About

The rise of affordable sequencing technologies is revolutionizing all areas of biology. This is most evident in the areas of areas of genetics, epigenetics, and genomics, where a number of faculty across the school of biological sciences and the medical school use genome-wide techniques to study gene regulation in development and disease, comparative genomics, the connection of epigenetic changes to metabolism, and cellular decision-making. Participants in this track benefit from interactions with students and faculty from UCI’s strong systems biology and modeling program as well as from workshops organized by the UCI Genomics High Throughput Facility.

The Genetics, Epigenetics, and Genomics program at UCI provides research training on the latest genome-wide techniques to study protein-DNA interactions, RNA expression, open chromatin, and long-range interaction in functional genomics, and personalized medicine. Students from this track will take graduate coursework in genetics and genomics while rotating through multiple laboratories to identify research topics of interest to them, which can span all of the areas of the CMB program in cell, developmental, cancer, immunology, and genetics with the emphasis on genome-wide analysis projects.

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Faculty

  • Steve Allison, allisons@uci.edu, Ecology & Evolutionary Biology
    Microbial ecology, modeling, and global environmental change
  • Bogi Andersen, bogi@uci.edu, Medicine and Biological Chemistry
    Transcriptional regulation in the developmental biology of epidermis and mammary gland
  • Tallie Z. Baram, tallie@uci.edu, Physiology & Biophysics and Anatomy & Neurobiology
    Epigenetic mechanisms in brain plasticity; stress, epilepsy, learning and memory
  • Emiliana Borrelli, borrelli@uci.edu, Microbiology & Molecular Genetics
    Dopaminergic system and glial cells in CNS development
  • Adriana Briscoe, abriscoe@uci.edu, Ecology & Evolutionary Biology.
    Evolution of sensory systems
  • Minji Byun, byunm1@uci.edu, Microbiology & Molecular Genetics
    Epigenetic modifiers in the regulation of immune cell function
  • J.J. Emerson, jje@uci.edu, Ecology & Evolutionary Biology
    Evolutionary genomics, population genetics, evolution of genetic novelty, natural genetic variation, structural genetic variation
  • Brandon Gaut, bgaut@uci.edu, Ecology & Evolutionary Biology
    Population genetics, molecular evolution, genome evolution.
  • Klemens Hertel, khertel@uci.edu, Microbiology & Molecular Genetics
    Regulation of gene expression by alternative splicing
  • Todd Holmes, tholmes@uci.edu, Physiology & Biophysics
    Phototransduction, non-image forming vision, circadian biology, voltage-gated potassium channels, neural circuit analysis, and behavior
  • Autumn S. Ivy, aivy@uci.edu, Physiology & Biophysics
    Role of exercise-induced chromatin modifications in brain plasticity and neural function, early-life periods of brain maturation
  • Evgeny Kvon, ekvon@uci.edu, Developmental and Cell Biology  Transcriptional regulation in the context of mammalian development, evolution, and human congenital disorders
  • Grace Lee, grylee@uci.edu, Ecology & Evolutionary Biology
    Population genetics, evolutionary genomics, epigenetics, transposable elements, Drosophila
  • Wei Li, wei.li@uci.edu, Biological Chemistry, Biological Chemistry Computational Cancer Epigenomics and Transcriptomics
  • Haoping Liu, h4liu@uci.edu, Biological Chemistry
    MAP kinase signal transduction; dimorphic regulation in yeast
  • Anthony Long, tdlong@uci.edu, Ecology & Evolutionary Biology
     Population genetics, the genetics of complex traits, the genetics of adaptation, and bioinformatics
  • Jennifer B.H. Martiny, jmartiny@uci.edu, Ecology & Evolutionary Biology
    Diversity, evolution, and functioning of microbial communities (microbiomes)
  • Ivan Marazzi, imarazzi@uci.edu, Biological Chemistry
    Epigenetic and chromatin-mediated control of gene expression in the context of the cellular response to pathogens or differentiation
  • Ali Mortazavi, ali.mortazavi@uci.edu, Developmental & Cell Biology
    Applications of genomics, computation, and sequencing technologies to the analysis of transcriptional regulation in development
  • Stanley Ng, sn16@sanger.ac.uk Biological Chemistry
    Advancing precision medicine with novel diagnostics and treatments at clonal resolution through multi-omic spatial and biofluid data generation and statistical learning using million-core machines
  • Trina M. Norden-Krichmar, tnordenk@uci.edu, Epidemiology  Bioinformatics, genomic and genetic factors in human health, computational methods
  • Feng Qiao, qiao@uci.edu, Biological Chemistry
    Telomeres & telomerase and their roles in cancer and stem cell diseases; Structural, biochemical and molecular genetic analyses of nucleoprotein assemblies
  • Jose M. Ranz, jranz@uci.edu, Ecology & Evolutionary Biology
    Functional and comparative genomics; Evolution of the expression network; Speciation.
  • Suzanne B. Sandmeyer, sbsandme@uci.edu, Biological Chemistry
    Molecular genetics of a position-specific yeast retrovirus-like element
  • Marcus Seldin, mseldin@uci.edu, Biological Chemistry
    Systems genetics approaches to understand metabolism and physiology with a special emphasis on mechanisms of tissue-tissue communication
  • Yongsheng Shi, yongshes@uci.edu, Microbiology & Molecular Genetics
    The role of post-transcriptional gene regulation in stem cells and cancer
  • Dorota Skowronska-Krawczyk, dorotask@hs.uci.edu, Ophthalmology and Physiology & Biophysics The focus of the lab is to understand the molecular mechanism of aging by studying the processes regulating age-related eye diseases, with an emphasis on coordinated changes in cellular, metabolic and transcriptional programs in conditions such as macular degeneration and glaucoma. Laboratory is a part of the Center for Translational Vision Research
  • Sha Sun, shasun@uci.edu, Developmental & Cell Biology
    Long noncoding RNAs in epigenetic programming
  • Vivek Swarup, vswarup@uci.edu, Neurobiology and Behavior Integrative functional genomics approaches to understand brain function and neurodegenerative diseases
  • Kevin Thornton, krthornt@uci.edu, Ecology & Evolutionary Biology
    Population genetics, quantitative genetics, and computational biology
  • Ping Wang, phwang@uci.edu, Biological Chemistry, Physiology & Biophysics, and Pathology & Laboratory Medicine
    Molecular hormone actions in diseases and stem cells
  • Katrine Whiteson, katrine@uci.edu, Molecular Biology & Biochemistry
    Metagenomics, metabolomics and community culture models of host-associated microbial and viral communities in health and disease; human microbiome; microbial ecology.
  • Xiaohui Xie, xhx@ics.uci.edu, Computer Science and Developmental & Cell Biology
    Computational biology, bioinformatics, and genomics
  • Qin Yang, qiny3@uci.edu, Medicine and Physiology & Biophysics
    Cellular and molecular mechanisms for insulin resistance and energy expenditure in obesity and type 2 diabetes
  • Kyoko Yokomori, kyokomor@uci.edu, Biological Chemistry
    Molecular mechanisms of chromosome dynamics and gene regulation
  • Michael Zaragoza,,mzaragoz@uci.edu, Biological Chemistry and Pediatrics
    Molecular mechanisms of inherited cardiovascular diseases

Faculty – Secondary Affiliation

  • Kavita Arora, karora@uci.edu, Developmental & Cell Biology
    Drosophila development; TGF-b signal transduction; cell signaling
  • Kevin Beier, kbeier@uci.edu, Physiology & Biophysics
    Identifying how experience modulates activity dynamics in neural circuits, both acutely and chronically
  • Claudia Benavente, claudia.benavente@uci.edu, Professor of Developmental & Cell Biology
    Understanding epigenetic deregulation in pediatric cancer tumorigenesis
  • Bruce Blumberg, blumberg@uci.edu, Developmental and Cell Biology
    Gene regulation by nuclear hormone receptors in vertebrate development and adult physiology
  • Anne L. Calof, alcalof@uci.edu, Anatomy & Neurobiology and Developmental & Cell Biology
    Regulation of stem cells in development and regeneration; genomic strategies for understanding the etiology and treatment of human neurodevelopmental disorders using transgenic mouse models
  • Ken W.-Y. Cho, kwcho@uci.edu, Developmental & Cell Biology
    Transcriptomic and epigenomic analysis in early vertebrate development
  • Jefferson Y. Chan, jchan@uci.edu, Pathology & Laboratory Medicine
    Regulation of genes associated with oxidative stress
  • Xing Dai, xdai@uci.edu, Biological Chemistry
    Skin and mammary stem cells, Wnt signaling, chromatin, transcription
  • Fangyuan Ding, dingfy@uci.edu, Developmental and Cell Biology Single molecule biology and engineering (such as in situ mapping currently inaccessible RNA, quantifying protein-nucleic acid kinetics in a high-throughput manner), emerging from basic single-cell research to tool developments
  • Nir Drayman, nirdra@uci.edu, Molecular Biology and Biochemistry
    Studies how cell-to-cell variability affects viral infection outcomes using technologies such as live-imaging, machine learning, single-cell RNA-sequencing and microfluidics
  • Robert Edwards , redwards@uci.edu, Pathology & Laboratory Medicine, In Residence
    Pathogenesis of inflammatory bowel disease
  • Michael Hicks, mrhicks1@hs.uci.edu, Physiology & Biophysics Skeletal muscle, muscle stem cells, and iPSCs with a focus on regeneration and cell therapies for muscle wasting diseases
  • Peter Kaiser, pkaiser@uci.edu, Biological Chemistry
    Cell cycle control; regulation of proteins by ubiquitination
  • Orkide Koyuncu, okoyuncu@hs.uci.edu, Microbiology and Molecular Genetics Virus infections of the nervous system, and understanding the molecular mechanisms of alpha herpesvirus (HSV, PRV, VZV) invasion, latency establishment and reactivation in the peripheral nervous system neurons
  • Gina Lee, ginalee@uci.edu Microbiology & Molecular Genetics RNA signaling and metabolism
  • Thomas Martinez, t.martinez@uci.edu, Biological Chemistry Discovery and characterization of unannotated small open reading frame-encoded microproteins using genomics, proteomics, and bioinformatics methods, with an emphasis on investigating microproteins in cancer
  • Selma Masri, smasri@uci.edu, Biological Chemistry Cancer and stem cell biology, immune microenvironment, young-onset cancer and circadian clock disruption
  • Krzysztof Palczewski, kpalczew@uci.edu, Physiology & Biophysics My research group uses multidisciplinary approaches aimed at developing a comprehensive understanding of vision, including gene expression and transcriptional regulation in phototransduction and the visual cycle to characterize the visual system in health and during diseases leading to blindness.
  • Nicholas Pannunzio, nrpann@uci.edu, Biological Chemistry
    Cancer genetics, genome integrity, and cancer health disparities in underrepresented groups
  • Matthew Rose, mfrose@hs.uci.edu, Pathology
    Mapping gene networks, cell fate, and wiring decisions with multi-omics and 3D imaging in neurodevelopment and neurologic disease
  • Leslie M. Thompson, lmthomps@uci.edu, Psychiatry and Biological Chemistry
    Molecular and biochemical mechanisms of disease pathogenesis and therapeutic approaches to human neurodegenerative disease
  • Rahul Warrior, rwarrior@uci.edu, Developmental & Cell Biology
    Developmental regulation of proteoglycan biosynthesis; Transcriptional response to BMP growth factor signaling
  • Travis Wiles, travis.wiles@uci.edu, Molecular Biology & Biochemistry Exploring the unseen connections between animals and the microbial world