Projects

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. We are following a large group of newborn children until they are at least 3 years of age.

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 good starting point for such an investigation due to its compact size and high mutation rate.

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, triplexes, slipped-strand structures, G-quadruplexes (G4s), Z-DNA, and bent DNA. They form at certain DNA sequence motifs that are ubiquitous in the genomes of prokaryotes and eukaryotes.

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 able to segment the genome into regions with high and low rates of different mutation types.

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 chromosomes in the mammalian genome due to a higher number of cell divisions in the male than female germ line.

Press Releases

More Press Releases

Listen to the Science Friday podcast where Adam Phillippy and Kateryna Makova discuss the challenges of sequencing the Y chromosome, …

New mutations occur at increasing rates in the mitochondrial genomes of developing egg cells in aging rhesus monkeys, but the increases …

UNIVERSITY PARK, PA. — Newly developed risk scores synthesize genetic information into an easy-to-interpret metric that could help …

Recent Publications

More Publications

. The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes. NATURE, in press, 2024.

Sex chromosome Paper Link

. Methylation profiles at birth linked to early childhood obesity. J DEV ORIG HEALTH DIS, 2024.

Childhood Obesity Paper Link

. In vivo detection of DNA secondary structures using Permanganate/S1 Footprinting with Direct Adapter Ligation and Sequencing (PDAL-Seq). METHODS IN ENZYMOLOGY, 2024.

Non-B DNA & Microsatellite Paper Link

. Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes. GENOME BIOL EVOL, 2023.

Sex chromosome Paper Link

. The complete sequence of a human Y chromosome. NATURE, 2023.

Sex chromosome Paper Link

. Accurate sequencing of DNA motifs able to form alternative (non-B) structures. GENOME RES, 2023.

Non-B DNA & Microsatellite Paper Link

. Constructing a polygenic risk score for childhood obesity using functional data analysis. ECONOM STAT, 2023.

Childhood Obesity Paper Link

Kaivan Kamali

Computational Scientist

Saswat Kumar Mohanty

Ph.D. student

Karol Pál

Postdoctoral Scholar

Hana Palova

Research Assistant

Jacob Sieg

Postdoctoral Scholar

Huiqing Zeng

Research Technologist

Xinru Zhang

Ph.D. student

Hui Zhao

Administrative Assistant

Contact

  • +1-814-863-1619
  • 310 Wartik Lab, University Park, Pennsylvania, 16802, USA