## Principal Investigators

## Javier Arsuaga

#### Professor of Mathematics, Professor of Molecular and Cellular Biology

Research Interests:

Applications of topology and stochastic methods to molecular biology and genetics.

- Development of topological and statistical methods for the reconstruction

of 3D structure of chromosomes across organisms (i.e. viruses, bacteria,

trypanosomes, mammalian) - Analysis of cancer genomic profiles using computational homology.

http://biosci3.ucdavis.edu/Faculty/Profile/View/14482

- Tel: (530) 754-0308
- Location: 0009 Briggs Hall

## Mariel Vazquez

#### Professor of Mathematics, Professor of Microbiology and Molecular Genetics

My research lies at the interface of mathematics, polymer physics, and molecular biology. I specialize in the application of topological tools to study DNA.

My work is currently focused on two lines of inquiry:

- DNA Topology: the mechanism of site-specific recombination, topoisomerase action, and the packing of chromosomes in human cells and viral capsids; using mathematical tools including know theory, low-dimensional topology, and Monte Carlo simulations.
- Chromosomal Aberrations and Cancer: analysis of cancer genomic data and mechanisms of repair pathways; using biophysical models, graph theory, and topological data analysis.

- Tel: (530) 754-0383
- Location: Mathematical Sciences Building (MSB) 2150

## Post Doctoral Researchers

## Allison Moore

I am postdoc with a background in pure math, particularly knot theory. In the Arsuaga Vazquez lab, I’ll be exploring how theoretical math (like knot theory and graph theory) and applied math (like statistics and data analysis) can be combined to tackle problems in molecular and cellular biology. Before coming to Davis, I was a RTG postdoc at Rice University in Houston. My research there was in low-dimensional topology, knot theory and Floer homology. I got my Ph.D. in pure math at the University of Texas at Austin, where my advisor was Cameron Gordon. My dissertation work involved the behavior of certain knot homology theories under topological mutation.

## PhD Students

## Shawn Witte

#### PhD Student

I am currently working with Mariel Vazquez in DNA topology. More specifically, using knot theory to examine bacterial DNA.

https://www.math.ucdavis.edu/~slwitte/

- Location: UC Davis Mathematics

## Maxime Pouokam

#### Junior Specialist

My scope of work includes computational mathematics, complexity of chromatin folding and the principle underlying the 3D architecture of chromosomes organization during the interphase, genomic, and data science.

- Location: Departments of Molecular and Cellular Biology | Mathematics

## Robert Stolz

#### PhD Student

I am a full-time graduate student studying Integrative Genetics and Genomics with an emphasis on Mathematical biology. I have an active mind with diverse areas of interest including human genomic organization, machine learning, knot theory, bayesian statistics, numerical analysis, polymer physics, combinatorics, algorithmic music, and data science.

- Location: UC Davis Department of Genetics and Genomics

## Ryan Polischuk

I am a graduate student in the Physics Department, who is interested in interdisciplinary problems in physics, biology, and applied mathematics. I am currently using biophysical tools to study the relationship between chromatin structure and cancer development. I like topics that touch on fundamental research questions in biology, while also bearing more or less directly on issues of human interest, like disease. I did my undergraduate work at Boston College, where I completed an experimental physics thesis on superconductivity and played ice hockey. At BC I developed an appreciation for interdisciplinarity and academic breadth, especially in the humanities. Please contact me if our research interests align or if you know of a good men’s ice hockey league anywhere in the vicinity of Davis!

## Research Specialists

## Gina Gonzalez

#### Assistant Specialist

I am a MSc in Applied Statistics and work on the project “Applications of computational homology to the analysis of copy number changes in breast cancer” analyzing genomic cancer data searching for oncogenes and tumor suppressor genes, classification of tumor subtypes and patient stratification using a combination of statistical and mathematical tools.

## Michelle Flanner

#### Applications Programmer

Attends to a variety of responsibilities within the research group; defines research goals, implements algorithms in C++, python and Matlab, develops algorithms for simulating molecular systems, drafts and co-authors scientific manuscripts, maintains various hosted services for the lab, maintains documentation webpages, cleans and documents software.

- Tel: 15309081584
- Location: Departments of Microbiology and Molecular Genetics

## Tamara Christiani

#### Junior Specialist

I am a recent transplant from NJ with a bachelor’s degree in Molecular Biology. My research involves investigating the 3D structure of bacteriophages, and more specifically the organization of DNA in their capsids. I am also interested in the relationship between phage packing motor mutations, knot distribution, and chirality of packaged phage genome.

- Location: Departments of Microbiology and Molecular Genetics

## Undergraduate Students

- Lara Ibrahim
- Gabriel Freund
- Melissa Spence
- Danny Halawi
- Jessica Au
- Carlos Palomo

## Previous Members

## Rachael Phillips

#### Masters Student

Throughout the lifespan of the human body, trillions of cell divisions occur. Every time a cell divides, a regulatory process can fail, causing alterations in the DNA. These alterations can cause diseases, including different types of cancer. My work focuses on different sub-types of breast cancer. Many researchers have previously found specific regions of the genome to be significant for different sub-types of breast cancer. My main goal of this project is to observe these regions and understand the relationship between copy number aberrations (changes in the DNA) and gene expression profiling (changes in the mRNA). This will give us an idea of how much the gene expression in these sub-types is being altered by copy number changes. This is done by using algebraic topology and different methods in statistics to understand the correlation of the relationships between these two types of data.

## Mimi Tsuruga

#### Arthur J. Krener Assistant Professor of Mathematics, Postdoctoral Researcher of Molecular and Cellular Biology

My research is in computational topology. I also have interests in low-dimensional topology in the PL setting, the construction of (potentially) exotic spheres, and topological combinatorics. I have a PhD in mathematics from TU Berlin. For my dissertation, I built simplicial complexes that have interesting topological properties and then used them as test objects to improve heuristic algorithms in topological software.

- Location: MSB 2149

## Judy Du

#### Junior Specialist

I am a recent UCD alumna who studied Biochemistry and Molecular Biology as a major and Statistics as a minor. I currently study the 3D architecture of chromosomes in different organisms, namely the relation of spatial proximity to:

-chromosomal aberrations witnessed in human cancer

-homologous recombination sites and sequence similarity in yeast genomes

Email: jdydu@ucdavis.edu Let us know if you might be interested in taking on my project!

- Location: Briggs 15