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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.

      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.

      Research Specialists

        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 subtypes and patient stratification using a combination of statistical and mathematical tools.

          Current Lab Members

          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 SARS-CoV-2 S-protein trimer.

                    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 fields of computational imaging and deep learning. My current research focuses on bridging the Knot Theory and PDEs of dsDNA in bacteriophage capsid.

                      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 by incorporating molecular techniques to enhance our knowledge about the arrangement of bacteriophage P4’s DNA.

                          • Location: 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 time I enjoy reading and playing guitar.

                                Jacob Lusk

                                Pronouns: He/Him/His

                                I’m a senior mathematics student at 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.

                                    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 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

                                      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)