Multi-copy genes are a major source of genetic material for genomic novelty and genome evolution in eukaryotes. I was focusing on the evolution of high-copy genes that encode for ribosomal RNA, which is a key component of an essential protein-making machine called the ribosome. I was interested in dissecting the role of evolutionary forces, molecular mechanisms, and genome organization in shaping sequences of ribosomal RNA by integrating 1) genomics data from hundreds of genomes, 2) structural data of the ribosome, 3) models of molecular evolution, and 4) genotype-phenotype data through ribosome engineering and fitness assays. My work expands our knowledge of evolution of the ribosome and multi-copy genes, adds another dimension to understanding how species can adapt to novel environments (e.g. how resistance to ribosome-targeting antibiotics emerges), and contributes to a better understanding of ribosome-associated diseases.• Developed multiple computational pipelines to mine large-scale genomics data and analyze RNA:protein structures• Described a new model of high-copy gene evolution by integrating comparative genomics, structural biology, genome biology, and experimental techniques• Created eukaryotic ribosome variants via evolution-guided computational design and ribosome engineering• Co-described molecular mechanisms that increase genomic instabilities of multi-copy genes using experimental techniques• Supervised the development of a database for ribosomal RNA mutations in human populations in health and disease

Graduate-level course• Prepared and taught material that covered protein structure and function, enzymology and catalysis, and protein evolution.

Undergraduate-level course• Facilitated discussions by using an interactive approach to teach broad topics in Biology to groups of 15-25 students twice a week

In eukaryotes, broken DNA must be recognized in the context of chromatin by repair factors, and PARP1 is one of the first proteins that is recruited to DNA breaks. I developed several experimental techniques to describe step-by-step reactions that involved recognition of DNA, biochemical modification of histones, and remodeling of nucleosomes by PARP1.• Developed single-molecule FRET microscopy assays to investigate changes in chromatin structure during DNA damage• Described a novel epigenetic mode of protein PARP1• Set up collaborations to use the developed methods in studying anti-cancer drugs in the context of chromatin

RNA polymerase II is responsible for transcribing protein-coding genes in eukaryotes, and it must do so in the context of nucleosomes and histone marks which forms chromatin. I was focusing on what structural rearrangements occur in nucleosomes when the RNA polymerase passes through it during RNA synthesis, by using chromatin assembly and in vitro transcription as my main experimental techniques.