Kateryna Makova
DIRECTOR of Center for Medical Genomics | Pennsylvania State University
University Park, PA, UNITED STATES
Kateryna Makova is an expert in molecular evolution, population genetics, evolutionary genomics, bioinformatics, and human genetics.
Media
Publications:
Documents:
Videos:
Audio/Podcasts:
Industry Expertise (2)
Research
Education/Learning
Areas of Expertise (5)
Molecular Evolution
Bioinformatics
Human Genetics
Population Genetics
Evolutionary Genomics
Biography
Dr. Makova is interested in molecular evolution, population genetics, evolutionary genomics, bioinformatics, and human genetics. Her laboratory employs a combination of molecular and computational approaches.
Education (2)
Texas Tech University: Ph.D., Biology 1999
Kiev State University: M.S., Biochemistry and Molecular Biology 1995
Links (2)
Articles (5)
RecoverY: K-mer based read classification for Y-chromosome specific sequencing and assembly
bioRxiv
Samarth Rangavittal, Robert S Harris, Monika Cechova, Marta Tomaszkiewicz, Rayan Chikhi, Kateryna Makova, Paul Medvedev
2017 The haploid mammalian Y chromosome is usually under-represented in genome assemblies due to high repeat content and low depth due to its haploid nature. One strategy to ameliorate the low coverage of Y sequences is to experimentally enrich Y-specific material before assembly. Since the enrichment process is imperfect, algorithms are needed to identify putative Y-specific reads prior to downstream assembly. A strategy that uses k-mer abundances to identify such reads was used to assemble the gorilla Y (Tomaszkiewicz et al 2016). However, the strategy required the manual setting of key parameters, a time-consuming process leading to sub-optimal assemblies.
Functional data analysis of “Omics” data: how does the genomic landscape influence integration and fixation of endogenous retroviruses?
Functional Statistics and Related Fields
Marzia A Cremona, Rebeca Campos-Sánchez, Alessia Pini, Simone Vantini, Kateryna D Makova, Francesca Chiaromonte
2017 We consider thousands of endogenous retrovirus detected in the human and mouse genomes, and quantify a large number of genomic landscape features at high resolution around their integration sites and in control regions. We propose to analyze this data employing a recently developed functional inferential procedure and functional logistic regression, with the aim of gaining insights on the effects of genomic landscape features on the integration and fixation of endogenous retroviruses.
Correcting palindromes in long reads after whole-genome amplification
bioRxiv
Sven Warris, Elio Schijlen, Henri van de Geest, Rahulsimham Vegesna, Thamara Hesselink, Bas te Lintel Hekkert, Gabino Sanchez-Perez, Paul Medvedev, Kateryna D Makova, Dick de Ridder
2017 Next-generation sequencing requires sufficient DNA to be available. If limited, whole-genome amplification is applied to generate additional amounts of DNA. Such amplification often results in many chimeric DNA fragments, in particular artificial palindromic sequences, which limit the usefulness of long reads from technologies such as PacBio and Oxford Nanopore. Here, we present Pacasus, a tool for correcting such errors in long reads. We demonstrate on two real-world datasets that it markedly improves subsequent read mapping and de novo assembly, yielding results similar to these that would be obtained with non-amplified DNA. With Pacasus long-read technologies become readily available for sequencing targets with very small amounts of DNA, such as single cells or even single chromosomes.
Y and W chromosome assemblies: approaches and discoveries
Trends in Genetics
Marta Tomaszkiewicz, Paul Medvedev, Kateryna D Makova
2017 Hundreds of vertebrate genomes have been sequenced and assembled to date. However, most sequencing projects have ignored the sex chromosomes unique to the heterogametic sex – Y and W – that are known as sex-limited chromosomes (SLCs). Indeed, haploid and repetitive Y chromosomes in species with male heterogamety (XY), and W chromosomes in species with female heterogamety (ZW), are difficult to sequence and assemble. Nevertheless, obtaining their sequences is important for understanding the intricacies of vertebrate genome function and evolution. Recent progress has been made towards the adaptation of next-generation sequencing (NGS) techniques to deciphering SLC sequences. We review here currently available methodology and results with regard to SLC sequencing and assembly. We focus on vertebrates, but bring in some examples from other taxa.
Elevated mitochondrial genome variation after 50 generations of radiation exposure in a wild rodent
Evolutionary Applications
Robert J Baker, Benjamin Dickins, Jeffrey K Wickliffe, Faisal AA Khan, Sergey Gaschak, Kateryna D Makova, Caleb D Phillips
2017 Currently, the effects of chronic, continuous low dose environmental irradiation on the mitochondrial genome of resident small mammals are unknown. Using the bank vole (Myodes glareolus) as a model system, we tested the hypothesis that approximately 50 generations of exposure to the Chernobyl environment has significantly altered genetic diversity of the mitochondrial genome. Using deep sequencing, we compared mitochondrial genomes from 131 individuals from reference sites with radioactive contamination comparable to that present in northern Ukraine before the 26 April 1986 meltdown, to populations where substantial fallout was deposited following the nuclear accident. Population genetic variables revealed significant differences among populations from contaminated and uncontaminated localities. Therefore, we rejected the null hypothesis of no significant genetic effect from 50 generations of exposure to the environment created by the Chernobyl meltdown.
Social