Jorge Mazza Rodrigues
Biologist Faculty Scientist
Professor, UC Davis
Building: Plant and Environmental Sciences Building, Room 3308
Mail Stop: One Shields Avenue, Davis, CA 95616-8627
Phone: (530) 752-1130
Fax: (530) 752-1552
jmrodrigues@ucdavis.edu
https://soilecogenomicslabs.weebly.com/
https://microbiome.ucdavis.edu/people/jorge-rodrigues
Links
Biography
Jorge “George” Mazza Rodrigues is a professor in the Department of Land, Air, and Water Resources at University of California, Davis. He graduated at the top of his class with a degree in agronomical engineering from the University of Sao Paulo, Brazil, and earned dual PhD degrees from Michigan State University. He was recognized as a UC Davis Faculty Leadership Fellow in 2022 and is currently a member of the First-Generation Faculty Learning Community.
Research Interests
Research in Rodrigues’s laboratory lies at the interface of soil microbial genomics and ecology and focuses on sustainable solutions for biodiversity maintenance in tropical forests and agricultural fields under increased world food demand. He uses a combination of molecular and physiological experimental data to study microbial phylogenetic and functional diversification and their consequences for global biogeochemical cycles. Results from this work have broad implications from basic research in evolutionary biology and ecology to applied aspects, such as conservation policies for natural ecosystems.
Recent Publications
Related News
UC Davis, Berkeley Lab Team up to Advance Green Agriculture
Three University of California, Davis, Faculty Fellows have been awarded $25,000 each to spearhead cross-campus research projects with Berkeley Lab scientists in the field of agricultural decarbonization. With agricultural activities contributing over 10% of the United States’ total greenhouse gas emissions, the sector is a prime target for lowering emissions and addressing the climate crisis. The teams will explore innovative methods to remove and store excess carbon dioxide from the atmosphere—a practice known as carbon sequestration—and minimize energy consumption in crop production.
Building: 91 and 977, Room 091-0450D4 and 977-225
Mail Stop: 977
Phone: MJoachimiak@lbl.gov
http://berkeleybop.github.io/people/marcin-joachimiak/
https://arkinlab.bio/lab-member/marcin-p-joachimiak/
Links
Biography
Marcin Joachimiak is a staff researcher in the Environmental Genomics and Systems Biology Division at Lawrence Berkeley National Laboratory (Berkeley Lab). His current research is performed as part of the DOE Systems Biology Knowledgebase (KBase), the NIH Bridge2AI project, as well as a Berkeley Lab-funded project for predicting microbial growth conditions. He has twenty-five years of experience and a publishing record (H-index 30) in developing and evaluating machine learning algorithms, methods for functional genomics, bioinformatics data science, knowledge modeling, and computational systems design for computational biology. For the past 17 years he has been a member of large distributed microbial and biomedical projects with either a large computational component interfacing with experimentalists (DOE ESPP, DOE ENIGMA Science Focus Area) or which are computational systems centered around modeling and inferring knowledge (KBase, Monarch Initiative, NCATS Biomedical Data Translator, NIH Phenomics First, NIH Bridge2AI). He has led or currently leads team efforts in functional genomics analysis (ENIGMA, KBase, NCATS Translator), knowledge modeling (KBase, Bridge2AI), and machine learning algorithm development (ENIGMA, KBase, NCATS Translator).
Research Interests
Marcin Joachimiak is a computational biologist dedicated to the integration of microbial biology with machine learning and semantic technologies. At the forefront of my research interests is the development of machine learning techniques, including graph learning and biclustering, to unravel the complex relationships in microbiology and metagenome data. Additionally, by leveraging semantic technologies and ontologies, I aim to enhance machine learning, data science, and knowledge graph construction for microbes and microbiomes – a more nuanced and dynamic framework for studying microbial life. As an example, I am developing advanced models for growth prediction and culturing medium optimization using knowledge graphs and graph learning, including tailoring to the unique environment characteristics of different microbiomes. This research has the potential to improve our ability to characterize microbes and develop new utilitarian purposes such as in biomanufacturing, environmental remediation, and human health. Via synthesis of these computational methods and harmonized metagenome and microbiological data, new possibilities emerge in managing and manipulating microbes and microbiomes.
Recent Publications
Related News
Biosciences FY25 LDRD Projects
The projects of 23 Biosciences Area scientists and engineers received funding through the FY25 Laboratory Directed Research and Development (LDRD) program.
Biosciences Area FY24 LDRD Projects
The projects of 21 Biosciences Area scientists and engineers received funding through the FY24 Laboratory Directed Research and Development (LDRD) program.
Biomedical Data Translator Consortium Reports Progress in Pair of Publications
In a pair of recently published papers, members of the Biomedical Data Translator Consortium detailed new features, functionality, and applications of the Translator system and its underlying data model, the Biolink Model.
Biography
Bronwyn Lucas is an assistant professor of biochemistry, biophysics and structural biology in the Department of Molecular and Cell Biology, as well as an assistant professor in the Center for Computational Biology at the University of California, Berkeley.
Research Interests
The Lucas Lab develops methods to visualize molecular structures in cells using focused ion beam (FIB-) milling and cryogenic electron microscopy (cryo-EM). They adapt structural biology techniques as tools for understanding the molecular mechanisms of RNA folding and RNA-protein complex formation within the native cellular environment.
Recent Publications
No publications are available at this time.
Building: 978, Room 4121E
Mail Stop: 978
Phone: (305) 323-8426
mthompson@lbl.gov
https://www.jbei.org/person/mitchell-thompson-2/
Research Interests
- Functional Genomics
- Synthetic Biology
- Microbiology
- Plant-Microbe Interactions
Recent Publications
Divisions
Engineering (Physical Sciences Area)
Secondary Affiliation:
Molecular Biophysics and Integrated Bioimaging
- Structural Biology
Biography
Joao Gabriel Felipe Machado Gazolla is currently a Computer Systems Engineer at The Berkeley Center for Structural Biology, and a former Postdoctoral Research Associate in Computational and Predictive Biology at Oak Ridge National Laboratory, where he worked with terabyte-level datasets and exascale computing. He holds a BS, MS, and Ph.D. in Computer Science and he is primarily interested in HPC, GPU Computing, Heterogeneous Computing, Optimization, and Performance. Previously, he worked as a Researcher and Software Engineer in the Media Lab at Federal Fluminense University (UFF) in Rio de Janeiro, Brazil. During his time there, he optimized GPU performance in various areas using CUDA, including the processing of generic workloads of tasks on heterogeneous machines, logistics, oil and gas, weather forecasting, and thermal image processing. Other interests include data structures, algorithms, C/C++, and Python. For more information, please visit https://www.linkedin.com/in/gabrielgazolla/.
Research Interests
- GPU Computing
- High Performance Computing
- Computational Biology
Research Interests
My research interest has been focused on how genetic and/or epigenetic variation is translated to complex phenotypic variation. I have been combining functional genomics and epigenomics as well as synthetic biology tools for my research.
Research areas are:
- Microbiology
- Plant Biology
- Crop and Pasture Production
- Industrial Biotechnology
Recent Publications
Building: 80A, Room 0100A
Mail Stop: 80R0114
Phone: (510) 486-7765
yangha@lbl.gov
https://bcsb.als.lbl.gov/
Research Interests
Protein crystallography
Recent Publications
Research Interests
I am interested in understanding metalloproteins with an active catalytic site with a focus on photosynthetic proteins, as well as the development of biomimetic catalytic systems relevant to the conversion and storage of renewable energies.
Keywords:
photosynthesis; protein function; light induced charge separation; proton coupled electron transfer; catalytic reactions; protein binding sites of substrates and cofactors; redox potentials; solar fuels; and design of catalytic systems.
Methods:
infrared spectroscopy; time-resolved spectroscopy; fluorescence methods; serial femtosecond crystallography; X-ray absorption and emission spectroscopy; and setup development.
Recent Publications
Related News
Congratulations to Biosciences Area Director’s Award Recipients
Several Biosciences Area personnel are among the 2024 recipients of Berkeley Lab Director’s Achievement Awards. The program recognizes outstanding contributions by employees to all aspects of Lab activities.
Research Interests
My research interests focus on the development of advanced cellular models to elucidate the mechanisms underlying disease and infection pathogenesis.
Biography
Cat Adams is a fungal ecologist interested in how chemistry such as toxins, light, or fragrances drive interactions between fungi and other living things. She earned her BS from the University of Washington in Biology with emphasis on Ecology and Evolution. For her Master’s at Harvard she studied how fungal seed pathogens of wild chili peppers evolved tolerance to spice. Her PhD at Cal examined the role of toxins in the invasion success of the death cap mushroom, Amanita phalloides. Her postdoctoral research examined how fragrances made by a plant root-associated fungus impact their friendly neighborhood bacteria. Cat is excited to join the Northen lab and learn more about mycorrhizal fungi!
Cat also enjoys embroidery, acrylic pour painting, and metal music.
Research Interests
Chemistry, ecology, fungi, mushrooms, signalling, soil, and toxins.
Recent Publications
Research Interests
Piya is a team member of the DOE BRaVE-funded Phage Foundry project for systematic characterization of phages and phage-tail like bacteriocins as a powerful countermeasure to tackle the antimicrobial resistance pandemic. He is currently interested in identifying factors that modulate interactions between phages and pathogenic bacteria so that machine learning tools can be employed to predict interaction between novel phages and their bacterial hosts. He is applying CRISPR and Dubseq technologies to study how genes affect fitness in the context of phage infection.
Recent Publications
Recent Publications
Related News
A New Genetic Hallmark for Predicting Breast Cancer Outcomes
Biosciences researchers have used Collaborative Cross mice, a mouse model system designed to mimic the diversity of human populations, to identify a set of genetic factors that could help refine treatment approaches for a fast-growing form of breast cancer.
Infrared and AI Detect Low-dose Radiation Long After Exposure
Biosciences researchers have established a powerful new method that couples advanced infrared imaging techniques with statistical machine learning models to quickly and non-invasively determine with high accuracy whether an animal was exposed to radiation—even at extremely low doses almost three months post exposure.
Toward a Genetic Understanding of Variability in Radiation Sensitivity
Injury to immune-system and blood-forming cells is a common side effect of radiation therapy, which more than half of all cancer patients receive as part of their treatment. Biosciences Area researchers and their collaborators used a genetically diverse mouse population to model individual differences in sensitivity to radiation exposure.
