Personal information

Genomics, genotyping, genomic tools, livestock, aquaculture
New Zealand

Activities

Employment (7)

AgResearch Ltd: Christchurch, NZ

Employment
Source: check_circle
AgResearch Ltd

University of Otago: Dunedin, NZ

2015 to present | Honorary Lecturer (Anatomy)
Employment
Source: Self-asserted source
Shannon Clarke

AgResearch Invermay: Mosgiel, NZ

2008 to present | Senior Scientist (Animal Genomics)
Employment
Source: Self-asserted source
Shannon Clarke

AgResearch Invermay: Mosgiel, NZ

2006 to 2008 | Scientist (Animal Genomics)
Employment
Source: Self-asserted source
Shannon Clarke

University of Otago: Dunedin, NZ

2003-05 to 2006-10 | FRST Post Doc (Biochemistry)
Employment
Source: Self-asserted source
Shannon Clarke

University of Otago Department of Biochemistry: Dunedin, NZ

2005 to 2006 | Lecturer
Employment
Source: Self-asserted source
Shannon Clarke

University of Wales Aberystwyth Institute of Biological Environmental and Rural Sciences: Aberystwyth, Ceredigion, GB

2000-03 to 2003-04 | BBSRC Post Doc
Employment
Source: Self-asserted source
Shannon Clarke

Education and qualifications (1)

University of Otago: Dunedin, NZ

1996 to 2000 | PhD
Education
Source: Self-asserted source
Shannon Clarke

Funding (4)

Fast-tracking Finfish Climate Change Adaptation

2023-10-01 to 2028-09-30 | Grant
Ministry of Business, Innovation and Employment (Wellington, Wellington, NZ)
GRANT_NUMBER:

CAWX2304

Source: check_circle
New Zealand Ministry of Business, Innovation and Employment

A transformative DNA diagnostic test for early-stage cancer detection

2021-10-01 to 2024-09-30 | Grant
Ministry of Business, Innovation and Employment (Wellington, Wellington, NZ)
GRANT_NUMBER:

UOOX2105

Source: check_circle
New Zealand Ministry of Business, Innovation and Employment

Beyond the genome: Exploiting methylomes to accelerate adaptation to a changing environment

2019-10-01 to 2025-03-31 | Grant
Ministry of Business, Innovation and Employment (Wellington, Wellington, NZ)
GRANT_NUMBER:

C10X1906

Source: check_circle
New Zealand Ministry of Business, Innovation and Employment

Developing and applying next generation genomic selection to rapidly improve honeybee performance

2017-10-01 to 2023-09-30 | Grant
Ministry of Business, Innovation and Employment (Wellington, Wellington, NZ)
GRANT_NUMBER:

UOOX1704

Source: check_circle
New Zealand Ministry of Business, Innovation and Employment

Works (39)

Genetic variation in skin traits in New Zealand lambs

Journal of the Science of Food and Agriculture
2022-08-30 | Journal article
Contributors: Kathryn M McRae; Sue M Cooper; John C McEwan; Rayna Anderson; Wendy E Bain; Hayley J Baird; Ken G Dodds; Shannon M Clarke; Natalie K Pickering; Geoff Holmes
Source: check_circle
Crossref

Population Genomics of New Zealand Pouched Lamprey (kanakana; piharau; Geotria australis)

Journal of Heredity
2022-07-23 | Journal article
Contributors: Allison K Miller; Nataliya Timoshevskaya; Jeramiah J Smith; Joanne Gillum; Saeed Sharif; Shannon Clarke; Cindy Baker; Jane Kitson; Neil J Gemmell; Alana Alexander et al.
Source: check_circle
Crossref

Development of Epigenetic Clocks for Key Ruminant Species

Genes
2021-12-30 | Journal article
Contributors: Alex Caulton; Ken G. Dodds; Kathryn M. McRae; Christine Couldrey; Steve Horvath; Shannon M. Clarke
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

Beyond the genome: a perspective on the use of DNA methylation profiles as a tool for the livestock industry

Animal Frontiers
2021-12-17 | Journal article
Contributors: Shannon Clarke; Alex Caulton; Kathryn McRae; Rudiger Brauning; Christine Couldrey; Ken Dodds
Source: check_circle
Crossref

Genomic Tools for the Identification of Loci Associated with Facial Eczema in New Zealand Sheep

Genes
2021-09 | Journal article | Author
Contributors: Kathryn McRae; suzanne rowe; Patricia L. Johnson; Hayley J. Baird; Neil G. Cullen; Matthew J. Bixley; Jeffrey E. Plowman; Santanu Deb-Choudhury; Rudiger Brauning; Neville C. Amyes et al.
Source: check_circle
Multidisciplinary Digital Publishing Institute

The Use of “Genotyping-by-Sequencing” to Recover Shared Genealogy in Genetically Diverse Eucalyptus Populations

Forests
2021-07-12 | Journal article
Contributors: Jaroslav Klápště; Rachael L. Ashby; Emily J. Telfer; Natalie J. Graham; Heidi S. Dungey; Rudiger Brauning; Shannon M. Clarke; Ken G. Dodds
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

Development of epigenetic clocks for New Zealand livestock

2021-07-02 | Other
Contributors: Alex Caulton; Ken G. Dodds; Kathryn M. McRae; Christine Couldrey; Steve Horvath; Shannon M. Clarke
Source: check_circle
Crossref

Genotyping-by-sequencing of pooled drone DNA for the management of living honeybee (Apis mellifera) queens in commercial beekeeping operations in New Zealand

Apidologie
2020 | Journal article
EID:

2-s2.0-85082860364

Part of ISBN:

12979678 00448435

Contributors: Petersen, G.E.L.; Fennessy, P.F.; Van Stijn, T.C.; Clarke, S.M.; Dodds, K.G.; Dearden, P.K.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

SNP discovery and population structure analysis in Lassi and Marecha camel breeds using a genotyping by sequencing method

Animal Genetics
2020-08 | Journal article
Contributors: S. Sabahat; R. Brauning; S. M. Clarke; A. Nadeem; P.C. Thomson; M. S. Khatkar
Source: check_circle
Crossref

Global analysis of transcription start sites in the new ovine reference genome (Oar rambouillet v1.0)

2020-07-06 | Preprint
Contributors: Mazdak Salavati; Alex Caulton; Richard Clark; Iveta Gazova; Timothy P. L. Smith; Kim C. Worley; Noelle E. Cockett; Alan L. Archibald; Shannon M. Clarke; Brenda M. Murdoch et al.
Source: check_circle
Crossref

A high density linkage map and quantitative trait loci for tree growth for New Zealand mānuka (Leptospermum scoparium)

New Zealand Journal of Crop and Horticultural Science
2019 | Journal article
EID:

2-s2.0-85055701008

Part of ISBN:

11758783 01140671

Contributors: Chagné, D.; Ryan, J.; Saeed, M.; Van Stijn, T.; Brauning, R.; Clarke, S.; Jacobs, J.; Wilcox, P.; Boursault, E.; Jaksons, P. et al.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

Applications of the soil, plant and rumen microbiomes in pastoral agriculture

Frontiers in Nutrition
2019 | Journal article
EID:

2-s2.0-85069768313

Part of ISBN:

2296861X

Contributors: Attwood, G.T.; Wakelin, S.A.; Leahy, S.C.; Rowe, S.; Clarke, S.; Chapman, D.F.; Muirhead, R.; Jacobs, J.M.E.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

Developing successful breeding programs for New Zealand aquaculture: A perspective on progress and future genomic opportunities

Frontiers in Genetics
2019 | Journal article
EID:

2-s2.0-85065848762

Part of ISBN:

16648021

Contributors: Symonds, J.E.; Clarke, S.M.; King, N.; Walker, S.P.; Blanchard, B.; Sutherland, D.; Roberts, R.; Preece, M.A.; Tate, M.; Buxton, P. et al.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

Exclusion and genomic relatedness methods for assignment of parentage using genotyping-by-sequencing data

G3: Genes, Genomes, Genetics
2019 | Journal article
EID:

2-s2.0-85072992728

Part of ISBN:

21601836

Contributors: Dodds, K.G.; McEwan, J.C.; Brauning, R.; Van, T.C.; Suzanne, S.J.; Mary McEwan, R.K.; Clarke, S.M.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier
grade
Preferred source (of 2)‎

Heritability of ram mating success in multi-sire breeding situations

Animal
2019 | Journal article
EID:

2-s2.0-85055513425

Part of ISBN:

1751732X 17517311

Contributors: Juengel, J.L.; Hickey, S.M.; Clarke, S.M.; Cullen, N.G.; McEwan, J.C.; Dodds, K.G.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

Using genotyping-by-sequencing to predict gender in animals

Animal Genetics
2019 | Journal article
EID:

2-s2.0-85064002401

Part of ISBN:

13652052 02689146

Contributors: Bilton, T.P.; Chappell, A.J.; Clarke, S.M.; Brauning, R.; Dodds, K.G.; McEwan, J.C.; Rowe, S.J.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

Genome-wide association study of lung lesions and pleurisy in New Zealand lambs

Journal of Animal Science
2018 | Journal article
EID:

2-s2.0-85057188184

Part of ISBN:

15253163 00218812

Contributors: McRae, K.M.; Rowe, S.J.; Baird, H.J.; Bixley, M.J.; Clarke, S.M.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

Linkage disequilibrium estimation in low coverage high-throughput sequencing data

Genetics
2018 | Journal article
EID:

2-s2.0-85047820013

Part of ISBN:

19432631 00166731

Contributors: Bilton, T.P.; McEwan, J.C.; Clarke, S.M.; Brauning, R.; van Stijn, T.C.; Rowe, S.J.; Dodds, K.G.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier
grade
Preferred source (of 2)‎

Reduced representation sequencing detects only subtle regional structure in a heavily exploited and rapidly recolonizing marine mammal species

Ecology and Evolution
2018 | Journal article
EID:

2-s2.0-85052572408

Part of ISBN:

20457758

Contributors: Dussex, N.; Taylor, H.R.; Stovall, W.R.; Rutherford, K.; Dodds, K.G.; Clarke, S.M.; Gemmell, N.J.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds /631/114 /631/181/735 /631/208/177 /631/553 /45/15 /45/23 article

Nature Communications
2018 | Journal article
EID:

2-s2.0-85042713595

Part of ISBN:

20411723

Contributors: Naval-Sanchez, M.; Nguyen, Q.; McWilliam, S.; Porto-Neto, L.R.; Tellam, R.; Vuocolo, T.; Reverter, A.; Perez-Enciso, M.; Brauning, R.; Clarke, S. et al.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

Estimation of linkage disequilibrium and effective population size in New Zealand sheep using three different methods to create genetic maps

BMC Genetics
2017 | Journal article
EID:

2-s2.0-85025111197

Part of ISBN:

14712156

Contributors: Prieur, V.; Clarke, S.M.; Brito, L.F.; McEwan, J.C.; Lee, M.A.; Brauning, R.; Dodds, K.G.; Auvray, B.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

Genetic diversity of a New Zealand multi-breed sheep population and composite breeds' history revealed by a high-density SNP chip

BMC Genetics
2017 | Journal article
EID:

2-s2.0-85014883424

Part of ISBN:

14712156

Contributors: Brito, L.F.; McEwan, J.C.; Miller, S.P.; Pickering, N.K.; Bain, W.E.; Dodds, K.G.; Schenkel, F.S.; Clarke, S.M.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

Genetic parameters for various growth, carcass and meat quality traits in a New Zealand sheep population

Small Ruminant Research
2017 | Journal article
EID:

2-s2.0-85026787235

Part of ISBN:

09214488

Contributors: Brito, L.F.; McEwan, J.C.; Miller, S.; Bain, W.; Lee, M.; Dodds, K.; Newman, S.-A.; Pickering, N.; Schenkel, F.S.; Clarke, S.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

Male–female relatedness at specific SNP-linkage groups influences cryptic female choice in Chinook salmon (Oncorhynchus tshawytscha)

Proceedings of the Royal Society B: Biological Sciences
2017 | Journal article
EID:

2-s2.0-85026481496

Part of ISBN:

14712954 09628452

Contributors: Geßner, C.; Johnson, S.L.; Fisher, P.; Clarke, S.; Rutherford, K.; Symonds, J.; Gemmell, N.J.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

Prediction of genomic breeding values for growth, carcass and meat quality traits in a multi-breed sheep population using a HD SNP chip

BMC Genetics
2017 | Journal article
EID:

2-s2.0-85010420489

Contributors: Brito, L.F.; Clarke, S.M.; McEwan, J.C.; Miller, S.P.; Pickering, N.K.; Bain, W.E.; Dodds, K.G.; Sargolzaei, M.; Schenkel, F.S.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

Assessing accuracy of imputation using different SNP panel densities in a multi-breed sheep population

Genetics Selection Evolution
2016 | Journal article
EID:

2-s2.0-84992202306

Contributors: Ventura, R.V.; Miller, S.P.; Dodds, K.G.; Auvray, B.; Lee, M.; Bixley, M.; Clarke, S.M.; McEwan, J.C.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

Incidence and heritability of ovine pneumonia, and the relationship with production traits in New Zealand sheep

Small Ruminant Research
2016 | Journal article
EID:

2-s2.0-84995554337

Contributors: McRae, K.M.; Baird, H.J.; Dodds, K.G.; Bixley, M.J.; Clarke, S.M.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

Construction of relatedness matrices using genotyping-by-sequencing data

BMC Genomics
2015 | Journal article
EID:

2-s2.0-84988267283

Contributors: Dodds, K.G.; McEwan, J.C.; Brauning, R.; Anderson, R.M.; Stijn, T.C.; Kristjánsson, T.; Clarke, S.M.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

A high throughput single nucleotide polymorphism multiplex assay for parentage assignment in new zealand sheep

PLoS ONE
2014 | Journal article
EID:

2-s2.0-84899666475

Contributors: Clarke, S.M.; Henry, H.M.; Dodds, K.G.; Jowett, T.W.D.; Manley, T.R.; Anderson, R.M.; McEwan, J.C.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

A high throughput single nucleotide polymorphism multiplex assay for parentage assignment in New Zealand sheep

PLoS ONE
2014 | Journal article
EID:

2-s2.0-84922394735

Contributors: Clarke, S.M.; Henry, H.M.; Dodds, K.G.; Jowett, T.W.D.; Manley, T.R.; Anderson, R.M.; McEwan, J.C.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

SNPs for parentage testing and traceability in globally diverse breeds of sheep

PLoS ONE
2014 | Journal article
EID:

2-s2.0-84925551985

Contributors: Heaton, M.P.; Leymaster, K.A.; Kalbfleisch, T.S.; Kijas, J.W.; Clarke, S.M.; McEwan, J.; Maddox, J.F.; Basnayake, V.; Petrik, D.T.; Simpson, B. et al.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

SNPs for parentage testing and traceability in globally diverse breeds of sheep

PLoS ONE
2014 | Journal article
EID:

2-s2.0-84899668758

Contributors: Heaton, M.P.; Leymaster, K.A.; Kalbfleisch, T.S.; Kijas, J.W.; Clarke, S.M.; McEwan, J.; Maddox, J.F.; Basnayake, V.; Petrik, D.T.; Simpson, B. et al.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

Jasmonates act with salicylic acid to confer basal thermotolerance in Arabidopsis thaliana

New Phytologist
2009 | Journal article
EID:

2-s2.0-61649094050

Contributors: Clarke, S.M.; Cristescu, S.M.; Miersch, O.; Harren, F.J.M.; Wasternack, C.; Mur, L.A.J.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

Salicylate accumulation inhibits growth at chilling temperature in Arabidopsis

Plant Physiology
2004 | Journal article
EID:

2-s2.0-3042630010

Contributors: Scott, I.M.; Clarke, S.M.; Wood, J.E.; Mur, L.A.J.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

Salicylic acid dependent signaling promotes basal thermotolerance but is not essential for acquired thermotolerance in Arabidopsis thaliana

Plant Journal
2004 | Journal article
EID:

2-s2.0-2342612864

Contributors: Clarke, S.M.; Mur, L.A.J.; Wood, J.E.; Scott, I.M.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

Amino acid deletions in the cytosolic domains of the chlorophyll a-binding protein CP47 slow Q<inf>A</inf><sup>-</sup> oxidation and/or prevent the assembly of Photosystem II

Plant Molecular Biology
2002 | Journal article
EID:

2-s2.0-0036790240

Contributors: Clarke, S.M.; Funk, C.; Hendry, G.S.; Shand, J.A.; Wydrzynski, T.; Eaton-Rye, J.J.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

Amino acid deletions in loop C of the chlorophyll a-binding protein CP47 alter the chloride requirement and/or prevent the assembly of photosystem II

Plant Molecular Biology
2000 | Journal article
EID:

2-s2.0-0034485076

Contributors: Clarke, S.M.; Eaton-Rye, J.J.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

Mutation of Phe-363 in the photosystem II protein CP47 impairs photoautotrophic growth, alters the chloride requirement, and prevents photosynthesis in the absence of either PSII-O or PSII-V in Synechocystis sp. PCC 6803

Biochemistry
1999 | Journal article
EID:

2-s2.0-0033514977

Contributors: Clarke, S.M.; Eaton-Rye, J.J.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

Specific requirements for cytochrome c-550 and the manganese- stabilizing protein in photoautotrophic strains of Synechocystis sp. PCC 6803 with mutations in the domain Gly-351 to Thr-436 of the chlorophyll-binding protein CP47

Biochemistry
1998 | Journal article
EID:

2-s2.0-0032514645

Contributors: Morgan, T.R.; Shand, J.A.; Clarke, S.M.; Eaton-Rye, J.J.
Source: Self-asserted source
Shannon Clarke via Scopus - Elsevier

Peer review (1 review for 1 publication/grant)

Review activity for BMC genomics (1)