Principal Investigator

Professor | Principal Investigator
aparkin@berkeley.edu Profile
Adam Arkin is the Dean A. Richard Newton Memorial Professor in the Department of Bioengineering at the University of California, Berkeley and Senior Faculty Scientist at the Lawrence Berkeley National Laboratory. He and his laboratory develop experimental and computational technologies for discovery, prediction, control and design of microbial and viral functions and behaviors in environmental contexts.
He is the chief scientist of the Department of Energy Scientific Focus Area, ENIGMA(Ecosystems and Networks Integrated with Genes and Molecular Assemblies, http://enigma.lbl.gov), designed to understand, at a molecular level, the impact of microbial communities on their ecosystems with specific focus on terrestrial communities in contaminated watersheds. He also directs the Department of Energy Systems Biology Knowledgebase (KBase) program: (http://kbase.us) an open platform for comparative functional genomics, systems and synthetic biology for microbes, plants and their communities, and for sharing results and methods with other scientists. He is director of the newly announced Center for Utilization of Biological Engineering in Space which seeks microbial and plant-based biological solutions for in situ resource utilization that reduce the launch mass and improves reliability and quality of food, pharmaceuticals, fuels and materials for astronauts on a mission to Mars. Finally, he is the Co-Director of the Berkeley Synthetic Biology Institute, which brings together U.C. Berkeley and Lawrence Berkeley National Laboratory Scientists with Industry Partners to forward technology and applications for sustainable biomanufacturing.
Administrator

Sr. Administrator
gaterry@lbl.gov
Gwyneth Terry is a senior administrator supporting Adam Arkin and his laboratory at Berkeley Lab and University of California, Berkeley. She has a BSc in geology from Cal State East Bay. She assists lab personnel with the UCB and LBL bureaucracy and helps moves science forward.
Project Managers

Project Coordinator
Project: PROTECT
Ezgi Booth is the PROTECT Project Coordinator, leveraging her BA in genetics and PhD in computational biology to excel in scientific project management. She bridges research with operations by overseeing administrative, reporting, procedural, and legal processes, while enhancing communication among multidisciplinary teams to support PROTECT’s objectives.

Project Manager
Project: ENIGMA
Astrid Terry is the ENIGMA Project Manager. Her role is to monitor and enable progress of each project and investigator in the program and closely manage the budget. She coordinates and communicates updates, reports & publications to DOE. A major goal is identifying opportunities for collaboration, and increasing awareness of capabilities and resources available across the Science Focus Area.
Staff Scientists

Project Scientist
Project: PROTECT & CUBES
Jake received his Bachelor’s degree in Genetics from the University of Wisconsin-Madison where he was introduced to the world of scientific research through the study of the evolution of gene expression regulation in the yeast Saccharomyces cerevisiae. Upon graduation, Jake began his graduate work in Marine Studies at the University of Delaware where he studied the regulation of energy metabolism in green sulfur bacteria (the Chlorobiaceae). Being a microbiologist that had always admired synthetic biology, and one that was enamored with space exploration, Jake joined the Arkin Lab at the University of California-Berkeley as a postdoc to pursue applications of microbial engineering to space exploration. Jake’s research interests include environmental microbiology, microbial physiology/systems biology, genetics, synthetic biology, and space bioengineering.

Data Scientist
Project: PROTECT
Spencer is a Data Scientist at UC Berkeley working with Dr. Adam Arkin on the ARPA-H funded PROTECT and ASMA initiatives. He joined the Arkin Lab to help build a structured, scalable data infrastructure to support multi-omic microbiome research in the human airway. His background spans astronomy, mathematics, bioinformatics, and machine learning, with experience integrating genomic and lifestyle data for predictive health modeling. Prior to joining the lab, he co-founded and led the bioinformatics division at a startup focused on personalized genetic health, where he developed risk prediction models for over 200 diseases.
In the Arkin Lab, Spencer is developing reproducible pipelines, metadata standards, and automated QC workflows for multi-modal datasets—including isolate genomics, metagenomics, metatranscriptomics, and cytokine data—to enable better understanding of host-microbiome interactions in airway health and disease. He is particularly interested in the intersection of synthetic microbial communities, host-pathogen exclusion, and data-driven hypothesis generation. Above all, he’s fascinated by science and deeply enjoys the research process—from the smallest technical challenge to the biggest biological questions.

Research Scientist
Project: ENIGMA
Lauren is interested in how we can use the latest sequencing technology to study environmental microbial communities, particularly nanopore sequencing. She studied mathematical biology and bioinformatics at UC Davis, and received her PhD in Biomolecular Engineering and Bioinformatics from UC Santa Cruz. Ever since she started doing research, Lauren has sought to integrate quantitative and computational methods with experimental biology. Currently, her projects include dissecting plant-microbe interactions with transposon mutant libraries, using synthetic microbial communities to understand the ecological and genetic factors of microbial interactions, and metagenomics of environmental microbes. Her ultimate goal is to be able to predict microbial interactions and community assembly from genome content and environmental measurements. In addition to her scientific work, Lauren is the co-secretary for the Women Scientists and Engineers Council at LBNL and loves doing photography, playing the ukulele, and illustrating with graphic arts.

Research Scientist
Project: ENIGMA
Thanks to cheap DNA sequencing, we are slowly starting to understand the incredible diversity of bacteria. Morgan Price builds 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.

Project Scientist
Project: CUBES
Kyle Sander earned a B.S. in Chemical Engineering and an M.S. degree in Biological and Ecological Engineering studying life cycle effects of algae production for fuels and co-products. He also investigated rapid sand filtration as an algal dewatering process step and enzymatic degradation of, and simultaneous saccharification and ethanol production from of algal cell biomass. Kyle earned his PhD from the University of Tennessee, Knoxville conducting his thesis research within the BioEnergy Science Center at Oak Ridge National Laboratory. Kyle characterized regulatory genes and related cellular redox in two candidate lignocellulolytic, ethanol-producing biocatalysts; Clostridium thermocellum and Caldicellulosiruptor bescii. Basic redox metabolism was characterized yielding an expanded view of redox metabolism in these organisms and effected bioprocessing improvements through genetically modifying redox-related regulation. A genotype-phenotype relationship was similarly identified between the FapR local fatty acid biosynthesis repressor and tolerance to elevated osmolarity conditions, a highly complex, bioprocess-limiting, and difficult-to-engineer trait in C. bescii. As a member of the CUBES project, Kyle studies unbalanced growth coupling of polyhydroyalkanoate production in species of Cupriavidus, and rhizosphere microbiome interspecies interactions toward improving reliability of probiotic species ingress in diverse community settings.
Postdoctoral Researcher

Postdoctoral Researcher
Project: PROTECT
Sun-Young is a postdoctoral researcher in the Arkin Lab at the University of California, Berkeley. He received his Ph.D. in Microbiology from the University of Texas at Austin, where he studied the molecular mechanisms of microcins, including their export, antibacterial activity, and self-immunity systems. At the Arkin Lab, he is involved in the ARPA-H PROTECT project, where he focuses on isolating microbial pathogens and commensals from the lower respiratory tract. He is also leading the phenotypic characterization of these isolates, including profiling antibiotic resistance, carbon source utilization, and antagonistic interactions against lung-infecting pathogens. His research interests lie in understanding microbial interactions within the oral and lower respiratory tract microbiota and in discovering novel antibacterial compounds and mechanisms.

Postdoctoral Researcher
Project: ENIGMA
Shekhar obtained his B.Tech and M.Tech in Chemical Engineering from the Indian Institute of Technology, Bombay in 2014. He discovered the joy of research through an internship in computational fluid dynamics, before moving into the field of systems biology with research on modeling the human cholesterol metabolism. After working as a Project Engineer for 9 months on fermentation technology at the DBT-ICT at Mumbai, India, Shekhar started his Ph.D. research at the University of Illinois, Urbana-Champaign in Chemical & Biomolecular Engineering. His doctoral research, in the lab of Huimin Zhao, involved the interdisciplinary application of computational modeling, CRISPR editing and mass spectrometric techniques to design rational strategies for metabolic engineering in yeast. Shekhar joined the Arkin Lab in September 2023 as a postdoctoral researcher with an eye on employing the toolkits of metabolic engineering for improving predictive microbial ecology within the ENIGMA project. Shekhar’s goal is to pursue advances in research that inform strategies for mitigating the adverse effects of anthropogenic climate change. In his spare time, Shekhar volunteers with the Citizen’s Climate Lobby, plays the guitar, goes rock climbing, does some gardening, and tries to catch up to an ever-growing list of books to read.

Postdoctoral Researcher
Project: NSF EDGE
lucasmoriniere@berkeley.edu
Lucas Morinière joined the Arkin Lab in April 2023 as a postdoctoral researcher in the EDGE project to work on phage-host interactions under Adam Arkin’s and Vivek Mutalik’s supervision. He completed his education at the University Claude Bernard Lyon 1 in France by earning his PhD in 2021 at the Microbial Ecology Lab of Lyon (UMR 5557). His thesis research was focused on the
ecology, genomics, and taxonomy of Xanthomonas hortorum pv. vitians (Xhv), the causal agent of the bacterial leaf spot of lettuce disease. As part of his research, he first conducted a thorough polyphasic taxonomical study which allowed to reshape the entire X. hortorum species. Then, he used transposon insertion sequencing (TnSeq) and comparative genomics to describe the in vitro and in planta essential genomes of this non-model plant-pathogenic bacterium. Afterwards, he pursued as a Temporary Lecturer and Research Assistant (ATER) for a year and used TnSeq to elucidate the molecular determinants of the interaction between Xhv and a new lytic phage. As part of the new NSF funded project, his present research in the Arkin Lab in collaboration with Mutalik lab focuses on uncovering the genetics of phage-host interactions by submitting large collections of Escherichia coli and coliphages to high-throughput susceptibility assays and high-throughput genetic screens (RB-TnSeq, DubSeq) based on a machine-learning-driven experimental workflow.

Postdoctoral Researcher
Project: BRAVE Phage Foundry
Avery is a postdoctoral researcher in the Environmental Genomics & Systems Biology Division at LBNL. Avery completed his BSc at the University of Toronto in Genetics and Geosciences in 2015 and his PhD at the University of British Columbia in the Genome Sciences and Technology program in 2023. His doctoral research related to the development of high-throughput screening paradigms for the study of photosynthetic microorganisms, as well as the application of computational tools to investigate microbial community structure and dynamics in natural and engineered environments, including photobioreactors and the human lung. In his role in the Arkin lab, Avery is using statistical and machine learning approaches to predict phage-host interactions with the goal of selecting or engineering phages to target specific human pathogens.
Staff

Research Associate Staff
Project: ENIGMA
Jennifer Kuehl is a staff research associate that has worked for LBNL since 2002. She graduated from the University of Missouri- St.Louis with a BS in Biology. After graduation she drove to California for a vacation and stayed to start a life there. Her career at the lab started at the Joint Genome Institute in the Sanger sequencing production line as they were completing the human genome. She then transferred to the evolutionary genomics group at the JGI where the research was focused on using plasmids genomes for reconstructing the evolutionary history of everything from lettuce to worm lizards to stony corals to stalk eyed flies. In 2008, she started in the Arkin lab constructing a barcoded mutant library in the non-model sulfate reducing bacteria, Desulfovibrio alaskensis G20 for improving gene annotations. Currently she is working on pipeline to identify microbial interactions important for fitness in a given growth condition using high throughput enrichment culturing and 16s amplicon community sequencing. She feels fortunate to be able to work with and develop friendships with so many interesting Berkeley students from around the world.

Research Assoc Sr
Project: ENIGMA
Hira Panna Lesea is a Research Associate in the Environmental Genomics and Systems Biology Division at Lawrence Berkeley National Laboratory working on isolating bacteria from groundwater and sediment from Oak Ridge National Laboratory that have been identified as important to the field site’s community function. She is measuring the growth phenotypes of ENIGMA isolates using a high throughput characterization pipeline under conditions relevant to the field site, such as low pH and high nitrate, in addition to providing high quality genomes of the characterized isolates. She is working with the Arkin lab on the ENIGMA project because of her interest in how microbes affect contaminated ecologies and her experience with studying the microbiome of the domestic cat at UC Davis. In addition to her passion for the unseen, she is also a chef and avid music lover.

Research Associate
Project: CUBES II
Cassandra is a motivated and curious senior undergraduate in the Bioengineering department at UC Berkeley with a specific focus on cell and tissue engineering. She has previously worked in immunology and polymer labs where she formulated and evaluated antibody-conjugated lipid nanoparticles as well as contributed to the standardization of nanoindentation as a modality for retrieval analysis of total knee replacement polymer components respectively. Through her coursework and research experiences, she has developed a strong interest in the field of synthetic biology which she hopes to utilize to solve problems caused by the climate crisis. Currently, she is working on the NASA CUBES to engineer Spirulina for pharmaceutical and flavor production with applications for supporting human exploration of space. In her free time, you can catch her at the roller rink, or on a hike in the Berkeley hills.
Graduate Students

Graduate Student
Project: ENIGMA
Cameron is a graduate student in Plant & Microbial Biology Dept and advised by Dr. Arkin

Graduate Student
Project: ENIGMA/BioDesign/MIM
Josh is a graduate student in the Dept. Comparative Biochemistry. He is working with Dr. Ruoshi Yuan on the time-lapse imaging project.

Graduate Student
Project: ENIGMA
Twitter(X)
Allison is an NSF fellow and graduate student in Molecular & Cell Biology. She obtained her BA in biology at Columbia University in 2020 while doing research on host-pathogen interactions and cell signaling in the Dietrich and Haeusler labs. As a student in the Arkin Lab, Allison is investigating bacterial colonization mechanisms in the context of the mammalian host gut. In her free time, Allison enjoys doing crosswords and practicing her German.

Graduate Student
Project: PROTECT/CUBES
Gwyneth graduated from UC Berkeley in 2020 where she did nearly 3 years of research and a fellowship in reproductive neuroendocrinology, chronobiology, and cellular biology. She then transitioned to the UCSF-Gladstone Institute of Neurological Disease where she pursued novel research into the contributions of cellular energy metabolism and bioenergetic failure to neurodegenerative disease pathogenesis. Following this, she worked as a Senior Research Associate at Conception Biosciences where she focused on the development of biotechnologies to turn stem cells into viable eggs for individuals and couples to overcome physiological, age-based, and sexuality-based barriers to reproductive success. With NASA CUBES and the Arkin Lab, Gwyneth is developing innovative approaches to build on the Arkin Lab’s recent successes engineering Spirulina for nutrient, pharmaceutical, and flavor production with applications for supporting human exploration of space. She is devising innovative ways to further improve the efficiency of engineering this previously recalcitrant organism and determining the best routes for metabolic engineering of these critical products. She is also interested in pursuing questions surrounding human physiology and reproduction in space with the goal of improving health outcomes for astronauts and space travelers both during missions and upon return to Earth. When she’s not in the lab, Gwyneth loves to spend time with her puppies—Willow and Pandora—and enjoys playing guitar and reading novels. She also fancies herself an amateur shark diver and is on the Board of Directors for a literacy nonprofit.

Graduate Student
Project: MTV/AI SynBio
Heather is a graduate student in the Chemical Biology program at UC Berkeley. She earned her BS in Biochemistry at UC Santa Barbara while working with Dr. Kalju Kahn to benchmark density functional methods for the prediction of gas-phase Vibrational Circular Dichroism spectra. She worked with Dr. David Bernstein on the Consortium for Monitoring, Technology and Verification Integrated University Program (IUP): Enabling Technologies and Innovation (ETI) & Monitoring, Technology and Verification (MTV). Dr. Arkin’s project is data integration to assist field sampling, with final model delivery. Heather and David worked on modeling the field data. They were responsible for collaboration between the groups of University of California, Berkeley, MIT and University of Tennessee/Oak Ridge National Laboratory.

Graduate Student
Project: KBase
Kate is a PhD student in the UC Berkeley–UCSF Graduate Program in Bioengineering, co-advised by Dr. Adam Arkin and Dr. Paramvir Dehal. Her research on the KBase project involves developing agentic AI models to improve microbial gene annotation by leveraging a diverse set of online resources. Before her PhD, she was raised in Los Angeles, CA, then earned her B.B.A. in Entrepreneurship and a Chemistry minor from the University of Miami, FL., followed by her M.Eng. in Artificial Intelligence from the University of Cincinnati, OH. Her prior work has included developing mass spectrometry assays in the Immunochemical Core Lab at Mayo Clinic in Rochester, MN, serving as an engineer on strategic aerospace projects in the Defense and Intelligence Solutions Division at Southwest Research Institute, and teaching undergraduate coursework on human sensation and perception at Sinclair Community College in Dayton, OH. In addition to her studies, Kate serves as Co-President of Biotech@Berkeley, an organization that connects and educates graduate students on opportunities for innovation in the life sciences. She is driven by an insatiable curiosity about the world, and by the belief that science and technology together hold the key to unlocking nature’s greatest mysteries.
Undergraduate Students

Project: CUBES
Undergraduate Hue Ahnn to work with Dr. Hilzinger to help develop innovative approaches to build on our recent successes engineering the cyanobacterial ‘superfood’, Spirulina (Arthrospira platensis) for production of pharmaceutical, nutrients, and flavors with application to supporting human exploration of space.

Project: PROTECT
Allie (Sarah) Cabiles is an undergraduate at UC Berkeley studying bioengineering. She is working with Dr. Jacob Hilzinger and Dr. Sun-Young Kim on PROTECT. Her interests lie at the intersection of biochemistry and synthetic biology, and she hopes to pursue a career in the biotech industry focused on harnessing these fields within translational medicine.

Malavika Garimella is a junior at UC Berkeley, studying Molecular & Cell Biology and Business Administration. She is working with Gwyneth Anne – Hutchinson on PROTECT because of her previous work with mammalian tissue culture and is interested in studying how cellular mechanisms can be leveraged for therapeutic discovery, particularly in the context of genetic disorders and antimicrobial resistance. Her experience spans genomic therapeutic research at MD Anderson Cancer Center and integrative biology research at UC Berkeley.

Malli is a senior at UC Berkeley studying both Molecular and Cellular Biology (MCB) as well as Business Administration. She is working under Gwyneth Hutchinson on the PROTECT project, focusing on tissue engineering with lung epithelia. Malli is interested in studying immunology and therapeutics development.

Snigdha is a freshman at UC Berkeley studying Genetics and Plant Biology. She is working with Dr.Sander on the CUBES project because of their work with the growth coupling of polyhydroxyalkanoate production in species of Cupriavidus for applications in space exploration. She is interested in studying the genetic engineering of metabolic pathways in bacteria and algae, especially in the broader context of sustainability.

Project: ENIGMA
Luz Arias is a sophomore at UC Berkeley studying bioengineering. She is working with Hira Lesea on the ENIGMA project exploring the impact of microorganisms on polluted ecosystems. Outside of the lab, she’s occupied with cooking and skateboarding.

Yihao is a first year undergraduate student at UC Berkeley studying Molecular Cell Biology. He is working with Jiaqi Huang on the C. necator imaging project. Through his work at this lab, Yihao is interested in exploring investigating diversity generating mechanisms in bacterial isolates.

Project: Phage Foundry
Jonathan Ngai is a senior at UC Berkeley studying Data Science and Political Science. He is working with Dr. Avery Noonan to build machine learning models for the prediction of phage-host interactions. Jonathan’s interests include deep learning, computer science, and multidisciplinary research approaches, and will apply his experience to support the objectives of the Phage Foundry.

Project: Phage Foundry
Cristina Prieto is a sophomore, studying both Molecular and Cell Biology and Data Science here at Berkeley. She works with Dr. Avery Noonan particularly the work conducted in KBase and biodesign.

Project: PROTECT
Erin Song is a sophomore at UC Berkeley studying Bioengineering. She is working with Gwyneth Hutchinson-Ramirez (PhD student) because of previous work with data collection/analysis, research methodology, and medical devices like fMRI as an undergraduate researcher at the Psychology Department Computational Neuroscience Lab. She is gaining experience in mammalian tissue culture and other molecular biology techniques/skills. She is growing her skill set as a bioengineer. She is expanding her expertise in lab techniques/technologies and contribute to the lab’s pioneering work in tissue culture and engineering!

Hanen is an undergraduate at UC Berkeley studying Bioengineering. He is interested in utilizing computational and synthetic biology to reduce plastic pollution, develop new drugs and diagnostics, and improve food production and the environment, especially in poorer regions of the world. At CUBES, he is focusing on engineering microbes to produce bioplastics useful for applications in space missions as well as on Earth.
After undergrad, Hanen plans to pursue a PhD in bioengineering or biotechnology to grow as a scientist. He aims to start a company one day focusing on using bioengineering to address environmental and food insecurity issues around the globe.

Luis is a Junior at UC Berkeley studying Bioengineering. He is working under Gwyneth Hutchinson on the PROTECT project, focusing on tissue engineering with lung epithelia. Luis is interested in pursuing a field in cell and tissue engineering.

CUBES
Justin Wahyudi is an undergraduate student at UC Berkeley studying Bioengineering. Justin is interested in exploring the field of synthetic biology and its applications in healthcare and pharmaceutical settings. He is working with Dr. Jacob Hilzinger on the CUBES project to help genetically engineer A. platensis for its potential applications in pharmaceutical production and supporting space exploration.

Xina Wang is a freshman at UC Berkeley studying chemical biology. She is working with Dr. Sanders on protein engineering for bioplastics production in space and is interested in how synthetic biology can enable human space exploration as well as how biosystems in nature can be engineered for applications in biomanufacturing and biomedicine.

Project: PROTECT
Sreshta is a sophomore at UC Berkeley studying Bioengineering and EECS. She is working with Dr. Jacob Hilzinger on Project PROTECT to genetically engineer P. Aeruginosa for antibiotic screening. Her interests lie in genetic engineering and computational biology.