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• Mark Akeson (BME) Control and Analysis of DNA and RNA Using Nanoscale Pores
• Manel Camps (METX) Use of Random Mutagenesis for Studies of Evolution and for Therapy
• David Deamer (BME) Nanopore Methods of DNA Analysis
• Rebecca DuBois (BME) Structure, Function, and Engineering of Virus Proteins
• David Haussler (BME) Bioinformatics, Computational Genomic Data Analysis, Molecular Evolution and Comparative Genomics
• Richard Hughey (CE) Bioinformatic Tools for Sequence Analysis and Prediction
• Mike Isaacson (EE) Nano- and Microfabrication Technology for Biomedical and Diagnostic devices
• Kevin Karplus (BME) Long-read DNA Sequencing
• Joel Kubby (EE) Applications of Adaptive Optics for Biological Microscopy
• Alan Litke (Physics) High Energy Physics Comes to the Aid of Neurobiology
• Roberto Manduchi, (CE) Assistive Technology for the Visually Impaired
• Nader Pourmand (BME) Single Cell Analysis and Manipulation, Biosensor, Nanotechnology, DNA Sequencing
• Holger Schmidt (EE) Integrated Optofluidics: Detecting and Analyzing Single Molecules on a Chip
• Alexander "Sasha" Sher (SCIPP) Neural Circuits: Function, Development, and Treatment
• Christopher Vollmers (BME) Development of DNA Sequencing Tools for the Analysis of B cells
• Ali Yanik (EE) Development of Nano-fluidic Platforms for Cancer Diagnostics
• Jin Zhang (Chem) The Application of Molecular and Nanomaterial Systems to the Detection and Treatment of Cancer

Prof Mark AkesonControl and Analysis of DNA and RNA Using Nanoscale Pores

Mark Akeson, Dept. of Biomolecular Engineering

Mark Akeson's research is focused on the use of nanopore detectors - instruments built around a tiny pore in a membrane or thin, solid-state wafer. These pores are just big enough to allow a single strand of DNA to pass through. Akeson and his collegues use the detectors to understand the dynamics and structure of DNA duplex ends, including those of retrotransposons and HIV. Akeson also investigates the coupling of processive DNA-modifying enzymes to nanopores, both protein and solid-state. Together with UCSC Professors William Dunbar and David Deamer, he has demonstrated enzymatic control of single DNA in nanopores with sequence specificity and real-time feedback control. [More]

Akeson Publications
Mark Akeson's Email

Prof Manel CampsUse of Random Mutagenesis for Studies of Evolution and for Therapy

Manel Camps, Microbiology and Environmental Toxicology

The laboratory of Dr. Manel Camps uses molecular genetic and computational approaches to study the biological consequences of random changes in genetic information mutations) that occur spontaneously or as a result of environmental insults. They couple the generation of random mutant libraries with specific selections or screens to study the functional impact of point mutations and to establish how genes evolve in response to selective pressure. This work is relevant for the identification of risk factors of disease, understanding the origins of drug resistance, and engineering biological activities. [More]

Camps' Publications Manel Camps' Email

Prof DeamerNanopore Methods of DNA Analysis

David Deamer, Biomolecular Engineering

Professor David Deamer and his collaborators have developed a nanopore device that captures single nucleic acid molecules and analyzes their structure, dynamic motion and base sequences. [More]

Deamer's Publications Dave Deamer's E-Mail


Prof DuBoisStructure, Function, and Engineering of Virus Proteins

Rebecca DuBois, Biomolecular Engineering

Professor DuBois is a structural biologist studying viral surface and replication proteins. She uses her discoveries to design novel vaccines, to develop nanoscale drug delivery vehicles, and to develop antiviral therapeutics. [More]

DuBois Publications Rebecca Dubois' E-Mail


Prof David HausslerBioinformatics, Computational Genomic Data Analysis, Molecular Evolution and Comparative Genomics

David Haussler, Dept. of Biomolecular Engineering

David Haussler’s research lies at the interface of mathematics, computer science, and molecular biology. He develops new statistical and algorithmic methods to explore the molecular function and evolution of the human genome, integrating cross-species comparative and high-throughput genomics data to study gene structure, function, and regulation. [More]

Haussler Publications David Haussler's E-Mail

Prof Richard HugheyBioinformatic Tools for Sequence Analysis and Prediction

Richard Hughey, Dept of Biomolecular Engineering and Dept. of Computer Engineering

Richard Hughey's research has focussed on two areas: high-performance VLSI computer architecture and biological sequence analysis. The Kestrel programmable sequence analysis accelerator was a single-board parallel processor designed to speed biological sequence analysis for Smith & Waterman searchin, HMMs, conformational chemistry, graph coloring, and other areas. Hughey, Dr. Anders Krogh, Professors Haussler and Karplus, and UC Santa Cruz student researchers developed developed the Sequence Analysis and Modeling (SAM) software suite. SAM is a a collection of algorithms and software used to create statistical models of RNA, DNA, and protein families with profile hidden Markov models. Dr. Hughey has been active in program development, including the UC Santa Cruz Bioinformatics and Bioengineering programs. He is presently Vice Provost and Dean of Undergraduate Education at UC Santa Cruz. [More]

Hughey's Publications Richard Hughey's Email

Prof Mike IsaacsonNano- and Microfabrication Technology for Biomedical and Diagnostic Devices

Mike Isaacson, Dept. of Electrical Engineering

Michael Isaacson's research group uses technology developed by the semiconductor industry to study biological systems and develop biomedical devices. The work involves fabrication techniques and imaging tools for making and visualizing devices and structures on the nanoscale. For example, the group has developed microelectronic devices that can be implanted into insect brains to record signals from the brain's neural circuits. Interestingly, information about how the neural circuits work can then be used to further improve microelectronic devices. [More]

  Mike Isaacson's Email


Prof Kevin KarplusLong-read DNA Sequencing

Kevin Karplus, Dept. of Biomolecular Engineering

Kevin Karplus' research group develops tools and techniques for genome assembly from next-generation sequence data, signal processing and machine learning for nanopores. [More]

Karplus Publications Kevin Karplus's E-Mail

Prof Joel KubbyApplications of Adaptive Optics for Biological Microscopy

Joel Kubby, Dept. of Electrical Engineering

Professor Joel Kubby is collaborating with engineers, physicists and biologists to utilize Adaptive Optics for the improvement of deep tissue imaging of living cells. Current biological microscopy is incapable of obtaining high quality live imaging in samples greater than 30 microns beneath the plasma membrane, where many critical cellular processes occur. Much of the degradation in image quality is the result of local differences in the refractive index, both within the sample and between the sample and the immersion lens. Adaptive optics was first used to correct for image aberrations in astronomical imaging. Kubby and his collaborators have shown that the same principles that improved resolution in telescopes can be adapted to improve wide-field, confocal, two-photon, super-resolution and spinning disk microscopy systems that are crucial for biological research. [More]
Kubby Publications Joel Kubby's Email

Prof Alan LitkeHigh Energy Physics Comes to the Aid of Neurobiology

Alan Litke, Santa Cruz Institute for Particle Physics

Alan Litke is physicist who is also interested in neurobiology. Several years ago, Litke began to utilize principles from his research on detection of particles in high-energy-physics collisions in order to develop electrode arrays that can be used to detect signals from the individual output neurons of live retinal tissue. Litke and neurobiologist E. J. Chichilnisky from the Salk Institute used this technology to discover a type of retinal cell that may help monkeys, apes, and humans see motion. [More]

Litke Publications Alan Litke Email

Prof ROBERTO MANDUCHI Assistive Technology for the Visually Impaired

Roberto Manduchi, Dept. of Computer Engineering

Dr. Manduchi's research focuses on computer vision and sensor processing, with application to assistive technology for the visually impaired. Specifically, I am exploring the use of mobile computer vision and wearable sensors for increased spatial awareness and information access. [More]

Manduchi Publications Roberto Manduchi's Email

Prof Nader PourmandSingle Cell Analysis and Manipulation, Biosensor, Nanotechnology, DNA Sequencing

Nader Pourmand, Dept. of Biomolucular Engineering

The Pourmand lab develops new tools and technologies that integrate biology, electronics, and nanofabrication for the detection and study of genes and proteins. These tools are specifically designed to increase the speed and lower the cost of sample analysis. The lab directs particular attention to the development of medically relevant technology, such as instruments for single cell analysis. Pourmand is also Director of Genome Technology Center. [More]

Pourmand Publications Pourmand's Email

Prof Holger SchmidtIntegrated Optofluidics: Detecting and Analyzing Single Molecules on a Chip

Holger Schmidt, Dept. of Electrical Engineering

Optofluidics describes the combination of optics and microfluidics and holds great promise for novel devices for biomedical instrumentation, analytical chemistry and other fields that deal with liquid analytes. A highly desirable extension of optofluidics is to use integrated optics to replace the bulky microscopy analysis that is still commonly in use. This would allow development of a fully planar, fully integrated lab on a chip. We are using optofluidic approaches for early infectious disease and cancer detection and genome analysis. [More]

Schmidt Publications Holger Schmidt's Emai

Prof Sasha SherNeural Circuits: Function, Development, and Treatment

Alexander "Sasha" Sher, Santa Cruz Institute for Particle Physics

Our brain is a highly sophisticated system that receives information about the outside world, processes it, and determines our reaction to it. These functions are realized through billions of individual neurons that are connected in vast and complicated circuits and use electrical signals to communicate with each other. The Sher lab is using unique large scale multielectrode recording systems developed by a collaboration of physicists, biologists, and engineers to study function, development and treatment of neural circuits. Sher's research is focused particularly on the retina and visual system. In addition, in collaboration with prof. Alan Litke, Sher lab participates in the development of new techniques for recording and stimulation of neural activity. [More]

Sher Publications Sasha Sher's Email

Prof Christopher VollmersDNA Sequencing Tools for the Analysis of B cells

Christopher Vollmers, Dept. of Biomolecular Engineering

Our adaptive immune systems is highly efficient in protecting us from the most diverse intruders. B cells are an essential part of the adaptive immune system. Each B cell uniquely rearranges its genome several times to produce an unique antibody. Until very recently, the analysis of B cell populations circulating in the periphery at any given time was labor intensive and low throughput. The Vollmers lab focuses on developing DNA sequencing tools to analyze B cells on a population and single cell level. [More]

Vollmers' Publications Christopher Vollmers' E-Mail

Prof Alli YanikDevelopment of Nano-fluidic Platforms for Cancer Diagnostics

Ali Yanik, Dept. of Electrical Engineering

Ali Yanik's current research focuses on Circulating Tumor Cell (CTC) detection from human blood, using nano-fluidic platforms for cancer diagnostics. His research interests includes nanoplasmonic and metamaterial devices for ultrasensitive infrared/terahertz spectroscopy of biomolecules/chemicals and high-throughput, cost-effective BioNEMS technologies for life sciences and point-of-care diagnostics. His expertise is in high-end nanolithography and bio-patterning as well as theory and engineering of nanophotonic devices. [More]

Yanik Publications Ali Yanik's Email

Prof Jin ZhangThe Application of Molecular and Nanomaterial Systems to the Detection and Treatment of Cancer

Jin Zhang , Dept. of Chemistry and Biochemistry

The Zhang research group is interested in the application of molecular and nanomaterial systems in conjunction with optical spectroscopy and related techniques for biomedical detection and treatment, with emphasis on cancer therapies and cancer biomarker detection.  Specific projects include: 1) investigation of mechanisms of photodynamic therapy and catalytic therapy based on porphyrins, phthalocyanines, and related compounds; 2) detection of small molecule, protein, and DNA cancer biomarkers using fluorescence based on quantum dots (QDs) and surface-enhanced Raman scattering (SERS) based on metal nanostrutcures; and 3) photothermal imaging and therapy of cancer using unique metal nanostructures.  This research involves systematic study of the structural, optical, and photophysical as well as photochemical properties of the materials using a combination of microscopy, x-ray, spectroscopy, and electrochemistry techniques. [More]
Zhang Publications Jin Zhang's Email

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