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David Winter

Evolution, computational biology and genomics

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Authors marked with asterisks contributed equally to the given paper.


  • Winter,D.J. et al. (In review PLOS Genetics) Repeat elements organize 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae. 10.1101/339010



  • Winter, D.J., Wu, S.H., Howell, A.A., Azevedo, R.B.R, Zufall, R.A, and Cartwrightt, R.A. (2018) accuMUlate: A mutation caller designed for mutation accumulation experiments Bioinformatics. 10.1093/bioinformatics/bty165


  • Winter, D.J. (2017) rentrez: An R package for the NCBI eUtils API The R Journal. 9:520—526 https://journal.r-project.org/archive/2017/RJ-2017-058/
  • Wu, S.H., Schwartz, R.S., Winter, D.J., Conrad, D.F., and Cartwright, R.A. (2017) Estimating error models for whole genome sequencing using mixtures of Dirichlet-multinomial distributions Bioinformatics. 33:2322—2329 10.1093/bioinformatics/btx133
  • Wallis, G.P., Cameron-Christie, S.R., Kennedy, H.L., Palmer, G., Sanders, T.R. and Winter, D.J. (2017) Interspecific hybridization causes long-term phylogenetic discordance between nuclear and mitochondrial genomes in freshwater fishes Molecular Ecology. 26:3116—3127 10.1111/mec.14096


  • Long, Hongan*., Winter, D.J.*, Chang, A.Y-C., Sung, W., Wu, S.H., Balboa, M., Azevedo, R.B.R., Cartwright, R.A., Lynch, M. and Zufall, R.A. (2016) Low Base-Substitution Mutation Rate in the Germline Genome of the Ciliate Tetrahymena thermophila Genome biology and evolution. 8:3629—3639 10.1093/gbe/evw223
  • Michonneau, F., Brown, J.W. and Winter, D.J. (2016) rotl: an R package to interact with the Open Tree of Life data Methods in Ecology and Evolution. 7:1476—1481 10.1111/2041-210X.12593
  • Smith, A.M., Clark, D.E., Lamare, M.D., Winter, David J. and Byrne, M. (2016) Risk and resilience: variations in magnesium in echinoid skeletal calcite Marine Ecology Progress Series. 561:1—16 10.3354/meps1190
  • Smith, AM., Key M.M., Henderson, Z.E., Davis, V.C., Winter, D.J. (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. 86:1425—1433 10.2110/jsr.2016.8


  • Winter,D.J., Pacheco, M.A., Vallejo, A.F.A, Schwartz, R.S., Arevalo-Herrera, M. Socrates, H., Cartwright, R.A. and Escalante, AE. (2015) Whole genome sequencing of field isolates reveals extensive genetic diversity in Plasmodium vivax from Colombia. PLOS Neglected Tropical Diseases. 9:e0004252 10.1371/journal.pntd.0004252
  • Donald, K.M., Winter, D.J., Ashcroft, A., and Spencer, H.G. (2015) Phylogeography of the whelk Cominella (Gastropoda, Buccinidae) suggests long-distance counter-current dispersal of a direct developer. Biological Journal of the Linnean Society. 114:315—332 10.1111/bij.12529


  • Bryne, M., Lamare, M., Winter, D.J., Dworjanyn, S.A., and Uthicke, S. (2013) Stunting effect of high CO 2 ocean on calcification and development in sea urchin larvae, a syn-thesis from tropics to the poles. Philosophical Transactions of the Royal Society B. 368 10.1098/rstb.2012.0439
  • Smith, A.M., Berman, J., Key, M.M. and Winter, D.J. (2013) Not all sponges will thrive in a high-CO2 ocean: Review of the mineralogy of calcifying sponges. Paleogeography, Paleo- climatology, Paleoecology. 392:463—472 10.1016/j.palaeo.2013.10.004


  • Smith, M., Riedi, M.A., and Winter, D.J. (2013.) Temperate reefs in a changing ocean: skeletal carbonate mineralogy of serpulids Marine Biology. 9:2281—2294 10.1007/s00227-013-2210-z


  • Smith, A.M., Sutherland, J.E., Kregting L., Farr, T.J., Winter, D.J. (2012) Phylomineralogy of the Coralline red algae: correlation of skeletal mineralogy with molecular phylogeny. Phytochemistry. 81:97-108 10.1016/j.phytochem.2012.06.003
  • Winter D.J. (2012) mmod : an R library for the calculation of population differentiation statistics. Molecular Ecology Resources.. 12 10.1111/j.1755-0998.2012.03174.x
  • Donald, K.M., Preston J., Williams, S.T., Reid, D.G., Winter, D.J., Alvarez, R., Buge, B., Hawkins S., Templado, J. and Spencer, H.G. (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. 62:35-45 10.1016/j.ympev.2011.09.002


  • Fraser, C.I., Winter, D.J., Spencer, H.G. and Waters, J.M. (2010) Molecular phylogeny of the southern bull-kelp genus Durvillaea (Phaeophyceae: Fucales). Molecular Phylogenetics and Evolution. 57:1301-11 10.1016/j.ympev.2010.10.011


  • Stevens, M. I., Winter, D. J., Morris, R., McCartney, J., & Greenslade, P. (2007) New Zealand’s giant Collembola: new information on distribution and morphology for Holacanthella Borner, 1906 (Neanuridae : Uchidanurinae) New Zealand Journal of Zoology. 34:63-78 10.1080/03014220709510065