Patrick Shih

Divisions

Environmental Genomics and Systems Biology

• Comparative and Functional Genomics

Research Interests

Much of the ingenuity of life has revolved around the evolution of metabolic pathways, which has unlocked novel chemistries and expanded the molecular repertoire of nature. In particular, plants have been especially successful through the evolution of many unique and relevant metabolisms, ranging from synthesis of specialized compounds that can be used as pharmaceuticals (e.g., morphine, artemisinin) to broad processes that drive our planet’s elemental cycles (e.g., photosynthesis). As a result, life as we know it could not exist without plants. Given the scale and utility of agriculture, plants offer a unique platform to address many imminent challenges facing society. My research focuses on developing the foundational knowledge needed to innovate, deploy, and engineer new traits in plants using synthetic biology. Beyond biotechnological applications, these approaches can also be utilized to provide more sophisticated tools to improve our basic understanding of plant systems.

Divisions

Molecular Biophysics and Integrated Bioimaging

• Bioenergetics

Secondary Affiliation:

Environmental Genomics and Systems Biology

• Comparative and Functional Genomics

Research Interests

Divisions

Molecular Biophysics and Integrated Bioimaging

• Cellular and Tissue Imaging

Biography

Markita Landry is an assistant professor in the department of Chemical and Biomolecular Engineering at the University of California, Berkeley.  She received a B.S. in Chemistry, and a B.A. in Physics from the University of North Carolina at Chapel Hill, a Ph.D. in Chemical Physics from the University of Illinois at Urbana-Champaign, and completed a postdoctoral fellowship in Chemical Engineering at the Massachusetts Institute of Technology.

She is a recent recipient of early career awards from the Brain and Behavior Research Foundation, the Burroughs Wellcome Fund, The Parkinson’s Disease Foundation, the DARPA Young Investigator program, the Beckman Young Investigator program, the Howard Hughes Medical Institute, is a Sloan Research Fellow, an FFAR New Innovator, and is a Chan-Zuckerberg Biohub Investigator.

Research Interests

My current research centers on the development of synthetic nanoparticle-polymer conjugates for imaging neuromodulation in the brain, and for the delivery of functional biomolecules and nutrients into living systems. The Landry lab exploits the highly tunable chemical and physical properties of nanomaterials for the creation of bio-mimetic structures, molecular imaging, and gene editing.

Divisions

Molecular Biophysics and Integrated Bioimaging

• Cellular and Tissue Imaging

Research Interests

Biomedical imaging instrumentation and physics

Divisions

DOE Joint Genome Institute

• Science Programs

Secondary Affiliation:

Environmental Genomics and Systems Biology

• Comparative and Functional Genomics

Research Interests

My research focuses on secondary metabolism of microbes. I am particularly interested in understanding how the production of secondary metabolites is controlled and what their roles are.

Programs & Initiatives

Biography

Nikki Humphreys has worked in the University of California (UC) System for over twenty years gathering a wealth of experience and honing her analytical, communication, planning, and project management skills. She has held management positions at UC Berkeley, UC Davis, and UC Agriculture & Natural Resources (UC ANR). Most recently, she has been serving as the Director of Administration of the Department of Bioengineering at the University of California, Berkeley. Humphreys has demonstrated strengths in financial management, strategic planning, and personnel administration, making her well suited for this integral position. She has a strong track record in management, having twice received the Berkeley Staff Assembly Excellence in Management Award.

Divisions

Climate and Ecosystems

Secondary Affiliation:

Environmental Genomics and Systems Biology

• Molecular EcoSystems Biology

Research Interests

My research focuses on understanding the impact of climate change on soil and aquatic biogeochemical cycles via studying microbial community functions and metabolism. I currently lead the permafrost microbiology component of the multi-institutional NGEE Arctic project of DOE in which we study microbial carbon cycling in climate sensitive regions in the arctic. I am also part of Terrestrial Ecosystem Science at Berkeley Lab team studying the consequences of increasing soil temperatures on soil carbon cycling in-situ manipulation experiments. Lastly, my most recent project aims to define microbial functions and their controls on terrestrial carbon and nutrient turn-over at terrestrial to aquatic interfaces.

Programs & Initiatives

• NGEE Arctic
  

Divisions

Environmental Genomics and Systems Biology

• Molecular EcoSystems Biology

Research Interests

The Coates lab is focus on environmental microbiology, specifically applied microbiology and bioremediation to clean up pollution and research environmentally friendly approaches to technology and oil extraction. We are located in the Department of Plant & Microbial Biology at UC Berkeley, as well as the Energy Biosciences Institute in Berkeley, CA.

Divisions

Molecular Biophysics and Integrated Bioimaging

• Structural Biology

Research Interests

Paul Williams’ expertise is in epidemiologic studies and analysis, including infectious disease. Recent studies have focused on striking a balance to maximize the health benefits of walking or running. Some press releases and science shorts can be seen here:

Excessive Running or Walking May Eliminate Health Gains in Heart Attack Survivors, Finds Berkeley Lab Research (August 12, 2014)

Running May Be Better Than Walking for Breast Cancer Survival (January 28, 2014)

Running, Even in Excess, Doesn’t Lead to More Osteoarthritis and Hip Replacements (February 28, 2013)

Divisions

Environmental Genomics and Systems Biology

• Molecular EcoSystems Biology

Research Interests

My research focuses on:

• Developing bioenergy crops for sustainable production of fuels and chemicals.
• Establishing novel approaches to modify lignin in plant biomass.
• Designing metabolic pathways for the production of value-added chemicals in plants.
• Identifying bio-engineering approaches to promote soil carbon sequestration.
• Engineering microorganisms for the synthesis of plant-specific metabolites.

Divisions

Biological Systems and Engineering

• BioEngineering & BioMedical Sciences

Biography

Polly Chang is the Senior Scientific Director of Nonclinical Development in SRI’s Biosciences Division. Chang received her PhD in Biophysics from University of California, Berkeley, and dedicated most of her early career in the area of radiation biology at Lawrence Berkeley National Laboratory, focusing on understanding the impact of highly energetic particle radiation on cells and tissues. This work transitioned to NASA-supported research using in vitro and in vivo models to understand the risks for manned space missions. Chang is Senior Scientific Director of Nonclinical Development in the Biosciences Division at SRI, an independent nonprofit R&D institute in Menlo Park, and remains active in the radiation biology community.

Divisions

Biological Systems and Engineering

• BioEngineering & BioMedical Sciences

Biography

Claire Tomlin is a Professor of Electrical Engineering and Computer Sciences at the University of California at Berkeley, where she holds the Charles A. Desoer Chair in Engineering. She held the positions of Assistant, Associate, and Full Professor at Stanford from 1998-2007, and in 2005 joined Berkeley. She received the Erlander Professorship of the Swedish Research Council in 2009, a MacArthur Fellowship in 2006, and the Eckman Award of the American Automatic Control Council in 2003. She works in hybrid systems and control, with applications to air traffic systems, robotics, and biology.

Research Interests

Hybrid Control Systems: These are systems which combine continuous time dynamics with discrete event dynamics. Research involves design, verification using new computational methods for computing reachable sets, and simulation of hybrid systems. We are currently developing the theory and designing models to predict the behavior of complex systems.
This work is supported by NSF, ONR, and AFOSR.

Air Traffic Control Automation: This is joint work with NASA Ames to design models of and control systems for Air Traffic dynamics. This research includes algorithms for automatic resolution of trajectory conflicts between multiple aircraft, as well as novel polynomial time scheduling algorithms.

Algorithms for Decentralized Optimization: In this project, we are designing algorithms with provable convergence properties for decentralized optimization — meaning that several interconnected units act as local decision-makers and optimize local costs, coordinating with each other through constraints. This work is supported by NSF, ONR, and AFOSR.

Human-automation Systems: This research involves analysis of systems for which the control authority is shared between human and automation. We work on the analysis of autopilot systems, driving systems, and robotic systems.

Modeling and Analysis of Biological Cell Networks: In this research project we are building models and analysis tools for helping to understand biological cell networks. Current research includes HER2+ breast cancer, early stage Drosophila development, and planar cell polarity in Drosophila. This is joint work with OHSU, LBNL, UCSF, and Stanford, and is supported by grants from the NCI and NIH.

Unmanned Aerial Vehicle Design and Control: In this project we are building a team of UAVs with the goals of studying formation flying, architectures for distributed control, and methods for reliable control over communication links.