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
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

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.


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.


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

Visiting Scholars

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.


Lucas Morinière
Lucas Morinière
Postdoctoral Researcher
Projects: 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.


Aaron Berliner
Aaron Berliner
Projects: CUBES
aaron.berliner@berkeley.edu   Profile   LinkedIn   Twitter  

Aaron Berliner is a Bioengineering postdoctoral 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
kelsey_hern@berkeley.edu  

Kelsey Hern completed her B.S. in Biochemistry in 2016 and went on to develop nanotechnologies to understand, diagnose and treat infectious respiratory diseases. She did her PhD work in Adam Arkin’s lab designing lower airway communities for protection against respiratory infection. As a Women in Enterprising Science Fellow at the Innovative Genomics Institute, Kelsey works to take the technology developed in her PhD and apply it to real-world clinical problems. Kelsey’s research interests include microbial interactions, synthetic biology and the development of living materials for improving health.


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


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.


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.


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

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

Cassandra Reyes
Cassandra Reyes

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 with Gwyneth Hutchinson and 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.


Eliana Matos
Eliana Matos

Eliana Matos is a highly motivated student pursuing her studies in Bioengineering, with a specific focus on cell and tissue engineering. She has experience working and volunteering with a myriad of organizations, which range from nonprofit hospitals to YMCA Camp Campbell. Here, she effectively applies her optimistic outlook and critical thinking skills. Throughout her undergraduate career, Eliana has explored a broad range of classes and clubs, delving into fields such as neurotechnology, health care advocacy, as well as advanced mathematics and sciences related to engineering. While she expresses an interest in the path towards medical school, she remains fascinated by the multitude of opportunities that bioengineering could potentially offer her. For instance, during her first year of college, she co-authored a research paper on the potential for bioengineering in space exploration, an experience that utterly astounded her. The prospect of integrating her major with space exploration filled her with an exhilarating sense of anticipation. Eliana also enjoys going to the beach and hiking in her free time.


Haoming Ma
Haoming Ma

Haoming is a rising senior year student at Wuhan University studying Life Sciences and Finance. He is an exchange student in Berkeley and is working with Ruoshi Yuan to develop high throughput platforms to study C.necator in low nutrition conditions. He is skilled in microfluidic chips design and fabrication and he is interested in understanding biological processes in economic terms.


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.


Katya Panchenko
Katya Panchenko

Katya is a 4th year undergrad studying Molecular and Cell Biology and Computer Science. She is passionate about the ways in which we can harness biology for sustainability and medical solutions, and is really inspired by the innovative applications of bioengineering at CUBES. She is working within the FPSD division at the Arkin Lab, engineering E.Coli to produce biopolymers suitable for additive manufacturing for human space exploration.


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.


Mindy Duong
Mindy Duong
mindy.duong@berkeley.edu  

Mindy Duong is a junior undergraduate at UC Berkeley studying Molecular & Cell Biology and Public Health. She joined the Arkin Lab as a student laboratory assistant to help with routine upkeep of the entire lab and assist individual researchers with their research projects. In her free time, she enjoys crocheting and learning other fiber arts.


Phillipe Wiederkehr
Phillipe Wiederkehr
Phillipe Wiederkehr is an undergraduate in Bioengineering Department 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 assists 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.

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.


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


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.