Graduate Division

Mathematical, Computational, and Systems Biology Ph.D.

Section 1


Biology is undergoing a revolution, and we are at the forefront. In this program, we seek to understand the living world as an interacting set of complex systems, crafted by natural selection to carry out defined tasks. The program is designed to meet the interdisciplinary training challenges of modern biology. Our students receive training and research experience in the tools of applied mathematics, computation, data analytics, and experimental methods in “-omics”, molecular, cellular and developmental biology.

What Sets Us Apart?

  • Faculty members from 22 departments, including biology, computing, engineering, mathematics, medicine, physics and statistics
  • After the rigorous first year “gateway”, the PhD program allows the flexibility to transfer into 10 departmental PhD programs or remain in the interdisciplinary PhD program
  • Close and continual interaction with the UCI Center for Complex Biological Systems, Center for Cancer Systems Biology, Center for Multiscale Cell Fate Research, Laboratory for Fluorescence Dynamics and many other campus resources

Quick Facts

Program Type

Doctoral Program

Normative Time to Degree

5 years

Capstone Type


Accordion Section

Admissions Requirements

The MCSB Director and Executive Committee annually appoint an Admissions Committee from MCSB associated faculty. Following an initial screening of applications, the Admissions Committee usually invites potential trainees for an interview at UCI. The Director makes the final offers of admissions to applicants, based on the recommendations of the interviewing faculty and the Admissions Committee.

Financial Support

A hallmark of the MCSB Program has been the strength of its student financial support. During the first year of Ph.D. study, the MCSB Gateway Program provides complete financial support to admitted Ph.D. students, which includes an annual stipend, as well as full tuition and fee remission, including health benefits. Typically, financial support for the three summer months after the first academic year at UCI will be through research funding provided or arranged by a student's primary thesis advisor. Since the fall of 2007 when the program admitted its first class of students, every student successfully completing the Gateway year has also been fully supported by the UCI Departments and faculty where they have chosen to continue their Ph.D. research.

Tuition & Fees

Graduate/Credential Student Fees 2019-20

  Fall 2019 Winter 2020 Spring 2020 Annual
Student Services Fee 376.00 376.00 376.00 1,128.00
Tuition 3,814.00 3,814.00 3,814.00 11,442.00
Assoc. Grad Students Fee 9.00 9.00 9.00 27.00
Student Center Fee 139.69 139.69 139.68 419.06
Bren Events Center Fee 23.00 23.00 23.00 69.00
Recreation Center Fee 88.00 88.00 88.00 264.00
Document Fee * 80.00 0.00 0.00 80.00
Student Health Insurance 1,459.18 1,459.18 1,459.18 4,377.54
Total California Resident $ 5,908.87 $ 5,908.87 $ 5,908.86 $ 17,726.60
Nonresident Supplemental Tuition 5,034.00 5,034.00 5,034.00 15,102.00
Total Nonresident $ 10,942.87 $ 10,942.87 $ 10,942.86 $ 32,828.60


Posted 12 July 2019 at

The tuition, fees, and charges posted to your billing statement or account are estimates based on currently approved amounts. These figures may not be final. Actual tuition, fees, and charges are subject to change by the Regents of the University of California and could be affected by increases or reductions in State funding, or other developments. Accordingly, final approved levels (and thus your final balance due) may differ from the amounts shown.

* The Document Fee provides lifetime access to official transcripts and academic verifications without a fee for in-person pickup or delivery by USPS. In addition, there is no fee for mailing the initial diploma. Effective Fall 2018, new undergraduate, professional, and graduate students are assessed the one-time document fee. Eligible students are able to use financial aid to cover the Document Fee.

Core Faculty

Allard, Jun     
Mathematical modeling of cell mechanics; How forces are used by cells for cell-cell communication, actin-based crawling, internal transport and cytoskeleton dynamics; Nonlinear partial differential equations, stochastic simulation and Bayesian statistics.

Allison, Steven     
Microbial enzymes, theoretical ecology, and biogeochemistry

Andersen, Bogi     
Transcriptional regulation in normal and diseased epithelia

Andricioaei, Ioan     
Interface of structural molecular biology and physical chemistry

Arora, Kavita     
Drosophila development, TGF-beta signal transduction, cell signaling

Atwood, Scott     
Cell fate decisions in skin cancer, skin and hair follicle development, and stem cells.

Baldi, Pierre 
Artificial Intelligence: Automated Reasoning / Machine Learning / Data Mining / Large-Scale Data Analysis: Information Access & Management / Computational Biology / Bioinformatics / Systems Biology

Bardwell, Lee     
Use of molecular biology, biochemistry, genetics, cell biology and math/computation to study fundamental questions of cell signaling and regulation

Bennett, Albert     
Evolutionary and comparative physiology

Blumberg, Bruce     
Molecular embryology, molecular biology, developmental biology, functional genomics, endocrinology, pharmacology, high-throughput screening

Botvinick, Elliot     
The relationship between mechanical stresses on cells and molecular signaling, or cellular mechanotransduction. Investigation of the role of the glycocalix in the transduction of fluid shear stress at the wall of blood vessels, and is constructing an instrument to study the scale of mechanical induction of vascular inflammation.

Brody, Jim     
Single molecule dynamics, bioinformatics, functional genomics, surface plasmon resonance

Calof, Anne     
Systems Biology of Stem Cells and Human Developmental Disorders

Chen, Long     
Theoretical analysis and practical application of Adaptive Finite Element Methods (AFEMs)

Cho, Ken     
Growth factor signaling and functional genomics in Xenopus and zebrafish, stem cell research and diabetes, Bioinformatics and functional genomics, Veterbrate embryology and growth factor signaling

Cinquin, Olivier 
Systems biology of cell differentiation.

Cocco, Melanie 
NMR spectroscopy, DNA-binding proteins, membrane proteins, cancer

Collins, Philip     
Nanomaterial Synthesis  & Characterization, Nanocircuit Behaviors, Single Molecule Circuits

Cooper, Dan     
Effect of exercise on gene and protein expression of key inflammatory and growth mediators in peripheral blood mononuclear cells in health children

Dai, Xing     
Role of the regulatory proteins Ovo in germ cell and epidermal differentiation

Dennin, Michael     
Biological physics, Langmuir monolayers, Foams

Emerson, J.J.     
Evolution of genetic novelty: copy number variation, gene duplication, sex chromosome evolution and the evolution of gene expression

Enciso, German     
Mathematical Biology; developing generic modules for biochemical reactions in little b and to study signal transduction pathways associated with EGF receptors.

Faiola, Celia 
Biosphere-atmosphere interactions, plant stress emissions in an evolving world, links between ecology and climate

Fowlkes, Charless     
Artificial Intelligence: Automated Reasoning / Machine Learning / Data MiningBio-Medical Informatics / Computational Biology

Frank, Steve     
Evolutionary genetics, host-parasite interactions, development of mathematical, computational and conceptual models to study complex phenotypes

Gaut, Brandon     
population genetics, molecular evolution, genome evolution

Gratton, Enrico     
Design of new fluorescence instruments, protein dynamics, hydration of proteins, and I.R. spectroscopy of biological substances

Grosberg, Anna     
Applying multiscale computational modeling and tissue engineering to stem cell-derived cardiomyocytes (heart muscle cells), cardiac morphogenesis (development of structure), and cardiac function.

Gross, Steve     
Biophysics of molecular motors and intracellular transport

Guidotti, Patrick 
Partial Differential Equations and Applied (Functional) Analysis

Haun, Jered     
Targeted drug delivery, clinical cancer detection, nanotechnology, molecular engineering, computational simulations

Hayes, Wayne     
Large-Scale Data Analysis: Information Access & Management / Databases / Information Infrastructure / Bio-Medical Informatics / Computational Biology

Hertel, Klemens     
Mechanisms of pre-mRNA splicing and the function of splicing enhancers  in exon definition, Regulation of pre-mRNA splicing and human genetic diseases, The coupling of transcription and pre-mRNA splicing

Huang, Lan     
Biological mass spectrometry/proteomics, ubiquitin-proteasome degradation pathways, protein complexes, posttranslational modifications, protein-protein interaction

Hughes, Christopher     
Blood vessel development, angiogenesis in cancer, bioengineering of blood vessels and tissues

Hui, Elliot     
MEMS, cell-cell interactions, tissue engineering, global health

Ihler, Alexander     
Artificial Intelligence: Automated Reasoning / Machine Learning / Data Mining

James, Anthony     
Molecular biology of insect vectors of disease, genetics of vector competence, malaria, dengue fever

Kaiser, Peter     
Control of the cell cycle through mechanisms involving ubiquitination

Kessenbrock, Kai     
Cellular communication in single cell resolution in the context of normal tissue homeostasis and in breast cancer.

Keyak, Joyce     
Bone biomechanics and structural analysis ; Effects of medications, aging, tumors, radiotherapy, and spaceflight on bone ; Cancer and radiotherapy ; Imaging using quantitative computed tomography

Kherardvar, Arash     
Cardiovascular engineering with emphasis on cardiac mechanics, cardiac imaging and cardiovascular devices

Khine, Michelle     
Quantitative Single-Cell Analysis of Receptor Dynamics and Chemotactic Response on a Chip

Komarova, Natalia     
Mathematical biology: modeling of cancer initiation and progression,  dynamics of DNA transcription and repair, modeling of learning and evolution of language

Lander, Arthur     
Systems biology of morphogenesis and pattern formation, proteoglycans, extracellular matrix, birth defects syndromes

Lanyi, Janos     
 Bacteriorhodopsin, spectroscopy, protein crystallography

Lathrop, Rick     
Artificial Intelligence: Automated Reasoning / Machine Learning / Data Mining / Bio-Medical Informatics / Computational Biology / Protein Structure Prediction / Drug Discovery / Genetic Regulation

Li, Han     
Metabolic engineering and Synthetic biology for production of chemicals from renewable resources.

Liu, Chang     
Synthetic biology, chemical biology, and directed evolution.

Liu, Haoping     
MAP kinase mediated signal transduction; dimorphic regulation in yeast

Liu, Wendy     
Understanding how microenvironmental cues regulate cell behavior in order to better understand and treat diseases of the cardiovasculature

Long, Anthony     
Quantitative and population genetics, genetic basis of quantitative variation for different phenotypes in different organisms, gene mapping and microarray analysis

Lowengrub, John     
Microstructured Materials, Multiphase Flows, Crystal Growth, Nanostructure Patterning, Metallic Alloys, Tumor Growth, Tissue Engineering

Leucke, Hartmut "Hudel" 
Protein crystallography, structure function studies, membrane proteins, bacteriorhodopsin, annexi, G protein-coupled receptors (GPCR), structure-based drug design

Luo, Ray     
Computational Biology, Protein Structure, Protein Function

Martens, Craig 
Theoretical Chemistry, Chemical Physics

Martiny, Adam     
Microbiology, Environmental Genomics, Oceanography

McHenry, Matthew
Biomechanics, Locomotion, Sensory Biology

Mjolsness, Eric     
Artificial Intelligence: Automated Reasoning / Machine Learning / Data Mining / Bio-Medical Informatics / Computational Biology / Systems Biology / Scientific Inference Systems / Mathematical Methods

Monuki, Edwin     
Roles of morphogens and transcription factors in early NSC fate control and boundary formation involving the cortex and specialized tissues at the midline

Mortazavi, Ali     
Applications of genomics, computation, and sequencing technologies to the analysis of transcriptional regulation in development. Emphasis on long-range protein-DNA interactions, ChIP-seq, RNA-seq, ChIA-PET, and comparative genomics

Mukamel, Shaul 
Theoretical studies of ultrafast dynamics and relaxation processes of large molecules, biological complexes, and semiconductors; Nonlinear ultrafast spectroscopy

Nenadic, Zoran     
Adaptive biomedical signal processing, control algorithms for biomedical devices, brain-machine interfaces, modeling and analysis of biological neural networks

Nguyen, Hung     
Self-assembly of biological and biomimetic nanoscale materials based on amino acids and on nucleic acids using computational and theoretical methods

Nie, Qing     
Computational Biology, Developmental and Cell Biology, Numerical Analsis, Interface Dynamics in Materials and Fluids, High-Performance Computing, Modeling and Simulation of Tissue Patterning, Systems Biology

Nowick, James  
Organic and Bioorganic Chemistry, Chemical Biology, Biomolecular Nanotechnology

Plikus, Maksim     
Stem cells and stem cell niche, Regeneration of tissues and organs, Biological pattern formation, Self-organization, Skin and hair follicles, Adipose tissue, WNT and BMP signaling pathways

Potma, Eric     
Molecular mobility in biological materials, vibrational coherences, ultrafast microscopy

Ranz, Jose     
Structural evolutionary genomics and evolution of the expression network

Read, Elizabeth     
Dynamics of complex biochemical systems and regulation of immune responses

Ritz, Thorsten     
Biological physics, magnetic sense of animals, quantum biology of photosynthesis

Sandmeyer, Suzanne     
Molecular genetics and biochemistry of retrotransposons and metabolic engineering in budding yeast

Schilling, Tom     
Zebrafish development, pattern formation, morphogenesis

Shahbaba, Babak     
Developing Bayesian methods and applying them to real-world problems; applying novel statistical methods to solve research questions in genetics, genomics, proteomics, and cancer studies

Shaka, A.J.     
Physical and Biophysical Chemistry; NMR Spectroscopy; Chemistry of Aging; Nuclear Power; Radiochemistry

Sheu, Phillip C-Y     
Database Systems, Object-Oriented Systems, Parallel Processing, Simulation, Interactive Multimedia Systems. Biomedical Database Management, Intranet/Internet Technologies

Siryaporn, Albert     
Biomechanics, Bacterial Signaling, Bacterial Pathogens, Biofilms

Siwy, Zuzanna     
Experimental Biophysics, Condensed Matter Physics

Smyth, Padhraic     
Artificial Intelligence: Automated Reasoning / Machine Learning / Data MiningLarge-Scale Data Analysis: Information Access & Management / Databases / Information Infrastructure; Internet Technologies / Applications; Statistics

Solna, Knut     
Applied mathematics, applied probablility, stochastic differential equations

Steele, Robert     
Molecular biology of Hydra development

Stern, Hal     
statistical inference using Bayesian methods, assessing the fit of statistical models, applications of statistics in the social and biological sciences, and statistics in sports.

Taborek, Peter     
Surface physics, sensors, high speed imaging, and fluid mechanics

Tan, Ming     
Gene Expression and Pathogenesis in Chlamydia Trachomatis

Thornton, Kevin     
Comparative genomics, Population Genetics, and statistical Genetics

Tobias, Douglas     
Computational Chemistry, Biophysical Chemistry, Atmospheric Chemistry

Tromberg, Bruce     
Lasers, near infrared spectroscopy, non-invasive diagnostics, photomedicine, biomedical optics, photodynamic therapy

Tsai, Sheryl     
Biochemistry, Chemical Biology, Structural Biology, Microbiology

Venugopalan, Vasan     
Biomedical laser applications, optical diffusion theory, photothermal and photomechanical phenomena

Wan, Frederic Y.M.     
Applied Mathematics, Solid Mechanics, Resource Economics, Biomathematics

Wang, Wenqi     
Protein-protein interaction network, Hippo signaling, Organ size control, Molecular mechanism of tumorigenesis

Warrior, Rahul     
Drosophila development, regulation of nuclear position and migration, effects of proteoglycans in growth factor signaling, regulation of developmental gene expression.  

Waterman, Marian     
Regulation of gene expression by LEF/TCF - beta-catenin complexes

Weiss, Gregory     
Bioorganic chemistry, chemical biology, protein engineering, molecular biology and biochemistry

Whiteson , Katrine     
Host-associated microbial communities, metabolomics, metagenomics, microbial ecology, phage, fermentation, polymicrobial infection, microbial interactions, human microbiome

Wickramasinghe, H. Kumar

Nano metrology to in-situ sensors that improve the throughput and/or yield in manufacturing lines to novel instruments for ultra fast sequencing of DNA and nanoscale metrology in biology

Wodarz, Dominik     
Mathematical and Computational Biology, Theoretical Biology, infectious diseases and the immune system, carcinogenesis & cancer treatment

Wunderlich, Zeba     
Experimental and computational approaches to studying the regulation of gene expression, Drosophila development, and interpreting natural variation in regulatory sequences

Xie, Xiaohui     
Computational Biology, Bioinformatics, Genomics, Neural Computation, and Machine Learning

Xin, Jack     
Analysis and Modeling of Reaction-Diffusion-Advection Fronts, Stochastic Partial Differential Equations, Asymptotics and Computations, Multiscale Analysis of Partial Differential Equations and Applications, Mathematical Modeling in Speech and Hearing Sciences.

Yokomori, Kyoko     
Mechanism and regulation of chromosome structural changes required for the maintenance of genome integrity

Yu, Clare     
Biological physics, Intracellular transport, Disordered systems

Zhao, Hong-kai     
The Level Set Method, Moving Interface and Free Boundary, Image Processing and Computer Graphics, Time Reversal and Wave Propagation, Domain Decomposition

Students & Alumni