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Kateryna Dmytrivna Makova, PhD

Kateryna Dmytrivna Makova, PhD

Francis R. and Helen M. Pentz Professor, Biology
Scientific Program:Cancer Control
Disease Teams:
Institute for CyberScience (ICS) - Associate
KDM16@psu.edu

Research Interests

  • Genome
  • Genes
  • Mutation
  • Human Genome
  • DNA
  • Microsatellite Repeats
  • Mitochondrial DNA
  • Population
  • Mutation Rate
  • Primates
  • Chromosomes
  • Pan troglodytes

Recent Publications

2024

Lahnsteiner, A, Craig, SJC, Kamali, K, Weissensteiner, B, McGrath, B, Risch, A & Makova, KD 2024, In vivo detection of DNA secondary structures using permanganate/S1 footprinting with direct adapter ligation and sequencing (PDAL-Seq). in G4 and i-motif biology. Methods in Enzymology, vol. 695, Academic Press Inc., pp. 159-191. https://doi.org/10.1016/bs.mie.2023.12.003
Lariviere, D, Craig, SJC, Paul, IM, Hohman, EE, Savage, JS, Wright, RO, Chiaromonte, F, Makova, KD & Reimherr, ML 2024, 'Methylation profiles at birth linked to early childhood obesity', Journal of Developmental Origins of Health and Disease, vol. 15, e7. https://doi.org/10.1017/S2040174424000060

2023

Weissensteiner, MH, Cremona, MA, Guiblet, WM, Stoler, N, Harris, RS, Cechova, M, Eckert, KA, Chiaromonte, F, Huang, YF & Makova, KD 2023, 'Accurate sequencing of DNA motifs able to form alternative (non-B) structures', Genome research, vol. 33, no. 6, pp. 907-923. https://doi.org/10.1101/gr.277490.122
Makova, KD & Weissensteiner, MH 2023, 'Noncanonical DNA structures are drivers of genome evolution', Trends in Genetics, vol. 39, no. 2, pp. 109-124. https://doi.org/10.1016/j.tig.2022.11.005
Rhie, A, Nurk, S, Cechova, M, Hoyt, SJ, Taylor, DJ, Altemose, N, Hook, PW, Koren, S, Rautiainen, M, Alexandrov, IA, Allen, J, Asri, M, Bzikadze, AV, Chen, NC, Chin, CS, Diekhans, M, Flicek, P, Formenti, G, Fungtammasan, A, Garcia Giron, C, Garrison, E, Gershman, A, Gerton, JL, Grady, PGS, Guarracino, A, Haggerty, L, Halabian, R, Hansen, NF, Harris, R, Hartley, GA, Harvey, WT, Haukness, M, Heinz, J, Hourlier, T, Hubley, RM, Hunt, SE, Hwang, S, Jain, M, Kesharwani, RK, Lewis, AP, Li, H, Logsdon, GA, Lucas, JK, Makalowski, W, Markovic, C, Martin, FJ, Mc Cartney, AM, McCoy, RC, McDaniel, J, McNulty, BM, Medvedev, P, Mikheenko, A, Munson, KM, Murphy, TD, Olsen, HE, Olson, ND, Paulin, LF, Porubsky, D, Potapova, T, Ryabov, F, Salzberg, SL, Sauria, MEG, Sedlazeck, FJ, Shafin, K, Shepelev, VA, Shumate, A, Storer, JM, Surapaneni, L, Taravella Oill, AM, Thibaud-Nissen, F, Timp, W, Tomaszkiewicz, M, Vollger, MR, Walenz, BP, Watwood, AC, Weissensteiner, MH, Wenger, AM, Wilson, MA, Zarate, S, Zhu, Y, Zook, JM, Eichler, EE, O’Neill, RJ, Schatz, MC, Miga, KH, Makova, KD & Phillippy, AM 2023, 'The complete sequence of a human Y chromosome', Nature, vol. 621, no. 7978, pp. 344-354. https://doi.org/10.1038/s41586-023-06457-y
Tomaszkiewicz, M, Sahlin, K, Medvedev, P & Makova, KD 2023, 'Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes', Genome biology and evolution, vol. 15, no. 11, evad205. https://doi.org/10.1093/gbe/evad205
Escalona, M, Vancampen, J, Maurer, NW, Haukness, M, Okhovat, M, Harris, RS, Watwood, A, Hartley, GA, O'neill, RJ, Medvedev, P, Makova, KD, Vollmers, C, Carbone, L & Green, RE 2023, 'Whole-genome sequence and assembly of the Javan gibbon (Hylobates moloch)', Journal of Heredity, vol. 114, no. 1, pp. 35-43. https://doi.org/10.1093/jhered/esac043

2022

Arbeithuber, B, Cremona, MA, Hester, J, Barrett, A, Higgins, B, Anthony, K, Chiaromonte, F, Diaz, FJ & Makova, KD 2022, 'Advanced age increases frequencies of de novo mitochondrial mutations in macaque oocytes and somatic tissues', Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 15, e2118740119. https://doi.org/10.1073/pnas.2118740119
Torres-Gonzalez, E & Makova, KD 2022, 'Exploring the Effects of Mitonuclear Interactions on Mitochondrial DNA Gene Expression in Humans', Frontiers in Genetics, vol. 13, 797129. https://doi.org/10.3389/fgene.2022.797129
Savage, JS, Hochgraf, AK, Loken, E, Marini, ME, Craig, SJC, Makova, KD, Birch, LL & Paul, IM 2022, 'INSIGHT responsive parenting educational intervention for firstborns is associated with growth of second-born siblings', Obesity, vol. 30, no. 1, pp. 183-190. https://doi.org/10.1002/oby.23301
Stein, ME, Hile, SE, Weissensteiner, MH, Lee, M, Zhang, S, Kejnovský, E, Kejnovská, I, Makova, KD & Eckert, KA 2022, 'Variation in G-quadruplex sequence and topology differentially impacts human DNA polymerase fidelity', DNA Repair, vol. 119, 103402. https://doi.org/10.1016/j.dnarep.2022.103402

2021

Carney, MC, Zhan, X, Rangnekar, A, Chroneos, MZ, Craig, SJC, Makova, KD, Paul, IM & Hicks, SD 2021, 'Associations between stool micro-transcriptome, gut microbiota, and infant growth', Journal of Developmental Origins of Health and Disease, vol. 12, no. 6, pp. 876-882. https://doi.org/10.1017/S2040174420001324
Craig, SJC, Kenney, AM, Lin, J, Paul, IM, Birch, LL, Savage, JS, Marini, ME, Chiaromonte, F, Reimherr, ML & Makova, KD 2023, 'Constructing a polygenic risk score for childhood obesity using functional data analysis', Econometrics and Statistics, vol. 25, pp. 66-86. https://doi.org/10.1016/j.ecosta.2021.10.014
Nandy, D, Craig, SJC, Cai, J, Tian, Y, Paul, IM, Savage, JS, Marini, ME, Hohman, EE, Reimherr, ML, Patterson, AD, Makova, KD & Chiaromonte, F 2022, 'Metabolomic profiling of stool of two-year old children from the INSIGHT study reveals links between butyrate and child weight outcomes', Pediatric Obesity, vol. 17, no. 1, e12833. https://doi.org/10.1111/ijpo.12833
Guiblet, WM, Cremona, MA, Harris, RS, Chen, D, Eckert, KA, Chiaromonte, F, Huang, YF & Makova, KD 2021, 'Non-B DNA: A major contributor to small-and large-scale variation in nucleotide substitution frequencies across the genome', Nucleic acids research, vol. 49, no. 3, pp. 1497-1516. https://doi.org/10.1093/nar/gkaa1269
Guiblet, WM, DeGiorgio, M, Cheng, X, Chiaromonte, F, Eckert, KA, Huang, YF & Makova, KD 2021, 'Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome', Genome research, vol. 31, no. 7, pp. 1136-1149. https://doi.org/10.1101/gr.269589.120
Rhie, A, McCarthy, SA, Fedrigo, O, Damas, J, Formenti, G, Koren, S, Uliano-Silva, M, Chow, W, Fungtammasan, A, Kim, J, Lee, C, Ko, BJ, Chaisson, M, Gedman, GL, Cantin, LJ, Thibaud-Nissen, F, Haggerty, L, Bista, I, Smith, M, Haase, B, Mountcastle, J, Winkler, S, Paez, S, Howard, J, Vernes, SC, Lama, TM, Grutzner, F, Warren, WC, Balakrishnan, CN, Burt, D, George, JM, Biegler, MT, Iorns, D, Digby, A, Eason, D, Robertson, B, Edwards, T, Wilkinson, M, Turner, G, Meyer, A, Kautt, AF, Franchini, P, Detrich, HW, Svardal, H, Wagner, M, Naylor, GJP, Pippel, M, Malinsky, M, Mooney, M, Simbirsky, M, Hannigan, BT, Pesout, T, Houck, M, Misuraca, A, Kingan, SB, Hall, R, Kronenberg, Z, Sović, I, Dunn, C, Ning, Z, Hastie, A, Lee, J, Selvaraj, S, Green, RE, Putnam, NH, Gut, I, Ghurye, J, Garrison, E, Sims, Y, Collins, J, Pelan, S, Torrance, J, Tracey, A, Wood, J, Dagnew, RE, Guan, D, London, SE, Clayton, DF, Mello, CV, Friedrich, SR, Lovell, PV, Osipova, E, Al-Ajli, FO, Secomandi, S, Kim, H, Theofanopoulou, C, Hiller, M, Zhou, Y, Harris, RS, Makova, KD, Medvedev, P, Hoffman, J, Masterson, P, Clark, K, Martin, F, Howe, K, Flicek, P, Walenz, BP, Kwak, W, Clawson, H, Diekhans, M, Nassar, L, Paten, B, Kraus, RHS, Crawford, AJ, Gilbert, MTP, Zhang, G, Venkatesh, B, Murphy, RW, Koepfli, KP, Shapiro, B, Johnson, WE, Di Palma, F, Marques-Bonet, T, Teeling, EC, Warnow, T, Graves, JM, Ryder, OA, Haussler, D, O’Brien, SJ, Korlach, J, Lewin, HA, Howe, K, Myers, EW, Durbin, R, Phillippy, AM & Jarvis, ED 2021, 'Towards complete and error-free genome assemblies of all vertebrate species', Nature, vol. 592, no. 7856, pp. 737-746. https://doi.org/10.1038/s41586-021-03451-0

2020

Arbeithuber, B, Hester, J, Cremona, MA, Stoler, N, Zaidi, A, Higgins, B, Anthony, K, Chiaromonte, F, Diaz, FJ & Makova, KD 2020, 'Age-related accumulation of de novo mitochondrial mutations in mammalian oocytes and somatic tissues', PLoS biology, vol. 18, no. 7, 3000745. https://doi.org/10.1371/journal.pbio.3000745
Vegesna, R, Tomaszkiewicz, M, Ryder, OA, Campos-Sanchez, R, Medvedev, P, DeGiorgio, M & Makova, KD 2020, 'Ampliconic genes on the great ape y chromosomes: Rapid evolution of copy number but conservation of expression levels', Genome biology and evolution, vol. 12, no. 6, pp. 842-859. https://doi.org/10.1093/GBE/EVAA088
Cechova, M, Vegesna, R, Tomaszkiewicz, M, Harris, RS, Chen, D, Rangavittal, S, Medvedev, P & Makova, KD 2020, 'Dynamic evolution of great ape Y chromosomes', Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 42, pp. 26273-26280. https://doi.org/10.1073/pnas.2001749117
Stoler, N, Arbeithuber, B, Povysil, G, Heinzl, M, Salazar, R, Makova, KD, Tiemann-Boege, I & Nekrutenko, A 2020, 'Family reunion via error correction: An efficient analysis of duplex sequencing data', BMC bioinformatics, vol. 21, no. 1, 96. https://doi.org/10.1186/s12859-020-3419-8
Chen, D, Cremona, MA, Qi, Z, Mitra, RD, Chiaromonte, F & Makova, KD 2020, 'Human L1 transposition dynamics unraveled with functional data analysis', Molecular biology and evolution, vol. 37, no. 12, pp. 3576-3600. https://doi.org/10.1093/molbev/msaa194
Barrett, A, Arbeithuber, B, Zaidi, A, Wilton, P, Paul, IM, Nielsen, R & Makova, KD 2020, 'Pronounced somatic bottleneck in mitochondrial DNA of human hair', Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 375, no. 1790, 20190175. https://doi.org/10.1098/rstb.2019.0175