- About Us
The UCSC Training Program in Systems Biology of Stem Cells, funded by the California Institute for Regenerative Medicine (CIRM), provides predoctoral and postdoctoral students with a solid understanding of the biology of stem cells, the skills to utilize stem cells in their own research, and the ability to devise and use computational approaches in their stem cell research.
Program trainees receive guidance from UCSC faculty mentors that possess a wide range of expertise in areas critical for advancing stem cell research. The mentors draw from four different departments in the School of Engineering and the Division of Physical & Biological Sciences: Biomolecular Engineering, Electrical Engineering, Molecular, Cell, & Developmental Biology, Applied Mathematics & Statistics, and Chemistry & Biochemistry.
David Haussler, Investigator, Howard Hughes Medical Institute, and Distinguished Professor, Biomolecular Engineering.
Using alternative splicing microarrays to profile changes in splicing and transcription during stem cell differentiation, as a means of understanding this form of regulation for cell type identity.
Researching gene regulation in cerebral cortex development, focusing on the processes that signal neural stem cells to generate the hundreds of different types of neurons and form the appropriate connections essential for brain function. Manipulating gene expression in embryonic stem cells to direct them to differentiate into corticospinal motor neurons.
Using stem cells to study molecules in the ephrin family and how their signaling pathways impact axon guidance and neural development in the central nervous system.
Studying what appear to be stem-progenitor cells that proliferate in hyperplasias and tumor formations resulting from loss-of-function mutations in a number of genes affecting mammary gland development.
Investigating the changes that occur in chromatin as stem cells differentiate, how transgene expression affects the chromatin structure at the site of integration in pluripotent stem cells, and how the chromatin at a particular locus affects transgene expression during differentiation. This research holds promise for understanding how to couple stem cells with gene therapy for the remediation of genetic defects.
Exploring the roles of the protein transformer 2B (Tra2B),a phylogenetically conserved regulator of alternative splicing, and alternative splicing in stem cell pluripotency and differentiation to elucidate an important and poorly understood element of the stem cell gene regulatory network.
Investigating the mechanisms used by germ cells to establish and maintain their identity, immortality, and totipotency, with a focus on epigenetic control of chromatin organization and gene expression. Studying germ cells using a wide variety of approaches, including forward genetics, RNAi, imaging, molecular biology, biochemistry, and whole genome microarray-based technologies.
Studying fundamental molecular and cellular mechanisms involved in stem cell renewal and differentiation. Focusing on the role of conserved cell-cycle checkpoint genes in controlling the stem cell division rate and daughter cell differentiation.
Using a combination of genetic, biochemical, and molecular approaches to study chromatin-remodeling complexes, including their roles in transcriptional regulation, structural maintenance, post-translational modifications, and cell fate specification.
Understanding how different cells behave during organ development and how their abnormalities lead to diseases such as cancer. Focusing on prostate organ development and homeostasis and cellular behaviors in the initiation of prostate cancer.
Understanding the role of epithelial cell differentiation in epidermal wound healing and in cutaneous immune responses. Characterizing the development and homeostatic maintenance of regulatory T cells.
Studying glia-neuron interaction, structural plasticity during learning, and brain pathologies. One goal is to reveal the structural basis of motor rehabilitation in the post-stroke brain, with the aim of facilitating the design of improved stem cell-based therapies.
Studying how stem cells make the decision to become a particular type of mature blood cell, and how this process goes wrong to cause disease. Using a variety of approaches, including bioinformatics. The long-term goal is to provide a comprehensive understanding of cell fate decisions at the molecular, cellular, and systems biology levels that will facilitate our ability to direct specific fates and improve clinical applications of stem cell therapy.
David Haussler (Program Director)
Investigating the ultraconserved elements in the human genome, which appear to be distal enhancers for key genes involved in early development. Exploring the role of non-coding RNAs in human stem cell differentiation through high-throughput RNA sequencing. Incorporating embryonic stem cell expression data into the UCSC Genome Browser.
On a genome-wide level, using computational inference of differently expressed genes to trace evolutionary origins, regulatory networks, and chromatin dynamics in the developmental processes involved in the differentiation of blood line stem cells.
Developing biomimetic systems, implantable electronic devices that interact with living tissues, to restore abilities that have been lost through injury or disease.
Bringing evolutionary considerations to the forefront as we move towards stem cell therapies by exploring the evolutionary biology of stem cells, especially the probability of renewal and the great variability shown by genetically identical stem cells from adjacent niches. Determining what sets the number of stem cells in the villi. Investigating the production of transit amplifying cells in response to challenges to the hematopoietic system.
Identifying the fundamental basis of crosstalk between the circadian clock and DNA damage checkpoint response to understand how disruption of the clock regulates oncogenesis. Integrating diverse experimental approaches from cell biology to solution NMR spectroscopy to gain an atomic-level understanding of the clock, as well as providing new targets and/or a temporal basis for improved therapeutic intervention in cancer.
Elucidating the biochemical determinants of protein interaction affinity and specificity and how these factors are affected by regulatory modifications to protein composition and structure. Applying a variety of structural and biochemical techniques to learn in molecular detail how structural changes and chemical modifications affect biological function.