Frederik Schulz

Divisions

DOE Joint Genome Institute

• Science Programs

Secondary Affiliation:

Environmental Genomics and Systems Biology

• Comparative and Functional Genomics

Biography

Frederik Schulz joined the DOE Joint Genome Institute in 2016 and is leading the New Lineages of Life Group. His research is focussed on the discovery of novel bacterial, archaeal and eukaryotic microbes and viruses in environmental sequence data. Schulz employs multi-omics (metagenomics, metatranscriptomics, single cell genomics and phylogenomics) and machine learning to find novel functions that may impact microbiome structure and biogeochemical cycles. He provides his expertise to the JGI user community and supports various user projects in the Microbial Program. In an LDRD-funded project, Schulz established a single-cell-based discovery pipeline and enrichment metagenomics for terrestrial protists. These approaches enable novel insights into the diversity and important ecological roles of microeukaryotes in terrestrial ecosystems. Additionally, Schulz is leading a DTRA-funded program on agnostic pathogen detection and surveillance in complex samples.

Research Interests

Microbial symbiosis
Giant viruses and other eukaryotic viruses
Protists
Pathogen agnostic detection
Strain-resolved sequencing



Programs & Initiatives

• New Lineages of Life Group
  

Divisions

Biological Systems and Engineering

• Process Engineering & Analytics

Divisions

DOE Joint Genome Institute

• Science Programs

Secondary Affiliation:

Environmental Genomics and Systems Biology

• Comparative and Functional Genomics

Research Interests

Dr. Li Lei is a Research Scientist at the DOE Joint Genome Institute. Her research uses pan-genomics, population genomics, and comparative genomics to explore the functional significance of the variants in plant genomes. Previous and current work has included investigating the abiotic stress responses for the model perennial grass Brachypodium sylvaticum, pan-genomics of Brachypodium species, drought and cold adaption in barley, comparative genomics to explore the variants which could decrease the crop yield, the evolution of gene family related to epigenetics following the whole genome duplications, and comparative transcriptomics in different tissues from different species.

Divisions

DOE Joint Genome Institute

• Science Programs

Secondary Affiliation:

Environmental Genomics and Systems Biology

• Molecular EcoSystems Biology

Research Interests

Bob uses single-cell genomics and metagenomics to explore how microbes influence people and the environment. This includes studying the diversity, physiology and community ecology of microbes sampled from the natural environment.

Divisions

Chemical Sciences Division

Secondary Affiliation:

Molecular Biophysics and Integrated Bioimaging

• Bioenergetics

Biography

B.A., Molecular Cell Biology, UC Berkeley, 2009

Ph.D., Chemistry, Caltech, 2014

Postdoctoral researcher, LBNL, 2014-2017 – f-element photospectroscopy

Research Interests

Fundamental & applied dark electrochemistry/photoelectrochemistry

Photophysics of lanthanide downconversion & spectral shifting

Algorithms for Tafel fitting

Inorganic emulation of biophysical systems/processes

Biochemical systems for atmospheric CO2 capture

Programs & Initiatives

• Berkeley Lab Carbon Negative Initiative
  
• Liquid Sunlight Alliance (LiSA)
  

Divisions

DOE Joint Genome Institute

• Genomic Technologies

Secondary Affiliation:

Environmental Genomics and Systems Biology

• Biosystems Data Science

Research Interests

My research interests center on systems biology and population genetics, and developing frameworks to draw insight from large-scale ‘omics data. I’m especially interested in using computational tools to understand how communities of all kinds–from collections of functionally specialized plant cells, to co-occurring sets of diverse microbial species, to genotypically heterogenous fruitfly populations–come together as a functional whole, and adapt to changing environments. Currently, my focus is on analyzing data from single cell technologies to profile individual community members, and integrating multi-omic data types to explore community function.

Divisions

DOE Joint Genome Institute

• Genomic Technologies

Secondary Affiliation:

Environmental Genomics and Systems Biology

• Molecular EcoSystems Biology

Research Interests

I work in the field of microbiology and synthetic biology, with a focus on technology development to facilitate strain engineering and microbial functional genomics studies. My background was in molecular genetics, and I use both traditional genetics approaches, and also cutting edge CRISPR-Cas9, Cre-lox recombineering techniques, to genetically engineer microbes from single gene to whole genome levels, in both aerobic and anaerobic organisms. I am passionate about how we could engineering microbes for useful outcomes, especially for new intervention in the prevention and treatment of environmental problems, and human health.

Divisions

Environmental Genomics and Systems Biology

• Molecular EcoSystems Biology

Research Interests

Exploration of Earth’s microbial and viral diversity is a major scientific frontier. Sequencing DNA – the blueprint of life – collected directly from the environment provides a powerful way to access the uncatalogued microbial diversity on our planet. These uncharacterized lifeforms are ripe with novel functions, metabolisms, the potential for biotechnological and medical applications, and will inform us on the evolution of all life.

My previous work has explored the nature and extent of microbial life underground and below the seafloor using tools rooted in molecular biology, biogeochemistry, and microbiology. Now I am working to explore novel microbial diversity in additional environments through the leveraging of ultra-powerful computational resources and true access to massive genome databases (i.e. big data).

Divisions

Biological Systems and Engineering

• Process Engineering & Analytics

Research Interests

Dr. Liu’s research is dedicated to the use of cutting-edge technologies for the production of renewable fuels and chemicals. His research interests are in catalysis, reaction engineering and process design. In particular, his research harnesses the unconventional solvents, such as supercritical fluids and gas-expanded liquids, as well as advanced membrane technology, e.g., nano filtration to develop resource-efficient process with reduced environmental footprint.  At the ABPDU, he plans, leads, and executes process development and piloting related projects in collaboration with R&D sponsors.

Divisions

Biological Systems and Engineering

• BioEngineering & BioMedical Sciences

Research Interests

Deepanwita Banerjee, PhD, is currently working on computationally driven host engineering for growth-coupled production of biofuels and bioproducts using the Product Substrate Pairing (PSP) approach. She uses computational strain optimization methods and genome scale metabolic models (GSM) to predict gene targets for engineering Pseudomonas putida. She is also working towards predicting PSP strategies in P. putida for utilization of lignocellulose derived carbon sources for bioenergy and biomanufacturing applications. The goal is to test and learn to better design robust and sustainable microbial hosts that maintain desirable phenotype across industrially relevant scales and conditions.

Deepanwita Banerjee’s research interests include understanding microbial systems for desirable phenotypes using multi-omics integrated systems biology approach. The applications are diverse ranging from improving production of value-added products or assessing microenvironments for a redox imbalance in vivo. She is also interested in understanding the emergent properties of a microbial hosts that are a result of the complex relationship between metabolism and transcriptional regulation. Currently there are digital resources available for model microbes that help inform such relationships but is lacking for non-model microbial systems. Genome-scale network reconstruction of a microbial system requires integration of more than one layer of biological networks (e.g., metabolism, regulation or signaling) as constraints to improve prediction power of such computational models for desirable phenotypes such as growth coupled production or maximum bioconversion of carbon sources.

Programs & Initiatives

• The Joint Bioenergy Institute
  

Divisions

DOE Joint Genome Institute

• Science Programs

Secondary Affiliation:

Environmental Genomics and Systems Biology

• Comparative and Functional Genomics

Biography

Stephen Mondo completed his PhD training at Cornell University in 2013, where he studied host-endosymbiont interactions with Dr. Teresa Pawlowska. After a brief postdoc in the Bogdanove lab at Cornell studying TAL effectors present in fungal endosymbiont he joined the Fungal amd Algal genomics team at the DOE Joint Genome Institute as a Data Scientist. Here, Stephen supports the fungal scientific community through annotation of fungal genomes, comparative genomic analyses for user-driven publications and tool development for improved quality of fungal genome annotations. Stephen also conducts his own independent research in support of DOE mission objectives, primarily in the areas of epigenomics an chromatin regulation. Additionally, he now leads multi-omics data analysis, integration and visualization efforts within the Fungal and Algal genomics program.

Research Interests

Epigenetics, chromatin regulation, fungal comparative genomics, evolutionary & co-evolutionary theory, host-endosymbiont interactions, phylogenomics, early-diverging fungi

Divisions

Molecular Biophysics and Integrated Bioimaging

• Bioenergetics

Biography

From the Molecular Foundry page:

Dr. Ajo-Franklin has been a Staff Scientist at the Molecular Foundry since 2007. Before that, she received her Ph.D. in Chemistry from Stanford University with Prof. Steve Boxer and was a post-doctoral fellow with Prof. Pam Silver in the Department of Systems Biology at Harvard Medical School.

Dr. Ajo-Franklin is fascinated by the incredible, diverse functionality of biological molecules and nanoassemblies, and seeks to engineer these complexes and their host organisms to address global challenges in energy and the environment.

Research Interests

Dr. Ajo-Franklin’s research creates engineered bioassemblies–electron nanoconduits–that direct the flow of charge between living cells and non-living materials. Though a combinatorial approach, she has established an unparalleled ability to genetically program the enormously complex biosynthesis of these electron nanoconduits and to quantitatively characterize their function at the biological-inorganic nanointerface. These capabilities have allowed her to discover design principles that govern the emergent processes of nanoconduit assembly and function. In future work, she will expand the combinatorial space through designed genetic variants and adaptive evolution approaches to dissect fundamental controls on charge transfer at this hybrid nanointerface.

ENGINEERING ELECTRONIC COMMUNICATION

Cellular-electrical connections would enable devices to combine specialties of the living world and the non-living technological world. This new class of smart, self-renewing nanostructured systems has the potential to revolutionize environmental sensing and energy harvesting applications and to open new avenues to program cellular behavior. Building towards this vision, the long-term objectives of the our research are to develop understanding of the principles which govern electron flow across living-non-living interfaces and to use those principles to create electron transfer pathways between individual living microbial cells and non-living electrodes. Our overall strategy is both to explore how naturally-occurring microbes achieve electron transfer to inorganic surfaces and to use genetic and materials surface engineering to create new ‘domesticated’ hybrid cell-electrode systems.

ASSEMBLY & APPLICATIONS OF S-LAYER PROTEINS

S (`surface’)-layer proteins form crystalline lattices on the outsides of many bacteria and archaea. These nearly ubquitous structures play a number of crucial biological roles: they serve as structural scaffolds, effect selective transport of ions and proteins, serve as templates for mineralization, and protect against phagocytosis. While the lattice structures of many S-layers are known, the dynamical mechanisms through which they form are poorly understood. A molecular-level picture of the assembly of the S-layer protein SbpA from Lysinibacillus sphaericus on lipid bilayers was obtained only recently by using in situ atomic force microscopy. AFM images elucidated the phase transition of amorphous precursors into the crystalline clusters composed of folded tetramers and subsequent growth without disappearance of any crystal clusters. Such a system demonstrates the non-classical crystallization behaviors in the S-layer assembly. Molecular dynamic simulations of the S-layer assembly using a coarse grain model also supported the non-classical nucleation arising from a dense liquid precursor, and subsequent growth of the crystal2. The long-term objectives of our research are to develop predictive understanding of S-layer protein nucleation and growth, so as to advance basic knowledge of the dynamics of coupled nanoscale phase separation and self-assembly and to enable control of the nanoscale structures. Together with the Whitelam, DeYoreo, and Bertozzi groups, we are using a combination of fluorescence microscopy, atomic force microscopy, and computer modeling to reveal the mechanisms underlying S-layer crystallization and to identify strategies for its control.