Researcher Profile

Researcher Profile

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

Recent Publications

2020

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

2019

Rangavittal, S, Stopa, N, Tomaszkiewicz, M, Sahlin, K, Makova, KD & Medvedev, P 2019, 'DiscoverY: A classifier for identifying y chromosome sequences in male assemblies', BMC genomics, vol. 20, no. 1, 641. https://doi.org/10.1186/s12864-019-5996-3
Vegesna, R, Tomaszkiewicz, M, Medvedev, P & Makova, KD 2019, 'Dosage regulation, and variation in gene expression and copy number of human Y chromosome ampliconic genes', PLoS genetics, vol. 15, no. 9, e1008369. https://doi.org/10.1371/journal.pgen.1008369
Cremona, MA, Xu, H, Makova, KD, Reimherr, M, Chiaromonte, F & Madrigal, P 2019, 'Functional data analysis for computational biology', Bioinformatics, vol. 35, no. 17, pp. 3211-3213. https://doi.org/10.1093/bioinformatics/btz045
Zaidi, AA & Makova, KD 2019, 'Investigating mitonuclear interactions in human admixed populations', Nature Ecology and Evolution, vol. 3, no. 2, pp. 213-222. https://doi.org/10.1038/s41559-018-0766-1
Harris, RS, Cechova, M, Makova, KD & Birol, I 2019, 'Noise-cancelling repeat finder: Uncovering tandem repeats in error-prone long-read sequencing data', Bioinformatics, vol. 35, no. 22, pp. 4809-4811. https://doi.org/10.1093/bioinformatics/btz484

2018

Wilton, PR, Zaidi, A, Makova, K & Nielsen, R 2018, 'A population phylogenetic view of mitochondrial heteroplasmy', Genetics, vol. 208, no. 3, pp. 1261-1274. https://doi.org/10.1534/genetics.118.300711
Craig, SJC, Blankenberg, D, Parodi, ACL, Paul, IM, Birch, LL, Savage, JS, Marini, ME, Stokes, JL, Nekrutenko, A, Reimherr, M, Chiaromonte, F & Makova, KD 2018, 'Child Weight Gain Trajectories Linked To Oral Microbiota Composition', Scientific reports, vol. 8, no. 1, 14030. https://doi.org/10.1038/s41598-018-31866-9
Warris, S, Schijlen, E, van de Geest, H, Vegesna, R, Hesselink, T, Te Lintel Hekkert, B, Sanchez Perez, G, Medvedev, P, Makova, KD & de Ridder, D 2018, 'Correcting palindromes in long reads after whole-genome amplification', BMC genomics, vol. 19, no. 1. https://doi.org/10.1186/s12864-018-5164-1
Sahlin, K, Tomaszkiewicz, M, Makova, KD & Medvedev, P 2018, 'Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon', Nature communications, vol. 9, no. 1, 4601. https://doi.org/10.1038/s41467-018-06910-x
Holland, MM, Makova, KD & McElhoe, JA 2018, 'Deep-coverage MPS analysis of heteroplasmic variants within the mtgenome allows for frequent differentiation of maternal relatives', Genes, vol. 9, no. 3, 124. https://doi.org/10.3390/genes9030124
Ye, D, Zaidi, AA, Tomaszkiewicz, M, Anthony, K, Liebowitz, C, DeGiorgio, M, Shriver, MD & Makova, KD 2018, 'High levels of copy number variation of ampliconic genes across major human Y haplogroups', Genome biology and evolution, vol. 10, no. 5, pp. 1333-1350. https://doi.org/10.1093/gbe/evy086
Cremona, M, Pini, A, Cumbo, F, Makova, KD, Chiaromonte, F & Vantini, S 2018, 'IWTomics: Testing high-resolution sequence-based 'Omics' data at multiple locations and scales', Bioinformatics, vol. 34, no. 13, pp. 2289-2291. https://doi.org/10.1093/bioinformatics/bty090
Guiblet, WM, Cremona, MA, Cechova, M, Harris, RS, Kejnovská, I, Kejnovsky, E, Eckert, K, Chiaromonte, F & Makova, KD 2018, 'Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate', Genome research, vol. 28, no. 12, pp. 1767-1778. https://doi.org/10.1101/gr.241257.118
Rangavittal, S, Harris, RS, Cechova, M, Tomaszkiewicz, M, Chikhi, R, Makova, KD & Medvedev, P 2018, 'RecoverY: K-mer-based read classification for Y-chromosome-specific sequencing and assembly', Bioinformatics, vol. 34, no. 7, pp. 1125-1131. https://doi.org/10.1093/bioinformatics/btx771

2017

Baker, RJ, Dickins, B, Wickliffe, JK, Khan, FAA, Gaschak, S, Makova, KD & Phillips, CD 2017, 'Elevated mitochondrial genome variation after 50 generations of radiation exposure in a wild rodent', Evolutionary Applications, vol. 10, no. 8, pp. 784-791. https://doi.org/10.1111/eva.12475
Tomaszkiewicz, M, Medvedev, P & Makova, KD 2017, 'Y and W Chromosome Assemblies: Approaches and Discoveries', Trends in Genetics, vol. 33, no. 4, pp. 266-282. https://doi.org/10.1016/j.tig.2017.01.008

2016

Tomaszkiewicz, M, Rangavittal, S, Cechova, M, Sanchez, RC, Fescemyer, HW, Harris, R, Ye, D, O'Brien, PCM, Chikhi, R, Ryder, OA, Ferguson-Smith, MA, Medvedev, P & Makova, KD 2016, 'A time- and cost-effective strategy to sequence mammalian Y chromosomes: An application to the de novo assembly of gorilla Y', Genome research, vol. 26, no. 4, pp. 530-540. https://doi.org/10.1101/gr.199448.115
Arbeithuber, B, Makova, KD & Tiemann-Boege, I 2016, 'Artifactual mutations resulting from DNA lesions limit detection levels in ultrasensitive sequencing applications', DNA research : an international journal for rapid publication of reports on genes and genomes, vol. 23, no. 6, pp. 547-559. https://doi.org/10.1093/dnares/dsw038
Campos-Sánchez, R, Cremona, MA, Pini, A, Chiaromonte, F & Makova, KD 2016, 'Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis', PLoS computational biology, vol. 12, no. 6, e1004956. https://doi.org/10.1371/journal.pcbi.1004956
Fungtammasan, A, Tomaszkiewicz, M, Campos-Sánchez, R, Eckert, KA, Degiorgio, M & Makova, KD 2016, 'Reverse Transcription Errors and RNA-DNA Differences at Short Tandem Repeats', Molecular biology and evolution, vol. 33, no. 10, pp. 2744-2758. https://doi.org/10.1093/molbev/msw139
Stoler, N, Arbeithuber, B, Guiblet, W, Makova, KD & Nekrutenko, A 2016, 'Streamlined analysis of duplex sequencing data with Du Novo', Genome biology, vol. 17, no. 1, 180. https://doi.org/10.1186/s13059-016-1039-4

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