Ning Sun

Divisions

Biological Systems and Engineering

• Process Engineering & Analytics

Research Interests

Dr. Sun’s research is devoted to biomass processing for production of renewable fuels and chemicals, which includes process design, optimization, and scale-up. Her research also includes characterization and evaluation of the solid and liquid streams from the biomass pretreatment process and development of integrated process for biomass conversion. She leads projects in ABPDU involving biomass conversion, and product recovery.

Divisions

Nuclear Science

Secondary Affiliation:

Molecular Biophysics and Integrated Bioimaging

• Cellular and Tissue Imaging

Research Interests

My research interests focus on the development of advanced imaging systems and techniques for biological research as well as for clinical applications. This includes developing advanced instrumentation for applications in medical imaging and homeland security, specifically developing advanced detector technologies and electronics to improve the performance and capability of radiation imaging detectors used in positron emission tomography (PET), single photon emission computed tomography (SPECT), and x-ray computed tomography (CT) systems. My current research areas focus on the development of: (1) novel photodetectors and radiation detectors, (2) custom integrated circuits and electronics, and (3) new detector design and camera geometries. Currently, I have a project developing an open, flexible, scalable, and high-performance electronics system for applications in radionuclide imaging called OpenPET. In addition, I am developing a novel photon-counting detector technology to improve the imaging performance of conventional x-ray imaging system as well as to transform it into a functional imaging platform. Another research area that I am investigating is developing advanced PET detector module that has excellent timing performance to enable the benefits of time-of-flight PET as well as providing a solution for developing advanced multimodality imaging systems. My research is primarily supported by the National Institute of Health.

Divisions

Environmental Genomics and Systems Biology

• Comparative and Functional Genomics

Research Interests

Computational reconstruction of transcriptional regulation in bacteria.
Integration of ENIGMA data and DOE KBase computational tools.
Development of bioinformatics tools and databases: RegPrecise, RegPredict, RegTransBase, Fama.

Divisions

DOE Joint Genome Institute

• Science Programs

Secondary Affiliation:

Environmental Genomics and Systems Biology

• Molecular EcoSystems Biology

Research Interests

Dr. Vogel’s research is focused on developing plant functional genomic resources and utilizing these resources to understand genome organization and regulation, abiotic stress tolerance, plant-microbe interactions, and the molecular basis of perenniality. Most projects in his lab utilize B. distachyon and related species as model systems to develop knowledge that will ultimately be used to improve biomass crops like switchgrass. Major projects currently underway include: 1) Defining the pan-genome of B. distachyon through de-novo assembly and annotation of 100 natural accessions 2) Using a trio of Brachypodium species as a model for polyploidy in order to understand polyploid genome evolution and regulation 3) Using a defined microbiome to identify plant genes that influence the composition and function of the root microbiome 4) Determining the molecular mechanism of engineered resistance to multiple abiotic stresses and the molecular basis of perenniality using the perennial model grass Brachypodium sylvaticum 5) Developing a comprehensive collection of defined grass mutants by sequencing chemical and radiation induced mutants.

Programs & Initiatives

• Plant Functional Genomics at JGI
  
• Microbes to Biomes (M2B)
  

Divisions

Environmental Genomics and Systems Biology

• Molecular EcoSystems Biology

Secondary Affiliation:

DOE Joint Genome Institute

• User Programs

Biography

Major foci of Tringe’s current research efforts are the roles of microbial communities in wetland carbon cycling and the interactions of plants with their associated microbiomes. She is the Laboratory Research Manager for the ENIGMA Scientific Focus Area. Tringe earned her bachelor’s degree in physics from Harvard University and her doctorate in biophysics from Stanford University. In her nearly two decades at Berkeley Lab, Tringe previously served in multiple roles at the DOE Joint Genome Institute (JGI), including Deputy of User Programs and head of the Metagenome Program. She is the 2021 recipient of the Ernest Orlando Lawrence Award, one of DOE’s highest honors, and was named a Fellow of the American Association for the Advancement of Science (AAAS) in 2018.

Research Interests

Sequence-based approaches to studying microbial community assembly, function and dynamics in terrestrial ecosystems.

Divisions

Environmental Genomics and Systems Biology

• Biosystems Data Science

Secondary Affiliation:

Molecular Biophysics and Integrated Bioimaging

• Structural Biology

Research Interests

John-Marc Chandonia is a computational biologist with a background in protein structure prediction, structure classification, and evolutionary analysis of proteins.

Programs & Initiatives

• Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA)
  
• Structural Classification of Proteins — extended (SCOPe)
  
• The ASTRAL Compendium for Sequence and Structure Analysis
  
• The Department of Energy Systems Biology Knowledgebase (KBase)
  

Divisions

Molecular Biophysics and Integrated Bioimaging

• Structural Biology

Research Interests

My research program is focused on understanding the molecular basis of cell mechanics and mechanotransduction with them aim to shed light on the role of these biological processes in human disease. Our specific attention is on the role of two macromolecular systems in cellular function, namely the integrin-mediated focal adhesions at the interface between the cell and extracellular matrix (ECM) and the nuclear pore complex (NPC). Focal adhesions are the immediate sites of cell interaction with the ECM, and as such they play a key role in mechanosensing and mechanotransduction at the edge of the cell. Nuclear pores could also play a role in the overall process of cellular mechanotransduction by exquisitely controlling the material transport in and out of the nucleus, thereby regulating the gene expression and protein synthesis.

Divisions

Molecular Biophysics and Integrated Bioimaging

• Structural Biology

Research Interests

Serial crystallography at modern lightsources, especially X-ray free electron lasers (XFELs), has allowed us to examine the time evolution of biomolecules, while avoiding the radiation damage commonly experienced with earlier single-crystal techniques. My group is developing the computational techniques needed to process XFEL data. One important target is photosystem II, where an extremely detailed structural description of the sunlight-driven water splitting process is emerging, based on work with collaborators in MBIB Division and elsewhere. Indeed, we hope to understand the sequential transfer of single electrons, using special diffraction experiments performed at the X-ray absorption edge of the Mn cofactor atoms. This entirely new analysis technique for metalloproteins will be enabled by cctbx.xfel, our open-source data processing package.

These challenging crystallography problems require ultrafast X-ray imaging detectors that produce massive datasets (100 TB/day), requiring radically scaled-up computer resources. Within the Exascale Computing Project (ECP) we have implemented a processing pipeline that utilizes GPU nodes at national supercomputing centers such as NERSC, thus turning around large datasets within a matter of minutes so experimental decisions can be made during data collection.

Profoundly detailed algorithms are needed to analyze every pixel of the diffraction pattern, using a Bayesian framework to “solve the inverse problem” to infer the best physics parameters that describe the data. For situations where we do not know the deterministic model, we are experimenting with machine learning approaches.

Divisions

Molecular Biophysics and Integrated Bioimaging

• Bioenergetics

Biography

Since 2015, Junko Yano has held leadership roles in the MBIB Division, first as head of the Bioenergetics Department, then as Deputy for Science, and most recently as interim Director. Yano is a senior scientist and has served as a member of the Lab Staff Committee since 2016 and the DOE Council on Chemical and Biochemical Sciences since 2015. She is a co-principal investigator of the multi-institutional Liquid Sunlight Alliance (LiSA), one of two projects in the Fuels from Sunlight Energy Innovation Hub funded by the DOE Office of Science, Basic Energy Sciences. Yano earned her doctorate in physical chemistry at Osaka University and came to the Lab as a postdoctoral fellow in 2001. Her research interests pertain to problems of importance in energy—particularly renewable energy sources. Her group uses X-ray spectroscopy and crystallography at X-ray free electron lasers and synchrotron facilities to understand biological and inorganic systems under functional conditions. They are studying how, during photosynthesis, plants use light to split water using a catalytic Mn4Ca cluster, converting light energy into chemical energy.

Research Interests

• Structure and function of active metal sites in metalloenzymes.
• X-ray crystallography and X-ray spectroscopy using an X-ray free electron laser.
• Application of X-ray-based techniques to artificial photosynthetic systems such as light-absorbers and catalysts to study electron transfer and catalytic reaction mechanisms in situ.
• Application of synchrotron X-ray absorption/diffraction methods for the analysis of molecular structures, crystal structures, and electronic structures of inorganic catalysts.
• Water oxidation reaction in natural photosynthesis
• Structure and function relationship using vibrational spectroscopy and EPR spectroscopy in organic/organometallic materials.

Divisions

Biological Systems and Engineering

• BioEngineering & BioMedical Sciences

Research Interests

A systems biology approach to identification of genetic networks controlling susceptibility to tumor development and progression induced by environmental exposure

Genetic susceptibility plays a role in many types of cancer. Identifying the genes involved in susceptibility to cancer may have potential utility in risk management, lead to greater understanding of the biological pathways involved in cancer development, and elucidate how environmental factors exert their effects in combination with genetic variants. One of the broad and long-term goals of my laboratory is to identify the combinations of genes and their functional polymorphisms that affect the susceptibility of individual human subjects to the effects of environmental exposure, such as thirdhand smoke and radiation. The detection and characterization of multiple low penetrance genetic variants that control many complex diseases is one of the major challenges of the future, but progress is hampered by formidable technical and conceptual difficulties. Mouse models offer many advantages for the study of the genetic basis of complex traits, including environmental exposure-induced cancers, because of our ability to control both the genetic and environmental components of risk. The goal is the understanding of all stages of multi-step carcinogenesis in the mouse, in particular the relationships between germ line predisposition and somatic genetic changes in tumors. The identification of human homologues of these predisposition genes and discovery of their roles in carcinogenesis will ultimately be important for the development of methods for prediction of risk, diagnosis, prevention and therapy for human cancers. We will use mouse population-based approach, such as Collaborative Cross system, to exploit the variation in susceptibility to environmental exposure-induced cancers and to identify the combinations of quantitative trait loci (QTLs) that control the radiation response. The power of classical mouse genetics will be complemented by new approaches involving haplotyping to refine the genomic locations of QTLs, together with sophisticated genetic analysis of the somatic events in environmental exposure-induced cancers using next generation sequencing technology.  This comprehensive systems biology approach may identify specific genes or pathways that are differentially controlled between mouse strains, and contribute to variation in susceptibility to environmental exposure-induced carcinogenesis.

Develop new mouse models for human cancer
Sporadic tumors, which account for the majority of all human cancers, evolve as the result of a step-wise accumulation of genetic alterations resulting in uncontrolled cell proliferation and a lack of response to apoptotic cues. Such genetic alterations include point mutations, deletions, duplication/amplification, and translocations and these alterations can lead to the enhanced or decreased activity of the expressed protein. These alterations are referred to as ‘gain-of-function’ or ‘loss-of-function’ mutations, respectively. The affected genes are termed oncogenes or tumor suppressors, respectively. Within the last decade, the availability of a complete sequence-based map of the human genome, coupled with significant technological advances, has revolutionized the search for somatic alterations in tumor genomes. Within a given tumor type there are many infrequently mutated genes and a few frequently mutated genes, resulting in incredible genetic heterogeneity. The resulting catalogues of somatic alterations will point to candidate cancer genes, but requiring further validation to determine whether they have a causal role in tumorigenesis. The availability of gene targeting and transgenic technology in the mouse gives us unparalleled opportunities to test the functional significance of genetic changes in tumor development. Another one of the broad and long-term goals of my laboratory is to develop new mouse models for human cancer. These mouse models not only will increase our understanding of genetic aberration associated with cancer progression, but also will potentially help to identify personalized medicine for cancer patients, which may eventually contribute to a decrease in morbidity and mortality of cancer.

Divisions

DOE Joint Genome Institute

• Science Programs

Secondary Affiliation:

Environmental Genomics and Systems Biology

• Comparative and Functional Genomics

Biography

Axel Visel joined the DOE Joint Genome Institute (JGI) in 2010 and currently serves as the Deputy of Science. He focuses on the development and implementation of strategic initiatives and leads the JGI Science Programs department. Visel received his Ph.D. in 2004 from the Max Planck Institute in Hanover, Germany, and performed postdoctoral training at Lawrence Berkeley National Laboratory (Berkeley Lab). In addition to his appointment at the JGI, Visel also holds appointments as a Senior Staff Scientist in the Environmental Genomics and Systems Biology Division at Berkeley Lab and as an Adjunct Professor at the School of Natural Sciences at the University of California, Merced.

Divisions

Environmental Genomics and Systems Biology

• Comparative and Functional Genomics

Research Interests

Thanks to cheap DNA sequencing, we are slowly starting to understand the incredible diversity of bacteria. I build computational tools to help us use all this data to understand how diverse bacteria work. This understanding can help us manage our environment, control the bacteria inside us, and develop new biotechnologies.