We develop quantitative proteomics technologies to study several key protein complexes involved in DNA replication and chromosome segregation, regarding their composition, dynamics, stability and regulation. Insights from the proteomics analysis are further pursued to study how cells maintain their genome integrity.

Using new 3rd-generation DNA sequencing technologies, it is now possible to perform complete assembly of chromosomes from telomere to telomere.  This project will investigate new categories of genetic variation that are detectable using the PacBio Sequel II whole genome sequencing (WGS) platform that are not detectable by traditional Illumina WGS, including structural variants (SVs) and tandem repeats (TRs). The trainee on this project will become familiar with basic tools for long read HiFi sequence analysis and will innovate upon current statistical genetic methods to investigate the association of SVs and TRs with disease with a focus on genes located within new regions of the human genome that have recently been assembled.

To get a more granular understanding of how rare variants and common variants contribute to quantitative variation in psychiatric traits, my lab is leading the whole genome analysis of rare genetic diseases that are being deeply characterized with dimensional measures of psychopathology. In collaboration with clinical research groups at several institutions, we have formed a consortium of rare disease research groups called the Genes to Mental Health Network (G2MH). This project will investigate how multiple genetic factors influence clinical features of autism using rare variant genotypes and polygenic risk scores derived from whole genome sequencing. The trainee on this project will learn how to carry out statistical genetic analysis of large whole genome and phenotype datasets.

Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers

The Lab of Dr. Joseph Califano under the sponsorship of the Japan Society for the Promotion of Science (JSPS) will conduct collaborative research on a new strategy for the treatment for HPV-associated oropharyngeal cancer based on comprehensive epigenetic analysis.  This year, we are proud to congratulate Postdoctoral Researcher, Dr. Takuya Nakagawa for his work entitled “Genetic and epigenetic analysis of HPV-positive and HPV-negative Oropharyngeal Squamous Cell Carcinoma”. Dr. Nakagawa graduated from Chiba University School of Medicine in Japan where he also received the Medical Pharmacy Director’s Award.