Mustafa Janabi

Divisions

Molecular Biophysics and Integrated Bioimaging

• Cellular and Tissue Imaging

Research Interests

Mustafa Janabi directs and manages operations of the Biomedical Isotope Facility, which means that he:
• Coordinates production schedule,
• Operates and maintains medical cyclotron (RDS-111),
• Hires, trains, and supervises new employees, and
• Coordinates with researchers on collaborative projects.

Divisions

Environmental Genomics and Systems Biology

• Molecular EcoSystems Biology

Research Interests

EcoFAB and EcoBOT development, environmental microbiology including plant-microbial interactions

Divisions

Molecular Biophysics and Integrated Bioimaging

• Bioenergetics

Research Interests

• Unravelling the relationship between structure, dynamics and function of enzymes using
  • Time-resolved structural studies at X-ray free-electron lasers (XFEL)
  • Simulating biological systems using Molecular Dynamics/Quantum mechanical methods
• X-ray crystallography data analysis – developing new methods for active sites of metalloenzymes
• Current systems of interest include Photosystem II, a multi-subunit membrane enzyme catalyzing the water oxidation reaction.

Divisions

Biological Systems and Engineering

• Biodesign

Research Interests

Bioenergy and Biomanufacturing by combining synthetic biology and metabolic engineering to develop microbial systems for better utilization of biomass and gaseous one-carbon substrates (CO2 and CH4). Further, redirecting the enhanced carbon utilization towards next-gen biofuel, green chemicals or biopolymer production.

Media
A Day in the Half Life Podcast: Biomanufacturing: Making Stuff with Microbes
YouTube video: Berkeley Lab in the fight against COVID-19: Researching an oral vaccine

Programs & Initiatives

• Joint BioEnergy Institute
  

Divisions

Environmental Genomics and Systems Biology

• Molecular EcoSystems Biology

Biography

Lauren was born and raised in Northern California.  She received her BS in Mathematical and Scientific Computation from UC Davis and her PhD in Biomolecular Engineering and Bioinformatics from UC Santa Cruz.

Research Interests

By working at the interface of microbiology and computational science, I study how microbial communities affect biogeochemical element cycling and how they respond to environmental changes and pressures.  Understanding biogeochemical cycling is critical for understanding the flow of energy and matter between major reservoirs of the Earth, such as the atmosphere, oceans, and terrestrial ecosystems.  Organisms transform matter to obtain nutrients they need to survive, and this transformed matter is used by other organisms.  Biogeochemical cycling research gives us insight into how we affect the earth and its organisms, and how they affect us.

I am developing computational and experimental methods to help us better interrogate and quantify microbial community members (bacteria, archaea, and viruses) to more accurately model population dynamics.   Namely, I am developing methods to improve long read metagenomics sequencing and assembly.

• Microbial Ecology
• Subsurface and Marine Microbiology
• Long reads for isolate and metagenomics assembly
• Metagenomics – improving assembly and analysis methods

Programs & Initiatives

• ENIGMA - Ecosystems and Networks Integrated with Genes and Molecular Assemblies
  
• LDRD - Ecogenomics and impact of viruses, plasmids, and strains on estuarine microbiome function
  

Divisions

Chemical Sciences

Secondary Affiliation:

Molecular Biophysics and Integrated Bioimaging

• Bioenergetics

Biography

Frances Houle is Deputy Director of the Liquid Sunlight Alliance, Deputy Director for Science and Research Integration of the Joint Center for Artificial Photosynthesis, and Senior Scientist in the Chemical Sciences and Molecular Biophysics and Integrated Bioimaging Divisions at Lawrence Berkeley National Laboratory. She received the BA from the University of California at Irvine and the PhD from the California Institute of Technology, both in chemistry. Prior to her current appointments she was a postdoctoral fellow at LBNL and the UC Berkeley Chemistry Department, Research Staff Member in the IBM Research Division in San Jose, California, Manager of Materials Development at InVisage Technologies, a startup company making nanoparticle-based image sensors that is now part of Apple Corporation, and Director of Strategic Initiatives in the Chemical Sciences Division at LBNL. She has received numerous awards including the 2009 American Vacuum Society John A. Thornton Memorial Award and Lecture, the 1999 American Institute of Chemical Engineers Northern California Section Research Project of the Year, and the 1998 IBM Environmental Affairs Excellence Award. She is a Fellow of the American Physical Society and Fellow of the AVS, and member of the American Chemical Society and the Materials Research Society. She has been active in professional service, and is currently Director of the Materials Research Society and Chair of the Ethics Committee of the American Physical Society in addition to serving as guest editor, and on conference organization and scientific advisory committees. She has over 150 publications and 28 US patents, and is co-author of the open-access stochastic reaction-diffusion simulation code Kinetiscope.

Research Interests

Houle’s scientific interests are in the areas of coupled reaction-transport processes in solar energy conversion systems and their components, and chemical modification of aerosols, nanoparticle, semiconductor, metal and polymer interfaces, surfaces and films using novel experimental and computational techniques.

Divisions

Molecular Biophysics and Integrated Bioimaging

• Cellular and Tissue Imaging

Research Interests

Our research interests bridge applied engineering with basic science. We are interested in mechanistic questions addressed at a molecular level using optical imaging acquired with high temporal and spatial resolution.

We are building the Advanced BioImaging Center (ABC), a global initiative where we will house cutting-edge pre-commercial imaging technologies, such as the next-generation Adaptive Optical Multi-functional Lattice Light-Sheet Microscope. The ABC will enable imaging across scales spanning several orders of magnitude in space and time in specimens up to several millimeters in extent, or over sessions lasting up to multiple days. These instruments consequently output explosive quantities of immensely complex data and the greatest challenge researchers face is the ability to visualize, analyze and understand the data in order to extract biologically meaningful insights. The prime goal of the ABC is therefore to not only provide cutting-edge microscopy, but also the dedicated human and hardware resources capable of handling tera- to petabyte scale projects and developing robust, open source computational workflows that allow biologists to easily mine the data. At the ABC, we are interested in leveraging the powerful combination of artificial intelligence tools with the cutting-edge multimodal imaging systems to accelerate the pace of discoveries in both fundamental and translational sciences.

Programs & Initiatives

• Advanced BioImaging Center
  

Divisions

Molecular Biophysics and Integrated Bioimaging

• Cellular and Tissue Imaging

Biography

Jinyi Qi a professor at the Department of Biomedical Engineering in the University of California, Davis. He was named Fellow of the Institute of Electrical and Electronics Engineers in 2014 for contributions to statistical image reconstruction for emission-computed tomography.

Research Interests

Dr. Qi aims to develop advanced image formation and processing tools to push the boundary of molecular imaging using positron emission tomography (PET)/computed tomography (CT). His lab combines in silico modeling of tracer kinetics, imaging system response and human observation to create new image reconstruction algorithms and design future imaging systems that provide higher sensitivity and specificity for lesion detection and staging. His work has specific applications in fighting cancer and Alzheimer’s disease.

Divisions

Molecular Biophysics and Integrated Bioimaging

• Cellular and Tissue Imaging

Biography

Suzanne Baker got her undergraduate degree in Biomedical Engineering from Tulane University and her PhD in Vision Science at University of California, Berkeley combining information from dipole source localization using EEG and fMRI.  The focus of her postdoc was on distortion correction in echo planar imaging (fMRI).

After her postdoc she was hired at Lawrence Berkeley National Laboratory (LBNL) to work for Bill Jagust where her primary responsibility was accurate PET quantification.  At LBNL, she got the opportunity to learn about PET scanners and imaging from Ron Huesman and Bill Moses.  In addition to applying and acquiring knowledge of image processing to PET, she also enjoyed dabbling in the world of instrumentation and was tasked with keeping the old Siemens (CTI) HR running.  She designed all aspects of PET data analysis in the Jagust lab, including detecting/fixing PET/CT overlay, DVR/SUVR/SRTM quantification, and partial volume correction.

Suzanne is experienced in PET analysis for multi-center studies.  She has served as the PET core (quality assurance and PET data analysis) for multisite studies (NGF, NIFD, 4RTNI), and works with Bob Koeppe on PET quality assurance for SCAN.

Currently Suzanne’s focus is on minimizing noise in cross-sectional and longitudinal tau imaging.  She and Tharick Pascoal are the PIs of an R01 to acquire head-to-head longitudinal tau PET data using MK6240 and Flortaucipir in over 600 participants at 8 different imaging sites with the purpose of comparing and harmonizing longitudinal change measured by these tau PET tracers.

Research Interests

My primary interest is the optimization quantification of PET imaging signal. I work in the field of aging and dementia and focus on:
– pharmacokinetic modeling
– partial volume correction
– analysis of multi-site data
– tracer comparison
– optimization of longitudinal measurements
– reference region analysis

Divisions

Molecular Biophysics and Integrated Bioimaging

• Structural Biology

Research Interests

I focus on serial crystallography computational methods development by researching new algorithms and methods for data reduction at high-energy XFEL sources and synchrotrons. I’m interested in all aspects of the process, from modeling the physics of photon diffraction to file formats and metadata standards to using supercomputers to process huge amounts of data in real time to data visualization.

I am a member of the data reduction team of the Computational Crystallography initiative (cci.lbl.gov), focused on analysis of diffraction data from advanced light sources, including X-ray free electron lasers (XFELs).

I am also researching as part of a large collaboration with the University of Connecticut and MIT the crystal engineering of hybrid coordination polymers towards achieving rational control over the optoelectronic properties of low-dimensional nanostructures.  We are using machine learning principles to add advanced spatial and symmetry aware neural network training methods to small-molecule chemical crystallography and material science data processing.  Press release.

Programs & Initiatives

• Computational Crystallographic Initiative (CCI)
  
• NeXus international advisory committee (NIAC)
  

Divisions

Molecular Biophysics and Integrated Bioimaging

• Structural Biology

Research Interests

Computational biophysics and bio-imaging, inverse problems and projection methods, algorithm development for X-ray diffraction and imaging data.

Divisions

Molecular Biophysics and Integrated Bioimaging

• Cellular and Tissue Imaging

Biography

Henry VanBrocklin, PhD, is a Professor in Residence, Director of the Radiopharmaceutical Research Program in the Center for Molecular and Functional Imaging (CMFI) at the University of California, San Francisco China Basin, and he is a Joint Faculty Scientist at the Lawrence Berkeley National Laboratory. Dr. VanBrocklin obtained his PhD in Radiopharmaceutical Chemistry from Washington University, St. Louis in 1990, and he completed a two-year postdoctoral program at the University of Illinois, Urbana in 1992. He maintains an active radiotracer research program in addition to providing tracers for collaborative basic science and translational clinical research. His research interests include short-lived radioisotope production to the creation of fluorine-18 and carbon-11 labeling chemistry strategies for new radiotracer preparations and applications.