Our publications are listed here by project.
We also publish Genomics Aotearoa blogs.
2021 Tee HS, Wood SA, Bouma-Gregson K, Lear G, Handley KM. Genome streamlining, plasticity and metabolic versatility distinguish co-occurring toxic and non-toxic cyanobacterial strains of Microcoleus. mBio. doi:10.1128/mBio.02235-21.
2021 Tee HS, Waite DW, Lear G, Handley KM. Microbial river-to-sea continuum: gradients in benthic and planktonic diversity, osmoregulation and nutrient cycling. Microbiome 9: 190. (video abstract:https://www.youtube.com/watch?v=smx-H3wVw_A)
2021 Chiri E, Nauer PA, Lappan R, Jirapanjawat T, Waite DW, Handley KM, Hugenholtz P, Cook PLM, Arndt SK, Greening C. Termite gas emissions select for hydrogenotrophic microbial communities in termite mounds. PNAS 118: e2102625118.
Genomic adaptations enabling Acidithiobacillus distribution across wide ranging hot spring temperatures and pHs.
Sriaporn C, Campbell KA, Van Kranendonk MJ, Handley KM.
Microbiome. 9,135, 2021, https://doi.org/10.1186/s40168-021-01090-1 (video abstract: https://www.youtube.com/watch?v=kqM1jPyMRyc)
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
mSystems 4(3), e00153-19, 2019, doi:10.1128/mSystems.00153-19
More on Environmental metagenomics
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
More on High quality genomes
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
More on Te nohonga kaitiaki
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
More on the Aotearoa New Zealand genomic variome
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
More on Genomic translational oncology
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