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Alex Gavryushkin - Senior Lecturer

Alex_226

Owheo Building, Room 244
Phone: +64 3 479 8494
Email: alex@cs.otago.ac.nz

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 BDS @Otago website.

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Publications

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. Advance online publication. doi: 10.1007/s00285-018-1237-7

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

Gavryushkin, A., Whidden, C., & Matsen IV, F. A. (2017). The combinatorics of discrete time-trees: Theory and open problems. Journal of Mathematical Biology. Advance online publication. doi: 10.1007/s00285-017-1167-9

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

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

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. Advance online publication. doi: 10.1007/s00285-018-1237-7

Gavryushkin, A., Whidden, C., & Matsen IV, F. A. (2017). The combinatorics of discrete time-trees: Theory and open problems. Journal of Mathematical Biology. Advance online publication. doi: 10.1007/s00285-017-1167-9

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

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

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

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

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

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

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

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

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 of London: Series B, 282(1806), 20150420. doi: 10.1098/rspb.2015.0420

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

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

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

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Journal - Research Other

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

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Conference Contribution - Published proceedings: Full paper

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

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

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