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University of California-Santa Cruz - 2016

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Research Description

Research Description By Graduate Engineering Department

Applied Mathematics and Statistics

The Department of Applied Mathematics and Statistics (AMS) is the campus focal point for research in statistics and in applied mathematics. The statistical part of AMS concentrates on theory, methodology, and applications in Bayesian statistics, an approach to uncertainty quantification which has been known for centuries to be the most general but which has only recently become feasible to use in complex applications by virtue of recent advances in computationally-intensive methods of inference and prediction. On the applied math side, AMS focuses on dynamic mathematical modeling of complex real-world phenomena, bringing expertise to bear principally in the fields of mathematical geosciences and mathematical biology.
Examples of recent research projects in AMS include geophysical modeling of lava flow, risk assessment in nuclear waste disposal, the statistical analysis of electroencephalograph (EEG) data to predict which psychiatric patients will respond best to treatment, the predictive modeling of rainfall at macro and micro levels of aggregation in space and time, the analysis of what discriminates between good and bad wines, the study of force generation mechanisms and the thermodynamics of molecular motors, and the mathematical modeling of liquid crystalline polymer fibers.

Biomolecular Engineering

The goal of the Biomolecular Engineering (BME) Department is to be a leader in integrating engineering, bioinformatics, and state-of-the-art genome and cell biology research to advance our understanding of human and microbial biology. Our current areas of expertise include bioinformatics tool development, genomics (computational, experimental, extremophile, evolutionary), stem cell research, and biomolecular technology development (single molecule DNA sequencing, molecular probes, extremozymes).

Our approach to bioinformatics is to combine advanced statistical methods, practical engineering, and biological insight to design new tools and methods of solving important problems. We employ these new tools to enable biological discovery.

Major accomplishments include the introduction of profile hidden Markov Models (HMMs) for sequence analysis; the co-introduction of the use of stochastic context-free grammars for RNA analysis; protein structure prediction using HMMs, neural nets, and conformational search; the use of HMMs and machine learning techniques for gene finding; small RNA gene finders; the assembly and analysis of the public human genome; and other tools to enable genome-scale comparisons.

New, expanding research areas include cancer genomics, metagenomics, pharmacogenetics (the influence of genetic factors on drug activity and metabolism), pharmacogenomics (the variability of patient responses to drugs due to genetic differences), and population genomics (the study of the relatedness of humans and other species to each other and the tree of life). UCSC develops and maintains the Human Genome Browser, which receives millions of visits each year, as well as genome browser resources for dozens of other vertebrates, and hundreds of microbial genomes (pathogens, model bacteria, and archaea). Using newly developed tools and comparative genomics, researchers have uncovered and begun characterizing a diverse array of novel non-protein coding RNA genes.

We are beginning genomic projects on diverse other non-model species, including alligators and banana slugs. We are undertaking or have completed sequencing of non-model microbial species (both pathogens and extremophiles), and we study genome dynamics, both in large (human) and small (archaeal and bacterial) genomes.

In collaboration with faculty in other departments, including Microbiology and Environmental Toxicology, and MCD Biology, we have developed techniques for generating and analyzing gene expression data, both from DNA microarrays and RNA-seq experiments.

Powerful new techniques have also been developed to infer complex molecular pathways from gene expression data in normal and tumor cancer cells.

Stem Cell Biology:
UCSC is an emerging leader in stem cell biology, with support from the California Institute for Regenerative Medicine to conduct research in hematopoietic (blood-forming) stem cells and neural precursor cells. A major recent advance is the discovery of a protein (ROBO4) that plays a key role in establishing blood stem cells in bone marrow.

Technology Development:
A major focus of technology development has been high-throughput DNA sequencing technologies, including single-molecule sequencing with nanopores and sequencing by synthesis techniques. A recent advance is the fabrication of a nanopore instrument that is capable of monitoring the function of a single DNA polymerase molecule in real time, which we are working with industry to develop into a device to perform rapid single-molecule sequencing of DNA at a tenth the cost of current methods.

We also manage the UCSC Genome Sequencing Center, with multiple commercial sequencing platforms, as well as doing research in improving and automating the sample-prep protocols.

Other biotech efforts include using nanopipettes as biosensors and other electronic means for chemical sensors.

Computational Media

The Computational Media Department is dedicated to the creation, enhancement, and study of media forms that can only be made using computers. The department emphasizes the construction of technologies that make possible novel media experiences, while simultaneously embracing and engaging in theoretical and practical approaches from the arts, humanities, and social sciences. UC Santa Cruz hosts the Center for Games and Playable Media, the largest games research group in the world, comprised of the Expressive Intelligence Studio, Computational Cinematics Studio, Natural Language and Dialog Systems Lab, Interactive Systems for Individuals with Special Needs Lab, Augmented Design Lab, and the Software Introspection Lab.

Computer Engineering

Research and teaching in the Department of Computer Engineering emphasizes interdisciplinary system design. Our research revolve around four foci. (1) Networks includes wireless networks, high-speed networks, sensor networks, algorithms and protocols for computer communication, and quality of service. Research areas presently include design and evaluation of protocols for wired and wireless networks, network switching, ad hoc networks, and internetworking research. (2) Robotics and Control includes autonomous vehicles, sensor fusion, exoskeletons, medical robots and biomolecular control. Research includes autonomous and embedded systems, robotics, robust and formal embedded software design, guidance, navigation and control, sensor and actuator fusion and fault detection. (3) Computer System Design studies the creation of computer and digital systems to solve problems. We currently perform work in Computer Aided Design (CAD) of VLSI, computer architecture, parallel and distributed computation, performance modeling, and in field-programmable gate array (FPGA) and very large scale integration (VLSI) system design. Research strengths in computer science complement several of these areas. (4) Sensing and Interaction research includes environmental monitoring, computer vision, remote sensing, telemetry, computer-based collaboration, multimedia systems, image and video reconstruction and modeling, human-computer interaction, and assistive and rehabilitative technology.

Computer Science

The Computer Science department has a substantial research program, and graduate students in both the M.S. and Ph.D. degree program participate in research. Focus areas include algorithms, logic and complexity; data science; database systems; games and playable media; graphics, animation and visualization; machine learning and artificial intelligence; programming languages; software engineering; and systems and storage. URL:

Electrical Engineering

The Electrical Engineering (EE) Department provides engineering students with a spectrum of excellent opportunities in electrical engineering education and research. The depth of these opportunities is possible because the student has at his or her disposal both EE and closely affiliated faculty in biology, biomolecular engineering, chemistry, computer engineering, computer science, applied mathematics and statistics and physics. Research is concentrated in the following areas: photonics and electronics; biophotonics and optofluidics; communications, signal processing, and image processing; sustainability engineering; bioelectronics and biomedical devices; nanotechnology and MEMS; nanoelectronics, spintronics, plasmonics and thermoelectricity. Many students work on interdisciplinary projects at the intersection of these areas. This environment is facilitated by the relatively small department size and strong interactions among the faculty.

Technology Management

Technology and Information Management (TIM) is a multi-disciplinary program that focuses on the integration of information systems, technology, and business management for two purposes: the technology of management, i.e., the use of information systems to solve business problems, and the management of technology, which includes new product development and enterprise management. Today, it is widely accepted that managing information resources to optimize enterprise performance is as important as managing resources such as labor, capital, and raw materials. TIM supports the management of the processes of collection, manipulation, storage, distribution, and utilization of an organization’s information resources as well as the use of these processes in the management of technology. Graduate research areas include: (1) information retrieval and knowledge management (e.g., data analytics, information filtering); (2) resource management (e.g., network management, cyber security, energy analytics); (3) engineering management and entrepreneurship; and (4) software engineering.

Research Description By Engineering Research Center

California Institute for Quantitative Biomedical Research (QB3)

The California Institute for Quantitative Biomedical Research (QB3) is one of four California Institutes for Science and Innovation. It unites quantitative, biological, and structural scientists at three University of California campuses Berkeley, San Francisco, and Santa Cruz with private industry collaborators to address problems concerning human health. QB3 aims to harness the quantitative sciences to integrate our understanding of biological systems at all levels of complexity from atoms and protein molecules to cells, tissues, organs, and the entire organism. QB3 scientists attack problems that have been simply unapproachable before, setting the stage for fundamental new discoveries, new products, and new technologies.The Institute builds on strengths in the engineering and physical sciences at UC Berkeley, engineering and mathematical sciences at UC Santa Cruz, and the medical sciences at UC San Francisco, as well as strong biology programs at the all three campuses. In addition to the creation of fundamental new knowledge and potent new technologies, a major goal of the Institute is to train a new generation of students able to fully integrate the quantitative sciences with biomedical research.

Center for Biomolecular Science and Engineering

The Center for Biomolecular Science and Engineering (CBSE) at the University of California at Santa Cruz fosters interdisciplinary research and academic programs that address the scientific questions of the post-genomic era. These are the scientific opportunities that have arisen from the completion of the Human Genome Project and the sequencing of other model organisms. From these roots, CBSE has grown to encompass a vast array of biological and engineering research that is fueling the biotechnology explosion.

CBSE serves as an umbrella organization at UC Santa Cruz spanning the Baskin School of Engineering and the Division of Physical and Biological Sciences. No longer limited to genome science, the research conducted by center affiliates reaches into bioelectronics, sensing technologies, and nanotechnology in addition to the biomolecular sciences. Much of the research incorporates the cutting-edge computational approaches that distinguish UCSC. In addition, through collaboration with UCSC affiliates in philosophy, community studies, and sociology, the center promotes the exploration of the ethical, social, and legal implications of the new biology.

The revolutionary technologies that have recently been developed to gather and analyze genomic information will help to forge a new understanding of biology with widespread applications to medicine, agriculture, and ecology. These technologies have been made possible by developments in structural biology, engineering, and computer science, and their further advancement requires a new blend of computational analysis, micromechanical robotics, microfluidics, bioelectronic chips, imaging, and new laboratory functional genomics methods.
UCSC's actively collaborating groups in molecular biology, protein and RNA biochemistry, computational biology, and the support for micro- and nanoscale engineering methods from both the older and newly emerging programs in the new School of Engineering, make this a natural research and academic focus area for this campus.

Center for Games and Playable Media

The Center for Games and Playable Media was formally established in 2010, building on work done since the founding of the game degree. The center houses the school's five games-related research labs including the Expressive Intelligence Studio â€" one of the largest technical game research groups in the world.
Projects range from work on artificial intelligence and interactive storytelling to natural language dialogue systems, cinematic communication, procedural content generation, human computer interaction, rehabilitation games, computational photography, and level design. Members of the group have published in some of the most respected journals in the fields of game studies, game AI, and game culture. Currently, the group has more than 11 active research grants on games and is the only non-European university taking part in the European Union's SIREN Project, a serious games initiative tackling conflict resolution. Agencies funding game research at UC Santa Cruz include the MacArthur Foundation, Knight Foundation, National Science Foundation (NSF) and Intelligence Advanced Research Projects Activity (IARPA).

Center for Information Technology Research in the Interest of Society

The Center for Information Technology Research in the Interest of Society (CITRIS) is a state-wide research institute focused on California's biggest challenges energy efficiency, transportation, earthquake preparedness, health care, education, and others on the horizon.

Center for Sustainable Energy and Power Systems (CenSEPS)

The Center for Sustainable Energy and Power Systems (CenSEPS) is poised to become a major hub for innovation in emerging clean energy technologies and tackling the challenges of energy sustainability. The Center explores the societal implications of new renewable energy technologies as well as prepares a new generation of 21st century engineers and scientists to address the problem of more efficient energy use with minimal carbon footprint. We promote and integrate the use of renewable energy technology to create sustainable communities and renewable energy districts.

Howard Hughes Medical Institute

The Howard Hughes Medical Institute is a nonprofit medical research organization dedicated to discovering and disseminating new knowledge in the basic life sciences. The HHMI appoints approximately 300 investigators at more than 60 universities, research institutes, and medical schools around the country. The scientists are supported by approximately 2,500 research associates, technicians, and other personnel employed by HHMI, as well as by a headquarters staff. By appointing scientists as investigators, rather than awarding research grants, the HHMI is guided by the principle of "people, not projects." The investigators are HHMI employees who also maintain their faculty positions at their host institutions. In addition, through its grants program and other activities, HHMI is helping to enhance science education at all levels and maintain the vigor of biomedical science worldwide.

Institute of Scalable Scientific Data Management

The Institute for Scalable Scientific Data Management (ISSDM) is an education and research collaboration with Los Alamos National Laboratory (LANL). The ISSDM focuses on Scientific Data Management advanced research and development topics in the areas of simulation and real time/experimental data collection, storage, analysis, and organization management. By working collaboratively with industry partners, LANL, and UCSC, the Institute will help solve Simulation Data Management problems at unprecedented scale and of national importance while also supporting CCN division, DOE/NNSA Advanced Simulation and Computing (ASC) program, and LANL Institutional Computing program goals.

Keck Center for Nanoscale Optofluidics

A joint endeavor of the Jack Baskin School of Engineering and the Division of Physical and Biological Sciences at UCSC, the Keck Center for Nanoscale Optofluidics explores the integration of nanotechnology and optofluidic silicon chips and how this technology can be used to improve biomedical analysis in a wide range of fields, including toxicology, immunology, disease detection, and diagnostics.

Storage Systems Research Center (SSRC)

The Storage Systems Research Center includes faculty from the Computer Science, Computer Engineering and Electrical Engineering departments. Research focuses on many aspects of file and storage systems. We have active projects in archival storage, scalable distributed indexing and non-hierarchical file systems, large-scale distributed storage systems, file systems for next-generation storage devices, and data deduplication. We also have particular focus in cross-cutting issues such as security and reliability in file and storage systems.