Jun Allard Receives NSF Career Award

Congratulations to Assistant Professor Jun Allard (Department of Mathematics and Physics & Astronomy) for receiving a 5-year NSF Career Award on the topic of "Mathematical Framework for Elucidating Mechanics at Immune Cell Interfaces."

Jun AllardDr. Allard's work will focus on developing mathematical models of the physical interactions at cell-cell interfaces, with particular emphasis on immune cells that need to decipher information - relevant to self and non-self recognition and disease processes - from transient dynamic cellular contacts. The dynamics at these interfaces involve an interplay between transport, mechanics and chemical kinetics, and play out over a range of length and time-scales, necessitating a combination of mathematical techniques, including systems of elliptic, parabolic and stochastic differential equations; computational fluid dynamics of liquid-structure interactions; Brownian dynamics; as well as Bayesian statistics that leverages quantitative experimental data. This work therefore aims to provide a deeper understanding of how cells overcome and exploit physical constraints to cell-cell contact, by developing a model that integrates motion of the intracellular and extracellular fluid, Brownian motion of molecules embedded in the cell's membranes and active forces. Dr. Allard will also explore the mechanism and evolutionary advantages of molecular clustering, and develop, validate and apply mesoscale models of large flexible biomolecules to decipher their mechanical properties and biological role. These mesoscale models are suitable to exploring timescales that all-atom molecular dynamics cannot, while capturing details that particle-based simulations miss.

Results from the work will have direct implications for understanding immune function, impacting research on autoimmune disease and immunotherapy. Students recruited to these projects will have the opportunity to gain exposure to contemporary work at the interface of mathematics, biology and physics.

2015 NSF Graduate Research Fellowship Awards

Congratulations to our MCSB graduate student award winners and honorable mentions.....

Award Winners:

Jaleal S. Sanjak for his project proposal "The Effects of Molecular Genetics Architecture and Deomgraphy on GWAS." Jaleal will be studying the "missing heritability" issue i.e. rare poylmorphisms with large effects that drive heritability of disease risk in humans, and which represents a significant problem for current genone wide association study (GWAS) approaches. He will develop and simulate predictive models that invoke population genetics theory and complex gene-gene interaction models to improve the predtictive power and GWAS study designs. He will be mentored by Professor Kevin Thornton, Department of Ecology and Evolutionary Biology.
Andrew J. Schaub for his project entitled "Engineering the Reductase Domain from the Non-Ribosomal Peptide Synthase Module in Myxalamid Biosynthesis System for Advanced Second-Generation Biofuel Production." Andrew will be studying methods to engineer improved metabolic pathways leading to polyketide synthesis that can be used for biofuel production. He will apply molecular dynamics (MD) simulations for the protein-protein interactions between the MxaA and PCP subunits bound to various alkyl-CoAs and polyketide mimics to guide the rational design and engineering of mutants able to accept different MxA upstream modules. His project mentors will be Professor Sheryl Tsai (Departments of Chemistry, Molecular Biology and Biochemistry and Pharmaceutical Sciences) and Professor Ray Luo (Departments of Molecular Biology and Biochemistry, Biomedical Engineering and Information and Computer Science).

Honorable Mentions:

Matthew Boyvn for his project entitled "Modeling Self-organization and Control in Motor Cargo Systems." Mathew hopes to investigate the properties that drive motor protein interactions with intracellular cargoes, and whether attachment/detachment occurs through stochastic events or is coordinated through various suspected mechanisms. He will use a combination of computational modeling and experimentation to address these questions. His mentor will be Professor Jun Allard (Department of Mathematics).
Anna LoPresti for her project entitled "An Evolutionary Model of Social Discounting and Implications for Climate Policy." Anna hopes to apply evolutionary theory to build a model of intergenerational social discounting in human populations related to implementation of policies addressing global climate change. In order to effectively tackle climate problems, current societies will have to forgo some benefits in order to provide future generations benefits, a process referred to as social discounting. This altruistic behavior is influenced by a combination of kin and group selection, and is subject to natural selection as well as the geogrpahic and temporal distributions of benefits and relatives in the future. Anna will be mentored by Professor Steven J. Davis (Department of Earth Systems Sciences).

Daniel Quang wins prize at Tsukuba Global Science Week, September 28-30, 2014

Quang award
Congratulations to MCSB student Daniel Quang for winning top prize as "Outstanding Student Speaker" for his presentation on "Motif Signatures in Stretch Enhancers" at the Tsukuba Global Science week in Tuskuba, Japan.
Professor Mitsuyasu Kato presented the awards. The prize includes an invitation for a future 1-week expenses paid return trip to Japan.

Colloquium on Genome Data Analysis Methods

UCLA is hosting a free 1-day colloquium on "Systems Biology Analysis Methods for Genomic Data"
on Tuesday, October 7th, 2014. Click here for schedule details and information on registration.

Genome Data Analysis Colloquium

UCLA is hosting a 1-day colloquium on Tuesday, October 7th 2014, on Systems Biology Analysis Methods for Genomic Data at the Center for the Health Sciences (13-105 CHS), University of California Los Angeles. 

This full day event is open to the public, but space is limited. To register for this event send an email with subject line "Network Analysis" to

Speakers will discuss network analysis methods widely used in systems biologic and systems genetic applications. The goal is to familiarize researchers with network methods and software for integrating genomic data sets with complex phenotype data. Participants will learn how to integrate disparate data sets (genetic variation, gene expression, complex phenotypes, gene ontology information) and use networks for identifying disease genes, pathways and key regulators. We also describe applications to DNA methylation data and the epigenetic clock software.

This full day event is open to the public, but space is limited. To register for this event send an email with subject line "Network Analysis" to


SHorvathSteve Horvath, PhD

Professor of Human Genetics & Biostatistics
PLangfelderPeter Langfelder, PhD
Department of Human Genetics

9:30am - 10:30am: Hierarchical clustering and the dynamic tree cut algorithm. Peter Langfelder

10:45am - noon: Weighted correlation network analysis. Steve Horvath

Noon - 1:30pm Break for lunch

1:30pm - 2:15pm: Consensus network analysis. Peter Langfelder

2:20pm - 3:15pm: R software tutorial for WGCNA. Steve Horvath

3:30pm - 4:15pm: Systems genetic analysis with structural equation models.Steve Horvath

4:30pm - 5:15pm: The epigenetic clock and user-friendly software. Steve Horvath

Advance notice: A week-long Network workshop will be held on the UCLA campus in the summer
of 2015. If you wish to be on the mailing list for this and future events, please email

2011 Recent News. Copyright © 2013. The Center for Complex Biological Systems, UC Irvine
Powered by Joomla 1.7 Templates