Graduate Program in

Mathematical, Computational & Systems Biology

Current MCSB Students

jose-bermudez

Jose Bermudez

UC San Diego

Salutations! My name is Jose Bermudez, and I am originally from the central valley town of Bakersfield, CA. I received my B.S. in Biochemistry and Cell Biology at the University of California San Diego and recently worked for a Women’s Health Biotech called Hologic, Inc. While at UCSD, I conducted immunological research for 5 years centered around the immunological dysfunction that arises during septic shock, its effect on macrophage polarization and the potential for small molecule therapeutics to upend this dysfunction. Upon entering the biotech industry and my 3+ years working at Hologic Inc., my interests have shifted to revolve around the applications of machine learning and deep-neural networks to complicated biological systems and processes like the immune system and cellular differentiation. Moreover, I am interested in how these tools illuminate the nuances of complex biological systems, and how we can leverage their predictive power to treat disease and benefit patient outcomes. Outside of lab, I enjoy being in nature with my family and friends, surfing, playing sports (most sports!), gardening and having good conversations with friends over a meal.

eric-bourgain-chang

Eric Bourgain-Chang

UC Los Angeles

Hi, my name’s Eric and I grew up in Riverside, CA. My undergrad I majored in Mechanical Engineering and Applied Math at UC Berkeley, followed by a masters in Mechanical Engineering (control theory) from UCLA. Afterwards, I worked at the Interdisciplinary Center for Quantitative Modeling in Biology at UC Riverside performing image analysis. My main projects were on the shoot apical meristem of Arabidopsis and fibrin/platelet behavior in blood clotting. I’m interested in applications of machine learning to biology, particularly deep learning for medical diagnosis. Outside of research, I enjoy being active and traveling.

pieter-derdeyn

Pieter Derdeyn

Pomona College

My name is Pieter Derdeyn and I graduated from Pomona College with a BA in mathematics in 2016. While there, I studied applied math and conducted a year-long senior thesis project simulating protein dynamics during cellular division using PDEs and numerical analysis. Since then I have worked as a QA for a software company in Long Beach and as a data scientist for a biotech startup in Tempe, Arizona. I’m excited to get into computational neuroscience research using both simulation and statistical methods, as well as learn about all the applications my cohort delves into! Non-academic interests include hiking, science fiction, and water polo.

junyan-duan

Junyan Duan

Bryn Mawr College

Hello! My name is Junyan and I am originally from Nanjing, China. I graduated from Bryn Mawr College with a B.A. degree in Mathematics and a minor in Biology. In 2018 summer, I participated in the SMALL REU program at Williams College and worked on two mathematical ecology projects: one delved into dynamics and controls of white-nose syndrome in little brown bats and the other one focused on transboundary disease management. For my senior thesis, I worked on modeling the development and transmission of HIV/AIDS. I am interested in using mathematical models to explore and understand cancer development, cell fate determination and morphogenesis. In my free time, I enjoy reading, hiking and traveling.

tatyana-lev

Tatyana Lev

University of North Carolina, Chapel Hill

Hello! I’m Tatyana Lev. I have a master's degree in Clinical Lab Science from the University of North Carolina, School of Medicine, and a graduate certificate in Applied Bioinformatics from Pennsylvania State University. Before deciding to pursue an MCSB PhD degree at UCI, I worked as a Molecular Technologist in clinical oncology labs for 5 years. At Quest Diagnostics, I most enjoyed assay validations and DNA sequence data analysis. At NYU Langone Health, I found my passion for integrating molecular biology with math and computer science through the various automation projects I completed to streamline the NYU molecular pathology lab. At UCI, I hope to further develop my analytical skills and become an interdisciplinary scientist ready to tackle complex issues in biomedical science. For fun, I like to watch forensics / detective documentaries and PBS “Space Time” astrophysics series.

margaret-myers

Margaret Myers

Rhodes College

I graduated in 2018 with a B.S. in Biomathematics from Rhodes College in Memphis, TN. My primary research background has been mathematical modeling of host immune responses to influenza virus, which began three years ago at St. Jude Children's Research Hospital. In addition, I have research experience in modeling radio-frequency ablation cancer therapy and also in modeling Wolbachia mosquito control methods. Systems of differential equations and agent-based models are my most familiar modeling techniques, and I have experience in scientific experiments. I am most interested in pursuing integrated mathematical and/or computational research in fields related to disease treatment or prevention.

narges-rezaie

Narges Rezaie

Sharif University of Technology

Hello! My name is Narges. I'm originally from Iran and recently graduated from Sharif University of Technology with a B.S in computer engineering. During my undergraduate study and working in Bioinformatics and Computational Biology (BCB) Laboratory at the Sharif University of Technology, I got interested in Bioinformatics and Machine Learning, including Computational Cancer Biology. During and after my graduation, I analyze long noncoding RNAs (lncRNAs) to find a potential role in breast cancer, because they are emerging important regulators of tissue physiology and disease processes, including cancer. In the other one, we try to create a statistical method to identify functional genomic interactions. Outside of the lab, I enjoy playing guitar, basketball, baking and cooking.

jonathan-rodriguez

Jonathan Rodriguez

Nottingham Trent University

Hello, my name is Jonathan, but I’ve been given many nicknames throughout the years ranging from J-Rod to California. I was born and raised in Southern California and spent most of my life here until I moved to Nottingham, England for college. While there I received a BSc Hons in Mathematics. For my final year dissertation I undertook independent research, with occasional guidance by my advisor, into cancer processes adapting that research into various mathematical models. Since graduating I spent a little time outside of higher math, but I eventually returned by joining a group run by Dr. Russell Rockne at City of Hope. In that group we discussed the group members’ current research and upcoming papers. I also was given some various assignments by Dr. Rockne to work on that were relevant to various ongoing topics. My main interest is in mathematical modeling of cancer and cancer treatments, but I am also interested in immunology and neurology. In my spare time I enjoy playing games in many forms whether it be video, board, or even D&D. I also enjoy a good TV show binge especially ones based upon organized crime, and on a healthier note I quite enjoy going for a jog or a hike.

harsh-shukla

Harsh Shukla

Nirma University

Hello!! My name is Harsh and I grew up in Ahmedabad, a city in western India. I finished my bachelors in Computer Science from Nirma University in 2014. Therein for my research project I worked on parallelizing pairwise sequence alignment algorithms. The reading I did during the project made me want to learn more of biology and I decided to pursue it a little further. I joined the Master’s (M.Sc.) program in Bioinformatics and Applied Biotechnology at IBAB, Bangalore in 2016. For my master’s thesis work I worked on improving the human reference genome by leveraging population level information derived from large scale resequencing studies like 1000 Genome project. After my graduation in 2018, I started working as a bioinformatician in Dr. Uma Ramakrishnan’s Lab at NCBS, Bangalore. I was part of the project tasked with generating a reference quality assembly for the Bengal Tiger. I am interested in the field of evolutionary and
population genomics and will be pursuing my doctorate in that. When I am not working or thinking about science I am usually off hiking or backpacking. I adore reading. For my daily dose of exercise, I try to cycle and swim every day with swimming being my go to stress buster.

cassandra-van

Cassandra Van

UC Berkeley

Hi, my name is Cassandra! I'm from the San Francisco Bay Area and graduated from UC Berkeley with a major in Molecular and Cell Biology, with a minor in Linguistics. After graduation, I've worked at: Spiral Devices, a start-up making a medical device; Crystal Bioscience making antibodies in chickens; and UCSF finding novel combination therapies for neuroblastoma. My projects at UCSF focused on cancer biology and in addition, I enjoy studying signaling pathways, systems biology, microscopy, and data analysis. Outside of lab, I enjoy doing puzzles (jigsaw and logic), board games, singing, baking, reading, and hiking. Nice to meet everyone!

jonathan-vo

Jonathan Vo

UC Irvine

I am very interested in data science, mathematical modeling, and computational science in the context of reverse-engineering the evolution of, emergence in, and complexity of biological systems. At UCI, I've implemented agent-based models simulating the dynamics of oncolytic viruses and analyzed bifurcations in many members of a family of self-regulating cell lineage models. At Sandia National Labs in Livermore, I evaluated different types of evolutionary algorithms for efficiency and accuracy, as well as ran computational experiments with the Uncertainty Quantification Toolkit (UQTk) and created a Python package for using k-Nearest Neighbors regression on time series data for nuclear waste management.

I graduated with a Mathematics degree with Biological Science minor from UCI. I enjoy singing, mathematical modeling, and playing violin, as well as analyzing anime and music, on the occasion. I highly value auto-didacticism, so I read widely on topics ranging from religion to mathematics to psychology.

karen-xiao

Karen (Hui) Xiao

UC Los Angeles

Hello I’m Karen (Hui). I was born and raised in Shenzhen, China and then moved to the US when I was a freshman in high school. I graduated from UCLA in 2018 with a BS in Biology and obtained a Certificate this Spring in Systems Analysis from UCLA-Extension. During my undergrad, I worked for two years at Dr. Zhefeng Guo Lab that studies the secondary structure of the Alzheimer’s-related proteins using EPR spectroscopy. Other than that, I am interested in Cancer Biology and Computational Biology. In my spare time I enjoy cooking and exploring yummy food in town.