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...
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...
Research Specialists
Jacob Lusk
Junior Specialist
Pronouns: He/Him/His I'm a recent mathematics graduate from UC Davis. I'm working on the "Predicting R-Loop Formation using a Formal Grammar" project which aims to predict the formation of R-loops using tools from computational linguistics.
Georgina 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...
Postdoctoral Fellows
Pengyu (Peter) Liu
Pronouns: He/Him/His I am a postdoc working on the topological entanglement of R-loops. I am interested applications of topology, discrete mathematics and data science in biology.
Graduate Students
Shuting Dai
Pronouns: She/Her/Hers I'm currently a PhD student in GGAM. I'm interested in using machine learning/deep learning methods for breast cancer prediction.
Michael Keith
Pronouns: He/Him/His 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...
Zhijie Wang
PhD Candidate
Pronouns: He/Him/His 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...
Jingwei Xiong
PhD Candidate
Pronouns: He/Him/His Ph.D student in biostatistic groups. I am currently in the breast cancer project group. I have 2 cute Guinea pigs.
Tamara Christiani
PhD Candidate
Pronouns: She/Her/Hers 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...
Departments of Microbiology and Molecular Genetics
Undergraduate Students
Claire Hsieh
Pronouns: She/Her/Hers I'm a third year majoring in Genetics and Genomics and have worked on adding weights to a profile HMM to predict mutations in SARS-CoV-2. My current interests are in Markov Models and algorithm design and in my free...
Camila Sanudo Thomas
Pronouns: She/Her/Hers 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...
Former Lab Members
Former Researchers/Postdocs
- 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)