Arsuaga Vazquez Lab

Topological Molecular Biology lab at UC Davis


Welcome to the Topological Molecular Biology Lab at UC Davis!

Our group is interested in applications of topological methods to understand the three dimensional organization of the genome in different organisms, to study genome rearrangements and copy number changes in cancer, and to model the action of enzymes such as recombinases and topoisomerases. We use a combination of mathematical and computational methods including tools from low-dimensional topology, computational knot theory, random knotting, algebraic topology, persistence homology, combinatorics, statistics, Monte Carlo methods and computer visualization.

We are deeply committed to promoting diversity in mathematics and the sciences. Our goal is to lead a truly interdisciplinary and vertically integrated group at the interface of mathematics and molecular biology. Find description of some of our research projects, our publications, and some of our dissemination and outreach efforts.

Untangling DNA with Knot Theory

Math shows how DNA twists, turns and unzips

Presentation from select sessions at the SIAM Annual Meeting (AN18) are now available on SIAM Presents

BaMBA 11 Biology and Mathematics in the Bay Area

Location: Genentech Hall, UCSF

Date: November 18th, 2017

Time: 9:00 am – 6:00 pm



BaMBA is a one-day meeting aimed at exploring the role of mathematics in biology in an informal atmosphere. Going beyond traditional applied mathematics, the topics include applications of algebraic, topological, statistical and computational methods. The goal is to encourage dialogue between researchers and students from different disciplines to promote the open exchange of scientific ideas and viewpoints.


Participation in BaMBA is free and open to everyone, but registration is required. Attendance is limited to 200 participants. The registration deadline is Monday November 13th, 2017. Undergraduates, graduates, and postdocs involved in mathematical and computational investigations of biological systems are invited to submit an abstract for a poster presentation.   

Please use this link to register for the meeting and submit a poster abstract: 



Polly Fordyce (Stanford University)

Nataša Jonoska (University of South Florida)

Tim Lewis (University of California Davis)

Marina Sirota (University of California San Francisco)

Josh Stuart (University of California Santa Cruz)


Organizing Committee

Javier Arsuaga (Mathematics and Molecular and Cellular Biology, UC Davis)

Sami Khuri (Computer Science, SJSU)

Michael Levitt (Computational Structural Biology, Stanford)

Mark Segal (Biostatistics, UC San Francisco)

Massa Shoura (Stanford School of Medicine, Fire lab)

Mariel Vazquez (Mathematics and Microbiology and Molecular Genetics, UC Davis)



UCSF Institute for Computational Health Sciences

Burroughs Wellcome Fund

UC Davis Mathematics Department

The DNA Topology table at Picnic Day 2017

This year the lab hosted the DNA Topology table outside the Math Sciences Building, open to the public for hands-on educational activities exploring the concepts behind DNA supercoiling, knotting and packaging.

Vazquez Receives Blackwell-Tapia Prize

View the original article here at


Over 100 researchers, faculty, graduate students and others gathered last week to witness Mariel Vazquez, a professor of mathematics and microbiology and molecular genetics at the University of California, Davis, receive the nation’s highest research award for minority mathematicians, the 2016 Blackwell-Tapia Prize, in Knoxville at the conclusion of the biennial Blackwell-Tapia Conference.

Before presenting the prize, Richard Tapia, professor of mathematics at Rice University, gave a stirring speech where he called upon all mathematicians from under-represented groups to achieve excellence both in research and service to the nation in training and inspiring the next generation of mathematicians.

Mariel Vazquez and Richard Tapia

Mariel Vazquez and Richard Tapia

In a moving acceptance speech, Vazquez spoke of how she felt the honor profoundly as an immigrant from Mexico with children born in the United States, together representing the changing face of America. She related how she came to the United States “with stars in her eyes” and urged the audience to recognize and reach out to all of the starry-eyed students to help them also follow their dreams.

The next Blackwell-Tapia conference will be lead by ICERM in Providence, RI in 2018.

Congratulations to Maxime Puoukam upon successfully defending his Master’s Thesis!

Congratulations to Maxime for successfully defending his Master’s Thesis from San Francisco State University in Mathematics! Maxime defended October 21st, 2016, at San Francisco State University.  He is pictured with Proffessors Federico Ardila, Alexandra Piryatinska and Serkan Hosten of San Francisco State University as well as Proffessor Javier Arsuaga of UC Davis.


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AMS celebrates Hispanic Heritage Month

The America Mathematical Society celebrates Hispanic Heritage month, September 15–October 15! ((Latinos and Latinas) and Hispanics in the mathematical sciences) will feature a prominent Mathematician every day during Hispanic Heritage Month.  Today, Friday September 16, Dr. Mariel Vazquez is being featured.


Read more here hispanicheritage

Congratulations to Judy, Maxime, Rachael and Lara

Congratulations to Judy Du on her acceptance to the Quantitative and Computational Biology program at Princeton University!

Congratulations to Maxime Pouokam on his acceptance to the Biostatistics program at UC Davis!

Congratulations to Rachael Phillips on her successful defense of her Master’s Thesis from San Francisco State University in Mathematics!

Congratulations to Lara Ibrahim on her award of a provost undergraduate fellowship! Her recent poster was accepted in the 2016 Stanford Research Conference for undergraduates. She has also presented in MIC 91/191.


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