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GRADUATE FELLOWS

Kwadwo Afriyie Bonsu

Kojo is a PhD student in the Chemical & Biomolecular Engineering department. His research seeks to elucidate the biological mechanisms which underlie DNA Methylation and its regulation, through mathematical modeling and statistical inference. In combination with experimental efforts, he hopes to create a toolkit capable of utilizing increasingly available epigenetic data, and draw conclusions regarding age-dependent methylation pattern inheritance.

Yingxin Cao

Yingxin Cao, Mathematical, Computational, and Systems Biology PhD program, supervised jointly by Xiaohui Xie in Computer Science and Qing Nie in Mathematics, working on deep learning for single-cell sequencing analysis in Mathematics Core. 

Morgan Dragan

Morgan Dragan is a PhD candidate under the direction of Dr. Xing Dai in the department of Biological Chemistry. Her current project attempts to elucidate the transcriptional regulation of skin barrier and immune cell recruitment and to understand how the skin can affect local and global metabolism (Theme A). She is also a collaborator on an IOA with Rachel Cinco to perform FLIM on skin wound healing.   

Alvaro Fletcher

Alvaro Fletcher is a PhD student of the Graduate Program in Mathematical, Computational and Systems Biology at UC Irvine. His research focuses on the development of stochastic and deterministic mathematical models to understand biological systems at multiple scales. Previous models have aimed to describe chromatin remodeling and, in collaboration with the Wunderlich lab, the activity of shadow enhancers in Drosophila. Other research interests include the application of chemical reaction network theory to cell signaling pathways.  
 

Lianna Fung

Lianna Fung is a PhD student in Thomas Schilling’s lab in the Department of Developmental and Cell Biology at UCI. Her research is on understanding vertebrate hindbrain development using zebrafish as a model organism. She is utilizing the MS2-MCP RNA labeling system and hybridization chain reaction (HCR) technique in zebrafish to visualize transcription dynamics and heterogeneity in the hindbrain during segment formation and boundary sharpening. In collaboration with Qing Nie’s Lab, they are also developing computational models for hindbrain segment boundary sharpening, cellular heterogeneity, and robustness.

Guadalupe Gutierrez

Lupe is a 4th year graduate student in Dr. Xing Dai’s lab in the Department of Biological Chemistry. He uses next generation sequencing approaches to characterize the transcriptomic heterogeneity of the mammary gland at a bulk and single cell level. He also uses in-vivo­ ­mouse models to uncover the function of genes within the mammary gland.

Yushang Lai

Yushang is currently working on statistical Bayesian inference methods such as Linear Noise Approximation (LNA) and Turing (HMC-MCMC) for the cell fate decision of hematopoiesis processes via gathering data from partially observed braining process as well as proposing biological-justified mathematical models.

Julien Morival

Julien Morival’s work focuses on trying to understand the impact of post-replication DNA methylation dynamics on cell fate decisions and age-related epigenetic drift, as well as the role of DNA methylation in LMNA-mutated patient-derived cells. Additional work concentrates on developing synthetic epigenetic modifiers to influence cellular fate. Julien is a 5th-year PhD candidate in the Biomedical Engineering Department in Dr. Timothy Downing’s laboratory.

Tessa Morris

Tessa Morris’s research focuses on developing computational tools for characterization of cardiac tissue architecture in order to contribute to an understanding of cardiac development and function. Specifically, this involves using and developing image analysis techniques to extract quantitative information about the biological constructs that comprise heart tissue. Tessa is a Mathematical, Computational, and Systems Biology PhD student in Dr. Anna Grosberg’s Cardiovascular Modeling Laboratory.  

Michelle Ngo

Michelle Ngo is a PhD candidate in the Mathematical, Computational, and Systems Biology PhD program supervised jointly between Shahbaba in Statistics and Lowengrub in Mathematics. She works on nonparametric Bayesian biclustering methods for single-cell RNA analysis in the Mathematics Core.

Trini Nguyen

Trini Nguyen is a Ph.D. student in the Mathematical, Computational, and Systems Biology graduate program. Supervised by Jun Allard, she is working on a number of projects as part of the Mathematics Core. One of the projects is funded by the 2019 CMCF IOA, in which she collaborates with a graduate student from the Andersen Lab (School of Medicine) to investigate the load tolerance advantages volar skin has over non-volar skin. Trini has been awarded the 2020 Graduate Research Fellowship by the NSF. 

Sohyeon Park

Sohyeon Park is a PhD student in the Mathematical, Computational, and Systems Biology program supervised by Dr. Jun Allard. Her current work focuses on airnemes, which are cellular protrusions that enable communication between different types of zebrafish pigment cells during pattern formation. It is important for the airineme to find the right target cell in order to send the signal for potential cell migration. Her research project uses mathematical modeling and image analysis of the airineme to understand how it optimizes efficient and accurate target search. Sohyeon presented her work at the SoCal Mechanobiology Day and won the best poster award. She also presented her work at the 2020 Biophysical Society Annual Meeting.

Honglei Ren

Honglei Ren is a PhD student in the Mathematical, Computational, and Systems Biology PhD program supervised jointly between Dr. Elizabeth Read in Chemical & Biomolecular Engineering and Dr. Qing Nie in Mathematics. He works on modeling the DNA methylation kinetics and single-cell method development in Mathematics Core and Theme.

Davie Tatarakis

David Tatarakis is a PhD student in the department of Developmental and Cell Biology at UC Irvine, studying the genetics of vertebrate embryo development in Dr. Thomas Schilling’s lab with particular emphasis on neural crest and craniofacial development. In collaboration with Dr. Qing Nie, David is working to elucidate the spatio-temporal dynamics and genetic mechanisms of cell fate determination in the early migrating neural crest in zebrafish using single cell RNA-seq and live in vivo imaging.

Remy Vu

Remy Vu is a PhD student in the Department of Biological Chemistry in Dr. Xing Dai lab. She utilizes single-cell RNA sequencing data to study molecular changes and interactions in different cell types during cutaneous wound healing (Theme A). Remy has been awarded the 2020 Graduate Research Fellowship by the NSF. 

POSTDOCTORAL FELLOWS

Axel Almet

Axel Almet is an NSF-Simons Postdoctoral Fellow in the Department of Mathematics and works with Professor Qing Nie. His research involves developing spatially-resolved mathematical and computational models to investigate the underlying processes governing skin function and pathology (in collaboration with the Plikus lab) and other biological systems. Current projects include: computational modelling of scar formation; mathematical modelling of skin stem cell lineage; and benchmarking cell-cell communication structures.

Zixuang Cang

Zixuan Cang is a postdoctoral scholar in the Department of Mathematics and NSF-Simons Center for Multiscale Cell Fate Research at UC, Irvine. His research interests include applied topology and numerical methods for PDEs with applications to biological systems of scales from molecular level to tissue level.

Christian F. Guerrero-Juarez

Christian F. Guerrero-Juarez is a postdoctoral fellow from the Department of Mathematics and Developmental & Cell Biology supervised by Dr. Nie. He works on skin wound healing and regeneration, hair follicle biology, single cell genomics and next generation lineage tracing and is involved in several projects related to Theme A.  He was a 2019 HHMI Hanna H. Gray Postdoctoral Fellowship Program Finalist ($10K) and received 2nd place for the virtual poster session at 2020 Inter-agency modeling and analysis group Multiscale Modeling annual meeting. 

Jinsu Kim

My research area lies at the interface of probability and mathematical biology. I am interested in stochastically modeled biochemical reaction networks, especially exploring connections between network topology and dynamical behaviors. I am also working on interdisciplinary research for various biological systems such as epigenome dynamics, designing synthetic control circuits, modeling protein aggregation, etc. My professional goal is to continue collaborative research to develop analytic and computational tools for problems arising in biology.

Wing Tat Leung

Wing Tat Leung is a postdoc fellow from Mathematics supervised by Lowengrub. He is developing a framework of dynamic density functional theory from statistical physics for bridging the scales between cells and tissues, a project in Mathematics Core.

Raul Ramos

Raul Ramos is a postdoctoral fellow in Dr. Maksim Plikus lab. Raul is interested in the mechanisms behind cell lineage specification and maintenance in various tissues, including the skin and the skeleton (Theme A). 

Yifan Wang

I am currently a visiting Assistant Professor in the Department of Mathematics at the University of California, Irvine (UC Irvine). Before joining UC Irvine, I worked as a postdoc researcher at UC Berkeley and the University of Houston. My research focuses on numerical solutions to fluid-structure interaction problems and its application such as modeling cardiovascular problems. I have expertise in developing numerical solvers, parallelizing codes, and conducting large-scale simulations on HPC clusters. Other areas of interest include machine learning and artificial intelligence.  
 

Xiaojie Wang

Xiaojie Wang, PhD, is a postdoctoral fellow in Dr. Maksim Plikus lab at the Department of Developmental and Cell Biology, UCI. She has been investigating the mechanism of regeneration using “multi-omics” platforms, focusing on “The Yin and Yang of adult skin stem cell niche”. 

Lihua Zhang

Lihua Zhang joined the Nie lab as a postdoctoral research scholar in August 2018. Before that she completed her Ph.D. in applied mathematics at Academy of Mathematics and Systems Science, Chinese Academy of Sciences: her thesis entitled “Research on Matrix Factorization Models, Algorithms and Applications of Big Omics Data”. Lihua’s research interests include computational biology, bioinformatics and optimization. Nowadays, single-cell data provides us unprecedented opportunity to understand the cellular heterogeneity in great details. She is actively developing new tools to model and analyze such data.

AY2019-2020 Fellows

Graduate Fellows

Yingxin Cao
Yingxin Cao, Mathematical, Computational, and Systems Biology PhD program, supervised jointly by Xiaohui Xie in Computer Science and Qing Nie in Mathematics, working on deep learning for single-cell sequencing analysis in Mathematics Core.
Lara Clemens
Lara Clemens was a PhD student supervised by Jun Allard. She worked on multiple projects in Mathematics Core and Theme C. Lara graduated and received her PhD degree in January 2020.
Morgan Dragan
Morgan Dragan is a PhD student under the direction of Dr. Xing Dai in the department of Biological Chemistry. Her current project centers around understanding transcriptional regulation of skin barrier and inflammation and understanding crosstalk between the skin and distal tissues (Theme A). She is also a collaborator on an IOA with Rachel Cinco to perform FLIM in skin wound healing.
Lianna Fung
Lianna Fung is a PhD student supervised by Schilling in the Dept. of Developmental and Cell Biology. She works on projects in Theme B on cell fate decisions during vertebrate hindbrain development using the MS2-MCP RNA labeling system and hybridization chain reaction (HCR) technique. She is closely working with a Mathematics PhD student on modeling aspect of the system.
Abdon Iniguez
Abdon Iniguez was a PhD student from MCSB supervised by Lowengrub. He worked on lineage models of tissue growth and parameter inference methods, projects in both Theme A and Mathematics Core.  He graduated with a PhD in January 2020.
Yushang Lai
Yushang Lai (a PhD student supervised by John Lowengrub) works on the Theme C projects in close collaboration with Dr. Vladimir Minin (faculty in statistics). He also uses stochastic analyses to designing new experiments for investigating hematopoiesis processes.
Julien Morival
Julien Morival (a PhD student supervised by Tim Downing) works on the Theme C projects in close collaboration with Dr. Elizabeth Read (a computational biologist). He also uses stochastic analyses to model temporal heterogeneity in post-replication DNA methylation.
Michelle Ngo
Michele Ngo is a PhD student in the Mathematical, Computational, and Systems Biology PhD program supervised jointly between Shahbaba in Statistics and Lowengrub in Mathematics. She works on nonparametric Bayesian bi-clustering method for single-cell RNA analysis in Mathematics Core.
Trini Nguyen
Trini Nguyen is a Ph.D. student in the Mathematical, Computational, and Systems Biology graduate program. Supervised by Jun Allard, she is working on a number of projects as part of the Mathematics Core. One of the projects is funded by the 2019 CMCF IOA, in which she collaborates with a graduate student from the Andersen Lab (School of Medicine) to investigate the load tolerance advantages volar skin has over non-volar skin.
Sohyeon Park
Sohyeon Park is a PhD student in the Mathematical, Computational, and Systems Biology program supervised by Dr. Jun Allard. She works on modeling cellular protrusion called Airineme, which is used for the long-distance cell signaling for stripe pattern formation in zebrafish. This project involves statistical inference and stochastic simulations in Mathematics Core. She presented her work at the SoCal Mechanobiology Day and won the best poster award. She also presented her work at the 2020 Biophysical Society Annual Meeting. 
Raul Ramos
Raul Ramos was a PhD student in the department of Developmental and Cell Biology and jointly supervised by professors Maksim Plikus and Qing Nie. He conferred his PhD degree in December 2019. Raul is interested in the mechanisms behind cell lineage specification and maintenance in various tissues, including the skin and the skeleton (Theme A).
Honglei Ren
Honglei Ren is a PhD student in the Mathematical, Computational, and Systems Biology PhD program supervised jointly between Dr. Elizabeth Read in Chemical & Biomolecular Engineering and Dr. Qing Nie in Mathematics. He works on modeling the DNA methylation kinetics and cell-cell communication in Mathematics Core and Theme C.
David Tatarakis
David Tatarakis is a PhD student in the Dept. of Developmental and Cell Biology supervised by Schilling. He works on the spatiotemporal dynamics and genetic mechanisms of cell fate determination in the early migrating neural crest in zebrafish using single-cell RNA-seq and live in vivo imaging, a project in Theme B. David is also interested in teaching and is receiving training in this area through his participation in the GAANN training grant on campus.
Remy Phong Vu
Remy Vu is a PhD student in the Department of Biological Chemistry in Dr. Xing Dai lab. She utilizes single-cell RNA sequencing data to study molecular changes and interactions in different cell types during cutaneous wound healing (Theme A). Remy has been awarded the 2020 Graduate Research Fellowship by the NSF.

 

Postdoctoral Fellows

Axel Almet
Axel Almet is a postdoctoral fellow from Mathematics supervised by Nie on research projects related to the Mathematics Core and Theme A. Current projects include spatial modelling of scar formation in skin tissue and mathematical modelling of skin stem cell lineage.
Zixuan Cang  
Zixuan Cang is a postdoctoral fellow from Mathematics supervised by Nie. He works on multiple projects on linking single-cell data with spatial modeling and imaging data in both Theme B and Mathematics Core.
Christian F. Guerrero-Juarez
Christian F. Guerrero-Juarez is postdoctoral fellow from Department of Developmental and Cell Biology jointly supervised by Plikus and Nie. He works on wound healing, adipocyte, and hair follicle biology and involves in several projects in Theme A.  He won a) 2019 HHMI Hanna H. Gray Postdoctoral Fellowship Program Finalist ($10K) and b) 2nd place for the virtual poster session at 2020 Inter-agency modeling and analysis group Multiscale Modeling annual meeting. 
Wing Tat Leung
Wing Tat Leung is a postdoc fellow from Mathematics supervised by Lowengrub. He is developing a framework of dynamic density functional theory from statistical physics for bridging the scales between cells and tissues, a project in Mathematics Core.
Xiaojie Wang
Xiaojie Wang is a postdoctoral fellow supervised by Plikus at the Department of Developmental and Cell Biology.  She is investigating the mechanism of regeneration using “multi-omics” platforms, focusing on “The Yin and Yang of adult skin stem cell niche”, a project in Theme A.
Lihua Zhang
Lihua Zhang is a postdoctoral fellow from Mathematics supervised by Nie. She is using optimization tools to develop new computational tools to analyze single-cell genomics data, a project in Mathematics Core.

AY2018-2019 Fellows

Graduate Fellows

Lianna Fung
Lianna Fung is a PhD student supervised by Schilling in the Dept. of Developmental and Cell Biology. She works on projects in Theme B on cell fate decisions during vertebrate hindbrain development using the MS2-MCP RNA labeling system and hybridization chain reaction (HCR) technique. She is closely working with a Mathematics PhD student on modeling aspect of the system.
Daniel Ramirez-Guerrero
Daniel Ramirez-Guerrero is a Math PhD student supervised by Lowengrub, working on projects in Mathematics Core and Theme A. He is developing a novel multiscale, tissue-level continuum model to understand how mechanical forces affect cell behaviors such as proliferation, differentiation and migration. He works on an IOA project with two students from BME and a student from Prof. Vivek Shenoy’s group in the Dept. of Materials Sci. at U. Pennsylvania.
Alvaro Fletcher
Alvaro Fletcher is a PhD student (with Hispanic heritage) in Mathematical, Computational, and Systems Biology PhD program supervised by Enciso. He works on developing stochastic models of cell fate, a project in Mathematics Core.
Daniel Haensel
Daniel Haensel is a 6th year graduate student in the Dept. of Biological Chemistry supervised by Dai. He uses adult mouse epidermis and hair follicle as model systems to study the regulation of epithelial stem cells during regeneration and wound repair. He works on research projects in Theme A. He will graduate in June 2019 and go to Stanford as a postdoctoral fellow.
Julien Morival
Julien Morival (a PhD student supervised by Tim Downing) works on the Theme C projects in close collaboration with Dr. Elizabeth Read (a computational biologist). He also uses stochastic analyses to model temporal heterogeneity in post-replication DNA methylation. Julien has presented a poster at the Biomedical Engineering Society (BMES) Annual Conference in Atlanta, (October 2018) and a poster and rapid-fire presentation at the UC System-wide Bioengineering Annual Symposium (June 2018) (received Best Poster Award).
Michelle Ngo
Michele Ngo is a PhD student in the Mathematical, Computational, and Systems Biology PhD program supervised jointly between Shahbaba in Statistics and Lowengrub in Mathematics. She works on nonparametric Bayesian bi-clustering method for single-cell RNA analysis in Mathematics Core.
Daniel Tatarakis
David Tatarakis is a PhD student in the Dept. of Developmental and Cell Biology supervised by Schilling. He works on the spatiotemporal dynamics and genetic mechanisms of cell fate determination in the early migrating neural crest in zebrafish using single-cell RNA-seq and live in vivo imaging, a project in Theme B. David is also interested in teaching and is receiving training in this area through his participation in the GAANN training grant on campus.
Rob Taylor
Rob Taylor is a PhD student in Physics supervised by Allard. He works on developing Weighted Ensemble methods to study cell surface evacuation, which plays important role in immune system response, a project in Theme C.

 

Postdoctoral Fellows

Zixuan Cang  
Zixuan Cang is a postdoctoral scholar in the Dept. of Math. supervised by Nie. He works on multiple projects on linking single-cell data with spatial modeling and imaging data in both Theme B and Mathematics Core.
Christian F. Guerrero-Juarez
Christian F. Guerrero-Juarez is a current UCI Chancellor’s ADVANCE Postdoctoral Fellow jointly supervised by Plikus and Nie. He works on wound healing, adipocyte, and hair follicle biology and involves in several projects in Theme A.  During the time as the center postdoctoral fellow, he won Premio Michoacano de la Juventud 2018 – Mérito Académico (2018 Michoacán Youth Prize – Academic Merit) – the highest distinction given by the State Government of Michoacán to excelling young professionals in their respective fields.
Theresa Loveless
Theresa Berens Loveless is a postdoctoral scholar in the Department of Biomedical Engineering, advised by Center faculty member Chang Liu. She is trained as a cell and molecular biologist, and now develops synthetic biology tools that increase the resolution and throughput of developmental biology. Currently, she is collaborating with Center Fellow Christian Guerrero-Juarez to trace cell lineage in regenerating mouse skin, part of Theme A.
Adam MacLean
Adam MacLean was a postdoctoral fellow in the Dept. of Math supervised by Nie. He worked on multiple projects in Mathematics Core and Theme A. In January 2019 he left UCI to start a tenure-track position as an assistant professor of quantitative and computational biology at USC.
Chris Rackauckas
Chris Rackauckas is a postdoc in the Dept. of Math. supervised by Nie. He studies multiscale mechanisms for controlling biological noise. He is the developer of many open-source Julia packages including DifferentialEquations.jl. He runs a blog on numerical computing where he details the methods using Julia effectively and numerical methods for solving differential equations. He worked on multiple projects in Mathematics Core and Theme B. He left in January 2019 to MIT as an Applied Mathematics Instructor. 
Xiaojie Wang
Xiaojie Wang is a postdoctoral fellow supervised by Plikus at the Department of Developmental and Cell Biology.  She is investigating the mechanism of regeneration using “multi-omics” platforms, focusing on “The Yin and Yang of adult skin stem cell niche”, a project in Theme A.
Lihua Zhang
Lihua Zhang is a postdoc fellow supervised by Nie. She is using optimization tools to develop new computational tools to analyze single-cell genomics data, a project in Mathematics Core.