Alex Gavryushkin, Our people, Department of Computer Science, University of Otago, New Zealand

Alex_226

Owheo Building, Room 244
Phone: +64 3 479 8494
Email: alex@biods.org

I joined the Department in 2018 as Rutherford Discovery Fellow. Prior to that I completed postdoctoral fellowships at ETH Zurich and the University of Auckland. I graduated from Novosibirsk University in 2009 with a PhD in Mathematics.

Currently I am leading the Biological Data Science lab here at Otago. We develop mathematical and computational methods for genomic data analysis, in close collaboration with our colleagues at the Division of Health Sciences.

Further information about the lab, including publications, projects, and open positions, can be found on the bioDS lab @Otago website.

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Publications

Gould, A. L., Zhang, V., Lamberti, L., Jones, E. W., Obadia, B., Korasidis, N., Gavryushkin, A., … Ludington, W. B. (2018). Microbiome interactions shape host fitness. PNAS, 115(51), E11951-E11960. doi: 10.1073/pnas.1809349115

Lienkaemper, C., Lamberti, L., Drain, J., Beerenwinkel, N., & Gavryushkin, A. (2018). The geometry of partial fitness orders and an efficient method for detecting genetic interactions. Journal of Mathematical Biology, 77, 951-970. doi: 10.1007/s00285-018-1237-7

Gavryushkin, A., Whidden, C., & Matsen IV, F. A. (2018). The combinatorics of discrete time-trees: Theory and open problems. Journal of Mathematical Biology, 76(5), 1101-1121. doi: 10.1007/s00285-017-1167-9

Robb, T., Blenkiron, C., Tsai, P., Parker, K., Drummond, A., Black, M., Gavryushkin, A., … Print, C. (2018). Investigating tumour evolution in a single patient with disseminated cancer. Annals of Oncology, 29(Suppl. 9), (pp. ix156). doi: 10.1093/annonc/mdy425.018

Crona, K., Gavryushkin, A., Greene, D., & Beerenwinkel, N. (2017). Inferring genetic interactions from comparative fitness data. eLIFE, 6, e28629. doi: 10.7554/eLife.28629

Journal - Research Article

Conference Contribution - Published proceedings: Abstract

Crona, K., Gavryushkin, A., Greene, D., & Beerenwinkel, N. (2017). Inferring genetic interactions from comparative fitness data. eLIFE, 6, e28629. doi: 10.7554/eLife.28629

Journal - Research Article

Gavryushkin, A., & Drummond, A. J. (2016). The space of ultrametric phylogenetic trees. Journal of Theoretical Biology, 403, 197-208. doi: 10.1016/j.jtbi.2016.05.001

Journal - Research Article

Robb, T., Blenkiron, C., Tsai, P., Parker, K., Drummond, A., Black, M., Gavryushkin, A., … Print, C. (2018). Investigating tumour evolution in a single patient with disseminated cancer. Proceedings of the New Zealand Society for Oncology (NZSO) Conference. Retrieved from http://www.nzsoncology.org.nz/

Conference Contribution - Published proceedings: Abstract

Zeidler, C., Weber, G., Gavryushkin, A., & Lutteroth, C. (2017). Tiling algebra for constraint-based layout editing. Journal of Logical & Algebraic Methods in Programming, 89, 67-94. doi: 10.1016/j.jlamp.2017.01.004

Journal - Research Article

Gavryushkin, P. N., Popov, Z. I., Litasov, K. D., Belonoshko, A. B., & Gavryushkin, A. (2016). Stability of B2-type FeS at Earth's inner core pressures. Geophysical Research Letters, 43(16), 8435-8440. doi: 10.1002/2016gl069374

Journal - Research Article

Gavryushkin, A., Khoussainov, B., Kokho, M., & Liu, J. (2016). Dynamic algorithms for multimachine interval scheduling through analysis of idle intervals. Algorithmica, 76(4), 1160-1180. doi: 10.1007/s00453-016-0148-5

Journal - Research Article

Gavryushkin, A., Khoussainov, B., & Stephan, F. (2016). Reducibilities among equivalence relations induced by recursively enumerable structures. Theoretical Computer Science, 612, 137-152. doi: 10.1016/j.tcs.2015.11.042

Journal - Research Article

Gavryushkin, P. N., Behtenova, A., Popov, Z. I., Bakakin, V. V., Likhacheva, A. Y., Litasov, K. D., & Gavryushkin, A. (2016). Toward analysis of structural changes common for alkaline carbonates and binary compounds: Prediction of high-pressure structures of Li₂CO₃, Na₂CO₃, and K₂CO₃. Crystal Growth & Design, 16(10), 5612-5617. doi: 10.1021/acs.cgd.5b01793

Journal - Research Article

Stadler, T., Vaughan, T. G., Gavryushkin, A., Guindon, S., Kühnert, D., Leventhal, G. E., & Drummond, A. J. (2015). How well can the exponential-growth coalescent approximate constant-rate birth–death population dynamics? Proceedings of the Royal Society B, 282(1806), 20150420. doi: 10.1098/rspb.2015.0420

Journal - Research Article

Gavruskin, A., Khoussainov, B., Kokho, M., & Liu, J. (2015). Dynamic algorithms for monotonic interval scheduling problem. Theoretical Computer Science, 562, 227-242. doi: 10.1016/j.tcs.2014.09.046

Journal - Research Article

Gavryushkin, P. N., Popov, Z. I., Litasov, K. D., & Gavryushkin, A. (2015). Unbiased crystal structure prediction of NiSi under high pressure [Short communication]. Journal of Applied Crystallography, 48(Part 3), 906-908. doi: 10.1107/s1600576715005488

Journal - Research Other

Gavryushkin, A. (2015). Decidable models of small theories. Lobachevskii Journal of Mathematics, 36(4), 446-449. doi: 10.1134/s1995080215040198

Journal - Research Article

Gavruskin, A., Khoussainov, B., Kokho, M., & Liu, J. (2014). Dynamic interval scheduling for multiple machines. In H.-K. Ahn & C.-S. Shin (Eds.), Algorithms and computation: Lecture notes in computer science (Vol. 8889). (pp. 235-246). Cham, Switzerland: Springer. doi: 10.1007/978-3-319-13075-0_19

Conference Contribution - Published proceedings: Full paper

Gavruskin, A., Jain, S., Khoussainov, B., & Stephan, F. (2014). Graphs realised by r.e. equivalence relations. Annals of Pure & Applied Logic, 165(7-8), 1263-1290. doi: 10.1016/j.apal.2014.04.001

Journal - Research Article

Gavruskin, A., & Nies, A. (2014). Universality for left-computably enumerable metric spaces. Lobachevskii Journal of Mathematics, 35(4), 292-294. doi: 10.1134/S1995080214040179

Journal - Research Article

Gavruskin, A., Khoussainov, B., Kokho, M., & Liu, J. (2013). Dynamising interval scheduling: The monotonic case. In T. Lecroq & L. Mouchard (Eds.), Combinatorial algorithms: Lecture notes in computer science (Vol. 8288). (pp. 178-191). Cham, Switzerland: Springer. doi: 10.1007/978-3-642-45278-9_16

Conference Contribution - Published proceedings: Full paper

Gavruskin, A., & Khoussainov, B. (2013). On decidable and computable models of theories. In P. Bonizzoni, V. Brattka & B. Löwe (Eds.), The nature of computation: Logic, algorithms, applications; Lecture notes in computer science (Vol. 7921). (pp. 200-209). Berlin, Germany: Springer. doi: 10.1007/978-3-642-39053-1_23

Conference Contribution - Published proceedings: Full paper

Gavryushkin, A. N. (2007). Spectra of computable models for Ehrenfeucht theories. Algebra & Logic, 46(3), 149-157. doi: 10.1007/s10469-007-0014-2

Journal - Research Other

Gavryushkin, A. N. (2006). Complexity of Ehrenfeucht models. Algebra & Logic, 45(5), 289-295. doi: 10.1007/s10469-006-0027-2

Journal - Research Other

More publications...

Alex Gavryushkin - Senior Lecturer

Publications