Research/Scholarly/Creative Works

• Moravec JC., Lanfear R., Spector DL., Diermeier SD. and Gavryushkin A. (2023) Testing for Phylogenetic Signal in Single-Cell RNA-Seq Data. Journal of Computational Biology 30(4): 518-537. http://dx.doi.org/10.1089/cmb.2022.0357. (Journal Articles)

• Chen K., Moravec JC., Gavryushkin A., Welch D. and Drummond AJ. (2022) Accounting for Errors in Data Improves Divergence Time Estimates in Single-cell Cancer Evolution. Molecular Biology and Evolution 39(8) http://dx.doi.org/10.1093/molbev/msac143. (Journal Articles)

• Elmes K., Heywood A., Huang Z. and Gavryushkin A. (2022) A fast lasso-based method for inferring higher-order interactions. PLoS Computational Biology 18(12) http://dx.doi.org/10.1371/journal.pcbi.1010730. (Journal Articles)

• Gardner PP., Paterson JM., McGimpsey S., Ashari-Ghomi F., Umu SU., Pawlik A., Gavryushkin A. and Black MA. (2022) Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software. Genome Biology 23(1) http://dx.doi.org/10.1186/s13059-022-02625-x. (Journal Articles)

• Powell RM., Pattison S., Moravec JC., Bhat B., Guirguis N., Markie D., Jones GT., Copedo J., Print CG. and Morison IM. (2022) Tuberous sclerosis complex: a complex case. Cold Spring Harbor Molecular Case Studies 8(3) http://dx.doi.org/10.1101/mcs.a006182. (Journal Articles)

• Collienne L. and Gavryushkin A. (2021) Computing nearest neighbour interchange distances between ranked phylogenetic trees. Journal of Mathematical Biology 82(1-2) http://dx.doi.org/10.1007/s00285-021-01567-5. (Journal Articles)

• Collienne L., Elmes K., Fischer M., Bryant D. and Gavryushkin A. (2021) Discrete coalescent trees. Journal of Mathematical Biology 83(5) http://dx.doi.org/10.1007/s00285-021-01685-0. (Journal Articles)

• Collienne L., Elmes K., Fischer M., Bryant D. and Gavryushkin A. (2021) The Geometry of the space of Discrete Coalescent Trees. . (Journal Articles)

• Elmes K., Heywood A., Huang Z. and Gavryushkin A. (2021) A Fast Lasso-Based Method for Inferring Pairwise Interactions. http://dx.doi.org/10.1101/2021.01.28.428698. (Journal Articles)

• Elmes K., Schmich F., Szczurek E., Jenkins J., Beerenwinkel N. and Gavryushkin A. (2021) Learning epistatic gene interactions from perturbation screens. PLoS ONE 16(7 July) http://dx.doi.org/10.1371/journal.pone.0254491. (Journal Articles)

• Moravec J., Lanfear R., Spector D., Diermeier S. and Gavryushkin A. (2021) Testing for phylogenetic signal in single-cell RNA-seq data. http://dx.doi.org/10.1101/2021.01.07.425804. (Journal Articles)

• Elmes K., Schmich F., Szczurek E., Jenkins J., Beerenwinkel N. and Gavryushkin A. (2020) Learning epistatic gene interactions from perturbation screens. http://dx.doi.org/10.1101/2020.08.24.264713. (Journal Articles)

• Collienne L., Elmes K., Fischer M., Bryant D. and Gavryushkin A. (2019) Geometry of Ranked Nearest Neighbour Interchange Space of Phylogenetic Trees. http://dx.doi.org/10.1101/2019.12.19.883603. (Journal Articles)

• Gavryushkin A., Whidden C. and Matsen FA. (2018) The combinatorics of discrete time-trees: theory and open problems. Journal of Mathematical Biology 76(5): 1101-1121. http://dx.doi.org/10.1007/s00285-017-1167-9. (Journal Articles)

• Gould AL., Zhang V., Lamberti L., Jones EW., Obadia B., Korasidis N., Gavryushkin A., Carlson JM., Beerenwinkel N. and Ludington WB. (2018) Microbiome interactions shape host fitness. Proceedings of the National Academy of Sciences of the United States of America 115(51): E11951-E11960. http://dx.doi.org/10.1073/pnas.1809349115. (Journal Articles)

• Lienkaemper C., Lamberti L., Drain J., Beerenwinkel N. and Gavryushkin A. (2018) The geometry of partial fitness orders and an efficient method for detecting genetic interactions. Journal of Mathematical Biology 77(4): 951-970. http://dx.doi.org/10.1007/s00285-018-1237-7. (Journal Articles)

• Ludington W., Beerenwinkel N., Carlson J., Gavryushkin A., Korasidis N., Obadia B., Jones E., Lamberti L., Zhang V. and Gould A. (2018) Microbiome interactions shape host fitness. Nextjournal http://dx.doi.org/10.33016/nextjournal.csi.kv6mmq6tbda4eelcehkxs. (Journal Articles)

• Crona K., Gavryushkin A., Greene D. and Beerenwinkel N. (2017) Inferring Genetic Interactions From Comparative Fitness Data. http://dx.doi.org/10.1101/137372. (Journal Articles)

• Crona K., Gavryushkin A., Greene D. and Beerenwinkel N. (2017) Inferring genetic interactions from comparative fitness data. eLife 6 http://dx.doi.org/10.7554/eLife.28629. (Journal Articles)

• Gould A., Zhang V., Lamberti L., Jones E., Obadia B., Gavryushkin A., Korasidis N., Carlson J., Beerenwinkel N. and Ludington W. (2017) High-dimensional microbiome interactions shape host fitness. http://dx.doi.org/10.1101/232959. (Journal Articles)

• Lienkaemper C., Lamberti L., Drain J., Beerenwinkel N. and Gavryushkin A. (2017) The Geometry of Partial Fitness Orders and an Efficient Method for Detecting Genetic Interactions. http://dx.doi.org/10.1101/180976. (Journal Articles)

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

• Gardner P., Paterson J., McGimpsey S., Ashari-Ghomi F., Ashari-Ghomi F., Umu S., Pawlik A., Gavryushkin A. and Black M. (2016) Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software. http://dx.doi.org/10.1101/092205. (Journal Articles)

• Gavryushkin A. (2016) THE SPACE OF SAMPLED ANCESTOR TREES. In Geological Society of America Abstracts with Programs Geological Society of America. http://dx.doi.org/10.1130/abs/2016am-278339. (Conference Contributions - Published)

• Gavryushkin A. and Drummond AJ. (2016) The space of ultrametric phylogenetic trees. Journal of Theoretical Biology 403: 197-208. http://dx.doi.org/10.1016/j.jtbi.2016.05.001. (Journal Articles)

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

• Gavryushkin A., Khoussainov B., Kokho M. and Liu J. (2016) Dynamic Algorithms for Multimachine Interval Scheduling Through Analysis of Idle Intervals. Algorithmica 76(4): 1160-1180. http://dx.doi.org/10.1007/s00453-016-0148-5. (Journal Articles)

• Gavryushkin A., Whidden C. and Matsen F. (2016) The combinatorics of discrete time-trees: theory and open problems. http://dx.doi.org/10.1101/063362. (Journal Articles)

• Gavryushkin PN., Behtenova A., Popov ZI., Bakakin VV., Likhacheva AY., Litasov KD. and 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 and Design 16(10): 5612-5617. http://dx.doi.org/10.1021/acs.cgd.5b01793. (Journal Articles)

• Gavryushkin PN., Popov ZI., Litasov KD., Belonoshko AB. and Gavryushkin A. (2016) Stability of B2-type FeS at Earth's inner core pressures. Geophysical Research Letters 43(16): 8435-8440. http://dx.doi.org/10.1002/2016GL069374. (Journal Articles)

• Gavruskin A., Khoussainov B., Kokho M. and Liu J. (2015) Dynamic algorithms for monotonic interval scheduling problem. Theoretical Computer Science 562(C): 227-242. http://dx.doi.org/10.1016/j.tcs.2014.09.046. (Journal Articles)

• Gavryushkin A. (2015) Decidable models of small theories. Lobachevskii Journal of Mathematics 36(4): 446-449. http://dx.doi.org/10.1134/S1995080215040198. (Journal Articles)

• Gavryushkin PN., Likhacheva AY., Popov ZI., Bakakin VV., Litasov KD., Shatskiy AF., Ancharov AI. and Gavryushkin A. (2015) Potassium carbonate under pressure: common structural trend for alkaline carbonates and binary compounds. . (Journal Articles)

• Gavryushkin PN., Popov ZI., Litasov KD. and Gavryushkin A. (2015) Unbiased crystal structure prediction of NiSi under high pressure. Journal of Applied Crystallography 48: 906-908. http://dx.doi.org/10.1107/S1600576715005488. (Journal Articles)

• Gavryushkin PN., Popov ZI., Litasov KD. and Gavryushkin AN. (2015) Unbiased crystal structure prediction of NiSi under high pressure. Journal of Applied Crystallography 48: 3. (Journal Articles)

• Stadler T., Vaughan TG., Gavryushkin A., Guindon S., Kühnert D., Leventhal GE. and Drummond AJ. (2015) How well can the exponential-growth coalescent approximate constant-rate birth–death population dynamics? Proceedings of the Royal Society B: Biological Sciences 282(1806) http://dx.doi.org/10.1098/rspb.2015.0420. (Journal Articles)

• Gavruskin A. and Nies A. (2014) Universality for left-computably enumerable metric spaces. Lobachevskii Journal of Mathematics 35(4): 292-294. http://dx.doi.org/10.1134/S1995080214040179. (Journal Articles)

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

• Khoussainov B., Gavruskin A., Kokho M. and Liu J. (2014) Dynamic interval scheduling for multiple machines. : 235-246. http://dx.doi.org/10.1007/978-3-319-13075-0_19. (Chapters)

• Gavruskin A. and Khoussainov B. (2013) On decidable and computable models of theories. : 200-209. http://dx.doi.org/10.1007/978-3-642-39053-1_23. (Chapters)

• Gavruskin A., Khoussainov B., Kokho M. and Liu J. (2013) Dynamising interval scheduling: The monotonic case. : 178-191. http://dx.doi.org/10.1007/978-3-642-45278-9_16. (Chapters)

• Gavryushkin A. (2012) On constructive models of theories with linear Rudin-Keisler ordering. Journal of Logic and Computation 22(4): 793-805. http://dx.doi.org/10.1093/logcom/exq043. (Journal Articles)

• Gavryushkin AN. (2007) Spectra of computable models for Ehrenfeucht theories. Algebra and Logic 46(3): 149-157. http://dx.doi.org/10.1007/s10469-007-0014-2. (Journal Articles)

• Gavryushkin AN. (2006) Complexity of Ehrenfeucht models. Algebra and Logic 45(5): 289-295. http://dx.doi.org/10.1007/s10469-006-0027-2. (Journal Articles)