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Kateryna Makova

Title
InstitutionEberly College of Science
DepartmentBiology
Address305 Wartik Lab
University Park, PA 16802
Phone8148631619
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    Other Positions
    TitleDirector of the Center for Medical Genomics
    InstitutionHuck Institutes of the Life Sciences


    Collapse Overview 
    Collapse overview
    PREFERRED TITLE/ROLE:

    Professor of Biology
    Director, Center for Medical Genomics

    GRADUATE PROGRAM AFFILIATIONS:

    Bioinformatics and Genomics, Genetics

    EDUCATION:

    M.S., Biochemistry and Molecular Biology, Kiev State University, Kiev, Ukraine, 1995
    Ph.D., Biology, Texas Tech University, 1999

    NARRATIVE:

    Dr. Makova's research focuses on molecular evolution, population genetics, evolutionary genomics, bioinformatics, and human genetics. Her lab employs both computational and experimental methods to investigate mutations, or the changes in DNA. They scrutinize the variability in the rates and patterns of different types of mutations among regions of vertebrate genomes. Such inquiries allow them to make inferences about the molecular mechanisms leading to mutations — thee cause of human genetic diseases and the source of genetic variation in natural populations.


    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    List All   |   Timeline
    1. Rangavittal S, Harris RS, Cechova M, Tomaszkiewicz M, Chikhi R, Makova KD, Medvedev P. RecoverY: K-mer based read classification for Y-chromosome specific sequencing and assembly. Bioinformatics. 2017 Nov 28. PMID: 29194476.
      View in: PubMed
    2. Baker RJ, Dickins B, Wickliffe JK, Khan FAA, Gaschak S, Makova KD, Phillips CD. Elevated mitochondrial genome variation after 50 generations of radiation exposure in a wild rodent. Evol Appl. 2017 Sep; 10(8):784-791. PMID: 29151870.
      View in: PubMed
    3. Tomaszkiewicz M, Medvedev P, Makova KD. Y and W Chromosome Assemblies: Approaches and Discoveries. Trends Genet. 2017 Apr; 33(4):266-282. PMID: 28236503.
      View in: PubMed
    4. Fungtammasan A, Walsh E, Chiaromonte F, Eckert KA, Makova KD. Corrigendum: A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome? Genome Res. 2016 10; 26(10):1451. PMID: 27698254.
      View in: PubMed
    5. Stoler N, Arbeithuber B, Guiblet W, Makova KD, Nekrutenko A. Streamlined analysis of duplex sequencing data with Du Novo. Genome Biol. 2016 08 26; 17(1):180. PMID: 27566673; PMCID: PMC5000403.
    6. Arbeithuber B, Makova KD, Tiemann-Boege I. Artifactual mutations resulting from DNA lesions limit detection levels in ultrasensitive sequencing applications. DNA Res. 2016 Dec; 23(6):547-559. PMID: 27477585.
      View in: PubMed
    7. Fungtammasan A, Tomaszkiewicz M, Campos-Sánchez R, Eckert KA, DeGiorgio M, Makova KD. Reverse Transcription Errors and RNA-DNA Differences at Short Tandem Repeats. Mol Biol Evol. 2016 Oct; 33(10):2744-58. PMID: 27413049.
      View in: PubMed
    8. Campos-Sánchez R, Cremona MA, Pini A, Chiaromonte F, Makova KD. Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis. PLoS Comput Biol. 2016 06; 12(6):e1004956. PMID: 27309962; PMCID: PMC4911145.
    9. Tomaszkiewicz M, Rangavittal S, Cechova M, Campos Sanchez R, Fescemyer HW, Harris R, Ye D, O'Brien PC, Chikhi R, Ryder OA, Ferguson-Smith MA, Medvedev P, Makova KD. A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y. Genome Res. 2016 Apr; 26(4):530-40. PMID: 26934921; PMCID: PMC4817776.
    10. Fungtammasan A, Ananda G, Hile SE, Su MS, Sun C, Harris R, Medvedev P, Eckert K, Makova KD. Accurate typing of short tandem repeats from genome-wide sequencing data and its applications. Genome Res. 2015 May; 25(5):736-49. PMID: 25823460; PMCID: PMC4417121.
    11. Makova KD, Hardison RC. The effects of chromatin organization on variation in mutation rates in the genome. Nat Rev Genet. 2015 Apr; 16(4):213-23. PMID: 25732611; PMCID: PMC4500049.
    12. Rebolledo-Jaramillo B, Su MS, Stoler N, McElhoe JA, Dickins B, Blankenberg D, Korneliussen TS, Chiaromonte F, Nielsen R, Holland MM, Paul IM, Nekrutenko A, Makova KD. Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA. Proc Natl Acad Sci U S A. 2014 Oct 28; 111(43):15474-9. PMID: 25313049; PMCID: PMC4217420.
    13. Paul IM, Williams JS, Anzman-Frasca S, Beiler JS, Makova KD, Marini ME, Hess LB, Rzucidlo SE, Verdiglione N, Mindell JA, Birch LL. The Intervention Nurses Start Infants Growing on Healthy Trajectories (INSIGHT) study. BMC Pediatr. 2014 Jul 18; 14:184. PMID: 25037579; PMCID: PMC4105401.
    14. Ananda G, Hile SE, Breski A, Wang Y, Kelkar Y, Makova KD, Eckert KA. Microsatellite interruptions stabilize primate genomes and exist as population-specific single nucleotide polymorphisms within individual human genomes. PLoS Genet. 2014 Jul; 10(7):e1004498. PMID: 25033203; PMCID: PMC4102424.
    15. McElhoe JA, Holland MM, Makova KD, Su MS, Paul IM, Baker CH, Faith SA, Young B. Development and assessment of an optimized next-generation DNA sequencing approach for the mtgenome using the Illumina MiSeq. Forensic Sci Int Genet. 2014 Nov; 13:20-9. PMID: 25051226; PMCID: PMC4580234.
    16. Campos-Sánchez R, Kapusta A, Feschotte C, Chiaromonte F, Makova KD. Genomic landscape of human, bat, and ex vivo DNA transposon integrations. Mol Biol Evol. 2014 Jul; 31(7):1816-32. PMID: 24809961; PMCID: PMC4069622.
    17. Kuruppumullage Don P, Ananda G, Chiaromonte F, Makova KD. Segmenting the human genome based on states of neutral genetic divergence. Proc Natl Acad Sci U S A. 2013 Sep 03; 110(36):14699-704. PMID: 23959903; PMCID: PMC3767554.
    18. Montgomery SB, Goode DL, Kvikstad E, Albers CA, Zhang ZD, Mu XJ, Ananda G, Howie B, Karczewski KJ, Smith KS, Anaya V, Richardson R, Davis J. The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes. Genome Res. 2013 May; 23(5):749-61. PMID: 23478400; PMCID: PMC3638132.
    19. Baptiste BA, Ananda G, Strubczewski N, Lutzkanin A, Khoo SJ, Srikanth A, Kim N, Makova KD, Krasilnikova MM, Eckert KA. Mature microsatellites: mechanisms underlying dinucleotide microsatellite mutational biases in human cells. G3 (Bethesda). 2013 Mar; 3(3):451-63. PMID: 23450065; PMCID: PMC3583453.
    20. Ananda G, Walsh E, Jacob KD, Krasilnikova M, Eckert KA, Chiaromonte F, Makova KD. Distinct mutational behaviors differentiate short tandem repeats from microsatellites in the human genome. Genome Biol Evol. 2013; 5(3):606-20. PMID: 23241442; PMCID: PMC3622297.
    21. Wilson Sayres MA, Makova KD. Gene survival and death on the human Y chromosome. Mol Biol Evol. 2013 Apr; 30(4):781-7. PMID: 23223713; PMCID: PMC3603307.
    22. Wagstaff BJ, Hedges DJ, Derbes RS, Campos Sanchez R, Chiaromonte F, Makova KD, Roy-Engel AM. Rescuing Alu: recovery of new inserts shows LINE-1 preserves Alu activity through A-tail expansion. PLoS Genet. 2012; 8(8):e1002842. PMID: 22912586; PMCID: PMC3415434.
    23. Fungtammasan A, Walsh E, Chiaromonte F, Eckert KA, Makova KD. A genome-wide analysis of common fragile sites: what features determine chromosomal instability in the human genome? Genome Res. 2012 Jun; 22(6):993-1005. PMID: 22456607; PMCID: PMC3371707.
    24. Wolfe K, Wayne ML, Makova K, Steen TY, Uyenoyama M, Takahata N. SMBE proposal to the government of Japan. Mol Biol Evol. 2012 Jan; 29(1):441. PMID: 22080475.
      View in: PubMed
    25. Afgan E, Baker D, Coraor N, Goto H, Paul IM, Makova KD, Nekrutenko A, Taylor J. Harnessing cloud computing with Galaxy Cloud. Nat Biotechnol. 2011 Nov 08; 29(11):972-4. PMID: 22068528; PMCID: PMC3868438.
    26. Wilson Sayres MA, Makova KD. Genome analyses substantiate male mutation bias in many species. Bioessays. 2011 Dec; 33(12):938-45. PMID: 22006834; PMCID: PMC4600401.
    27. Kelkar YD, Eckert KA, Chiaromonte F, Makova KD. A matter of life or death: how microsatellites emerge in and vanish from the human genome. Genome Res. 2011 Dec; 21(12):2038-48. PMID: 21994250; PMCID: PMC3227094.
    28. Goto H, Ryder OA, Fisher AR, Schultz B, Kosakovsky Pond SL, Nekrutenko A, Makova KD. A massively parallel sequencing approach uncovers ancient origins and high genetic variability of endangered Przewalski's horses. Genome Biol Evol. 2011; 3:1096-106. PMID: 21803766; PMCID: PMC3194890.
    29. Goto H, Dickins B, Afgan E, Paul IM, Taylor J, Makova KD, Nekrutenko A. Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study. Genome Biol. 2011; 12(6):R59. PMID: 21699709.
      View in: PubMed
    30. Wilson Sayres MA, Venditti C, Pagel M, Makova KD. Do variations in substitution rates and male mutation bias correlate with life-history traits? A study of 32 mammalian genomes. Evolution. 2011 Oct; 65(10):2800-15. PMID: 21967423.
      View in: PubMed
    31. Lombard Z, Park C, Makova KD, Ramsay M. A computational approach to candidate gene prioritization for X-linked mental retardation using annotation-based binary filtering and motif-based linear discriminatory analysis. Biol Direct. 2011 Jun 13; 6:30. PMID: 21668950; PMCID: PMC3142252.
    32. Ananda G, Chiaromonte F, Makova KD. A genome-wide view of mutation rate co-variation using multivariate analyses. Genome Biol. 2011; 12(3):R27. PMID: 21426544; PMCID: PMC3129677.
    33. Kelkar YD, Strubczewski N, Hile SE, Chiaromonte F, Eckert KA, Makova KD. What is a microsatellite: a computational and experimental definition based upon repeat mutational behavior at A/T and GT/AC repeats. Genome Biol Evol. 2010; 2:620-35. PMID: 20668018; PMCID: PMC2940325.
    34. Park C, Carrel L, Makova KD. Strong purifying selection at genes escaping X chromosome inactivation. Mol Biol Evol. 2010 Nov; 27(11):2446-50. PMID: 20534706; PMCID: PMC2981488.
    35. Kvikstad EM, Makova KD. The (r)evolution of SINE versus LINE distributions in primate genomes: sex chromosomes are important. Genome Res. 2010 May; 20(5):600-13. PMID: 20219940; PMCID: PMC2860162.
    36. Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, Muzny DM, Reid JG, Nazareth LV, Wang Q, Burhans R, Riemer C, Wittekindt NE, Moorjani P, Tindall EA, Danko CG, Teo WS, Buboltz AM, Zhang Z, Ma Q, Oosthuysen A, Steenkamp AW, Oostuisen H, Venter P, Gajewski J, Zhang Y, Pugh BF, Makova KD, Nekrutenko A, Mardis ER, Patterson N, Pringle TH, Chiaromonte F, Mullikin JC, Eichler EE, Hardison RC, Gibbs RA, Harkins TT, Hayes VM. Complete Khoisan and Bantu genomes from southern Africa. Nature. 2010 Feb 18; 463(7283):943-7. PMID: 20164927; PMCID: PMC3890430.
    37. Wilson MA, Makova KD. Evolution and survival on eutherian sex chromosomes. PLoS Genet. 2009 Jul; 5(7):e1000568. PMID: 19609352; PMCID: PMC2704370.
    38. Kvikstad EM, Chiaromonte F, Makova KD. Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions. Genome Res. 2009 Jul; 19(7):1153-64. PMID: 19502380; PMCID: PMC2704434.
    39. Park C, Makova KD. Coding region structural heterogeneity and turnover of transcription start sites contribute to divergence in expression between duplicate genes. Genome Biol. 2009; 10(1):R10. PMID: 19175934; PMCID: PMC2687787.
    40. Goto H, Peng L, Makova KD. Evolution of X-degenerate Y chromosome genes in greater apes: conservation of gene content in human and gorilla, but not chimpanzee. J Mol Evol. 2009 Feb; 68(2):134-44. PMID: 19142680.
      View in: PubMed
    41. Wilson MA, Makova KD. Genomic analyses of sex chromosome evolution. Annu Rev Genomics Hum Genet. 2009; 10:333-54. PMID: 19630566.
      View in: PubMed
    42. Lau AN, Peng L, Goto H, Chemnick L, Ryder OA, Makova KD. Horse domestication and conservation genetics of Przewalski's horse inferred from sex chromosomal and autosomal sequences. Mol Biol Evol. 2009 Jan; 26(1):199-208. PMID: 18931383.
      View in: PubMed
    43. Tyekucheva S, Makova KD, Karro JE, Hardison RC, Miller W, Chiaromonte F. Human-macaque comparisons illuminate variation in neutral substitution rates. Genome Biol. 2008 Apr 30; 9(4):R76. PMID: 18447906.
      View in: PubMed
    44. Kelkar YD, Tyekucheva S, Chiaromonte F, Makova KD. The genome-wide determinants of human and chimpanzee microsatellite evolution. Genome Res. 2008 Jan; 18(1):30-8. PMID: 18032720; PMCID: PMC2134767.
    45. Kvikstad EM, Tyekucheva S, Chiaromonte F, Makova KD. A macaque's-eye view of human insertions and deletions: differences in mechanisms. PLoS Comput Biol. 2007 Sep; 3(9):1772-82. PMID: 17941704; PMCID: PMC1976337.
    46. Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun; 17(6):960-4. PMID: 17568012; PMCID: PMC1891355.
    47. Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007 Apr 13; 316(5822):222-34. PMID: 17431167.
      View in: PubMed
    48. Goetting-Minesky MP, Makova KD. Mammalian male mutation bias: impacts of generation time and regional variation in substitution rates. J Mol Evol. 2006 Oct; 63(4):537-44. PMID: 16955237.
      View in: PubMed
    49. Carrel L, Park C, Tyekucheva S, Dunn J, Chiaromonte F, Makova KD. Genomic environment predicts expression patterns on the human inactive X chromosome. PLoS Genet. 2006 Sep 29; 2(9):e151. PMID: 17009873; PMCID: PMC1584270.
    50. Chung WY, Albert R, Albert I, Nekrutenko A, Makova KD. Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network. BMC Bioinformatics. 2006 Jan 27; 7:46. PMID: 16441884; PMCID: PMC1403810.
    51. Taylor J, Tyekucheva S, Zody M, Chiaromonte F, Makova KD. Strong and weak male mutation bias at different sites in the primate genomes: insights from the human-chimpanzee comparison. Mol Biol Evol. 2006 Mar; 23(3):565-73. PMID: 16280537.
      View in: PubMed
    52. Makova K, Norton H. Worldwide polymorphism at the MC1R locus and normal pigmentation variation in humans. Peptides. 2005 Oct; 26(10):1901-8. PMID: 15979202.
      View in: PubMed
    53. Nekrutenko A, Wadhawan S, Goetting-Minesky P, Makova KD. Oscillating evolution of a mammalian locus with overlapping reading frames: an XLalphas/ALEX relay. PLoS Genet. 2005 Aug; 1(2):e18. PMID: 16110341; PMCID: PMC1186735.
    54. Makova KD, Yang S, Chiaromonte F. Insertions and deletions are male biased too: a whole-genome analysis in rodents. Genome Res. 2004 Apr; 14(4):567-73. PMID: 15059997; PMCID: PMC383300.
    55. Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004 Apr 01; 428(6982):493-521. PMID: 15057822.
      View in: PubMed
    56. Miller W, Makova KD, Nekrutenko A, Hardison RC. Comparative genomics. Annu Rev Genomics Hum Genet. 2004; 5:15-56. PMID: 15485342.
      View in: PubMed
    57. Makova KD, Li WH. Divergence in the spatial pattern of gene expression between human duplicate genes. Genome Res. 2003 Jul; 13(7):1638-45. PMID: 12840042; PMCID: PMC403737.
    58. John PR, Makova K, Li WH, Jenkins T, Ramsay M. DNA polymorphism and selection at the melanocortin-1 receptor gene in normally pigmented southern African individuals. Ann N Y Acad Sci. 2003 Jun; 994:299-306. PMID: 12851329.
      View in: PubMed
    59. Li WH, Yi S, Makova K. Male-driven evolution. Curr Opin Genet Dev. 2002 Dec; 12(6):650-6. PMID: 12433577.
      View in: PubMed
    60. Mu J, Duan J, Makova KD, Joy DA, Huynh CQ, Branch OH, Li WH, Su XZ. Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum. Nature. 2002 Jul 18; 418(6895):323-6. PMID: 12124624.
      View in: PubMed
    61. Makova KD, Li WH. Strong male-driven evolution of DNA sequences in humans and apes. Nature. 2002 Apr 11; 416(6881):624-6. PMID: 11948348.
      View in: PubMed
    62. Nekrutenko A, Makova KD, Li WH. The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study. Genome Res. 2002 Jan; 12(1):198-202. PMID: 11779845; PMCID: PMC155263.
    63. Makova KD, Ramsay M, Jenkins T, Li WH. Human DNA sequence variation in a 6.6-kb region containing the melanocortin 1 receptor promoter. Genetics. 2001 Jul; 158(3):1253-68. PMID: 11454772; PMCID: PMC1461732.
    64. Liu JC, Makova KD, Adkins RM, Gibson S, Li WH. Episodic evolution of growth hormone in primates and emergence of the species specificity of human growth hormone receptor. Mol Biol Evol. 2001 Jun; 18(6):945-53. PMID: 11371582.
      View in: PubMed
    65. Makova KD, Nekrutenko A, Baker RJ. Evolution of microsatellite alleles in four species of mice (genus Apodemus). J Mol Evol. 2000 Aug; 51(2):166-72. PMID: 10948273.
      View in: PubMed
    66. Nekrutenko A, Makova KD, Baker RJ. Isolation of binary species-specific PCR-based markers and their value for diagnostic applications. Gene. 2000 May 16; 249(1-2):47-51. PMID: 10831837.
      View in: PubMed
    67. Nekrutenko A, Makova KD, Chesser RK, Baker RJ. Representational difference analysis to distinguish cryptic species. Mol Ecol. 1999 Jul; 8(7):1235-8. PMID: 10447864.
      View in: PubMed
    68. Baker RJ, Makova KD, Chesser RK. Microsatellites indicate a high frequency of multiple paternity in Apodemus (Rodentia). Mol Ecol. 1999 Jan; 8(1):107-11. PMID: 12187947.
      View in: PubMed
    69. Makova KD, Patton JC. Microsatellite markers in wood mouse and striped field mouse (genus Apodemus). Mol Ecol. 1998 Feb; 7(2):247-9. PMID: 9532763.
      View in: PubMed
    70. Makova KD, Patton JC. Increased yield of tri- and tetranucleotide heterospecific microsatellites from unenriched small-insert libraries. Biotechniques. 1998 Jan; 24(1):38, 40, 42-3. PMID: 9454948.
      View in: PubMed
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