The Makova Lab at Penn State

Regional variation in mutation rates R

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.

Mitochondrial mutation dynamics Mt

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.

Childhood obesity O

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.

Microsatellite variation and evolution Mc

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.

Sex chromosome evolution S

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 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

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
  • Rebeca Campos-Sanchez

    PhD student, Program in Genetics
    rxc327@psu.edu
    Genome Evolution, Cancer Genomics, Population Genetics

  • Sarah J. Carnahan Craig

    Postdoctoral Scholar
    sarah@bx.psu.edu 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.

  • Di (Bruce) Chen

    Ph.D student, Program in Integrative Bioscience - Genetics
    di.bruce.chen@gmail.com
    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.

  • Arkarachai Fungtammasan

    PhD student, Program in Integrative Bioscience - Bioinformatics and Genomics
    azf127@psu.edu
    My research goal is to differentiate real biological variation from technical errors in Short Tandem Repeats (STRs). I'm interested in mutation pattern of these repeats and how they affect genome and transcriptome stability. I enjoy developing tools (in Python and R) and share them on github and Galaxy.

  • Wilfried Guiblet

    PhD stduent, Program in Integrative Bioscience - Bioinformatics and Genomics
    wmg133@psu.edu
    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.

  • Bonnie K Higgins

    Research Technician
    bkg102@psu.edu
    Mitochondrial change and inheritance patterns

  • Kateryna Makova, Ph.D.

    Professor, Department of Biology Director, Center for Medical Genomics
    kmakova@bx.psu.edu 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.

  • Monika Michalovova

    PhD student, Program in Biology
    biomonika@psu.edu
    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.

  • Samarth Rangavittal

    Ph.D student, Program in Integrative Bioscience - Bioinformatics and Genomics
    szr165@psu.edu
    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, Program in Integrative Bioscience - Bioinformatics and Genomics - Co-advised by Anton Nekrutenko
    ber5099@psu.edu
    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.

  • Marcia Shu-Wei Su

    Postdoctoral Scholar
    marcia@bx.psu.edu 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.

  • Nick Stoler

    Ph.D student, Program in Integrative Bioscience - Bioinformatics and Genomics - Co-advised by Anton Nekrutenko
    nicholas.stoler@gmail.com
    ?

  • Marta Tomaszkiewicz

    Postdoctoral Scholar
    marta@bx.psu.edu 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.

  • Danling Ye

    Undergraduate Student, Program in Veterinary and Biomedical Sciences
    dxy5063@psu.edu
    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.

  • Rahulsimham Vegesna

    Ph.D student, Program in Integrative Bioscience - Bioinformatics and Genomics - Co-advised by Paul Medvedev
    rxv923@psu.edu
    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.

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.

Lab address:
305 Wartik Lab
University Park, PA 16802
Phone: (814) 863-1619 Fax: (814) 865-9131

Advertised positions:

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 kdm16@psu.edu, indicating “mtDNA postdoc” in the subject line.

Galaxy
We contribute our tools to Galaxy, a free software for genomic research.

X inactivation
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

Indels
Human-specific indels identified in the non-coding non-repetitive (NCNR) portion of hg18 according to methods described in (Kvikstad et al 2007)
Online Supplemental materials

Duplicate genes
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