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
  • Mitochondrial DNA
  • Chromosomes
  • Pan troglodytes

Recent Publications

2020

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
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

Zaidi, AA, Wilton, PR, Su, MSW, Paul, IM, Arbeithuber, B, Anthony, K, Nekrutenko, A, Nielsen, R & Makova, KD 2019, 'Bottleneck and selection in the germline and maternal age influence transmission of mitochondrial DNA in human pedigrees', Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 50, pp. 25172-25178. https://doi.org/10.1073/pnas.1906331116
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, 798. 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

Clinical Trials Search


Children (age < 18 years)
Adults (age >= 18 years)