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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  • Tallie Z. Baramtallie@uci.edu, Physiology & Biophysics 
    Epigenetic mechanisms in brain plasticity; stress, epilepsy, learning and memory
  • Kevin T. Beierkbeier@uci.edu, Physiology & Biophysics
    Molecular and neural circuit basis of mental illness, substance use disorders, Alzheimer’s disease – genetic/epigenetic individual vulnerability factor identification
  • Emiliana Borrelliborrelli@uci.edu,  Microbiology & Molecular Genetics
    Involvement of dopamine in addiction and in neurological and psychiatric disorders
  • Minji Byun, byunm1@uci.edu, Microbiology & Molecular Genetics
    Epigenetic modulator dysfunction in human developmental and immune disorders
  • Timothy Lamont Downingtim.downing@uci.edu, Microbiology & Molecular Genetics
    The Downing Lab explores new and innovative approaches to cell and tissue engineering. We are particularly interested in understanding how the genome is regulated through non-sequence-based changes to DNA (epigenetics) during healthy tissue development and disease progression.
  • J.J. Emersonjje@uci.edu, Ecology & Evolutionary Biology
    Population genetics and molecular evolution of genome structure
  • Klemens Hertelkhertel@uci.edu, Microbiology & Molecular Genetics
    Regulation of gene expression by alternative splicing, bioinformatics, human genetic disease
  • Evgeny Kvon, ekvon@uci.edu, Developmental & Cell Biology
    The Kvon lab investigates mammalian gene regulation using cutting-edge genomics, genome editing, and transgenic tools. We are particularly interested in studying the role of gene regulation in development and evolution and how its malfunction leads to congenital disease.
  • Albert La Spada, alaspada@uci.edu, Pathology & Laboratory Medicine
    Our research seeks the mechanisms that underlie neurodegeneration and neuron cell death in spinal & bulbar muscular atrophy, spinocerebellar ataxia type 7, Huntington’s Disease, ALS, Parkinson’s disease, and Alzheimer’s disease, and by reproducing molecular pathology in mice and in neurons, astrocytes, and skeletal muscle cells derived from human patient stem cells, we are developing therapies to treat these diseases.
  • Grace Yuh Chwen Lee, grylee@uci.edu, Ecology & Evolutionary Biology
    I study how the widespread genomic parasite, transposable element, influences health and the myriad diversity of life, by combining population genomics, epigenomics, and computational biology
  • Wei Li, wei.li@uci.edu, Biological Chemistry
    Computational Biomedicine: Epigenetics Liquid Biopsy and Alternative Polyadenylation Therapy
  • Anthony D. Longtdlong@uci.edu, Ecology & Evolutionary Biology
    Population genetics, the genetics of complex traits, the genetics of adaptation, and bioinformatics
  • Ivan Marazzi, imarazzi@uci.edu, Biological Chemistry
    The Marazzi Laboratory studies epigenetic and chromatin-mediated control of gene expression in the context of the cellular response to pathogens or cellular differentiation.
  • Ali Mortazaviali.mortazavi@uci.edu, Developmental & Cell Biology
    Our lab is focused on mammalian functional genomics using short and long-read sequencing to understand gene regulatory networks.
  • Stanley W.K. Ng, stanlewn@uci.edu, Biological Chemistry
    The Ng Lab uses multiple spatial and omics sequencing technologies to profile tissue clones and assess their contribution to overall disease state, treatment response, and patient outcomes
  • Trina M. Norden-Krichmar, tnordenk@uci.edu, Biological Chemistry
    Bioinformatics; genetic factors in human diseases; medical, environmental and marine genomics; computational drug discovery; machine learning
  • Jose Ranzjranz@uci.edu, Ecology & Evolutionary Biology
    Insect functional and comparative genomics, evolution of the expression network, speciation
  • Marcus Seldin, mseldin@uci.edu, Biological Chemistry
    Population genetics approaches to investigate inter-organ signaling
  • Yongsheng Shiyongshes@uci.edu, Microbiology & Molecular Genetics
    Our laboratory studies the mechanism and regulation of mRNA processing in development and in pathogen-host interactions.
  • Dorota Skowronska-Krawczyk, dorotask@hs.uci.edu, Physiology & Biophysics
    Skowronska-Krawczyk’s laboratory focuses on understanding the molecular mechanism of aging in the eye and on discovering novel treatments to prevent age-related vision loss.
  • Bryan Sun, sunb8@uci.edu, Biological Chemistry
    The Sun Laboratory studies genetic mechanisms of skin tissue development and disease with a particular interest on regulatory elements of the noncoding genome. We use primary cell culture, skin organoids, and human/patient samples for our research.
  • Sha Sunshasun@uci.edu, Developmental & Cell Biology
    The main focus of our research involves the functional roles of long noncoding RNAs (lncRNAs) in epigenetic programming.
  • Vivek Swarup, vswarup@uci.edu, Neurobiology & Behavior
    Genomics of Neurodegenerative dementia
  • Kevin Thorntonkrthorn@uci.edu, Ecology & Evolutionary Biology
    Computational methods in population genetics.
  • Katrine Whiteson, katrine@uci.edu, Molecular Biology & Biochemistry
    The Whiteson lab studies human associated microbial and viral communities. We use metagenomics, metabolomics, microbiology and bioinformatics to answer questions about how microbes and viruses (especially phages!) affect human health.
  • Marcelo A. Wood, mwood@uci.edu, Neurobiology & Behavior
    Research in the Wood lab is focused on understanding the epigenetic mechanisms underlying long-lasting forms of synaptic plasticity and memory in the adult and aging brain, as well as maladaptive memory processes underlying addiction.
  • Xiangmin Xuxiangmix@uci.edu, Microbiology & Molecular Genetics
    Neural circuits, brain diseases, Viral genetic tool development
  • Qin Yang, qiny3@uci.edu, Physiology & Biophysics
    Identifying novel targets and developing new tools for the treatment of obesity and diabetes
  • Kyoko Yokomorikyokomor@uci.edu, Biological Chemistry

    We study the mechanism and function of heterochromatin dynamics in human cells using muscular dystrophy FSHD and DNA damage response as the model systems.

Faculty – Secondary Affiliation

  • Bogi Andersenbogi@uci.edu, Biological Chemistry
    The goal of my research is to understand the role of the circadian clock in skin and the gene-regulatory mechanisms underlying epidermal differentiation and repair.
  • Kavita Arorakarora@uci.edu, Developmental & Cell Biology
    We are interested in the diverse cellular responses triggered by TGF-ß signaling proteins in development. Recent areas of study are: the neuroendocrine control of developmental timing, and the regulation of metabolism by TGF-ß ligands.
  • Claudia Benaventeclaudia.benavente@uci.edu, Developmental & Cell Biology
    Identifying therapeutic vulnerabilities in solid malignancies harboring RB1 mutations, with special emphasis on epigenetics.
  • Bruce Blumbergblumberg@uci.edu,  Developmental & Cell Biology
    My lab focuses on multi-‘omic analyses of gene environment interactions important for development, adult physiology and disease predisposition using in vitro and in vivo models.
  • Anne L. Calofalcalof@uci.edu,  Developmental & Cell Biology
    My laboratory uses genetic model organisms to study how stem cell behaviors and gene expression changes both direct normal development and contribute to the etiology of syndromic and non-syndromic birth defects.
  • Ken W.Y. Chokwcho@uci.edu, Developmental & Cell Biology
    Using genomics, we study how early cellular differentiation events, particularly in the endodermal lineage leading to an animal’s gut and extraembryonic structures, are programmed.
  • Xing Daixdai@uci.edu, Biological Chemistry
    Intrinsic and microenvironmental control of skin and mammary epithelial stem cell function in development and repair/regeneration, and how such control mechanisms go awry in disease and aging.
  • Nir Drayman, nirdra@uci.edu, Molecular Biology & 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
  • Todd C. Holmestholmes@uci.edu, Physiology & Biophysics
    We study non-image forming visual mechanisms controlling arousal, phototaxis/light avoidance, time-of-day information behaviors in Drosophila (Fogle et al., 2011, Science; Ni, Baik et al., 2017, Nature).
  • Peter Kaiserpkaiser@uci.edu, Biological Chemistry
    Our lab studies the ubiquitin proteasome pathway, cell cycle, and cancer metabolism, focusing on mechanism of diet/therapeutics interactions and development of mutant p53 reactivation compounds.
  • Mei Kong, meik1@uci.edu, Molecular Biology & Biochemistry
    Nutritional microenvironment in tumor development and drug response, metabolism, epigenetics and cancer stem cells, protein phosphatase regulation in diabetes and obesity.
  • Orkide Koyuncu, okoyuncu@hs.uci.edu, Microbiology & Molecular Genetics
    In the Koyuncu lab, we study virus infections of the nervous system with a focus on local and global changes in neuronal biology during alpha herpesvirus infection
  • Wei Ling Lauwllau@uci.edu, Physiology & Biophysics
    Vascular injury and gut dysbiosis in chronic kidney disease
  • Gina Leeginalee@uci.edu Microbiology & Molecular Genetics
    Elucidate oncogenic signaling pathways that rewire cellular metabolism, RNA biogenesis and RNA epigenetic modification in human cancer
  • Chang Liu, ccl@uci.edu, Molecular Biology & Biochemistry
    What does the map between macromolecular sequence and function look like? How does a gene’s evolutionary past shape its future?
  • Haoping Liuh4liu@uci.edu, Biological Chemistry
    We study the human fungal pathogen Candida albicans, Candida-host cell interaction, mechanisms of pathogenesis and drug resistance.
  • Andrej Luptakaluptak@uci.edu, Molecular Biology & Biochemistry
    RNA biology and chemistry
  • Rachel W. Martinrwmartin@uci.edu, Molecular Biology & Biochemistry
    Structural biology and biophysics of both highly soluble proteins and protein aggregates; enzyme discovery; NMR methods development.
  • Thomas F. Martinez, t.martinez@uci.edu, Biological Chemistry
    Unannotated microprotein discovery and characterization, proteomics, genomics, cell biology, protein biochemistry
  • Krzysztof Palczewski, kpalczew@uci.edu, Molecular Biology & Biochemistry, Physiology & Biophysics
    Kris Palczewski’ s laboratory is focused on the fundamental process of vision taking place in rod and cone photoreceptors of the retina and the adjacent pigment epithelium.
  • Nicholas Pannunzio, nrpann@uci.edu, Biological Chemistry
    Cancer etiology, cancer genetics, genome integrity, DNA double-strand break repair, and cancer health disparities in underrepresented groups
  • Farah Rahmatpanah, frahmatp@uci.edu, Pathology & Laboratory Medicine
    Prostate cancer disparities, ovarian cancer, cervical cancer, bioinformatics, epigenetics
  • Matt Rose, mfrose@hs.uci.edu, Pathology & Laboratory Medicine
    Mapping gene networks, cell fate, and neural wiring decisions with multi-omics and 3D-cleared and live imaging in neurodevelopment and models of neurologic disease
  • Thomas F. Schillingtschilli@uci.edu, Developmental & Cell Biology
    Our laboratory is generally interested in the early embryonic development of the vertebrate nervous and musculoskeletal systems. We study zebrafish, small teleost fish that have emerged as a powerful new genetic system for studying how genes control early development. The genetic mechanisms we are studying have important implications for human craniofacial birth defects and cancers.
  • Leslie M. Thompsonlmthomps@uci.edu, Biological Chemistry
    Molecular and biochemical mechanisms of disease pathogenesis and therapeutic approaches to human neurodegenerative disease
  • Momoko Watanabe, momokow@uci.edu, Anatomy & Neurobiology
    We use brain organoids derived from hPSCs to study human neural development and disease using molecular, cellular, and bioinformatic approaches
  • Travis Wilestravis.wiles@uci.edu, Molecular Biology & Biochemistry
    Wiles Lab research focuses on the form and function of microbiomes, the ecology and evolution of antibiotic resistance, and immune sensing of gut bacterial communities.