Professor of Mathematics, Professor of Molecular and Cellular Biology
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,
- Analysis of cancer genomic profiles using computational homology.
- Tel: (530) 754-0308
- Location: 0009 Briggs Hall
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
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.
Current Lab Members
I am an applied mathematics PhD student at UC Santa Barbara. My current interests lie in mathematical biology, single-particle analysis/cryo-EM, the calculus of variations, and numerical analysis. Currently, my work focuses on creating a 3D reconstruction of the SARS-CoV-2 S-protein trimer.
My name is Zhijie Wang, and I earned my Bachelor’s degree in Mathematical and Scientific Computation at the University of California, Davis in Dec, 2020, with a minor in Computer Science.
I am interested in the intersection of fields of computational imaging and deep learning. My current research focuses on bridging the Knot Theory and PDEs of dsDNA in bacteriophage capsid.
- Website: Link
I am currently a Ph.D student in the Integrative Genetics and Genomics program. For my Master’s thesis, I focused on constructing a cryo-electron microscopy structure for the nucleocapsid of bacteriophage P4. I am continuing to advance this project by incorporating molecular techniques to enhance our knowledge about the arrangement of bacteriophage P4’s DNA.
- Location: Departments of Microbiology and Molecular Genetics
Camila Sanudo Thomas
I am a second year majoring in quantitative biology. In my free time, I love playing ultimate frisbee and hiking in the wilderness. In my studies, I am interested in harnessing matrices and linear algebra to model biological processes. I am working on the project “Applications of computational homology to the analysis of copy number changes in breast cancer” to analyze genomic cancer data. This project includes the search for oncogenes and tumor suppressor genes, classification of tumor subtypes, and patient stratification using a combination of statistical and mathematical tools.
Former Lab Members
- Allison Moore 2019
- Judy Du
- Lara Ibrahim
- Maxime Pouokam (PhD, Biostatistics 2020) Statistical Topology of Genome Analysis: From Chromosome Conformation Capture data to 3D structure
- Michelle Flanner
- Mimi Tsuruga
- Monica Nicolas
- Rachael Phillips (MA, Mathematics 2016):
Relating Gene Expression Profiling and Copy Number Changes with Different Sub-types
of Breast Cancer
- Robert Stolz (PhD)
- Ryan Polischuk (PhD)
- Shawn Witte (PhD, Mathematics 2019) Markov Chains Applied to Cubic Lattice Links, Grid Diagrams, and Writhe
Former Undergraduate Researchers
- Anthony Jajeh (BS, Math, 2020)
- Caitlin Brown (BS, Math, 2020)
- Ismail Daud (BS, Computer Science, 2020)
- Teresa Diaz (Polytechnic University of Valencia, Honors Thesis) Characterization of Horizontal Evolution of RNA viruses using topological data analysis
- Sofia Jakovcevic (BS, Physics, 2020)
- Wangbo Tang (BS, Math, 2020)