Héctor García Martín
Computational Biologist Staff Scientist
Building: 978, Room 4244
Mail Stop: 978-4121
Phone: (510) 495-2505
Fax: (510) 486-4252
hgmartin@lbl.gov
https://hectorgarciamartin.com/
https://qmm.lbl.gov/
Links
Divisions
Biological Systems and Engineering
- Process Engineering & Analytics
Secondary Affiliation:
Environmental Genomics and Systems Biology
- Biosystems Data Science
Biography
I was born and raised in the basque city of Bilbao, in northern Spain. From every early on I was fascinated by science and math, so I studied physics for my bachelors, and specialized in solid state physics at the University of the Basque Country. Afterwards, I did my Ph. D. in condensed matter physics at the University of Illinois at Urbana-Champaign. Very soon I became fascinated by emergent properties in biology, like e.g. the species area rule. Hence, I decided to work on metagenomics for my postdoc at the Joint Genome Institute, obtaining blueprints of microbial community metabolism. Irked by the difficulty of creating predictive models for microbial communities, I focused on an easier target: pure cultures for which we have the tools to change their genome. This took me to my current position, developing predictive models for biological systems to produce renewable biofuels and other products using synthetic biology. You can read the expanded version of this story here.
Research Interests
My research interests focus on mathematical modeling of biological systems: from synthetic biology, machine learning, systems biology, metabolic flux analysis, data visualization, scientific software development, ecology, to automation and complexity
My research is divided among machine learning, metabolic flux analysis, retrobiosynthesis, automation and software development for visualization and acquisition of data. I am also using mathematical approaches to try and develop quantitative predictive models for microbial communities. You can find more detailed information on my research interests here and the full story of how a physicist ended up working in biology here.
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.
Making Sustainable Products Faster with AI and Automation
Héctor García Martín, a staff scientist in the Biological and Systems Engineering (BSE) Division, is working to accelerate and refine the synthetic biology landscape by applying artificial intelligence and the mathematical tools he mastered during his training as a physicist.
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.
Divisions
- Genomic Technologies
Secondary Affiliation:
Environmental Genomics and Systems Biology
- Biosystems Data Science
Research Interests
Transcriptomics, Metagenomics, High-performance Computing, Machine Learning
Recent Publications
Related News
GenomeOcean Leverages AI to Decode Nature’s Secret Language
Trained on environmental data, a new JGI tool more accurately facilitates microbial genome discoveries.
Case Study: JGI Leveraging HPC Resources
The JGI partnered with Science IT in a deep research collaboration to build an AI-powered model capable of transforming genomic research. This effort has involved active collaboration, weekly meetings, and iterative refinement to turn experimental ideas into functional AI tools.
JGI, JBEI Partner on Successful RENEW Proposals
The Joint BioEnergy Institute (JBEI) and Joint Genome Institute (JGI) are part of three DOE-funded initiatives under the RENEW program, which supports internships, training, and mentoring to foster diverse talent in the energy workforce.
Building: 978, Room 4452
Mail Stop: 978R4412
Phone: (510) 486-7371
HScheller@lbl.gov
https://www.jbei.org/person/henrik-vibe-scheller/
Divisions
Environmental Genomics and Systems Biology
- Molecular EcoSystems Biology
Secondary Affiliation:
Biological Systems and Engineering
- BioEngineering & BioMedical Sciences
Recent Publications
Related News
How Plants and Mycorrhizal Fungi Cooperate
Researchers have studied both sides of plant-fungi symbiosis in one of the first cross-kingdom spatially-resolved transcriptomics studies to date.
Report from Second Plant Single-cell Solutions for Energy and the Environment Workshop Available
On April 29, 2021, Berkeley Lab hosted a second workshop to identify the most pressing barriers to wider adoption of single-cell sequencing and omics technologies, and to discuss solutions to remedy those barriers in order to drive discovery. The workshop report is now available for download.
Finding the Missing Step of an Important Molecular Process
Lysine is an important amino acid that must be supplied in our diets, as our bodies can’t produce lysine on their own. Most cereal grains have low levels of lysine, and scientists have worked to breed crops with higher lysine levels. However, the biochemical processes that break down lysine in plants weren’t fully understood. New Joint BioEnergy Institute (JBEI) research, published in Nature Communications, reveals this last missing step of lysine catabolism.
Research Interests
In my research group, we are particularly inspired by how nature manages complex interactions at interfaces and self-assembles functional bionanomaterials. Therefore, we use bioengineering approaches to both study and mimic these processes. Specifically, we use genetic engineering techniques to design novel peptides/proteins or virus particles and then use them to create functional nanostructures for regenerative medicine, therapeutics, biosensing and energy generation.
Recent Publications
Related News
Two PBD Scientists Win 2013 R&D 100 Awards
Presented by R&D Magazine, the R&D 100 Awards recognize the year’s top 100 technology products from industry, academia, and government-sponsored research, ranging from chemistry to materials to biomedical breakthroughs.
Bacteriophage Power Generator: Viruses Generate Electricity
The Bacteriophage Power Generator generates power using harmless viruses that convert mechanical energy into electricity, providing a sustainable, cost-effective, nontoxic energy source capable of powering electronics and microdevices. It is unique in addressing the energy challenge of predominantly battery-driven devices.
Building: Aquatic Park Station 717 Potter St #180B, 977-0180B, CA 94710, Room 180B
Mail Stop: 977-180B
VKMutalik@lbl.gov
Links
Divisions
Environmental Genomics and Systems Biology
- Comparative and Functional Genomics
Secondary Affiliation:
Biological Systems and Engineering
- BioEngineering & BioMedical Sciences
- Biodesign
Research Interests
- Developing high-throughput functional discovery platform for thousands of microbial genes, phage genes and extending it to metagenomic samples
- Discovery of bacteriophage-host interaction determinants, mechanistic insights into antibiotic resistance and phage resistance, and how they impact host fitness
- Approaches for doing esigned manipulation of microbial communities
- Engineering of phages, phage particles for diverse applications
- Rational design of phage cocktails with antibiotics for phage therapy applications
- Synthetic genetic parts for phylogenetically distinct and industrially important microbes and rules for their functional composition.
PRESS:
Cataloging Nature’s Hidden Arsenal: Viruses that Infect Bacteria
https://naturemicrobiologycommunity.nature.com/posts/a-tale-of-tailocins-bacterial-stabbing-tools
https://mammoth.bio/2020/10/28/mammoth-interviews-vivek-k-mutalik-phd-scientist-at-lbnl-and-co-founder-of-felix-biotechnology/
https://phage.directory/capsid/interview-vivek-mutalik
Programs & Initiatives
Recent Publications
Related News
Biosciences Researchers Launching Biopreparedness Projects
Two scientists in the Area, Greg Hura and Vivek Mutalik, are heading up research projects that are part of the Department of Energy's Biopreparedness Research Virtual Environment (BRaVE) initiative. Yasuo Yoshikuni, a scientist at the Joint Genome Institute, is part of a third project that is being led by Brookhaven National Laboratory. These projects will leverage bioimaging expertise to develop better therapies and vaccines for viruses, develop a high-throughput platform to rapidly design countermeasures to drug-resistant pathogens, and unlock the molecular basis of plant-pathogen interactions to create resilient bioenergy crops.
Dub-seq Used to Screen Phage Proteins for Antibiotic Properties
A team of researchers from Berkeley Lab, UC Berkeley, and Texas A&M University worked together on a high-throughput genetic screen to identify which part of the bacteria bacteriophage viruses were targeting.
Research Interests
Our current research focuses on the development of next-generation microscopy and spectroscopy tools to address pressing questions in cell biology. We developed a new method to enable electron microscopy, and correlated super-resolution microscopy, of fully hydrated animal cells by employing graphene, a single-atom-thick carbon meshwork, as the thinnest possible impermeable and conductive membrane to protect cells from vacuum. We also recently introduced and realized the new concept of spectrally resolved, “true-color” super-resolution microscopy, in which we synchronously obtain the fluorescence spectra and positions of millions of single molecules in densely labeled cell samples in minutes. Based on this approach, we have demonstrated in our work high-quality multicolor 3D super-resolution microscopy for 4 dyes only 10 nm separated in emission wavelength.
Recent Publications
Related News
Ke Xu Receives NIH New Innovator Award
Ke Xu, a faculty scientist in Molecular Biophysics and Integrated Bioimaging, has been awarded a NIH Director’s New Innovator Award as part of the National Institutes of Health's High-Risk, High-Reward Research program. Supported by the NIH Common Fund, these grants catalyze exceptionally innovative biomedical research with transformative potential from early career investigators who have never received an NIH grant before. An assistant professor of chemistry at UC Berkeley, Xu develops new physical and chemical tools to explore biological, chemical, and materials systems at the nanoscale with extraordinary resolution and sensitivity. He takes a multidimensional approach that integrates advanced microscopy, spectroscopy, cell biology, and nanotechnology. Xu is among 89 New Innovator Award recipients for 2018. Each grant comes with $1.5 million in direct funds for five years. Read more from UC Berkeley News.
Super-Resolution Microscopy Reveals Fine Detail of Cellular Mesh
Ke Xu, faculty scientist in the Molecular Biophysics and Integrated Bioimaging Division, used super-resolution microscopy to reveal the geodesic mesh supporting red blood cells, enabling them to be sturdy yet flexible enough to squeeze through narrow capillaries as they carry oxygen to tissues. The discovery could help uncover how malaria parasites hijack this mesh and destroy red blood cells. Read more at UC Berkeley News.
The Strings That Bind Us: Cytofilaments Connect Cell Nucleus to Extracellular Microenvironment
New images of structural fibers inside a cell appear in a study featured on the cover of the Journal of Cell Science special issue on 3D Cell Biology, published this month. The images, obtained by scientists in the Biosciences Area, show thread-like cytofilaments reaching into and traversing a human breast cell’s chromatin-packed nucleus. 
It provides the first visual evidence of a physical link by which genes can receive mechanical cues from its microenvironment.
The work leading up to the images began in the early 1980s when Biological Systems & Engineering's Mina Bissell proposed the idea that gene expression and cell fate were dependent on their physical surroundings called extracellular matrix. The images were captured by Manfred Auer, staff scientist, and Ke Xu, faculty scientist, both in the Molecular Biophysics & Integrated Bioimaging Division. Read more at the Berkeley Lab News Center.
Divisions
Molecular Foundry
Secondary Affiliation:
Molecular Biophysics and Integrated Bioimaging
- Structural Biology
Research Interests
Beamline instrumentation, macromolecular crystallography and X-ray footprinting technique development.
Recent Publications
Related News
Biosciences FY26 LDRD Projects
The Laboratory Directed Research and Development program at Berkeley Lab produces cutting-edge research for the DOE and the nation. Read about the Biosciences Area–led projects and multi-Area collaborations with Biosciences co-investigators receiving funding this cycle.
Towards a New Framework for Radiation Cancer Treatment
Biosciences Area researchers have developed a novel approach for studying the FLASH effect, an emerging frontier in radiation oncology.
Gemini Beamline Banks First Protein Structure
A protein structure obtained at Beamline 2.0.1 (“Gemini”) at the Advanced Light Source (ALS) has recently been published in the literature and deposited into the Protein Data Bank—two significant firsts for this beamline.
Research Interests
Deepti Tanjore is Director of the ABPDU and Head of the Department, Process Engineering and Analytics at Berkeley Lab. She interfaces with several scientists from industry, academia, and start-ups in strategizing and resolving scale-up challenges for their synthetic biology-based technologies. Her research focuses on developing self-driving bioreactor capabilities by modeling the impact of bioprocess conditions on microbial heterogeneity and developing in-line analytical tools for real-time adaptation of process development. She has a PhD from Penn State University in Biological Engineering, BTech from Andhra University in Chemical Engineering, and an MBA from Haas School of Business.
Recent Publications
Related News
Accelerating Science with Digital Twins
Researchers at ABPDU are developing a biological digital twin to model the scaled production of lipids for jet fuel from engineered microbes.
Science Power-up: Where Biomanufacturing Can Take Us This Century
Scientists at the ABPDU are perfecting the science of scale up — transforming biological breakthroughs into commercial products for use in our everyday lives, and growing an industry that can help secure our supply chain and create generational jobs.
The ABPDU: A Catalyst for the U.S. Biomanufacturing Sector
The ABPDU helps biomanufacturing companies scale up innovative biotechnologies and transition them to the marketplace.
Research Interests
My research group at the Joint BioEnergy Institute is focusing on identifying potential drop-in biofuels and building and optimizing the metabolic pathway to produce these target fuels in microbes. Our major target fuels are isoprenoid-based compounds that can be alternative to gasoline, jet, and diesel fuels. To improve fuel production titer and yield, we study the producing host and fuel biosynthetic pathway intensively using various advanced analytical tools such as targeted proteomics, metabolomics, and transcriptomics; and engineer the metabolic pathway in the producing host using synthetic biology tools.
Recent Publications
Related News
AI, Automation, and Biosensors Speed the Path to Synthetic Jet Fuel
Two breakthrough strategies are rewriting the playbook for designing microbes that make synthetic aviation fuels.
Congratulations to Biosciences Area Director’s Award Recipients
Numerous Biosciences Area personnel are among the 2021 Berkeley Lab Director’s Awards honorees. This annual program recognizes outstanding contributions by employees to all facets of Lab activities. A complete list of winners can be found here. The 10th annual Director’s Awards ceremony will take place on November 18 at noon.
Biosciences Area Projects Receive Technology Commercialization Funding Awards from Department of Energy
Two projects from the Biosciences Area were awarded $1 million from the DOE’s Technology Commercialization Fund (TCF) to further collaborative research with industry partners. The research will enable rapid strain engineering for the production of biofuels and bioproducts from low-cost gas feedstock, and produce a new aviation biofuel precursor from cellulosic biomass.
Building: 978, Room 4128
Mail Stop: 978R4121
Phone: (510) 486-6754
NJHillson@lbl.gov
https://www.jbei.org/person/nathan-hillson/
Links
Research Interests
To develop and demonstrate experimental wetware, software, and laboratory automation devices that facilitate, accelerate, and standardize the engineering of microbes.
Recent Publications
No publications are available at this time.
Related News
Biological Systems and Engineering Division and Program Leadership Changes
Division Director Blake Simmons announced that, effective March 2, Chris Petzold will lead the Biodesign Department as Interim Head following Nathan Hillson’s departure. Petzold will also assume the role of Chief Information Officer for the Joint BioEnergy Institute, as announced by CEO Jay Keasling. Katy Christiansen will serve as the lead principal investigator of the Agile BioFoundry.
Foundational AI Models to Accelerate Biological Discovery
Berkeley Lab is helping build AI models for autonomous research that will enable prediction and precise design of biological systems.
Biosciences FY26 LDRD Projects
The Laboratory Directed Research and Development program at Berkeley Lab produces cutting-edge research for the DOE and the nation. Read about the Biosciences Area–led projects and multi-Area collaborations with Biosciences co-investigators receiving funding this cycle.
Research Interests
Metagenomics, Microbial Genomics, Microbial Diversity, Microbiology, Bioinformatics
Recent Publications
Related News
Taking Stock of the Known and Unknown Microbial Space
In Science Advances, JGI researchers have taken stock of the current state of microbial genomic biodiversity. Using publicly available genome sequence data generated over the past three decades, their study assesses what fraction of the microbial diversity we know about, and proposes a path forward to curate and cultivate what is still unknown.
University of Duisburg-Essen Delegation Explores Collaborative Opportunities with Lawrence Berkeley National Laboratory
Building on a Memorandum of Understanding signed between UDE and Berkeley Lab researchers, a kick-off meeting focused on future collaborations in the fields of genomics, structural biology, bioimaging, and water research.
Doubling Down on Known Protein Families
Through a novel approach detailed in Nature, a massive computational analysis of microbiome datasets by the JGI focuses on unveiling protein functional diversity.
Divisions
Molecular Biophysics and Integrated Bioimaging
- Structural Biology
Secondary Affiliation:
Biological Systems and Engineering
- BioEngineering & BioMedical Sciences
Research Interests
Applied Mathematics
Machine Learning
Scattering
Crystallography
Synchrotron radiation
Free Electron Laser
Recent Publications
Related News
Biosciences FY26 LDRD Projects
The Laboratory Directed Research and Development program at Berkeley Lab produces cutting-edge research for the DOE and the nation. Read about the Biosciences Area–led projects and multi-Area collaborations with Biosciences co-investigators receiving funding this cycle.
University of Duisburg-Essen Delegation Explores Collaborative Opportunities with Lawrence Berkeley National Laboratory
Building on a Memorandum of Understanding signed between UDE and Berkeley Lab researchers, a kick-off meeting focused on future collaborations in the fields of genomics, structural biology, bioimaging, and water research.
Congratulations to Biosciences Area Director’s Award Recipients
Numerous Biosciences Area personnel are among the 2021 Berkeley Lab Director’s Awards honorees. This annual program recognizes outstanding contributions by employees to all facets of Lab activities. A complete list of winners can be found here. The 10th annual Director’s Awards ceremony will take place on November 18 at noon.
