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 able to segment the genome into regions with high and low rates of different mutation types.
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 good starting point for such an investigation due to its compact size and high mutation rate.
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. We are following a large group of newborn children until they are at least 3 years of age.
We have investigated microsatellite evolution in the framework of a life-cycle hypothesis, according to which microsatellites are born and expand into adulthood, until their degradation and death. Microsatellites are implicated in numerous diseases and used as markers in population genetics and forensics.
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 chromosomes in the mammalian genome due to a higher number of cell divisions in the male than female germ line.
Congratulations to the Gorilla Y Chromosome group for their paper being accepted in Genome Research !
Congratulations to Malika Laurence for her grant awarded by the Undergraduate Research Fund !
Congratulations to Marta Tomaszkiewicz for her 3rd place during the 8th Annual Postdoc Research Exhibition !
Congratulations to Wilfried Guiblet on winning the Huck Dissertation Research Award 2015!
Monika Michalovova receives the CBIOS predoctoral training grant from the NIH's National Institute of General Medical Sciences !
Read about our latest research on the maternal age affect on human mtDNA in the October 28, 2014 edition of PNAS.
Makova Lab graduate students Rebeca and Samarth awarded the Jeanette Ritter Mohnkern Graduate Student Scholarship in Biology and Huck Dissertation Research Award respectively
Congratulations to Sarah on winning the Penn State Clinical and Translational Science Institute Novel Methodologies in Health Research Award!
Read Rebeca's latest article in Molecular Biology and Evolution : Genomic Landscape of Human, Bat and Ex Vivo DNA Transposon Integrations
|2016||Tomaszkiewicz, Rangavittal, Cechova et al.||A Time- and Cost-Effective Strategy to Sequence Mammalian Y Chromosomes: An Application to the de novo Assembly of Gorilla Y||Genome Research||S|
|2015||Fungtammasan, Ananda et al.||Accurate Typing of Short Tandem Repeats from Genome-wide Sequencing Data and its Applications||Genome Research||Mc|
|2015||Makova, Hardison||The effects of chromatin organization on variation in mutation rates in the genome||Nature Reviews Genetics||R|
|2014||Chiaromonte, Makova||Using Statistics to Shed Light on the Dynamics of the Human Genome: A Review. Advances in Complex Data Modeling and Computational Methods in Statistics||Contributions to Statistics||R|
|2014||Rebolledo-Jaramillo, Su et al.||Maternal Age Effect and Severe Germline Bottleneck in the Inheritance of Human Mitochondrial DNA||PNAS||Mt|
|2014||Paul et al.||The Intervention Nurses Start Infants Growing on Healthy Trajectories (INSIGHT) study||BMC pediatrics||O|
|2014||Ananda et al.||Microsatellite Interruptions Stabilize Primate Genomes and Exist as Population-Specific Single Nucleotide Polymorphisms within Individual Human Genomes||PLoS Genet.||Mc|
|2014||McElhoe et al.||Development and assessment of an optimized next-generation DNA sequencing approach for the mtgenome using the Illumina MiSeq||Forensic Science International: Genetics||Mt|
|2014||Campos-Sanchez, Kapusta et al.||Genomic Landscape of Human, Bat, and Ex Vivo DNA Transposon Integrations||Molecular Biology and Evolution||R|
|2014||Dickins, Rebolledo-Jaramillo et al.||Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach||BioTechniques||Mt|
|2013||Kuruppumullage Don, Ananda et al.||Segmenting the human genome based on states of neutral genetic divergence||Proceedings of the National Academy of Sciences||R|
|2013||Steiner et al.||Mitochondrial Genome: Clues about the Evolution of Extant Equids and Genomic Diversity of Horse Breeds, in Equine Genomics||(ed B. P. Chowdhary), Blackwell Publishing Ltd., Oxford, UK||Mt|
|2013||Montgomery et al.||The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes||Genome Research||Mc|
|2013||Baptiste et al.||Mature Microsatellites: Mechanisms Underlying Dinucleotide Microsatellite Mutational Biases in Human Cells||Genes, Genomes, and Genetics||Mc|
|2013||Ananda et al.||Distinct mutational behaviors distinguish short tandem repeats from microsatellites in the human genome||Genome Biology and Evolution||Mc|
|2013||Wilson Sayres, Makova||Gene survival and death on the human Y chromosome||Molecular Biology and Evolution||S|
|2012||Wagstaff et al.||Rescuing Alu: recovery of new inserts shows LINE-1 preserves Alu activity through A-tail expansion||PLoS Genetics||R|
|2012||Fungtammasan et al.||A Genome-wide Analysis of Common Fragile Sites: What Features Determine Chromosomal Instability in the Human Genome?||Genome Research||R Mc|
|2012||Wolfe et al.||SMBE Proposal to the Government of Japan||Molecular Biology and Evolution|
|2011||Wilson Sayres, Makova||Genome analyses substantiate male mutation bias in many species||Bioessays||S|
|2011||Kelkar et al.||A matter of life or death: How microsatellites emerge in and vanish from the human genome||Genome Research||Mc|
|2011||Afgan et al.||Harnessing cloud-computing for biomedical research with Galaxy Cloud||Nature Biotechnology||Mt|
|2011||Goto et al.||A massively parallel sequencing approach uncovers ancient origins and high genetic variability of endangered Przewalski s horses||Genome Biology and Evolution||Mt|
|2011||Lombard et al.||A Computational Approach to Candidate Gene Prioritization for X-Linked Mental Retardation using Annotation-based Binary Filtering and Motif-Based Linear Discriminatory Analysis||Biology Direct||S|
|2011||Goto et al.||Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study||Genome Biology||Mt|
|2011||Wilson et al.||Do variations in substitution rates and male mutation bias correlate with life history traits? A study of 32 mammalian genomes||Evolution||R S|
|2011||Ananda et al.||A genome-wide view of mutation rate co-variation using multivariate analyses||Genome Biology||R|
|2010||Kelkar et al.||What Is a Microsatellite: A Computational and Experimental Definition Based upon Repeat Mutational Behavior at A/T and GT/AC Repeats||Genome Biol. Evol.||Mc|
|2010||Park et al.||Strong Purifying Selection at Genes Escaping X Chromosome Inactivation||Molecular Biology and Evolution||S|
|2010||Kvikstad, Makova||The (r)evolution of LINE and SINE distribution in the primate genomes: Sex chromosomes are important||Genome Research||R|
|2010||Schuster et al.||Complete Khoisan and Bantu genomes from southern Africa||Nature|
|2009||Wilson, Makova||Evolution and survival on eutherian sex chromosomes||PLoS Genetics||S|
|2009||Wilson, Makova||Genomic analyses of sex chromosome evolution||Annual Reviews of Human Genetics and Genomics||S|
|2009||Kvikstad et al.||Ride the wavelet: a multi-scale analysis of genomic contexts flanking small insertions and deletions||Genome Research||R|
|2009||Park, Makova||oding region structural heterogeneity and turnover of transcription start sites contribute to divergence in expression between duplicate genes||Genome Biology|
|2009||Goto et al.||Evolution of X-degenerate Y chromosome genes in greater apes: Conservation of gene content in human and gorilla, but not chimpanzee||Journal of Molecular Evolution||S|
|2009||Allison et al.||Horse Domestication and Conservation Genetics of Przewalski's Horse Inferred from Sex Chromosomal and Autosomal Sequences||Molecular Biology and Evolution|
|2008||Tyekucheva et al.||Human-macaque comparisons illuminate variation in neutral substitution rates||Genome Biology||R|
|2008||Kvikstad et al.||Rapid Evolution of Genes on the Human X-chromosome. Encyclopedia of Life Sciences (ELS)||John Wiley & Sons||S|
|2008||Kelkar et al.||The genome-wide determinants of microsatellite evolution||Genome Research||Mc|
|2007||Kvikstad et al.||A macaque's-eye view of human insertions and deletions: differences in mechanisms||PLoS Computational Biology||R|
|2007||Blankenberg et al.||A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly||Genome Research|
|2007||Rhesus Macaque Genome Sequencing and Analysis Consortium (K. D. Makova - member)||Evolutionary and Biomedical Insights from the Rhesus Macaque Genome||Science||S|
|2006||Carrel et al.||Genomic environment predicts expression patterns on the human inactive X chromosome||PLoS Genet||S|
|2006||Goetting-Minesky, Makova||Mammalian Male Mutation Bias: Impacts of Generation Time and Regional Variation in Substitution Rates||Journal of Molecular Evolution||R S|
|2006||Chung et al.||Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network||BMC Bioinformatics|
|2006||Taylor et al.||Strong and Weak Male Mutation Bias at Different Sites in the Primate Genomes: Insights from the Human-Chimpanzee Comparison||Molecular Biology and Evolution||R|
|2005||Makova, Norton||Worldwide polymorphism at the MC1R locus and normal pigmentation variation in humans||Peptides|
|2005||The Chimpanzee Sequencing and Analysis Consortium (K. D. Makova - member)||Initial sequence of the chimpanzee genome and comparison with the human genome||Nature|
|2005||Nekrutenko et al.||Oscillating Evolution of a Mammalian Locus with Overlapping Reading Frames: An XLas/ALEX Relay||PloS Genetics|
|2004||Makova et al.||Indels are male-biased too: a whole genome analysis in rodents||Genome Research||R|
|2004||Miller et al.||Comparitive Genomics||Annual Review of Genomics and Human Genetics|
|2004||Rat Genome Sequencing Project Consortium (K. D. Makova - member)||Evolution of the Mammalian Genome: sequence of the genome of the brown Norwegian Rat||Nature||R S|
|2004||International Chicken Genome Sequencing Consortium (K. D. Makova - member)||Sequence and comparitive analysis of the chicken genome provide unique perspectives on vertebrate evolution||Nature||R S|
|2003||Makova, Li||Divergence in the spatial pattern of gene expression between human duplicate genes||Genome Research|
|2003||John et al.||DNA polymorphism and selection at the melanocortin-1 receptor gene in normally pigmented southern African individuals||Ann N Y Acad Sci|
|2003||Li, Makova||Molecular Clocks||Encyclopedia of the Human Genome (Nature Publishing Group)|
|2003||Li, Makova||Domain duplication and gene elongation||Encyclopedia of the Human Genome (Nature Publishing Group)|
|2002||Li et al.||Male-driven evolution||Current Opinions in Genetics and Development.|
|2002||Mu et al.||Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum||Nature|
|2002||Makova, Li||Strong male-driven evolution of DNA sequences in humans and apes||Nature|
|2002||Nekrutenko et al.||The KA/KS ratio test for assessing the protein-coding potential of genomic regions: An empirical and simulation study||Genome Research|
|2001||Makova et al.||Human DNA sequence variation in a 6.6-kilobase region containing the melanocortin 1 receptor promoter||Genetics|
|2001||Liu, Makova et al.||Periods of rapid evolution of growth hormone in primates and emergence of species specificity of growth hormone receptor||Molecular Biology and Evolution|
|2001||Li, Makova||Molecular Clocks||Encyclopedia of Genetics (Academic Press)|
|2001||Longmire et al.||Tetranucleotide microsatellite markers for the brown-headed cowbird (Molothrus ater)||Journal of Avian Biology|
|2000||Makova et al.||Evolution of Microsatellite Alleles in Four species of mice (genus Apodemus)||Journal of Molecular Evolution|
|2000||Nekrutenko et al.||Isolation of binary species-specific PCR-based markers and their value for systematic applications||Gene|
|1999||Nekrutenko et al.||Representational Difference Analysis to distinguish cryptic species||Molecular Ecology|
|1999||Baker et al.||Microsatellites indicate high frequency of multiple paternity in Apodemus (Rodentia)||Molecular Ecology|
|1998||Makova et al.||Microsatellite markers in wood mouse and striped field mouse (genus Apodemus)||Molecular Ecology|
|1998||Makova et al.||Increased yield of tri- and tetranucleotide microsatellite markers from unenriched small-insert libraries||BioTechniques|
email@example.com Lab : (814) 863-2185
I am generally interested in human evolution with a specific emphasis on genetic variation within and between species, gene duplication, and the evolution of regulatory elements. I find 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. My current project in the Makova Lab focuses on childhood obesity.
Ph.D student, Program in Biology
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.
Ph.D student, Intercollege Graduate Program in Genetics
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.
Ph.D student, Program in Integrative Bioscience - Bioinformatics and Genomics
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.
Mitochondrial change and inheritance patterns
Professor, Department of Biology Director, Center for Medical Genomics
firstname.lastname@example.org Office: (814) 863-1619
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.
Ph.D student, Program in Integrative Bioscience - Bioinformatics and Genomics
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.
Ph.D student, Program in Integrative Bioscience - Bioinformatics and Genomics - Co-advised by Anton Nekrutenko
I am from Chile, and I am a Fulbright Ph.D. student in the Bioinformatics and Genomics program. I am currently a member of the mitochondrial team. I develop computational pipelines for the understanding of mitochondrial DNA variation and evolution in natural populations.
email@example.com Lab : (814) 863-2185
My research focuses on molecular microbiology and genetics. I am currently investigating the variation of mitochondrial DNA (mtDNA) between humans using the Next Generation Sequencing and computational analyses. My goal is to discover how mtDNA mutations correlate with diseases to aid the development of personalized and preventative medicine.
Ph.D student, Program in Integrative Bioscience - Bioinformatics and Genomics - Co-advised by Anton Nekrutenko
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. More information at https://nstoler.com https://github.com/NickSto/
firstname.lastname@example.org Lab : (814) 863-2185
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.
Undergraduate Student, Program in Veterinary and Biomedical Sciences
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.
Ph.D student, Program in Integrative Bioscience - Bioinformatics and Genomics - Co-advised by Paul Medvedev
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.
Zaky Adam - Postdoctoral Scholar
Guru Ananda - Postdoctoral Scholar
Amanda Breski - Undergraduate student - Biology
Rebeca Campos-Sanchez - Ph.D student, Intercollege Graduate Program in Genetics
Benjamin Dickins - Postdoctoral Scholar
Prabhani Kuruppumullage Don - Ph.D. student - Statistics
Allison Fisher - Undergraduate student - Biology
Arkarachai Fungtammasan - Ph.D student, Program in Integrative Bioscience - Bioinformatics and Genomics
Matthew Ghent - Undergraduate - Biochemistry
Aparna Goel - Undergraduate student
Paula Goetting - Senior research assistant
Hiroki Goto - Postdoctoral Scholar
Yogeshwar Kelkar - Ph.D. student - Biology
Lydia Krasilnikova - Undergraduate student - Computer Science
Erika Kvikstad - Ph.D. student - Genetics
Allison Lau - Undergrad - Biology
Malika Laurence - Undergraduate Student, Premedical-Medical Program
Ali Martinson - Undergraduate student - Biology
Matthew Nielsen - Undergraduate student - Biology
Chungoo Park - Ph.D. student - Biology
Lei Peng - Undergrad - Biology
Adil Sarwar - Ph.D. student - Computer Science
Melissa A. Wilson Sayres - Ph.D. student - Integrative Biosciences
Bryant Schultz - Undergraduate student - Biology
Carolyn Rogers - Undergraduate Student - Program in Biology
Department of Statistics - Pennsylvania State University
Department of Biology
Associate Professor of Reproductive Biology
Emeritus Professor of Pathology - University of Cambridge
Associate Professor, Biochemistry & Molecular Biology
San Diego Zoological Society
Post-doctoral applicants : Please mail a copy of your CV and reference letters to Kateryna Makova.
Graduate students may apply through the Huck Institutes Program or the Department of Biology.
Rotation candidates may email Kateryna Makova.
Postdoctoral position: Computational Biologist :
The Makova lab is looking to hire a computational postdoctoral researcher with knowledge of genomics for a project examining mitochondrial mutations and their transmission in humans from an evolutionary perspective (please see our recent publication in PNAS. Such knowledge is vital in a clinical setting when transmission risk for pathogenic mutations must be estimated. Our resources and links with medical researchers at Penn State College of Medicine and computational biologists from the Galaxy team put us in a great position to address these questions. A PhD in Computational Biology or related field is required. Candidates should be familiar with scientific programming and statistical analysis techniques. Experience with next-generation sequencing data analyses is desirable. You will be joining an established dynamic group. Penn State is a vibrant scientific community with particular strengths in computational genomics and molecular evolution. Our location, in State College, Pennsylvania, is known for excellent public schools, low cost of living, and numerous opportunities for outdoor activities. The starting date is flexible, with an earlier date preferred. Interested applicants should send a pdf with a CV, a statement of research interests, and contact information of three referees to Kateryna Makova at email@example.com, indicating “mtDNA postdoc” in the subject line.
We contribute our tools to Galaxy, a free software for genomic research.
Genomic Environment Predicts Expression Patterns on the Human Inactive X Chromosome.
Carrel L, Park C, Tyekucheva S, Dunn J, Chiaromonte F, Makova KD. PLoS Genet 2(9): e151. doi:10.1371/journal.pgen.0020151
Online Supplemental materials
Coding region structural heterogeneity and turnover of transcription start sites contribute to divergence in expression between duplicate genes Chungoo Park and Kateryna Makova.
Genome Biology 2009, 10:R10 (doi:10.1186/gb-2009-10-1-r10)
Duplicate genes from FASTA
Duplicate genes by TRIBE-MCL
Expression data for human tissues in U133A and GNF1H affymetrix arrays
Genes mapping to probes with a one-to-one correspondence
X and Y-added Region
Evolution and Survival on Eutherian Sex Chromosomes
Wilson MA and Makova KD.
PLoS Genet. 2009 Jul;5(7):e1000568. Epub 2009 Jul 17.
Unmasked FASTA files for XAR/YAR genes
Sample Gene Reads
Sample Gene Reads