic resources for New Zealand
S P Robertson et al.
New Zealand Medical Journal, 131(1480), 81-89, 2018

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Genomic translational oncology

PDX1 DNA methylation distinguishes two subtypes of pancreatic neuroendocrine neoplasms with a different prognosis
G Boons et al.
Cancers, 12(6), 1461, 2020, https://doi.org/10.3390/cancers12061461

Genomic and signalling pathway characterisation of the NZM panel of melanoma cell lines: A valuable model for studying the impact of genetic diversity in melanoma
K Tran et al.
Pigment Cell & Melanoma Research, June 2020, https://doi.org/10.1111/pcmr.12908

An estimate of limited duration cancer prevalence in New Zealand using ‘big’ data
N Brewer, J Atkinson, P Guilford, C Print, T Blakely, A Teng
New Zealand Medical Journal, 133(1514), May 2020

Accessing a new dimension in TP53 biology: Multiplex long amplicon digital PCR to specifically detect and quantitate individual TP53 transcripts
A Lasham, R Tsai, S Fitzgerald, S Mehta, N Knowlton, A Braithwaite, C Print
Cancers, 12(3), 769, 2020, https://doi.org/10.3390/cancers12030769

A predictor of early disease recurrence in breast cancer patients using a cell-free RNA and protein liquid biopsy
A Lasham et al.
Clinical Breast Cancer, 20(2), 2020, https://doi.org/10.1016/j.clbc.2019.07.003

Tailoring a rapid autopsy protocol to explore cancer evolution: A patient collaboration
C Blenkiron, T Robb, K Parker, N Kramer, S Stables, R Tse, L Modahl, E Coats, C Print, B Lawrence
New Zealand Medical Journal, 132(1503), October 2019

Mapping a route to Indigenous engagement in cancer genomic research
K Henare, K Parker, H Wihongi, C Blenkiron, R Jansen, P Reid, M Findlay, B Lawrence, M Hudson, C Print
The Lancet Oncology, 20(6), 2019, https://doi.org/10.1016/S1470-2045(19)30307-9

Recurrent loss of heterozygosity correlates with clinical outcome in pancreatic neuroendocrine cancer
B Lawrence et al.
NPJ Genomic Medicine, 3(18), 2018, https://doi.org/10.1038/s41525-018-0058-3

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Epigenome-wide association study technology

DNA methylation profiling identifies a high effect genetic variant for lipoprotein(a) levels
GT Jones, J Marsman, B Bhat, VL Phillips, A Chatterjee, EJ Rodger, MJA Williams, AM van Rij, SPA McCormick.
Epigenetics, 15(9), 2020, https://doi.org/10.1080/15592294.2020.1739797 

A variant of the castor zinc finger 1 (CASZ1) gene is differentially associated with the clinical classification of chronic venous disease
G Jones et al.
Scientific Reports, 9, 14011, 2019, https://doi.org/10.1038/s41598-019-50586-2

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