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, PRANA, MIM, MTV, BioDesign, TrIP
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

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.


Manoshi Sen Datta
Manoshi Sen Datta
Manoshi is a computational microbial ecologist interested in harnessing the power of microbial consortia for sustainability.  During her academic training, Manoshi explored how microscale eco-evolutionary dynamics in wild microbial ecosystems drive ecosystem-level properties. She employed a variety of approaches, including novel experimental model systems (with Otto Cordero), mathematical modeling of laboratory ecosystems (with Jeff Gore), and comparative genomics of wild bacteria (with Martin Polz and Roy Kishony).  Manoshi then joined Boost Biomes, an agtech start-up, where she developed data science approaches to accelerate microbial interaction discovery in complex soil communities.  In the Arkin Lab, she aims to combine her expertise in computational genomics and data science to design synthetic microbial consortia for bioremediation of nitrate and heavy metals.

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.


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 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.


Cameron Hearne
Cameron Hearne
Projects: ENIGMA

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


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

Joshua is a graduate student in the Dept. Comparative Biochemistry. He is working with Dr. Ruoshi Yuan on the time-lapse imaging project.


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.


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

Gwyneth Hutchinson
Gwyneth Hutchinson

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.


Hira Panna Lesea
Hira Panna Lesea

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.


Undergraduate Students

Asa Garner
Asa Garner

Asa Garner is a Sophomore studying Mechanical Engineering at Cal. He is a member of the CUBES project and is working under Aaron Berliner to study offworld nuclear engineering & develop methods to additively manufacture fissile material. He is also a lead for the Cal liquid rocket propulsion group ‘Space Enterprise at Berkeley’


Cameran Casale
Cameran Casale

Cameran Casale is a second year undergraduate student at UC Berkeley studying bioengineering. She is currently working with Aaron Berliner on the CUBES project. Through her work at this lab, Cameran is interested in exploring different biological applications within space systems, such as the utilization of biologically derived materials in the development of nanoscale devices.


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.


Isra Raza
Isra Raza
isra.raza@berkeley.edu  

Isra is a rising senior undergraduate at UC Berkeley in Environmental Sciences. She is working with Dr. Bradley Biggs on ENIGMA to conduct research focusing on pairwise microbial interactions under low pH and anaerobic conditions, with aims of applying this to broader biological modeling efforts.


Jasmine Escobedo
Jasmine Escobedo
ENIGMA

Jasmine is an undergraduate bioengineering major at UC Berkeley. She works with Dr. Bradley Biggs using genomic fragments to analyze the function of particular bacterial enzymes. This involves genetic recombination and cultivation of bacteria to study the observed behavior 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 function of the microbial communities.


Joyleen Abou Hamad
Joyleen Abou Hamad

Joyleen is a freshman studying Aerospace Engineering (part of the inaugurating class) at UC Berkeley. She will work with Dr. Aaron Berliner a postdoc in the Arkin Lab on the development of Space Bioprocess Engineering metrics involving sustainability and supportability.


Katie Sie
Katie Sie

Katie is an undergraduate studying Bioengineering and Electrical Engineering and Computer Science at UC Berkeley. She is mentored by Cameron Hearne and Dr. Mutalik. Her focuses will be to use phage isolation techniques to optimize the engineering of phage-like molecules.


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.


Phillipe Wiederkehr
Phillipe Wiederkehr
Phillipe Wiederkehr is a sophomore bioengineering student at UC Berkeley with a major emphasis in synthetic biology. His interest in microbiology is tailocins, which he hopes could be utilized to revolutionize medicine in the future. He is very interested in just how precise bacteria-tailocin interactions are, and how surface proteins on a cell can have counter-intuitive effects on such events. The overall complexity of viruses interests him, and he will be able to contribute to a greater understanding of their interactions with cells.
He will assist with phage-related projects. He has done biological research since high school and co-authored a paper on the effects of cannabinoids on the brain that was published in the Journal of Investigative Medicine in 2019. He is also involved with Berkeley iGEM, a club focussing on synthetic and computational biology.

Rahil Shaik
Rahil Shaik

Rahil Shaik is a second-year chemical engineering undergraduate at UC Berkeley with an interest in studying manufacturing automation, battery materials, and semiconductor design. He is working with Dr. Kyle Sander to develop process models and 3D design modeling.


Shobhin Logani
Shobhin Logani

Shobhin Logani is a sophomore at UC Berkeley studying Molecular and Cell Biology, and is working with Kelsey Hern on engineering probiotic biosensors for detecting respiratory disease. He is interested in studying functional and comparative genomics, and his research interests lie in manipulating natural biological systems to address issues in human and environmental health. He is also passionate about making new biotechnologies more accessible and cost-effective.


Skyler Chan
Skyler Chan

Skyler Chan is studying Electrical Engineering and Computer Science at UC Berkeley, and he has wanted to become an astronaut since he was 3. In high school, he learned how to fly gliders, and was involved in various student-led space organizations. One of his goals is to make humanity an interplanetary species within our lifetime, and he joined CUBES to advance this mission. Currently, he builds in the Systems Design and Integration Division of CUBES. He is interested in exploring sustainable design on Mars, such as, how to build the first self-sufficient Martian cities. To Skyler, the idea that the choices we make designing the first Martian habitats today will have an impact on the future of humanity never gets old. In his free time, he can be found flying drones, PR-ing at the gym, and filming videos with friends.


Snigdha Jagarlapudi
Snigdha Jagarlapudi
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.

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


Sophia Bertoldo
Sophia Bertoldo

Sophia is a sophomore at UC Berkeley studying Molecular & Cellular Biology and Economics. She was initially drawn to CUBES because of their work with In-situ Resource Utilization and is interested in studying different forms of life in strenuous environments. In her free time she enjoys surfing, playing soccer and reading novels.


Spencer Zezulka
Spencer Zezulka
spencer_zezulka@berkeley.edu  

Spencer Zezulka is a senior at UC Berkeley studying MCB and astrophysics. He joined CUBES in October 2021 and is working with Aaron Berliner to computationally model compact object accretion disks in search of a potentially habitable region. Outside of his own aforementioned project, he assists his teammates at CUBES in data visualization and mathematical modeling. Aside from astrobiology and data science, Spencer is interested in music and education, and helps direct an organization providing free college admissions prep to communities in the Bay Area. In his spare time, Spencer likes to read, play piano, and game.


Yihao (Harry) Ma
Yihao (Harry) Ma

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.