arkinlab

Principal Investigator

Adam Arkin
Adam Arkin
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

Gwyneth Terry
Gwyneth Terry
Projects: KBase, ENIGMA, CUBES, BioDesign, IGI
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.


Program Manager

Astrid Terry
Astrid Terry
Affiliate
Projects: ENIGMA
AYTerry@lbl.gov  

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

Lauren Lui
Lauren Lui
Projects: ENIGMA
lmlui@lbl.gov  

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.


Vivek Mutalik
Vivek Mutalik
Collaborator
Projects: BioDesign, Phage
VKMutalik@lbl.gov  

Dr. Mutalik is a research scientist at Environmental Genomics and Systems Biology Division, Functional genomics Department, and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; and Principal Investigator at Innovative Genomics Institute. Dr. Mutalik works in the area of synthetic biology and functional genomics of diverse microbes and phages. Dr. Mutalik is currently working towards establishing Berkeley Phage Foundry, a unified facility for engineering phages and phage-like particles for diverse applications within Innovative Genomics Institute, Berkeley. Previously, Dr. Mutalik lead the BIOFAB project, the world’s first biological design-build facility in Emeryville, CA, funded by NSF. Dr. Mutalik received his PhD in Chemical engineering from the Indian Institute of Technology Bombay, India and was a Postdoctoral Fellow in Prof Carol Gross at University of California, San Francisco. Dr. Mutalik has three years of experience in the Biotechnology Industry in handling more than hundred kiloliter industrial fermentation units, bulk drug manufacturing and resource management. He has recently cofounded Felix Biotechnology, focused on accelerating the deployment of novel biotherapeutics targeting urgent microbial challenges in human health and beyond.


Morgan Price
Morgan Price
Projects: ENIGMA
mnprice@lbl.gov  

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.


Research Scientists

Software Engineer

Omree Gal-Oz
Omree Gal-Oz
Projects: BioDesign
ogaloz@lbl.gov  

Omree Gal-Oz is a software developer with the Arkin Laboratory at UC Berkeley/ LBNL. Throughout college he was primarily interested in mathematics and music, and found an intersection between them in software. Afterwards he tutored high-schoolers in math and software and taught piano privately before moving to Berkeley to work at the California Jazz Conservatory. He gained experience in software-oriented companies by writing software for Magisto and working on product development with Blue Cedar. He is currently working on integrating biology software into KBase and creating in-browser visual displays. Besides writing software, he still enjoys playing and producing music and can occasionally be found playing music in the wilderness.


Postdoctoral Researcher

Bradley Biggs
Bradley Biggs
Projects: ENIGMA
bbiggs@lbl.gov  

Bradley completed his B.S. in Chemical Engineering at the University of Southern California, where he worked on silicon-based optical biosensors. As his research interests evolved, he pursued an M.S. in Biotechnology at Northwestern University, and subsequently worked for a time at a metabolic engineering startup based in Cambridge, MA called Manus Bio. He later returned to Northwestern University to pursue his Ph.D. in Chemical Engineering working with advisor Keith Tyo in synthetic biology and metabolic engineering, with his thesis work focusing on engineering the soil bacterium Acinetobacter baylyi for applications in lignin upgrading. In the Arkin Lab, Bradley’s work focuses on integrating synthetic biology and systems biology approaches to the ENIGMA project, continuing to explore soil bacterium and their relevance to engineering applications and the environment.


David Bernstein
David Bernstein
Projects: BioDesign

David is a postdoctoral researcher in the Arkin Laboratory at UC Berkeley. He received his Bachelor’s degree in Mechanical Engineering from the University of Vermont. He then earned his PhD in Biomedical Engineering from Boston University working in the lab of Daniel Segrè where he developed computational approaches to study the metabolic properties of microbes and microbial communities. In the Arkin lab, he is focused on combining genome-scale metabolic modeling and machine learning to predict microbial phenotype from genotype. Outside of the lab, David enjoys spending time outdoors skiing (both downhill and cross-country) and hiking.


Jacob Hilzinger
Jacob Hilzinger
Projects: CUBES
jhilzinger@berkeley.edu  

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.


Yolanda (Yue) Huang
Yolanda (Yue) Huang
Projects: ENIGMA
yolandahuang@lbl.gov  

Yolanda is a postdoc in the Arkin lab and a Life Sciences Research Foundation (LSRF) fellow sponsored by Astellas Pharmaceuticals. She received her Bachelor’s from McGill University in Biochemistry. She completed her PhD in Chemical Biology with Emily Balskus at Harvard University where she characterized a new glycyl radical enzyme responsible for 4-hydroxyproline metabolism that is prevalent among gut anaerobes. In the Arkin lab, she is working to identify phage factors that influence bacterial physiology through multiple approaches – computational tools, data mining, and functional genomics. Outside of the lab, she can be found active in the outdoors, travelling, cooking, and filling up space with plants.


Kyle Sander
Kyle Sander
Projects: CUBES
kbsander@berkeley.edu  

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.


Fangchao Song
Fangchao Song
Projects: ENIGMA
fsong@lbl.gov  

Fangchao Song is a postdoctoral fellow in Arkin Lab at Lawrence Berkeley National Laboratory. He is working on droplet-based high throughput method to reveal bacterial interactions in complex microbial community and profile the microbial physiology in different nutrients and environments, under the project of Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA). Before joining the lab, Fangchao was a graduate student working on mathematical modeling of polymerization and biodegradable polymer manufacturing. In 2010, he started a new journey in the microbiology world during his Ph.D research on microbial biofilms and their antibiotic resistance. Since then, he is fascinated by the complexity and orderliness of microbiome, and enthusiastic about designing new method by combining experiments and modeling to better understand the function and dynamics of microbiome. Fangchao obtained his B.S. from Shandong University in 2003, M.S. from Zhejiang University in 2010, and Ph.D. from Syracuse University in 2016, all in Chemical Engineering. He wants to be a researcher and educator in the future.


Ruoshi Yuan
Ruoshi Yuan
Projects: ENIGMA
ruoshi_yuan@berkeley.edu  

Ruoshi Yuan is currently a postdoc researcher in the Arkin lab at UC Berkeley/LBNL. He obtained his PhD in 2016 at Shanghai Jiao Tong University, China, supervised by Dr. Ping Ao. Then he did postdoctoral research at Harvard Medical School with Dr. Johan Paulsson. Ruoshi’s research interests include stochastic and nonlinear dynamics, mathematical modeling of biological phenomena, microbial interactions, complex diseases, and synthetic biology. Besides theory, he also works on high-throughput microfluidic experiments to obtain single cell time series data.


Staff Research Associates

Jennifer Kuehl
Jennifer Kuehl
Projects: ENIGMA
jvkuehl@lbl.gov  

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.


Graduate Students

Allison Hung
Allison Hung
allison_hung@berkeley.edu   Twitter  

Allison is a graduate student in the department of 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.


Cameron Hearne
Cameron Hearne
Projects: ENIGMA

Cameron is a graduate student in Plant & Microbial Biology Dept and jointly advised by Drs. Mutalik and Arkin


Aaron Berliner
Aaron Berliner
Projects: CUBES
aaron.berliner@berkeley.edu  

Aaron Berliner is a Bioengineering graduate student in the Arkin Laboratory at UC Berkeley/UCSF. He studied bioengineering, control theory, and synthetic and systems biology at Boston University. In 2012, he began working as a research associate at the NASA Ames Research Center on projects involving 3D printing, bioelectrochemistry, and astrobiology. In 2013, he started as a research scientist in the Life Sciences group of Autodesk Research in San Francisco. At Autodesk, Aaron’s work ran the gamut from bioprinting, software engineering, synthetic virology, and DNA origami until 2016 when he moved back to space biology. Forming a partnership between UC Berkeley, Autodesk, and NASA Ames, Aaron began construction on Crucible, an open-source reactor for space synthetic biology experiments until 2017 when he started as a graduate student with Adam Arkin. He enjoys playing with his Mars-in-a-jar reactors. Aaron helped author the STRI grant that launched CUBES and is an NSF graduate fellow. His alternative scientific interests are terraforming and radiation biology. In his spare time, Aaron explores terraforming and space radiation


Kelsey Hern
Kelsey Hern
Projects: Phage
kelsey_hern@berkeley.edu  

Kelsey Hern is a Microbiology graduate student in the Arkin Lab at UC Berkeley. Kelsey completed her bachelors in Biochemistry at Simmons college in 2016. She went on to work at the Laboratory for Multiscale Regenerative Technologies at MIT designing nanotechnologies to understand, diagnose and treat infectious respiratory diseases. As a student in the Arkin lab, Kelsey is interested in using functional genomics approaches to better understand human respiratory pathogens and inform treatment. Outside of the lab, Kelsey works to develop strategies to address and dismantle racial inequities in STEM. In her free time she enjoys powerlifting, historical fiction and cooking Sunday dinner for her friends and family.


William Krinsman
William Krinsman
Projects: KBase, ENIGMA
williamkrinsman@lbl.gov  

William Krinsman is a PhD student from the Interdepartmental Group in Biostatistics at UC Berkeley working in the Arkin Laboratory at LBNL as a developer for KBase and data analyst for ENIGMA. William’s research focuses on developing novel computational methods for the statistical analysis of biological datasets. William majored in mathematics at Northwestern University, during which time William also studied at the universities TUM and LMU in the German city of Munich. Before moving to Berkeley, William was a Fulbright scholar for one year in the German capital Berlin. Afterwards, and prior to joining the Arkin Laboratory, William previously worked at LBNL’s supercomputing center NERSC and Computational Research Division (CRD), developing software to help scientists fully and easily access NERSC’s computing resources via interactive computing platforms from the open-source Jupyter project. William is fluent in German, as well as conversational in Russian and Spanish, and grew up in a household with two dogs and five cats.


Kelly Wetmore
Kelly Wetmore
Projects: ENIGMA, CUBES
kmwetmore@lbl.gov  

Kelly Wetmore is a graduate student in Adam Arkin’s lab at UC Berkeley with over 15 years of experience in microbial physiology and genetics before and during graduate school. She has been instrumental in developing a number of next-generation tools and protocols for microbial functional genomics. Kelly is supporting the CUBES team in applying these tools to optimize the core biomanufacturing microbes in physiologically more-or-less relevant conditions. She is also part of a large DOE environmental systems biology project in which she is developing a new technology to query high-throughput genetic interactions.


Research Associates

Undergraduate Students

Batu Akkas
Batu Akkas
batuakkas@berkeley.edu  

Batu is an undergraduate in the Bioengineering Dept. Batu works with Dr. Bernstein utilizing high-throughput genomics data and machine learning to improve the accuracy of genome scale metabolic modeling in predicting biological outcomes.


Dexter Lai
Dexter Lai
Projects: ENIGMA

Dexter works with Dr. Bradley Biggs on the cloning and testing of genomic fragments into bacterial strains to test for the activity of unknown genes. This work is part of the broader ENIGMA goals of understanding the metagenomic data gathered at the site and improving our ability to move from metagenomic DNA to practical biological function of the microbial communities.


Divya Sivanandan
Divya Sivanandan
Projects: CUBES

Divya is an undergraduate in the Bioengineering Dept. Divya is working with Dr. Hilzinger to screen Spirulina mutants as they are generated (gDNA preps, PCR, possible Illumina sequencing preps), and help develop better transformation methods for this organism.


Farrah Kaiyom
Farrah Kaiyom
CUBES
farrahk@berkeley.edu  

Farrah is a second year undergraduate student studying Bioengineering and Electrical Engineering and Computer Science. She is a member of CUBES project working under Aaron Berliner. Farrah is currently developing a model that simulates how metabolic rate of crew members fluctuate during space travel and extravehicular activity under varying conditions. She is also researching data for microbial biomanufacturing.


Gretchen Vengerova
Gretchen Vengerova
Projects: CUBES

Gretchen is an undergraduate in the Bioengineering Dept. She works with Aaron Berliner on CUBES project specifically Modeling a Martian Biomanufactury


Hanqiao	Zhang
Hanqiao Zhang
Projects: MTV Consortium for Monitoring, Technology and Verification
hanqiaoz@berkeley.edu  

Han is a senior undergraduate in the Bioengineering Dept. He works with Dr. Bernstein on mechanistic modeling and machine learning to monitor environmental contamination through genomics.


Jiaqi (Joshua) Huang
Jiaqi (Joshua) Huang
Projects: ENIGMA/BioDesign
joshuah2000@berkeley.edu  

Joshua is an undergraduate in the Bioengineering Dept. He is work with Dr. Ruoshi Yuan on the time-lapse imaging project.


Kim Pham
Kim Pham
Projects: CUBES

Kim Pham is an undergraduate in the Bioengineering Dept. She works with Dr. Jake Hilzinger to develop a pan-genome on the CUBES project


Kylie Akiyama
Kylie Akiyama
Projects: CUBES
kylie.akiyama@berkeley.edu  

Kylie Akiyama is a second-year bioengineering undergraduate at UC Berkeley with an interest in the convergence of synthetic biology and space exploration. She is currently within the FPSD division of CUBES, working with Dr. Jake Hilzinger to improve the group’s capacity to metabolically engineer A. platensis for small molecule production.


Sofia Milian
Sofia Milian
Projects: ENIGMA

Sofia Milian is an undergraduate student attending Berkeley City College (BCC). Works on ENIGMA project assisting the researchers in the preparation of material. Due to graduate from BCC in the fall of 2023 then transfer to a four-year university, to pursue career in BioTechnology


Davian Ho
Davian Ho
Projects: BioDesign, ENIGMA, CUBES
davian@berkeley.edu  

Davian is an undergraduate student interested in bioengineering and EECS. He previously worked on extracellular contractile injection systems, and now investigates phages in the gut microbiome and makes vector art for synthetic biology. Davian also a member of CUBES, where he is developing the interface for space resource modeling software.


Isaac Lipsky
Isaac Lipsky
Projects: CUBES
isaaclipsky@berkeley.edu  

Isaac Lipsky is a third year undergraduate student at UC Berkeley studying environmental science and public policy. In concert with Aaron Berliner, he is working on developing cost-benefit metrics for Mars surface operations. His interests include planetary science and the tantalizing prospect of Martian terraforming.