GRADUATE FELLOWS
Carmen Al Masri
My research aims at understanding transcription factor (TF) search and binding mechanisms through various computational biophysics methods. Our lab employs a multidisciplinary approach that involves molecular modeling and simulation techniques, statistical mechanics, and stochastic methods. We also incorporate experimental information from single molecule measurements and genome profiling.
Currently, I have three ongoing projects: the first employs all-atom MD simulations and statistical mechanics methods to explore the WRKY domain plant TF dissociation from the DNA by constructing the corresponding free energy landscape. The second project involves deep learning methods to predict the change in binding affinity of the WRKY domain TF upon mutating the DNA binding site. The features used are energy terms obtained from MD simulations (MMGBSA) and the model is trained using experimental data for binding affinities. The third project, selected for Interdisciplinary Opportunity Award from NSF/Simons Center for Multiscale Cell Fate Research Center, involves studying the Myc/Max search dynamics on the DNA by determining binding and diffusion energetics through all-atom and coarse-grained MD simulations, but also by studying the genome-wide binding profile.
Thomas Beardsley
Thomas Beardsley is a PhD candidate in the Mathematics department advised by Dr. Natalia Komarova. His research focuses on developing dynamical models to describe the evolutionary behavior of bacterial populations. In particular, he is interested in developing numerical tools to describe the evolutionary dynamics in serial propagation experiments of E.Coli and other unicellular populations.
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.
Stephenson Chea
Multiscale Analysis of Early Cell Fate and Gene Expression Transitions in Human Developmental Disorders – Developmental disorders are structural or physiological impairments to an individual’s physical and/or cognitive functions. Although developmental disorders are very common, they often lack reliable treatment options. Generating treatments for developmental disorders requires that we reproduce them in animals, but the genetic origins of many developmental disorders are unknown and appear to be polygenic. Since this is the case, how do we reproduce developmental disorders in animals when we don’t know which genes cause them and how they cause them? A promising solution to this problem is found in the study of transcriptomopathies, genetic syndromes in which a mutation to a ubiquitous transcriptional control gene results in quantitative changes in the expression of hundreds or thousands of other genes from the beginning of development. In the Nipbl+/- mouse, which models the transcriptomopathy, Cornelia de Lange Syndrome (CdLS), these gene expression changes give rise to developmental disorders in multiple tissues and organs common to non-syndromic cases in man. Recently, I used early Nipbl+/- mouse embryos (at late-gastrulation stage and cardiac crescent stage) and single-cell transcriptomics (scRNA-seq) to study the developmental origins of congenital heart defects. I found that changes in the allocation of cells to early heart cell lineages and changes in function of the Nanog gene regulatory network foreshadow the structural heart defects that emerge at birth in the Nipbl+/- mouse and CdLS, thereby identifying both the cells and genes responsible for those anomalies. I am currently using the same model system to identify gene regulatory networks that are key drivers of progenitor cell allocation in the emerging neural ectoderm, as a means to discover cell and gene targets for the treatment of neurodevelopmental disorders. In the very near future, I plan on using single-cell epigenomics (ATAC-seq) to study how changes to chromatin topology (Nipbl regulates gene expression by affecting chromatic interactions) cause gene regulatory network dysfunction in the Nipbl+/- mouse.
Emmanuel Dollinger
Emmanuel uses a combination of short read single cell transcriptomic data, cutting edge deep learning and experimental validation to characterize the immune system response to different stimuli. He focuses on the immune response to basal cell carcinoma and how these interactions change with different immunotherapeutic treatments in vivo. Emmanuel collaborates with the UCI Vaccine Center to understand the systems-level effects of vaccine adjuvants on the immune system. Emmanuel also co-founded the genomics Practical Applications and Learning Seminar (genPALS), a CMCF seminar series dedicated to building a community of biological big data researchers at UCI. He can be found on LinkedIn.
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.
Junyan Duan
Junyan Duan is a PhD student in the Mathematical, Computational and Systems Biology program supervised jointly by Dr. Bogi Andersen in Biological Chemistry and Dr. John Lowengrub in Mathematics. She analyzes single cell sequencing data to understand skin development and the circadian rhythm in the skin. She also works on developing an algorithm for predicting circadian time in single cell data with Michelle Ngo.
Renzhi Hou
I am a PhD student in the Cellular and Molecular Biosciences program supervised by Dr. Maksim Plikus in Developmental and Cell Biology. I am interested in the wound healing process in amphibian that are capable of scarless wound repair. I hope to study the tissue dynamics and cell fate during early wound healing event.
Yushang Lai
Yushang is a Mathematical, Computational, and Systems Biology Ph.D candidate co-advised by Prof. Vladimir Mini and John Lowengrub. He is interested in integrating statistical Bayesian probabilistic learning and mathematical mechanistic ODE modeling in fundamental biology Hematopoiesis process.
Pavan Nayak
Pavan is a Ph.D. student in the Mathematical, Computational, and Systems Biology program, conducting research in the Schilling Lab. His current research is focused on understanding the cellular diversity of cranial tendon fibroblasts (called tenocytes) using single-cell sequencing in transgenic zebrafish.
Sohyeon Park
Sohyeon is a Mathematical, computational, and systems biology PhD student co-advised by Profs. Jun Allard and Xiaoyu Shi. She is interested in mathematical modeling and structural biology and studies how signalling molecules are transported in primary cilia by developing a stochastic model with super resolution microscopy.
Andrew Phan
Tri Andrew Phan is a PhD student in Dr. Timothy Downing’s lab in the Department of Biomedical Engineering. Andrew’s research focuses on understanding how biophysical cues influence cell fate decisions in the context of stemness acquisition. His current work highlights a potential role for cell adhesion to influence both human fibroblast reprogramming efficiency and cancer stemness using data collected from scRNA-seq, traction force microscopy, and bioinformatic analyses of cancer genomic databases.
Honglei Ren
Honglei is a Ph.D. student in the Mathematical, Computational, and Systems Biology program supervised jointly by Dr. Qing Nie and Dr. Elizabeth Read. His current research focuses on developing computational methods for spatial transcriptomic data, especially for understanding the pseudo-spatiotemporal relationship between cells in tissue.
Brian Schetzsle
Brian Schetzsle is a third-year PhD student in the Statistics department under the supervision of Professor Babak Shahbaba. His research focuses on modeling functional relationships between regions of the brain using time-varying autoregressive models applied to fMRI data from human subjects. The size of fMRI data poses a perennial problem in research. Necessary dimensionality reduction is achieved through tensor decomposition of coefficient matrices in combination with Bayesian methodology imposing sparsity inducing Ising prior densities.
Rachel Sousa
Rachel is a PhD student in the Mathematical, Computational, and Systems Biology program co-advised by Dr. John Lowengrub and Dr. Francesco Marangoni. She is developing mathematical models of the tumor-immune system with the aim of identifying the key features that distinguish the ability of the immune system to eliminate a tumor from those features that allow a tumor to evade the immune system and persist in the body. By understanding these differences, she will be able to to predict responses to immunotherapies and design new combinations of drugs, doses, and schedules that can optimize treatment response and minimize unwanted side-effects.
Adam Stabell
Adam Stabell is a PhD candidate in the department of Developmental and Cell Biology, mentored by Dr. Scott Atwood. His research seeks to elucidate the cell-cell communication between the heterogenous stem cell populations present in human epidermis and the role they play in the morphogenesis of this tissue. He is currently using single-cell RNA sequencing data to impute active signaling pathways in the skin and perturbing them using in vitro and in vivo model systems.
Kirsten Wong
Kirsten Wong is a PhD candidate in the Department of Developmental and Cell Biology in Dr. Scott Atwood’s lab. She is studying the mechanisms that drive tumor regression in basal cell carcinoma. She currently uses transgenic mouse models and single-cell RNA sequencing data to investigate the role of immune system interactions in regulating spontaneous tumor regression (Theme A).
Yinyin Zhuang
Yinyin Zhuang is a PhD student supervised by Dr. Xiaoyu Shi in the Department of Developmental and Cell Biology. Her current research aims to dissect the structural organization of nuclear lamina via label-retention expansion microscopy and reveals lamina’s functions on cell senescence/proliferation from structural angle.
POSTDOCTORAL FELLOWS
Axel Almet
Axel Almet is an NSF-Simons Postdoctoral Fellow in the Nie Lab (Department of Mathematics). His current projects include: developing a spatially-resolved computational model of scar formation in skin; analyzing the transcriptional landscape of fibroblasts during wound healing using single-cell RNA-sequencing; and dissecting causal mechanisms in cell-cell communication using single-cell RNA-sequencing and spatial transcriptomics.
Federico Bocci
Federico Bocci integrates systems biology modeling with bioinformatics methods on single cell transcriptomics to investigate complex biological processes. Currently, his major biological interests include the regulation of the Epithelia-Mesenchymal Transition (EMT) during cancer progression, the spatial and temporal dynamics of cell-cell communication, and the heterogeneity and signaling in the epidermis.
Zhuoxin Chen
Zhuoxin Chen is a postdoc fellow in Department of Developmental & Cell Biology supervised by Dr. Evgeny Kvon. My research focuses on characterizing chromatin interactions during mammal development and integrating expression, histone modification and interaction data to understand gene regulation process.
Theresa Loveless
Theresa Berens Loveless is a postdoctoral researcher and MOSAIC K99/R00 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. She will be starting her own group at Rice University in July 2023.
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).
Benjamin Walker
Benjamin Walker is a CMCF postdoctoral fellow in the Nie Lab focusing on research involving spatial transcriptomic (ST) data. Current research interests include understanding multiscale organization in tissue through computational analysis of ST datasets and applications of machine learning methods in ST.
Yubai Yuan
Yubai Yuan is a Postdoc researcher in Statistics at UC Irvine. He is under the supervision of Professor Annie Qu, and his research focuses on complex network analysis, causal inference, and optimal transport with their application to the study of cross- specie neuron dynamics relevant to memory. His other research interests are community detection, link prediction, causal inference, metric learning, active learning, crowdsourcing, and latent modeling.
AY2021-2022 Fellows
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.
Emmanuel Dollinger
Emmanuel uses a combination of short read single cell transcriptomic data, cutting edge deep learning and experimental validation to characterize the immune system response to different stimuli. He focuses on the immune response to basal cell carcinoma and how these interactions change with different immunotherapeutic treatments in vivo. Emmanuel collaborates with the UCI Vaccine Center to understand the systems-level effects of vaccine adjuvants on the immune system. Emmanuel also co-founded the genomics Practical Applications and Learning Seminar (genPALS), a CMCF seminar series dedicated to building a community of biological big data researchers at UCI. He can be found on LinkedIn.
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.
Junyan Duan
Junyan Duan is a PhD student in the Mathematical, Computational and Systems Biology program supervised jointly by Dr. Bogi Andersen in Biological Chemistry and Dr. John Lowengrub in Mathematics. She analyzes single cell sequencing data to understand skin development and the circadian rhythm in the skin. She also works on developing an algorithm for predicting circadian time in single cell data with Michelle Ngo.
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.
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.
Michelle Ngo
Michelle Ngo is a PhD candidate in the Mathematical, Computational and Systems Biology program supervised jointly by Dr. Babak Shahbaba in Statistics and Dr. John Lowengrub in Mathematics. She works on nonparametric Bayesian biclustering methods for single cell RNA analysis in the Mathematics Core, and with Junyan Duan on developing an algorithm for predicting circadian time in single cell data.
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 is a Mathematical, computational, and systems biology PhD student co-advised by Profs. Jun Allard and Xiaoyu Shi. She is interested in mathematical modeling and structural biology and studies how signalling molecules are transported in primary cilia by developing a stochastic model with super resolution microscopy.
Honglei Ren
Honglei Ren is a Ph.D. student in the Mathematical, Computational, and Systems Biology program supervised jointly between Dr. Elizabeth Read in Chemical & Biomolecular Engineering and Dr. Qing Nie in Mathematics. He is currently working on developing deep learning methods for spatial transcriptomic data and modeling the DNA methylation kinetics during cell cycles.
Rachel Sousa
Rachel is a PhD student in the Mathematical, Computational, and Systems Biology program co-advised by Dr. John Lowengrub and Dr. Francesco Marangoni. Her research aims to understand responses to immunotherapy via mathematical modeling. Currently, she is working to model the response of T regulatory cells, CD8-positive T cells, and dendritic cells to anti-PD-1 and anti-ICOSL treatments.
Adam Stabell
Adam Stabell is a PhD candidate in the department of Developmental and Cell Biology, mentored by Dr. Scott Atwood. His research seeks to elucidate the cell-cell communication between the heterogenous stem cell populations present in human epidermis and the role they play in the morphogenesis of this tissue. He is currently using single-cell RNA sequencing data to impute active signaling pathways in the skin and perturbing them using in vitro and in vivo model systems.
Annie Trinh
Annie Trinh is a Microbiology & Molecular Genetics Ph.D. student in the lab of Dr. Timothy Downing. Her research aims to investigate the role of maintenance methylation in governing cell fate decisions through the introduction of engineered mutant methyltransferases or small molecule inhibitors during cellular differentiation processes. While small molecular inhibitors of DNA methylation act globally, Annie’s work also involves developing tools for targeted epigenetic editing.
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.
Kirsten Wong
Kirsten Wong is a PhD candidate in the Department of Developmental and Cell Biology in Dr. Scott Atwood’s lab. She is studying the mechanisms that drive tumor regression in basal cell carcinoma. She currently uses transgenic mouse models and single-cell RNA sequencing data to investigate the role of immune system interactions in regulating spontaneous tumor regression (Theme A).
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.
Federico Bocci
Federico Bocci is an NSF-Simons Postdoctoral Fellow in the Department of Mathematics and NSF-Simons Center for Multiscale Cell Fate Research. His research focuses on integrating computational modeling and single cell data analysis to uncover the dynamics of Epithelial-Mesenchymal Transition during cancer progression.
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.
Theresa Loveless
Theresa Berens Loveless is a postdoctoral researcher and MOSAIC K99/R00 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. Among other projects, she is collaborating with the Nie lab to trace cell lineage in regenerating mouse skin.
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).
Benjamin Walker
My research focuses on developing computational tools for modeling and analysis of biological systems, with a goal of using mathematical modeling to inform future biological research. I am currently working in the Nie lab using spatial transcriptomics data to study cell development, interaction, and tissue structure in several biological systems. By integrating spatial data, a much more detailed picture of interactions between cells can be obtained than from single cell transcriptomics alone.
Xiaojie Wang
Xiaojie Wang, PhD, is a postdoctoral fellow in Dr. Maksim Plikus lab at the Department of Developmental and Cell Biology, UCI. Her research is focused on understanding dynamics of biological switches for activation (ON) versus quiescence (OFF). In order to identify how individual cells respond to and interact with each other to perform logical functions, both traditional one-at-a-time assays and systemic approaches are used.
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.
AY2020-2021 Fellows
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.
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 C.
David 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.
Federico Bocci
Federico Bocci is an NSF-Simons Postdoctoral Fellow in the Department of Mathematics and NSF-Simons Center for Multiscale Cell Fate Research. His research focuses on integrating computational modeling and single cell data analysis to uncover the dynamics of Epithelial-Mesenchymal Transition during cancer progression.
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