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Dr David Winter staff profile picture

Contact details +64 (06) 356 9099  ext. 85734

Dr David Winter PhD

Lecturer

School of Fundamental Sciences

I am a computational biologist who develops bioinformatic and genomic approaches to answer fundamental questions about evolutionary change. I am particularly interested in analysing functional genomic data in an evolutionary context. Applying the principals of evolutionary biology to functional data allows me to answer questions about the genomic basis of adaptation and the origin and maintenance of functional diversity within populations.

 

Professional

Qualifications

  • Doctor of Philosophy - University of Otago (2012)

Research Expertise

Research Interests

Evolutionary Biology

Genomics

Bioinformatics

Development of scientific sofware

Area of Expertise

Field of research codes
Biological Sciences (060000): Evolutionary Biology (060300): Genetics (060400): Genome Structure and Regulation (060407): Genomics (060408): Molecular Evolution (060409): Population, Ecological and Evolutionary Genetics (060411): Quantitative Genetics (incl. Disease and Trait Mapping Genetics) (060412)

Research Projects

Summary of Research Projects

Position Current Completed
Project Leader 1 1

Current Projects

Project Title: Treasure from the junk pile. Do transposable elements drive the evolution of gene expression?

Date Range: 2019 - 2022

Funding Body: Royal Society of New Zealand

Project Team:

Research Outputs

Journal

Lukito, Y., Lee, K., Noorifar, N., Green, K., Winter, D., Ram, A., . . . Scott, B. (2020). Host infection by the grass-symbiotic fungus Epichloë festucae requires catalytically active H3K9 and H3K36 methyltransferases.
[Journal article]Authored by: Cox, M., Winter, D.
Gemmell, NJ., Rutherford, K., Prost, S., Tollis, M., Winter, D., Macey, JR., . . . Edmonds, H. (2020). Publisher Correction: The tuatara genome reveals ancient features of amniote evolution (Nature, (2020), 584, 7821, (403-409), 10.1038/s41586-020-2561-9). Nature. 585(7823), E3
[Journal article]Authored by: Winter, D.
Gemmell, NJ., Rutherford, K., Prost, S., Tollis, M., Winter, D., Macey, JR., . . . Edmonds, H. (2020). The tuatara genome reveals ancient features of amniote evolution. Nature. 584(7821), 403-409
[Journal article]Authored by: Winter, D.
Hassing, B., Eaton, CJ., Winter, D., Green, KA., Brandt, U., Savoian, MS., . . . Scott, B. (2020). Phosphatidic acid produced by phospholipase D is required for hyphal cell-cell fusion and fungal-plant symbiosis. Molecular Microbiology. 113(6), 1101-1121
[Journal article]Authored by: Hassing, B., Mesarich, C., Savoian, M., Scott, D., Winter, D.
Winter, DJ., Charlton, ND., Krom, N., Shiller, J., Bock, CH., Cox, MP., . . . Young, CA. (2020). Chromosome-level reference genome of venturia effusa, causative agent of pecan scab. Molecular Plant-Microbe Interactions. 33(2), 149-152
[Journal article]Authored by: Cox, M., Winter, D.
Gemmell, N., Rutherford, K., Prost, S., Tollis, M., Winter, D., Macey, R., . . . Board, NT. (2019). The tuatara genome: insights into vertebrate evolution from the sole survivor of an ancient reptilian order.
[Journal article]Authored by: Winter, D.
Hassing, B., Winter, D., Becker, Y., Mesarich, CH., Eaton, CJ., & Scott, B. (2019). Analysis of Epichloëfestucae small secreted proteins in the interaction with Lolium perenne. PLoS ONE. 14(2)
[Journal article]Authored by: Hassing, B., Mesarich, C., Scott, D., Winter, D.
Chujo, T., Lukito, Y., Eaton, CJ., Dupont, PY., Johnson, LJ., Winter, D., . . . Scott, B. (2019). Complex epigenetic regulation of alkaloid biosynthesis and host interaction by heterochromatin protein I in a fungal endophyte-plant symbiosis. Fungal Genetics and Biology. 125, 71-83
[Journal article]Authored by: Cox, M., Scott, D., Winter, D.
Winter, DJ., Ganley, ARD., Young, CA., Liachko, I., Schardl, CL., Dupont, PY., . . . Cox, MP. (2018). Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae. PLoS Genetics. 14(10)
[Journal article]Authored by: Berry, D., Cox, M., Scott, D., Winter, D.
Winter, DJ., Wu, SH., Howell, AA., Azevedo, RBR., Zufall, RA., & Cartwright, RA. (2018). accuMUlate: a mutation caller designed for mutation accumulation experiments. Bioinformatics (Oxford, England). 34(15), 2659-2660
[Journal article]Authored by: Winter, D.
Winter, D., Wu, S., Howell, A., Azevedo, R., Zufall, R., & Cartwright, R. (2017). accuMUlate: A mutation caller designed for mutation accumulation experiments.
[Journal article]Authored by: Winter, D.
Winter, D. (2017). rentrez: An R package for the NCBI eUtils API.
[Journal article]Authored by: Winter, D.
Winter, DJ. (2017). rentrez: An R package for the NCBI eUtils API. R Journal. 9(2), 520-526
[Journal article]Authored by: Winter, D.
Wu, SH., Schwartz, RS., Winter, DJ., Conrad, DF., & Cartwright, RA. (2017). Estimating error models for whole genome sequencing using mixtures of Dirichlet-multinomial distributions. Bioinformatics. 33(15), 2322-2329
[Journal article]Authored by: Winter, D.
Wallis, GP., Cameron-Christie, SR., Kennedy, HL., Palmer, G., Sanders, TR., & Winter, DJ. (2017). Interspecific hybridization causes long-term phylogenetic discordance between nuclear and mitochondrial genomes in freshwater fishes. Molecular Ecology. 26(12), 3116-3127
[Journal article]Authored by: Winter, D.
Michonneau, F., Brown, JW., & Winter, DJ. (2016). rotl: an R package to interact with the Open Tree of Life data. Methods in Ecology and Evolution. 7(12), 1476-1481
[Journal article]Authored by: Winter, D.
Smith, AM., Key, MM., Henderson, ZE., Davis, VC., & Winter, DJ. (2016). Pretreatment for removal of organic material is not necessary for x-ray-diffraction determination of mineralogy in temperate skeletal carbonate. Journal of Sedimentary Research. 86(12), 1425-1433
[Journal article]Authored by: Winter, D.
Long, H., Winter, DJ., Chang, AYC., Sung, W., Wu, SH., Balboa, M., . . . Zufall, RA. (2016). Low base-substitution mutation rate in the germline genome of the ciliate tetrahymena thermophila. Genome Biology and Evolution. 8(12), 3629-3639
[Journal article]Authored by: Winter, D.
Smith, AM., Clark, DE., Lamare, MD., Winter, DJ., & Byrne, M. (2016). Risk and resilience: Variations in magnesium in echinoid skeletal calcite. Marine Ecology Progress Series. 561, 1-16
[Journal article]Authored by: Winter, D.
Winter, D., Pacheco, M., Vallejo, AF., Schwartz, R., Arevalo-Herrera, M., Herrera, S., . . . Escalante, A. (2015). Whole genome sequencing of field isolates reveals extensive genetic diversity in Plasmodium vivax from Colombia.
[Journal article]Authored by: Winter, D.
Long, H., Winter, D., Chang, AY-C., Sung, W., Wu, S., Balboa, M., . . . Zufall, R. (2015). Low base-substitution mutation rate in the germline genome of the ciliate Tetrahymena thermophila.
[Journal article]Authored by: Winter, D.
Winter, DJ., Pacheco, MA., Vallejo, AF., Schwartz, RS., Arevalo-Herrera, M., Herrera, S., . . . Escalante, AA. (2015). Whole Genome Sequencing of Field Isolates Reveals Extensive Genetic Diversity in Plasmodium vivax from Colombia. PLoS Neglected Tropical Diseases. 9(12)
[Journal article]Authored by: Winter, D.
Donald, KM., Winter, DJ., Ashcroft, AL., & Spencer, HG. (2015). Phylogeography of the whelk genus Cominella (Gastropoda: Buccinidae) suggests long-distance counter-current dispersal of a direct developer. Biological Journal of the Linnean Society. 115(2), 315-332
[Journal article]Authored by: Winter, D.
Smith, AM., Berman, J., Key, MM., & Winter, DJ. (2013). Not all sponges will thrive in a high-CO<inf>2</inf> ocean: Review of the mineralogy of calcifying sponges. Palaeogeography, Palaeoclimatology, Palaeoecology. 392, 463-472
[Journal article]Authored by: Winter, D.
Smith, AM., Riedi, MA., & Winter, DJ. (2013). Temperate reefs in a changing ocean: Skeletal carbonate mineralogy of serpulids. Marine Biology. 160(9), 2281-2294
[Journal article]Authored by: Winter, D.
Byrne, M., Lamare, M., Winter, D., Dworjanyn, SA., & Uthicke, S. (2013). The stunting effect of a high CO<inf>2</inf> ocean on calcification and development in sea urchin larvae, a synthesis from the tropics to the poles. Philosophical Transactions of the Royal Society B: Biological Sciences. 368(1627)
[Journal article]Authored by: Winter, D.
Winter, DJ. (2012). MMOD: An R library for the calculation of population differentiation statistics. Molecular Ecology Resources. 12(6), 1158-1160
[Journal article]Authored by: Winter, D.
Smith, AM., Sutherland, JE., Kregting, L., Farr, TJ., & Winter, DJ. (2012). Phylomineralogy of the Coralline red algae: Correlation of skeletal mineralogy with molecular phylogeny. Phytochemistry. 81, 97-108
[Journal article]Authored by: Winter, D.
Donald, KM., Preston, J., Williams, ST., Reid, DG., Winter, D., Alvarez, R., . . . Spencer, HG. (2012). Phylogenetic relationships elucidate colonization patterns in the intertidal grazers Osilinus Philippi, 1847 and Phorcus Risso, 1826 (Gastropoda: Trochidae) in the northeastern Atlantic Ocean and Mediterranean Sea. Molecular Phylogenetics and Evolution. 62(1), 35-45
[Journal article]Authored by: Winter, D.
Fraser, CI., Winter, DJ., Spencer, HG., & Waters, JM. (2010). Multigene phylogeny of the southern bull-kelp genus Durvillaea (Phaeophyceae: Fucales). Molecular Phylogenetics and Evolution. 57(3), 1301-1311
[Journal article]Authored by: Winter, D.
Steens, MI., Winter, DJ., Morris, R., McCartney, J., & Greenslade, P. (2007). New Zealand's giant Collembola: New information on distribution and morphology for Holacanthella Börner, 1906 (Neanuridae: Uchidanurinae). New Zealand Journal of Zoology. 34(1), 63-78
[Journal article]Authored by: Winter, D.

Teaching and Supervision

Summary of Doctoral Supervision

Position Current Completed
Co-supervisor 1 0

Current Doctoral Supervision

Co-supervisor of:

  • Sidra Hussain - Doctor of Philosophy
    Evolution of Cytonuclear Coordination in Tragopogon (Asteraceae) Allopolyploids

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