Publications

1. Wolfsberger, W.W., K. Chhugani, K. Shchubelka, A. Frolova, Y. Salyha, O. Zlenko, O. V. Ivashchenko, M. Arych, D. Dziuba, A. Parkhomenko, V. Smolanka, S. Reinsone, Z. H. Gümüş, E. Sezgin, A. Diaz-Lameiro, M. Maci, E. Bortz, F. Kondrashov, P. Morton, P.P. Łabaj, V. Romero, J. Hlávka, S. Mangul, and T.K. Oleksyk. 2023. Scientists without Borders: Lessons from Ukraine. GigaScience 12: giad045 https://doi.org/10.1093/gigascience/giad045

2. Chhugani, K., Frolova, A., Salyha, Y., Fiscutean, A., Zlenko, A., Reinsone, S., Wolfsberger, W.W., Ivashchenko, O.V., Maci, M., Dziuba, D., Parkhomenko, A., Bortz, E., Kondrashov, F., Łabaj, P., Romero, V., Hlávka, J., Oleksyk, T.K. and S. Mangul. 2022. Remote opportunities for scholars in Ukraine. Science 378 (6626) 1285-1286. https://www.science.org/doi/10.1126/science.adg0797

3. Hains T., Pirro, S., O’Neill, K., Valez, J., Speed, N., Clubb, S., Oleksyk, T.K., Bates J., and S. Hackett . 2022. The Complete Genome Sequences of 94 Species of Parrots (Psittaciformes, Aves). Biodiversity Genomes, https://doi.org/10.56179/001c.40338

4. Majeske, A.J., Mercado-Capote, A.J., Komissarov, A., Bogdanova, A., Schizas, N.V., Castro-Márquez, S.O., Hilkert, K., Wolfsberger, W.W., and T. K. Oleksyk. 2022. The first complete mitochondrial genome of Diadema antillarum (Diadematoida, Diadematidae). GigaByte 1:gigabyte.73, https://doi.org/10.46471/gigabyte.73

5. Oleksyk, T.K., Wolfsberger, W.W., Shchubelka, K., Mangul, S and S.J. O’Brien. 2022. The Pioneer Advantage: Filling the Blank Spots On the Map of Genome Diversity in Europe. GigaScience, 11: giac081. https://doi.org/10.1093/gigascience/giac081

6. Díaz-Lameiro, A. M., C. I. Villamil, T. Gamble, B. J. Pinto, A. Herrera-Martínez, R. Thomas, J. M. Bernstein, J. E. Titus-McQuillan, S. V. Nielsen, E. Agosto-Torres, A. R. Puente-Rolón, F. J. Bird-Picó, T. K. Oleksyk, J. C. Martínez-Cruzado, and J. D. Daza. 2022. A New Species of Sphaerodactylus (Gekkota: Sphaerodactylidae) from the Northwest Limestone Region of Puerto Rico. Ichthyology & Herpetology, 110(3):449–465. https://doi.org/10.1643/h2020123

7. Wolfsberger, WW, FU Battistuzzi, and T.K. Oleksyk. 2022. Genomics of Adaptation and Speciation. Genes 13 (7), 1187 https://doi.org/10.3390/genes13071187

8. Shchubelka K., W.W. Wolfsberger, O.T. Oleksyk, and T.K. Oleksyk. 2022. Estimation of the frequency of genetic variants associated with vitamin d levels and osteoporosis in the population of Ukraine. Problems of Endocrine Pathology 79 (2), 53-59 https://doi.org/10.21856/j-PEP.2022.2.08

9. Wolfsberger, W.W, N.M. Ayala, A. Potapchuk, K. Schubelka, S. O. Castro-Marquez, V. Irizarry, L. Potish, A.J. Majeske, L. Figueroa Oliver, Alondra Diaz Lameiro , J. Carlos Martínez-Cruzado, G. Lindgren, and T. K Oleksyk. 2022. Genetic Diversity and Selection in Puerto Rican Horses. Scientific Reports Sci Rep. 12(1):515 https://doi.org/10.1038/s41598-021-04537-5

10. Totikov, A., A Tomarovsky, D Prokopov, A Yakupova, T Bulyonkova, T.K. Oleksyk and S. Kliver. 2021. Chromosome-level genome assemblies expand capabilities of genomics for conservation biology. Genes 12 (9), 1336 https://doi.org/10.3390/genes12091336

11. Oleksyk, T.K., W. W Wolfsberger, A. M Weber, K. Shchubelka, O. T Oleksyk, Olga Levchuk, A. Patrus, N. Lazar, S. O Castro-Marquez, Y. Hasynets, P. Boldyzhar, M. Neymet, A. Urbanovych, Viktoriya Stakhovska, K. Malyar, S. Chervyakova, O. Podoroha, N. Kovalchuk, J. L Rodriguez-Flores, W. Zhou, S. Medley, F. Battistuzzi, R. Liu, Y. Hou, S. Chen, H. Yang, M. Yeager, M. Dean, R. E Mills, V. Smolanka, 2021. Genome diversity in Ukraine, GigaScience, 10(1), giaa159 https://doi.org/10.1093/gigascience/giaa159

12. Kolchanova, S.; Komissarov, A.; Kliver, S.; Mazo-Vargas, A.; Afanador, Y.; Velez-Valentín, J.; de la Rosa, R.V.; Castro-Marquez, S.; Rivera-Colon, I.; Majeske, A.J.; Wolfsberger, W.W.; Hains, T.; Corvelo, A.; Martinez-Cruzado, J.-C.; Glenn, T.C.; Robinson, O.; Koepfli, K.-P.; and Oleksyk, T.K. 2021. Molecular Phylogeny and Evolution of Amazon Parrots in the Greater Antilles. Genes, 12, 608. https://doi.org/10.3390/genes12040608

13. Totikov, A.; Tomarovsky, A.; Prokopov, D.; Yakupova, A.; Bulyonkova, T.; Derezanin, L.; Rasskazov, D.; Wolfsberger, W.W.; Koepfli, K.-P.; Oleksyk, T.K.; and Kliver, S. 2021, Chromosome-Level Genome Assemblies Expand Capabilities of Genomics for Conservation Biology. Genes 12, 1336. https://doi.org/10.3390/genes12091336

14. Hains T, O’Neill K, Velez J, N. Speed, Susan Clubb, T. K. Oleksyk, Stacy Pirro. 2020. The complete genome sequences of 22 parrot species (Psittaciformes, Aves). F1000Research , 9:1318 https://doi.org/10.12688/f1000research.25560.1

15. Zhernakova, D.V., Brukhin, V., Malov, S. Oleksyk, T.K., Koepfli, K.P., Zhuk, A., Dobrynin, P., Kliver, S., Cherkasov, N., Tamazian, G., Rotkevich, M., Krasheninnikova, K., Evsyukov, I., Sidorov, S., Gorbunova, A., Chernyaeva, E., Shevchenko, A., Kolchanova, S., Komissarov, A., Simonov, S., Antonik, A., Logachev, A., Polev, D.E., Pavlova, O.A., Glotov, A.S., Ulantsev, V., Noskova, E., Davydova, T.K., Sivtseva, T.M., Limborska, S., Balanovsky, O., Osakovsky, V., Novozhilov, A., Puzyrev, V., and S.J. O’Brien. 2020. Genome-wide sequence analyses of ethnic populations across Russia. Genomics 112(1):442-458. https://doi.org/10.1016/j.ygeno.2019.03.007

16. Shchubelka, K.M., Oleksyk, O. T. Oleksyk T.K, and Y.S. Hasynets. 2019. Vitamin D in the genetic aspect the role in type 1 diabetes mellitus. Endokrynologia, 24(4), 367-372. https://doi.org/10.31793/1680-1466.2019.24-4.367

17. Kolchanova, K., Kliver, S., Komissarov, A., Dobrinin, P., Tamazian, G., Grigorev, K., Wolfsberger, W.W., Majeske, A.J., Velez-Valentın, J., Valentın de la Rosa, R., Paul-Murphy, J. R., Sanchez-Migallon Guzman D., Court , M.H., Rodriguez Flores, J.L., Martínez Cruzado, J.C. and T. K. Oleksyk. 2019. Genomes of three closely related Caribbean Amazons provide insight for species history and conservation. Genes 10(1), 54. https://doi.org/10.3390/genes10010054

18. Diaz-Zabala, H.J., Ortiz, Ana P., Garland, L., Jones, K., Perez, C.M., Mora, E., Arroyo, N., Oleksyk, T.K., Echenique, M., Matta, J. L., Dean, M., and J. Dutil. 2018. A recurrent BRCA2 mutation explains the majority of Hereditary Breast and Ovarian Cancer Syndrome cases in Puerto Rico. Cancers 10(11), 419. https://doi.org/10.3390/cancers10110419

19. Grigorev, K., Kliver, S., Dobrynin, P., Komissarov, A., Wolfsberger, W., Krasheninnikova, K., Yashira M Afanador-Hernández, Y.M., Paulino, L.A., Carreras, R., Rodríguez, L.E., Núñez, A., Silva, F., Hernández-Martich, D., Majeske, A.J, Antunes, A., Roca, A.L., O’Brien, S.J., Martinez-Cruzado, J.C., and T.K. Oleksyk. 2018. Innovative assembly strategy contributes to the understanding of evolution and conservation genetics of the critically endangered Solenodon paradoxus from the island of Hispaniola. GigaScience, 7(6):giy025. https://doi.org/10.1093/gigascience/giy025

20. Brandt A., K. Grigorev, Y.M. Afanador-Hernández, L.A. Paulino, W.J. Murphy, A. Núñez, A. Komissarov, J.R. Brandt, P. Dobrynin, J. D. Hernández-Martich, R. María, S.J. O’Brien, L.E. Rodríguez, J.C. Martínez-Cruzado, T.K. Oleksyk and A.L. Roca. 2016. Mitogenomic sequences support a north-south subspecies subdivision within Solenodon paradoxus. Mitochondrial DNA A, 20:1-9. https://doi.org/10.3109/24701394.2016.1167891

21. Cosme, S.; Cuevas, H.E.; Zhang, D.; Oleksyk, T.K., and B. Irish. 2016 .Genetic diversity of naturalized cacao (Theobroma cacao L.) in Puerto Rico. Tree Genetics & Genomes, 12:88 https://doi.org/10.1007/s11295-016-1045-4

22. Dobrynin, P., Liu, S., Tamazian. G., Xiong, Z., Yurchenko, A., Krasheninnikova, K., Kliver, S., Koepfli, K.P., Johnson, W., Kuderna, L., García-Pérez., L. de Manuel Montero, M., Godinez, R., Makunin, A., Komissarov, A., Brukhin, V., Qiu, W., Zhou, L., Li, F., Jian, J., Driscoll, C., Antunes, A., Oleksyk, T.K., Eizirik, E., Perelman, P., Roelke, M., Wildt, D., Diekhans, M., Marques-Bonet, T., Schmidt-Küntzel, A., Marker, L., Bhak, J., Wang, J., Zhang, G., and S.J. O’Brien. 2015. Genomic Legacy of the African Cheetah, Acinonyx jubatus. Genome Biology, 16 (1), 1-20 https://doi.org/10.1186/s13059-015-0837-4

23. Oleksyk T.K., Brukhin V, and O’Brien SJ. 2015. Putting Russia on the genome map. Science 350(6262), 747. https://doi.org/10.1126/science.350.6262.747-a

24. Oleksyk T.K., Brukhin V, and O’Brien SJ. 2015. The Genome Russia project: closing the largest remaining omission on the world Genome map. GigaScience 4:53 https://doi.org/10.1186/s13742-015-0095-0

25. The 1000 Genomes Project Consortium. 2015. A global reference for human genetic variation. Nature 526, 68–74 https://doi.org/10.1038/nature15393

26. Guiblet, W.M., Zhao, K., O’Brien, S.J., Massey S., Roca. A.L. and T.K. Oleksyk. 2015. SmileFinder: a resampling-based platform to evaluate signatures of selection from genome-wide sets of matching allele frequency data between populations. GigaScience 4:1 https://doi.org/10.1186/2047-217X-4-1

27. Limou, S., Nelson, G.W., Lecordier, L., An, P., O’hUigin, C.S., David, V.A., Binns-Roemer, E.A., Guiblet, W.M., Oleksyk, T.K., Pays, E., Kopp, J.B., and C. A Winkler. 2015. Sequencing rare and common APOL1 coding variants to determine kidney disease risk. Kidney International 88:754–763. https://doi.org/10.1038/ki.2015.151

28. Afanador, Y., Velez-Valentín, J. Valentín de la Rosa, R., Martínez-Cruzado, J.-C., vonHoldt, B., and T. K. Oleksyk. 2014. Isolation and characterization of microsatellite loci in the critically endangered Puerto Rican parrot (Amazona vittata). Conservation Genetics Resources. 6: 4, p. 885–889. https://doi.org/10.1007/s12686-014-0232-6

29. Svitin, A. Malov, S., Cherkasov, N., Dobrynin, P., Guan, L., Geerts, P., Troyer, J. Hendrickson-Lambert, S., Sezgin, E., Hutcheson Dilks, H., Carrington, M., Lautenberger, J., Oleksyk, TK., Goedert, J., Vlahov, D., Kirk, G., Buchbinder, S., Kingsley, L., Donfield, S., Gomperts, E., Jabs, DA., VanNatta, M., Harrigan, R. ,SOCA Research Group, HGDS, MHCS, SFCC, MACS, ALIVE, HOMER, and SJ. O’Brien. 2014. Gene Discovery and Data Sharing in Disease Association Analyses Across the Genome. GigaScience 3:18

30. Gravel, S., Zakharia, F., Byrnes, J.K., Muzzio, M., Moreno-Estrada, A. Rodriguez-Flores, A.L., Kenny, E.E., Gignoux, C.R., Maples, B.K., Guiblet, W.G., Dutil, J., Sandoval, K., Bedoya, G., The 1000 Genomes Project, Oleksyk, T.K., Ruiz-Linares, A., Burchard, E.G., Martinez-Cruzado, J.C., and Bustamante, CD. 2013. Reconstructing Native American Migrations from Whole-genome and Whole-exome Data. PLoS Genetics. 9(12) e1004023

31. Díaz-Lameiro AM, Oleksyk TK, Bird-Picó FJ, Martínez-Cruzado JC. 2013. Colonization of islands in the Mona Passage by endemic dwarf geckoes (genus Sphaerodactylus) reconstructed with mitochondrial phylogeny. Ecol Evol. 3(13):4488-500

32. Oleksyk TK, Pombert JF, Siu D, Mazo-Vargas A, Ramos B, Guiblet W, Afanador Y, Ruiz-Rodriguez CT, Nickerson ML, Logue D., Figueroa L., and Martinez-Cruzado, JC. 2012. A Locally Funded Puerto Rican Parrot (Amazona vittata) Genome Sequencing Project Increases Avian Data and Advances Young Researcher Education. GigaScience, 1:14

33. Zhao, K., Ishida, Y., Oleksyk, TK., Winkler CA, and Roca AL, 2012. Evidence for selection at HIV host susceptibility genes in a West Central African human population. BMC Evolutionary Biology 12:237

34. The 1000 Genomes Project Consortium. 2012. An integrated map of genetic variation from 1,092 human genomes. Nature 491:56-65

35. Majeske, A,M., Oleksyk, T.K., Smith C.L., 2012. The Sp185/333 immune response genes and proteins are expressed in cells dispersed within all major organs of the adult purple sea urchin. Innate Immunity 19(6):569-87

36. Ishida Y, Oleksyk TK, Georgiadis NJ, David VA, Zhao K, et al. 2011 Reconciling Apparent Conflicts between Mitochondrial and Nuclear Phylogenies in African Elephants. PLoS ONE 6(6): e20642

37. Oleksyk TK, O’Brien SJ and Smith MW. 2010. Scanning genomes for the footprints of historic selection. Phil Trans R Soc B 365:185-205

38. Genovese G, Friedman DJ, Ross MD, Lecordier L, Uzureau P, Freedman BI, Bowden DW, Langefeld CD, Oleksyk TK, Uscinski Knob AL, Bernhardy AJ, Hicks PJ, Nelson GW, Vanhollebeke B, Winkler CA, Kopp JB, Pays E, Pollak MR. 2010. Association of trypanolytic ApoL1 variants with kidney disease in African Americans. Science. 329(5993):841-5.

39. Oleksyk TK, Nelson GW, An P, Kopp JB and Winkler CA. 2010. Worldwide distribution of the MYH9 kidney disease susceptibility alleles and haplotypes: evidence of historical selection in Africa. PLoS One. 5(7):e11474

40. Winkler CA, Nelson G, Oleksyk TK, Nava MB, Kopp JB. 2010 Genetics of focal segmental glomerulosclerosis and human immunodeficiency virus-associated collapsing glomerulopathy: the role of MYH9 genetic variation. Seminars in Nephrology. 30(2):111-25

41. Via M, Gignoux CR, Roth L, Fejerman L, Galanter J, Choudhry S, Toro-Labrador G, Viera-Vera J, Oleksyk TK, Beckman K, Ziv E, Risch N, Burchard EG, and Martínez-Cruzado JC. 2010. Geography and history shape fine-scale genomic admixture patterns in the island of Puerto Rico . PLoS One. 2011 6(1):e16513.

42. Volfovsky N, Oleksyk TK, Cruz KC, Truelove AL, Stephens RM, and Smith MW. 2009. Chimpanzee chromosome 23 vs. human 22: genomic insertion, deletion and ancestral indel polymorphisms. BMC Genomics, 10 (51)

43. Oleksyk TK, Shrestha S, Truelove AL, O’Brien SJ, and Smith MW. 2009. Association of extended IL10 haplotypes with HIV progression to AIDS. Genes of Immunity 10(4):309-22

44. Oleksyk TK., Zhao K, O’Brien SJ, and Smith MW. 2008. Identifying selected regions from heterozygosity and divergence using a light-coverage genomic dataset from two human populations PLoS One, 3(3): e1712

45. Kopp JB., Smith MW, Johnson R, Freedman BI, Bowden DW, Oleksyk TK, McKenzie LM, Ahuja TS, Cho ME, Dart RA, Kimmel PL, Korbet SM, Michael DM, Mokryzcki MH, Schelling JR, Simon E, Trachtman H, Vlahov D, Hiroshi K, Nelson GW, and Winkler CA. 2008. Genome wide admixture mapping identifies MYH9 as a major effect risk gene for FSGS in African-Americans. Nature Genet, 40(10):1175-84

46. Truelove AL, Oleksyk TK, Shrestha S, Thio CL, Goedert JJ, Donfield SM, Thomas DL, O’Brien SJ, and Smith MW. 2008. Hepatitis B viral persistence is associated with polymorphisms in the IL10 and IL20 region. International Journal of Immunogenetics, 35(3):255-64

47. Purdue, J. R., Oleksyk, T.K. and M. H. Smith. 2006. Independent occurrences of multiple repeats in the control region of mitochondrial DNA of white-tailed deer. Journal of Heredity, 97(3): 235-243, 2006

48. Tsyusko, O.V., Michael H. Smith, T. K. Oleksyk, Julia Goryanaya, and Travis C. Glenn. 2006. Radiation effects of the Chornobyl accident on the genetics of cattails. Molecular Ecology, 15(9): 2611-2625

49. Shrestha, S., S.A Strathdee, N. Galai, T.K. Oleksyk, D. Fallin, D. Schaid, D. Vlahov, D. Thomas, S. J. O’Brien, and M.W. Smith. 2006. Behavioral Risk Exposure and Host Genetics of Susceptibility to HIV-1 Infection. Journal of Infectious Diseases, 193:16-26

50. Oleksyk, T. K, C. L. Thio, A.L. Truelove, J.J. Goedert, S.M. Donfield, G.D. Kirk, D.L. Thomas, S.J. O’Brien, and M.W. Smith. 2005. Single nucleotide polymorphisms and haplotypes in the IL10 region associated with HCV clearance. Genes and Immunity, 6(4):347-57

51. Oleksyk, TK, Thio CL, Truelove AL, Goedert JJ, Donfield SM, Kirk GD, Thomas DL, O’Brien SJ, and Smith MW. 2005. Single nucleotide polymorphisms and haplotypes in the IL10 region associated with HCV clearance. Genes and Immunity, 6(4):347-57

52. Oleksyk TK, Goldfarb LG, Shrestha S, O’Brien SJ, and Smith MW. 2004. Associations of the inflammatory gene polymorphisms and the Viliuisk Encephalomyelitis syndrome. European Journal of Immunogenetics, 31:121-128

53. Oleksyk, T.K., L.G. Goldfarb, S. Shrestha, S.J. O’Brien, and M.W. Smith. 2004 Associations of the inflammatory gene polymorphisms and the Viliuisk Encephalomyelitis syndrome. European Journal of Immunogenetics, 31:121-128

54. Oleksyk, T.K., M.H. Smith, J.M. Novak, J.R. Purdue, and S.P. Gashchak. 2004. High levels of fluctuating asymmetry in populations of Apodemus flavicollis from the most contaminated areas in Chornobyl. Journal of Environmental Radioactivity, 73:1-20

55. Oleksyk, T.K., F.B. Golley, O.S. Sydor, R. Kish, M.H. Smith and S. Shevera. 2003. Eugene Odum: Nature has answers to the questions we ask [In Ukrainian]. Visnyk Nacionalnoi Akademii Nauk Ukrainy (Herald of the Ukrainian National Academy of Sciences), 6: 61-65

56. Smith, M.H., T. K. Oleksyk, and O. Tsyusko-Omeltchenko. 2003. Effect of trophic level on the radiocesium frequency distribution in aquatic and terrestrial ecosystems at Chornobyl and nuclear sites in the United States. In: Proceedings of the International Symposium: Transfer of Radionuclides in Biosphere – Prediction and Assessment. Mito Japan December 18-19, 2002. Japanese Atomic Energy Research Institute. Amano, H. and S. Uchida (eds.). pp. 37-48

57. Oleksyk, T.K., M.H. Smith, T.G. Glenn, J.R. Purdue, C.H. Jagoe, and M.W. Smith. 2002. Radioactivity and genetic diversity in populations of Apodemus flavicollis from Chornobyl, Ukraine. In: International Conference on Radioactivity in the Environment. Eds. P. Borretzen, T. Jolle and P. Strand. Monaco: The International Union of Radioecology (IUR), in association with the Norwegian Radiation Protection Authority (NRPA), and the Journal of Environmental Radioactivity (JER), and in co-operation with the International Atomic Energy Agency (IAEA), pp. 167-171, 2002

58. Oleksyk, T.K., S.P. Gaschak, T.C. Glenn, C.H. Jagoe, J.D. Peles, J.R. Purdue, O.V. Tsyusko, O.O. Zalissky, and M.H. Smith. 2002. Frequency distributions of 137Cs in fish and mammal populations. Journal of Environmental Radioactivity 61:55-74

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