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  • Projects
    • Childhood obesity
    • Mitochondrial mutation dynamics
    • Non-B DNA and microsatellite variation and evolution
    • Regional variation in mutation rates
    • Sex chromosome evolution
  • News
    • Congratulations to Saswat Mohanty for winning the the 2026-27 Alumni Association Graduate Fellowship
    • Congratulations to Kateryna on her interview with Roxanne Khamsi in a new book Beyond Inheritance
    • Congratulations to Saswat Mohanty for winning the Jeanette Ritter Mohnkern Graduate Student Scholarship in Biology
    • Congratulations to Huiqing Zeng for winning the Biology 2025 Research Staff Excellence Award
    • Congratulations to Edmundo Torres-González on his successful PhD defense
    • Congratulations to Saswat Mohanty for winning an EXPLORER grant to support his summer internship at the University of Montpellier, which will strengthen collaborations between PSU and UoM.
    • Congratulations to Xinru Zhang who has been named as one of the recipients of the Jeanette Ritter Mohnkern Graduate Student Scholarship in Biology for the 2022/2023 fiscal year!
    • Congratulations to Xinru Zhang on publishing a manuscript in Nature Communications
    • Congratulations to Edmundo Torres-González for winning the GlaxoSmithKline (GSK) Graduate Fellowship from the Eberly College of Science in partnership with the College of Medicine and the Huck Institutes of the Life Sciences for the 2023-2024 academic year.
    • Congratulations to Sarah Craig on winning the Center for Human Evolution and Diversity grant
    • Congratulations to Barbara Arbeithuber, a former postdoc from the lab, on winning the 2021 EMGS New Investigator Presentation Award!
    • Congratulations to Bonnie Higgins on winning the 2020 Biology Research Staff Award!
    • Marta Tomaszkiewicz won the first prize for the poster presentation at the 13th Research Exhibition for postdocs and assistant research professors at Penn State
    • Congratulations to Wilfried Guiblet on his successful PhD defense
    • We are proud of Allison Watwood on her selection as a trainee of the CBIOS (Computation Bioinformatics, and Statistics) NIH Training Grant
    • Congratulations to Monika Cechova and Rahul Vegesna on their graduation. We hope you both come back to work after the pandemic
    • We are proud of Edmundo Torres Gonzalez on being awarded the NSF Graduate Fellowship
    • Good luck to Rahul Vegesna as he starts his postdoctoral position at the National Cancer Institute
    • Frontiers public lecture presented by Kateryna Makova: Predicting mutation and disease occurrence from DNA and omics data
    • Congratulations to Rahul Vegesna on his successful PhD defense
    • Good luck to Monika Cechova as she moves back to Czech Republic to start her postdoctoral position at the Central European Institute of Technology in Brno
    • Congratulations to Monika Cechova on her successful PhD defense
    • Barbara Arbeithuber awarded best poster presentation
    • Marzia Cremona awarded best presentation
    • Bruce is runner-up in poster competition
    • Barbara Arbeithuber awarded Erwin Schrödinger fellowship
    • Danling receives 2017 Douglas and Regina Award for Research Achievement
    • Marta Tomaszkiewicz reviews W and Y chromosome assemblies
    • Sarah Craig and Marta Tomaszkiewicz win 1st and 2nd poster awards
    • Monika Cechova (Michalovova) wins 2016 Dr. John Randall Shuman Troxell Memorial Scholarship in Biology
    • Gorilla Y Chromosome paper accepted by Genome Research
    • Marta Tomaszkiewicz wins 3rd place award
    • Wilfried Guiblet wins 2015 Huck Dissertation Research Award
    • Malika Laurence receives grant from the Undergraduate Research Fund
    • Monika Cechova (Michalovova) receives CBIOS predoctoral training grant
    • Read about our latest research on the maternal age affect on human mtDNA
    • Rebeca and Samarth win awards
    • Sarah wins Novel Methodologies in Health research award
    • Read Rebeca's latest article in Molecular Biology and Evolution
  • Press Releases
    • In brief: Certain age-related DNA mutations are less common in human eggs
    • Beyond the double helix: Alternative DNA conformations in ape genomes
    • Complete genome sequences of six ape species unveiled
    • Complete X and Y chromosome sequences of living great ape species determined
    • DNA sequence of the human Y chromosome fully determined for first time
    • Are egg cells in aging primates protected from mutations?
    • New approach can help identify young children most at risk for obesity
    • A new class of functional elements in the human genome?
    • Unusual DNA folding increases the rates of mutations
    • Evolution of the Y chromosome in great apes deciphered
    • Scientists take a step toward understanding 'jumping genes' effect on the genome
    • New mutations accumulate in reproductive cells of older mice
    • Connecting the dots
    • Tracking inheritance of human mitochondrial DNA
    • Differences in genes’ geographic origin influence mitochondrial function
    • DNA structure impacts rate and accuracy of DNA synthesis
    • Young children’s oral bacteria may predict obesity
  • Publications
    • Single-stranded and non-canonical DNA formation in human and other ape cells with telomere-to-telomere genomes
    • Protocol for Duplex Sequencing of Mitochondrial DNA in Single Human Oocytes
    • Nuclear Mitochondrial Sequences in Great Ape Telomere-to-Telomere Genomes
    • The complete genome of a songbird
    • A Complete Genome for the Common Marmoset
    • Jim Watson (1928–2025): a genomics visionary
    • HPRC2: A human pangenome reference with near-complete coverage of common genetic variation
    • Direct detection of alternative DNA conformations with long-read sequencing and machine learning approaches
    • The Vertebrate Genomes Project Phase I: A global reference genome resource
    • Variation and selection at predicted G-quadruplexes across the human pangenome
    • Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures
    • Unraveling Non-B DNA Structures in the Era of Telomere-to-Telomere Genomes
    • How and why ampliconic genes survive on the human Y chromosome
    • Uncertainty-aware benchmarking reveals ambiguous transcripts in mRNA-lncRNA classification
    • Non-canonical DNA and sequencing challenges in bird genomes
    • Substitution spectrum and selection at G-quadruplexes in great ape telomere-to-telomere genomes
    • Mammalian Mitochondrial DNA Accumulates Insertions and Deletions with Age in Energetically Demanding Tissues
    • Allele frequency selection and no age-related increase in human oocyte mitochondrial mutations
    • Evolutionary Dynamics of G-Quadruplexes in Human and Other Great Ape Telomere-to-Telomere Genomes
    • Replicative DNA polymerase Epsilon and Delta holoenzymes show wide ranging inhibition at G-Quadruplexes in the human genome
    • Complete sequencing of ape genomes
    • Non-canonical DNA in human and other ape telomere-to-telomere genomes
    • The ape Y chromosome evolves extremely rapidly, but the X chromosome is conserved
    • The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes
    • Methylation profiles at birth linked to early childhood obesity
    • In vivo detection of DNA secondary structures using Permanganate/S1 Footprinting with Direct Adapter Ligation and Sequencing (PDAL-Seq)
    • Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes
    • The complete sequence of a human Y chromosome
    • Accurate sequencing of DNA motifs able to form alternative (non-B) structures
    • Transcription factor binding sites are frequently under accelerated evolution in primates
    • Constructing a polygenic risk score for childhood obesity using functional data analysis
    • Noncanonical DNA structures are drivers of genome evolution
    • Whole-genome sequence and assembly of the Javan gibbon (Hylobates moloch)
    • Variation in G-quadruplex Sequence and Topology Differentially Impacts Human DNA Polymerase Fidelity
    • Exploring the effects of mitonuclear interactions on mitochondrial DNA gene expression in humans
    • Advanced age increases frequencies of de novo mitochondrial mutations in macaque oocytes and somatic tissues
    • INSIGHT responsive parenting educational intervention for firstborns is associated with growth of secondborn siblings
    • Metabolomic profiling of stool of two-year old children from the INSIGHT study reveals links between butyrate and child weight outcomes
    • Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome
    • Towards complete and error-free genome assemblies of all vertebrate species
    • Non-B DNA: A major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome
    • Associations between stool micro-transcriptome, gut microbiota, and infant growth
    • Dynamic evolution of great ape Y chromosomes
    • Human L1 Transposition Dynamics Unraveled with Functional Data Analysis
    • Age-related accumulation of de novo mitochondrial mutations in mammalian oocytes and somatic tissues
    • Ampliconic genes on the great ape Y chromosomes: Rapid evolution of copy number but conservation of expression levels
    • Family reunion via error correction: an efficient analysis of duplex sequencing data
    • Pronounced somatic bottleneck in mitochondrial DNA of human hair
    • Bottleneck and selection in the germline and maternal age influence transmission of mitochondrial DNA in human pedigrees
    • Dosage regulation, and variation in gene expression and copy number of human Y chromosome ampliconic genes
    • DiscoverY: a classifier for identifying Y chromosome sequences in male assemblies
    • Noise-Cancelling Repeat Finder: Uncovering tandem repeats in error-prone long-read sequencing data
    • High Satellite Repeat Turnover in Great Apes Studied with Short- and Long-read Technologies
    • Polygenic risk score based on weight gain trajectories is a strong predictor of childhood obesity
    • Functional data analysis for computational biology
    • Investigating mitonuclear interactions in human admixed populations
    • Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate
    • Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon
    • Correcting palindromes in long reads after whole-genome amplification
    • Child Weight Gain Trajectories Linked To Oral Microbiota Composition
    • IWTomics: testing high-resolution sequence-based `Omics' data at multiple locations and scales
    • High Levels of Copy Number Variation of Ampliconic Genes across Major Human Y Haplogroups
    • RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly
    • A Population Phylogenetic View of Mitochondrial Heteroplasmy
    • Deep-Coverage MPS Analysis of Heteroplasmic Variants within the mtGenome Allows for Frequent Differentiation of Maternal Relatives
    • Elevated mitochondrial genome variation after 50 generations of radiation exposure in a wild rodent
    • Y and W Chromosome Assemblies: Approaches and Discoveries
    • Artifactual mutations resulting from DNA lesions limit detection levels in ultrasensitive sequencing applications
    • Reverse Transcription Errors and RNA–DNA Differences at Short Tandem Repeats
    • Streamlined analysis of duplex sequencing data with Du Novo
    • Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis
    • A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y
    • The effects of chromatin organization on variation in mutation rates in the genome
    • Accurate typing of short tandem repeats from genome-wide sequencing data and its applications
    • Using Statistics to Shed Light on the Dynamics of the Human Genome: A Review
    • Development and assessment of an optimized next-generation DNA sequencing approach for the mtgenome using the Illumina MiSeq
    • Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA
    • Genomic Landscape of Human, Bat, and Ex Vivo DNA Transposon Integrations
    • Microsatellite Interruptions Stabilize Primate Genomes and Exist as Population-Specific Single Nucleotide Polymorphisms within Individual Human Genomes
    • The Intervention Nurses Start Infants Growing on Healthy Trajectories (INSIGHT) study
    • Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach
    • Rapid Evolution of Genes on the Human X Chromosome
    • Segmenting the human genome based on states of neutral genetic divergence
    • Gene Survival and Death on the Human Y Chromosome
    • Mature Microsatellites: Mechanisms Underlying Dinucleotide Microsatellite Mutational Biases in Human Cells
    • Mitochondrial Genome: Clues about the Evolution of Extant Equids and Genomic Diversity of Horse Breeds
    • Distinct Mutational Behaviors Differentiate Short Tandem Repeats from Microsatellites in the Human Genome
    • The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes
    • Rescuing Alu: Recovery of New Inserts Shows LINE-1 Preserves Alu Activity through A-Tail Expansion
    • A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?
    • SMBE Proposal to the Government of Japan
    • Genome analyses substantiate male mutation bias in many species
    • Harnessing cloud computing with Galaxy Cloud
    • DO VARIATIONS IN SUBSTITUTION RATES AND MALE MUTATION BIAS CORRELATE WITH LIFE-HISTORY TRAITS? A STUDY OF 32 MAMMALIAN GENOMES
    • A computational approach to candidate gene prioritization for X-linked mental retardation using annotation-based binary filtering and motif-based linear discriminatory analysis
    • Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study
    • A genome-wide view of mutation rate co-variation using multivariate analyses
    • A Massively Parallel Sequencing Approach Uncovers Ancient Origins and High Genetic Variability of Endangered Przewalski's Horses
    • A matter of life or death: How microsatellites emerge in and vanish from the human genome
    • Strong Purifying Selection at Genes Escaping X Chromosome Inactivation
    • Complete Khoisan and Bantu genomes from southern Africa
    • The (r)evolution of SINE versus LINE distributions in primate genomes: Sex chromosomes are important
    • What Is a Microsatellite: A Computational and Experimental Definition Based upon Repeat Mutational Behavior at A/T and GT/AC Repeats
    • Genomic Analyses of Sex Chromosome Evolution
    • Evolution and Survival on Eutherian Sex Chromosomes
    • Evolution of X-Degenerate Y Chromosome Genes in Greater Apes: Conservation of Gene Content in Human and Gorilla, But Not Chimpanzee
    • Coding region structural heterogeneity and turnover of transcription start sites contribute to divergence in expression between duplicate genes
    • Horse Domestication and Conservation Genetics of Przewalski's Horse Inferred from Sex Chromosomal and Autosomal Sequences
    • Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions
    • Molecular Clocks
    • Human-macaque comparisons illuminate variation in neutral substitution rates
    • The genome-wide determinants of human and chimpanzee microsatellite evolution
    • A Macaque's-Eye View of Human Insertions and Deletions: Differences in Mechanisms
    • Evolutionary and Biomedical Insights from the Rhesus Macaque Genome
    • A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly
    • Mammalian Male Mutation Bias: Impacts of Generation Time and Regional Variation in Substitution Rates
    • Genomic Environment Predicts Expression Patterns on the Human Inactive X Chromosome
    • Domain Duplication and Gene Elongation
    • Strong and Weak Male Mutation Bias at Different Sites in the Primate Genomes: Insights from the Human-Chimpanzee Comparison
    • Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network
    • Worldwide polymorphism at the MC1R locus and normal pigmentation variation in humans
    • Initial sequence of the chimpanzee genome and comparison with the human genome
    • Oscillating Evolution of a Mammalian Locus with Overlapping Reading Frames: An XLαs/ALEX Relay
    • Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
    • COMPARATIVE GENOMICS
    • Genome sequence of the Brown Norway rat yields insights into mammalian evolution
    • Insertions and Deletions Are Male Biased Too: A Whole-Genome Analysis in Rodents
    • DNA Polymorphism and Selection at the Melanocortin-1 Receptor Gene in Normally Pigmented Southern African Individuals
    • Divergence in the Spatial Pattern of Gene Expression Between Human Duplicate Genes
    • Tetranucleotide microsatellite markers for the Brown-headed Cowbird Molothrus ater
    • Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum
    • Strong male-driven evolution of DNA sequences in humans and apes
    • Male-driven evolution
    • The K A/K S Ratio Test for Assessing the Protein-Coding Potential of Genomic Regions: An Empirical and Simulation Study
    • Human DNA Sequence Variation in a 6.6-kb Region Containing the Melanocortin 1 Receptor Promoter
    • Episodic Evolution of Growth Hormone in Primates and Emergence of the Species Specificity of Human Growth Hormone Receptor
    • Evolution of Microsatellite Alleles in Four Species of Mice (Genus Apodemus)
    • Isolation of binary species-specific PCR-based markers and their value for diagnostic applications
    • Representational difference analysis to distinguish cryptic species
    • Microsatellites indicate a high frequency of multiple paternity in Apodemus (Rodentia)
    • Microsattelite markers in wood mouse and striped field mouse (genus Apodemus)
    • Increased Yield of Tri- and Tetranucleotide Heterospecific Microsatellites from Unenriched Small-Insert Libraries
  • Videos
    • How and why multicopy genes survive on the human Y chromosome
    • Complete X and Y chromosome sequences of living great ape species
    • The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes
    • Detection and dynamics of mitochondrial mutations in mammalian populations and single cells with applications to aging and diseases
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Complete X and Y chromosome sequences of living great ape species

Jul 24, 2024 · 0 min read
video
Last updated on Jul 24, 2024
← How and why multicopy genes survive on the human Y chromosome May 27, 2026
The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes May 29, 2024 →

© 2026 The Makova Lab at Penn State. This work is licensed under CC BY NC ND 4.0

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