Projects
Childhood obesity featured image

Childhood obesity

Obesity is becoming the major epidemic of the 21st century, and we are studying this disease in an integrated way - from the perspective of genomics, microbiomics, and epigenomics. …

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Mitochondrial mutation dynamics featured image

Mitochondrial mutation dynamics

With sequencing now possible at high depth, we aim to examine mutation process directly, by examining the DNA of children and their parents. Mitochondrial DNA (mtDNA) provides a …

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Non-B DNA and microsatellite variation and evolution featured image

Non-B DNA and microsatellite variation and evolution

Approximately 13% of the genome can fold into DNA structures different from the B-form double-helix discovered by Watson and Crick. Such "non-B DNA" structures include cruciforms, …

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Regional variation in mutation rates featured image

Regional variation in mutation rates

Mutation rates vary at a fine scale - even within individual chromosomes. We are using statistical modeling to study such regional variation in mutation rates. Moreover, we are …

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Sex chromosome evolution featured image

Sex chromosome evolution

We are determining the gene repertoire and structure of the Y chromosome in several mammalian species. The Y chromosome has very high rates of mutation compared with other …

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News
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Press Releases

In brief: Certain age-related DNA mutations are less common in human eggs

UNIVERSITY PARK, Pa. — Unlike other tissues in the human body, human eggs don’t pick up as many mutations in some of their DNA as they age. The findings from a new study, published in Science Advances and led by researchers at Penn State, suggests that human eggs — the reproductive cells that, when…

Beyond the double helix: Alternative DNA conformations in ape genomes

UNIVERSITY PARK, Pa. — Certain DNA sequences can form structures other than the canonical double helix. These alternative DNA conformations — referred to as non-B DNA — have been implicated as regulators of cellular processes and of genome evolution, but their DNA tends to be repetitive, which…

Complete genome sequences of six ape species unveiled

UNIVERSITY PARK, Pa. — Differences among the DNA of seven ape species — including humans — are greater than originally thought, according to an international team led by researchers at Penn State, the National Human Genome Research Institute (NHGRI) and the University of Washington. They revealed…

Complete X and Y chromosome sequences of living great ape species determined

Newly generated, complete “end-to-end” reference genomes for the sex chromosomes of five great ape species and one lesser ape species — produced by an international collaborative team led by researchers at Penn State, the National Human Genome Research Institute and the University of Washington —…

DNA sequence of the human Y chromosome fully determined for first time

Listen to the Science Friday podcast where Adam Phillippy and Kateryna Makova discuss the challenges of sequencing the Y chromosome, and what doing so might mean for medical research. UNIVERSITY PARK, Pa. — The first full sequence of the last human chromosome — the Y chromosome — to be assembled is…

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Publications
A Chakravarti, EE Eichler, AC Ferguson-Smith, RA Gibbs, ED Green, JR Inglis, Kateryna Makova, Ph.D., RM Myers, HE Sussman (2026). Jim Watson (1928–2025): a genomics visionary. GENOME RES.
Edmundo Torres-González, Marzia Cremona, JM Storer, M Ventura, RJ O’Neill, Kateryna Makova, Ph.D. (2026). Nuclear Mitochondrial Sequences in Great Ape Telomere-to-Telomere Genomes. GENOME RES, ACCEPTED.
Paper Link Mitochondrial
P Hebbar, TA Potapova, H Loucks, K Ray, MF Rodrigues, F Ryabov, J Malukiewicz, D Yoo, LG de Lima, A Haber, S Kumar, S Banerjee, M Borchers, GH Garcia, J Gardner, S Hachem, HD Heath, SK Ha, M Mastoras, B McNulty, KM Munson, Karol Pal, JE Park, S Plosch, C Roos, WE Seligmann, V Shepelev, C Spruce, I Violich, L Walter, Kateryna Makova, Ph.D., A Thathiah, SJS Rizzo, AC Silva, GW Carter, KH Miga, EE Eichler, DF Conrad, JL Gerton, I Alexandrov, B Paten (2026). A Complete Genome for the Common Marmoset. CELL, ACCEPTED.
Paper Link Sex chromosome
G Formenti, DE Absolon, LAL Abueg, F Ackerman, FO Al-Ajli, A Aleixo, A Antunes, D Arcila, J-N Audet, JR Balacco, AJS Beavan, K Belov, R Betancur-R, SL Bidwell, MT Biegler, I Bista, M Blaxter, K Boyer, I Braasch, IR Bradbury, N Brajuka, AM Bronikowski, T Brown, G Butler, S Cao, E Charvel, Y Chen, C Ciofi, HM Clawson, JC Collins, S Correard, S Corrigan, M Couture, AJ Crawford, ND D’Alessandre, HB da Conceicao, RR da Fonseca, M Daigavane, J Dalapicolla, M de Bruyn, E de Jong, DN De Panis, HW Detrich III, C DeWeese Scott, M Diekhans, E Duarte, R Durbin, M Escalona, M Eschenbrenner, O Fedrigo, J Fenn, P Flannery, N Forde, SM Gable, PA Galante, R Ganesan, A Gardiner, E Garrison, NJ Gemmell, MTP Gilbert, F Giudicelli, TM Gonçalves, GDA Guardia, A Guarracino, A Gupta, B Haase, D Hays, G Hickey, M Hiller, PM Hime, CJ Hogg, KM Horan, K Howe, D Jackson, N Jain, L Kang, S Kliver, Byung June Ko, K-P Koepfli, A Komissarov, LM Komoroske, B Koo, S Koren, J Korlach, I Kovacic, K Krasheninnikova, LF Kuderna, RA Langlois, D Lariviere, DM Larkin, C Lee, YH Lee, HA Lewin, D Lim, RN Lou, SS Mak, Kateryna Makova, Ph.D., L Marín-Gual, T Marques-Bonet, FJ Martin, TC Mathers, CJ Mazzoni, K McCaffrey, SA McCarthy, JA Medico, RLV Mercuri, A Meyer, P Michalak, S Mirarab, PA Morin, J Mountcastle, RW Murphy, TD Murphy, EW Myers, GJ Naylor, T Near, Anton Nekrutenko, Z Ning, BJ Novak, MF O’Brien, MJ O’Connell, BP O’Toole, S Paez, B Paten, M Paulini, SE Pelan, M Pennell, AR Pfenning, Adam M. Phillippy, B Pinto, M Pippel, M Popova, M Prylutskyi, A Rhie, H Roest Crollius, A Ruiz-Herrera, O Ryder, Y Safonova, CA Santos, MC Schatz, S Secomandi, HB Shaffer, L Shalmiyev, B Shapiro, JJ Smith, M Sollitto, CG Sotero-Caio, CC Steiner, PH Sudmant, DJ Sweeney, SC Talbot, CH Taylor, EC Teeling, F Thibaud-Nissen, T Tilley, N Timoshevskaya, P Traore, Y Turakhia, M Uliano-Silva, C Venditti, B Venkatesh, SC Vernes, WC Warren, CV Whelan, Melissa A. Wilson Sayres, S Winkler, JM Wood, G Zhang, G Zhao, ED Jarvis, the Vertebrate Genomes Project Consortium Phase I (2026). The Vertebrate Genomes Project Phase I: A global reference genome resource. BIORXIV.
Paper Link Sex chromosome
Saswat Kumar Mohanty, MG Marin, Linnéa Smeds, Francesca Chiaromonte, CD Huber, Kateryna Makova, Ph.D., Human Pangenome Reference Consortium (2026). Variation and selection at predicted G-quadruplexes across the human pangenome. BIORXIV.
Paper Link Non-B DNA & Microsatellite
P Hallast, A Rhie, M Loftus, M Mazzetto, P Ebert, S Gao, GV Martino, PA Audano, H Ashraf, Karol Pal, R Siford, J Ebler, S Koren, D Yoo, K Kim, Y Jiang, NF Hansen, P Hebbar, T Kanno, O Purnoch, C Montano, J Lin, KK Oshima, L Ren, A Guarracino, M Jensen, BJ Pinto, D Porubsky, S Kuziel, L Ni, J Li, P Balachandran, F Yilmaz, Human Genome Structural Variation Consortium (HGSVC), Human Pangenome Reference Consortium (HPRC), JO Korbel, B Paten, M Gerstein, Kateryna Makova, Ph.D., X Shi, Evan E. Eichler, CR Beck, MR Wilson, MK Konkel, T Marschall, Monika Cechova (Michalovova), G Logsdon, Adam M. Phillippy, C Lee (2026). Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures. BIORXIV.
Paper Link Sex chromosome
Kateryna Makova, Ph.D., S Mohanty, Linnéa Smeds, Jacob Sieg, A Lahnsteiner (2026). Unraveling Non-B DNA Structures in the Era of Telomere-to-Telomere Genomes. ANNU REV GENOMICS HUM GENET.
Paper Link Non-B DNA & Microsatellite
G Formenti, N Jain, JA Medico, M Sollitto, D Antipov, S Barcellos, M Biegler, I Borges, JK Chang, Y Chen, H Cheng, H Conceição, M Davenport, L De Oliveira, E Duarte, G Durham, J Fenn, N Forde, PA Galante, K Gerhardt, AM Giani, S Giunta, J Kim, A Komissarov, B Koo, S Koren, D Larkin, C Lee, H Li, K Makova, P Masterson, T Murphy, K McCaffrey, RLV Mercuri, Y Na, MJ O’Connell, S Ou, A Phillippy, M Popova, A Rhie, FJ Ruiz-Ruano, S Secomandi, Linnéa Smeds, A Suh, T Tilley, N Vontzou, PD Waters, J Balacco, ED Jarvis (2026). The complete genome of a songbird. CELL, ACCEPTED.
Paper Link Non-B DNA & Microsatellite
Karol Pal, Alexandra Greshnova, S Park, Byung June Ko, Hana Palova, M Steinegger, SLK Pond, S Canzar, Kateryna Makova, Ph.D. (2026). How and why ampliconic genes survive on the human Y chromosome. BIORXIV.
Paper Link Sex chromosome
D García-Ruano, M Georges, Saswat Kumar Mohanty, R Baaziz, Kateryna Makova, Ph.D., M Nikolski, D Chalopin (2026). Uncertainty-aware benchmarking reveals ambiguous transcripts in mRNA-lncRNA classification. BIORXIV.
Paper Link Non-B DNA & Microsatellite
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Videos
How and why multicopy genes survive on the human Y chromosome featured image

How and why multicopy genes survive on the human Y chromosome

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Complete X and Y chromosome sequences of living great ape species featured image

Complete X and Y chromosome sequences of living great ape species

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The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes featured image

The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes

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Detection and dynamics of mitochondrial mutations in mammalian populations and single cells with applications to aging and diseases featured image

Detection and dynamics of mitochondrial mutations in mammalian populations and single cells with applications to aging and diseases

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Members

Kateryna Makova, Ph.D.

Kateryna Makova, Ph.D.

Professor

Department of Biology

Kateryna is interested in genomics, evolution, and human genetics. Her lab studies mutations using both computational and experimental approaches. Additional topics of interest include sex chromosome evolution and genomics of childhood obesity.

Genesis Castillo

Genesis Castillo

Byung June Ko

Byung June Ko

Postdoctoral Scholar

Currently, Byung June focuses on telomere-to-telomere genome assembly and the functional research of chromatin's complex structure, particularly in sex chromosomes. Prior to bioinformatics, Byung June majored in conservation genetics, focusing on identifying the genetic diversity and structure of the leopard cat in the South Korea during his M.S. course, supervised by Prof. Soo Hyung Eo. This research sparked his interest in bioinformatics and genome functionality, leading to his false gene gain research collaboration with the Vertebrate Genomes Project during his Ph.D. course at Seoul National University, supervised by Prof. Heebal Kim. Outside of science, Byung June enjoyed playing bass and electric guitar and now enjoys weight lifting and walking in peaceful towns.

Saswat Kumar Mohanty

Saswat Kumar Mohanty

Ph.D. Student

Saswat is interested in understanding the evolution of non-B-DNA structures in primates. Currently, he is working mainly on a specific type of non-B-DNA structure called the G-quadruplex or G4, for example, developing bioinformatic tools to analyze genome-wide distribution of these structures.

Karol Pal

Karol Pal

Postdoctoral Scholar

Karol has a Computer Science background but also enjoys the biological aspect of his work. He did his PhD in Oncology analyzing clonal evolution in leukemias. Currently he is focusing on a more standard type of evolution, that of the primate sex chromosomes. He enjoys creating interactive visual representations of his findings. Outside of the lab Karol likes playing music and scuba diving.

Hana Palova

Hana Palova

Researcher

Before joining Makova Lab, Hana worked for six years in the field of molecular genetic characterization of pediatric solid tumors and hereditary diseases in Prof. Slaby’s research group at CEITEC, Masaryk University, Brno, Czechia. She got familiar with the interpretation of next generation sequencing data (mainly WES, RNA seq) and a spectrum of molecular genetic methods. She collaborated on several publications and grant projects. In Makova Lab she is responsible for cell cultivation, performing molecular biology methods, and has recently started a new project focusing on the study of telomeres in macaques. Apart from work, she enjoys spending time with her husband and 3 year-old son.

Jacob Sieg

Jacob Sieg

Postdoctoral Scholar

Jacob's current research in Makova Lab uses a combination of experimental and computational approaches to characterize the role of non-canonical DNA secondary structures in primate genomes. Before joining Makova Lab, Jacob studied RNA biochemistry. His Ph.D. thesis work with Dr. Philip Bevilacqua updated thermodynamic models that describe RNA secondary structures to better reflect the cellular environment. His undergraduate thesis work focused on drug targeting RNA thermometers in bacteria.

Johanna Stepanian

Johanna Stepanian

Ph.D. Student

Johanna has a background in microbiology and computational biology, with a strong interest in the study of evolution. She currently works on the evolution of sex chromosomes across primates. Although skilled in both wet and dry lab work, she is more drawn to the computational side of research. Her long term interests lie in bioinformatics and evolutionary biology, including RNA-seq, genomic diversity, and population structure, driven by a continued interest in bringing computational approaches to biological questions. Outside the lab, she enjoys biking, traveling, and crafts.

Huiqing Zeng

Huiqing Zeng

Research Technologist

Huiqing's current interest in Makova Lab is using new technologies, such as ddPCR, next generation sequencing, etc., to study genomics and human genetics. Before joining Makova Lab, she studied signaling pathway in mouse embryonic development.

Hui Zhao

Hui Zhao

Administrative Assistant

Hui obtained her M.S. in Biology from McMaster University, Canada, in the year of 2013. After living in Canada for 4 years, she moved to US and settled down in State College along with her family. She joined Makova Lab as an administrative assistant in 2024. Apart from her work, Hui likes cooking, karate, excercise, or watching animal documentaries.

All members

Collaborators

Laura Carrel

Laura Carrel

Department of Biochemistry and Molecular Biology, Huck Institutes of the Life Sciences, Penn State University

Department of Biochemistry and Molecular Biology, Huck Institutes of the Life Sciences, Penn State University

Prof. Carrel focuses on genetic, epigenetic, and genomic regulation of expression on the mammalian X chromosome.

Francesca Chiaromonte

Francesca Chiaromonte

Pennsylvania State University

Pennsylvania State University

Francesca is a statistician developing methods for the analysis of large, high-dimensional and complex data, and applying such methods in contemporary “Omics” sciences and other scientific fields – including Meteorology and Economics.

Barbara Arbeithuber

Barbara Arbeithuber

Postdoctoral scholar

University Clinic of Gynaecology, Obstetrics and Gynaecological Endocrinology, Johannes Kepler University Linz, Austria

In Prof. Makova's lab Barbara was interested in the accurate measurement of rare mutations. Her project was focused on the inheritance of mitochondrial DNA; particularly, analysis of de novo mutations in the germ line, as well as the inheritance of low-level variants.

Marzia Cremona

Marzia Cremona

Visiting Research Professor

Université Laval, Canada

Marzia develops statistical techniques for the analysis of large, high-dimensional and complex data – in particular functional data. An important aspect of her research is its collaborative and multidisciplinary nature. Indeed, much of her work is at the interface between statistics and computational biology, and her main application area is in the “Omics” sciences.

Michael DeGiorgio

Michael DeGiorgio

Department of Electrical Engineering and Computer Science, Florida Atlantic University

Department of Electrical Engineering and Computer Science, Florida Atlantic University

Michael leads a data science research group focusing on the development and application of statistical and machine learning techniques in genomics.

Francisco J. Diaz

Francisco J. Diaz

Pennsylvania State University

Pennsylvania State University

Francisco's research focuses on understanding the molecular and functional interactions between oocytes and granulosa cells that promote production of a fertile oocyte. This knowledge can then be used to (1) develop better therapeutic interventions for infertility or species preservation and (2) develop better reproductive management tools for animal agriculture.

Kristin Eckert

Kristin Eckert

Department of Pathology and Laboratory Medicine and Department of Biochemistry and Molecular Biology

Department of Pathology and Laboratory Medicine and Department of Biochemistry and Molecular Biology

Prof. Eckert is focused on mechanisms of human cell mutagenesis and repetitive DNA replication in relation to genome evolution.

Evan E. Eichler

Evan E. Eichler

Department of Genome Sciences, University of Washington

Department of Genome Sciences, University of Washington

Prof. Eichler's research is focused on understanding the evolution, pathology and mechanism(s) of recent gene duplication and DNA transposition within the human genome. His work involves the systematic discovery of these regions, the development of methods to assess their variation, the detection of signatures of rapid gene evolution and ultimately the correlation of this genetic variation with phenotypic differences within and between species.

Malcolm Ferguson-Smith

Malcolm Ferguson-Smith

University of Cambridge

University of Cambridge

Malcolm Ferguson-Smith's significant contributions to human genetics and cytogenetics range from early studies applying the sex chromatin method to the analysis and frequency of intersexual states, and to genome mapping using chromosome rearrangements. Malcolm was the first to report the now familiar phenomenon of satellite association, the 48 XXXY karyotype, the specificity of location of secondary constrictions in the human chromosome set and gene location by in situ hybridization.

Christian Huber

Christian Huber

Biology department of The Pennsylvania State University

Biology department of The Pennsylvania State University

Christian is an Assistant Professor in the Biology department of The Pennsylvania State University. He is interested in quantifying positive and negative natural selection in the genome. Currently he's been working on methods for inferring demographic history and genetic adaptation from ancient DNA.

Adam M. Phillippy

Adam M. Phillippy

Genome Informatics Section at the National Human Genome Research Institute

Genome Informatics Section at the National Human Genome Research Institute

Dr. Adam Phillippy is a Senior Investigator and head of the Genome Informatics Section at the National Human Genome Research Institute. His lab develops and applies computational methods for the analysis of massive genomics datasets, focusing on the challenges of genome sequencing and comparative genomics. He is a pioneer of single-molecule sequencing for the reconstruction of complete genomes and is best known for his work on completing the human genome from “telomere to telomere”.

Zachary Szpiech

Zachary Szpiech

Department of Biology, Institute for Computational and Data Sciences, Penn State University

Department of Biology, Institute for Computational and Data Sciences, Penn State University

Zachary works at the interface of population genetics and evolutionary genomics. His work has relevance to a number of fields including medical genetics, anthropology, and conservation genetics.

Mitchell M. Holland

Mitchell M. Holland

Pennsylvania State University

Pennsylvania State University

Dr. Holland is a Fellow in the American Academy of Forensic Sciences, and has served as an associate professorial lecturer and adjunct faculty member at various colleges and universities. Dr. Holland has been on the Editorial Board of the Journal of Forensic Sciences and a member of the Advisory Board of the International Journal of Legal Medicine. He has held positions on governmental and company advisory boards and has been recognized by the FBI and others for his work. Dr. Holland has had extensive experience with human remains identification cases, including the identification of victims from the World Trade Center disasters and from numerous commercial airline accidents. His rearch group is focused on advancing forensic DNA applications, especially in the area of forensic mitochondrial (mt) DNA analysis.

Yifei Huang

Yifei Huang

Yifei is an Assistant Professor in the Biology Department and the Huck Institutes at the Pennsylvania State University. He is interested in developing novel machine learning models to study how natural selection shapes the distribution of human genomic variation and the architectures of genetic diseases.

Paul Medvedev

Paul Medvedev

Pennsylvania State University

Pennsylvania State University

Paul Medvedev is a Professor in the Department of Computer Science and Engineering and the Department of Biochemistry and Molecular Biology and the Director of the Center for Computational Biology and Bioinformatics at the Pennsylvania State University. His research is focused on developing computer science techniques for analysis of biological data and on answering fundamental biological questions using such methods.

Anton Nekrutenko

Anton Nekrutenko

Pennsylvania State University

Pennsylvania State University

Prof. Nekrutenko performed postdoctoral work at the University of Chicago where he found his interest in computational genomics. After moving to the Pennsylvania State University as an Assistant Professor, he and his collaborators developed the Galaxy platform for analysis of biological data. He is now a professor of biochemistry and molecular biology and founding member of galaxyproject.org.

Rasmus Nielsen

Rasmus Nielsen

Department of Integrative Biology and the Department of Statistics, University of California at Berkeley

Department of Integrative Biology and the Department of Statistics, University of California at Berkeley

Rasmus focuses on the development and application of statistical and computational methods for analyzing genomic data in the context of evolutionary genetics, population genetics, and medical genetics.

Ian Paul

Ian Paul

Penn State College of Medicine

Penn State College of Medicine

Ian Paul, MD, MSc, graduated from Penn State College of Medicine and completed his residency training at Duke University Medical Center in Durham, N.C. In addition to his responsibilities as a general pediatrician at Penn State Pediatrics and in the newborn nursery, Dr. Paul spends much of his time working on a variety of research projects and clinical trials that seek to improve health care for children and their families. His current research includes studies to prevent obesity and help breastfeeding newborns.

Matthew Reimherr

Matthew Reimherr

Department of Statistics, Pennsylvania State University

Department of Statistics, Pennsylvania State University

Matthew's research interests include functional data analysis, longitudinal data analysis, and data privacy with applications to Omics data.

Oliver Ryder

Oliver Ryder

Zoological Society of San Diego

Zoological Society of San Diego

Dr. Oliver Ryder serves San Diego Zoo Wildlife Alliance as the Kleberg Endowed Director of Conservation Genetics. He oversees research activities in the areas of molecular genetics, genomic studies, and genetic rescue efforts, including stem cell applications – all focused on reducing extinction risk and contributing to species recovery and sustainable populations. He guides the strategic development of efforts to develop and expand a global network of cryobanking facilities, especially for viable tissue culture cells.

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310 Wartik Lab

University Park, Pennsylvania 16802

United States

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kdm16@bx.psu.edu

Phone

+1-814-863-1619

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