Members
Members
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.
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
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
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
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
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
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
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
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.
Former Members
Zaky Adam
Postdoctoral Scholar
Guru Ananda
Postdoctoral Scholar
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.
Amanda Breski
Undergraduate student
Rebeca Campos-Sanchez
Ph.D. student
Sarah J. Carnahan Craig
Research Assistant Professor
Sarah is interested in human evolution with a specific emphasis on genetic variation within and between species, gene duplication, and the evolution of regulatory elements. She found that the application of knowledge from these genetic investigations to explain (or help explain) phenotypic observations in humans (especially related to reproduction and human health) to be particularly exciting. Her project in the Makova Lab was focused on childhood obesity.
Monika Cechova (Michalovova)
Ph.D. student
I enjoy bioinformatics as a tool to study evolution of sex chromosomes, transposable elements and gene expression. I am interested in topics covering RNASeq, variant calling, mapping, genome assembly and new sequencing technologies.
Di (Bruce) Chen
Ph.D. student
Born and raised up in Nanjing, China. Trained as a computational biologist and amateur violinist. Big fan of backpacking, sci-fi, and research. Current work leverages bioinformatics tools and statistics in comparative genomics, with special interest in the regional variation of mutation rate in human genome.
Benjamin Dickins
Postdoctoral Scholar
Allison Fisher
Undergraduate student
Arkarachai Fungtammasan
Ph.D. student
Matthew Ghent
Undergraduate student
Aparna Goel
Undergraduate student
Paula Goetting
Senior research assistant
Hiroki Goto
Postdoctoral Scholar
Wilfried Guiblet
Ph.D. student
I am interested in the relationship between genomics and human physiology. My current project is to relate the different type of DNA polymerases and their variability to specific mutation patterns.
Kaivan Kamali
Computational Scientist
Kaivan is a computer scientist/software engineer, specializing in AI/ML. He enjoys data analysis and applying AI/ML techniques to bioinformatics data. Currently, his research focuses on non-B DNA data.
Yogeshwar Kelkar
Ph.D. student
Lydia Krasilnikova
Undergraduate student
Arpita Dey
Postdoctoral Scholar
Arpita has a background in studying the molecular biophysical interactions of G-quadruplex and other quadruplex DNA structures involved in anticancer mechanisms. With a strong interest in cancer biology, she is now exploring the molecular evolutionary medicine of non-B-DNA structures in primates, focusing on G-quadruplexes (G4). Outside the lab, Arpita enjoys singing, cooking, and traveling to explore new places.
Lauren Anna Heverly
Undergraduate Student
Lauren is broadly interested in studying the mechanisms and genetic markers of human disease. She is currently working on a project investigating non-canonical DNA structures, specifically, examining the conditions of G-quadraplex formation. She plans to pursue a Ph.D. in the Biomedical Sciences field after completing her undergraduate education.
Prabhani Kuruppumullage Don
Ph.D. student
Erika Kvikstad
Ph.D. student
Allison Lau
Undergraduate student
Malika Laurence
Undergraduate student
Ali Martinson
Undergraduate student
Matthew Nielsen
Undergraduate student
Chungoo Park
Ph.D. student
Lei Peng
Undergraduate student
Samarth Rangavittal
Ph.D. student
I am a grad student in the Bioinformatics and Genomics program. My primary interest is in genome assembly of short and long read sequence data. I also spend time thinking about topics like the sex chromosomes of primates, and how to mix computer science with biology in new and interesting ways.
Boris Rebolledo-Jaramillo
Ph.D. student
Carolyn Rogers
Undergraduate student
Adil Sarwar
Ph.D. student
Bryant Schultz
Undergraduate student
Linnéa Smeds
Postdoctoral Scholar
Linnéa's research in the Makova lab involves investigating selection in non-canonical DNA from primates, especially G4 quadruplexes, using bioinformatics methods. Linnéa worked for 8 years as a bioinformatician in Dr. Hans Ellegren's lab, developing approaches to study speciation, mutation rate and sex chromosome evolution in birds, before taking on a Ph. D. in evolutionary genetics. Her thesis "Conservation genomics in inbred Scandinavian wolves using bioinformatic methods" involved work on Y chromosome evolution, admixture, genetic load and structural variation.
Nick Stoler
Ph.D. student
My focus is on variation in mitochondrial DNA. I develop methods and software tools to analyze mitochondrial sequencing data, as well as data from other non-diploid systems like viral populations, cancer, and somatic variation.
Marcia Shu-Wei Su
Postdoctoral Scholar
Marta Tomaszkiewicz
Research Assistant Professor
From the very beginning of my studies, I have been trying to understand the evolution of sex chromosomes across invertebrate and vertebrate taxa. Now, my postdoctoral research is focused on the Y chromosomes of primates. Using comparative genomics tools I am trying to answer important questions linked to the male heterogamety of our closest relatives.
Edmundo Torres-González
Ph.D. student
Before starting his PhD in the Makova lab, Edmundo worked on regional human variation as an undergraduate in Puerto Rico and on translational cancer genomics as a postdoc in NIH. As part of this thesis work, he focuses on mitochondrial genomics that cover its evolution, and relation to complex phenotypes.
Rahulsimham Vegesna
Ph.D. student
I am interested in understanding the mechanism that give rise to complex genomic structural variants in cancer. I am studying the role of different DNA polymerases in the formation of different structural variations.
Melissa A. Wilson Sayres
Ph.D. student
Danling Ye
Undergraduate student
I am an undergraduate student currently pursuing a degree in Veterinary and Biomedical Sciences. In the lab, I am helping with a project involving genetics on the Y chromosome. I am also interested in research about the genetics involved in reproduction.
Arslan Zaidi
Postdoctoral Scholar
I am interested in studying both the proximal (developmental) and ultimate (evolutionary) causes of human genetic variation. I am currently examining the transmission of mitochondrial heteroplasmies in families to understand the biological processes governing mitochondrial DNA inheritance in humans. When I’m not science-ing, I’m drawing or re-reading The Lord of the Rings.
Xinru Zhang
Ph.D. student
Xinru is a Ph.D. student in the Bioinformatics and Genomics Program co-advised by Dr. Kateryna Makova and Dr. Yi-Fei Huang. Currently, she is studying the evolution of human genome, specifically G-quadruplexes and regulatory elements. By integrating machine learning and phylogenetic inferences, she aims to explore the connection between evolutionary biology and human health.
Collaborators
Collaborators
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
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
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
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
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
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
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
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
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
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
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
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
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 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
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
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
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
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
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
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.