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 Lui is a postdoctoral fellow in the Arkin Lab at Lawrence Berkeley National Laboratory. She was born and raised in Northern California and has been bumming around the UC system her whole career. 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. As an undergraduate she studied vernal pool ecology and DNA supercoiling. As a graduate student she used RNAseq and bioinformatics to study small RNAs in archaea. Currently, her postdoctoral research 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

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.


Denish Piya
Denish Piya
Projects: BioDesign
denish.piya@berkeley.edu  

Denish Piya is a postdoctoral scholar in the Arkin Laboratory at UC Berkeley. He completed his PhD from Texas A&M University focusing on phage research. He is applying CRISPR and Dubseq technologies to study how genes affect fitness in context of phage infection.


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

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

Heloise Carion
Heloise Carion
Projects: ENIGMA
heloisecarion@berkeley.edu  

Heloise Carion is a fourth year Bioengineering undergraduate student at UC Berkeley with a concentration in synthetic and computational biology. Her interests include genetics, systems biology, and computation. In 2018, she joined the Arkin Laboratory, and has helped develop technology for high-throughput characterization of phage genes.


Drew Hendrickson
Drew Hendrickson
Projects: ENIGMA
ajhendrickson@lbl.gov  

Drew Hendrickson is a researcher with the Arkin Lab at LBNL. He graduated from UC Berkeley in 2019 with his B.S. in Chemical Biology and Microbial Biology with a focus in environmental and ecological microbiology. Previously, Drew worked in bioremediation to elucidate the microbial transformations of hydrocarbon contaminants by using advanced mass spectrometry and sequencing techniques. He is interested in systems biology, data science, and “-omics” to understand our microbial world. Since joining the ENIGMA team, he employs improved sequencing techniques to study novel microbes from diverse environments. Outside of the lab, he enjoys dance, LGBTQ advocacy, and hiking across the California landscape.


Madeline Moore
Madeline Moore
Technical Staff
Projects: COVID-19
mlmoore@lbl.gov  

Madeline graduated from UC Berkeley in 2020 with a degree in Molecular Environmental Biology. She began her research career as a field biologist where she quickly discovered her interest in microbial communities within soil. In 2016, she traveled to Antarctica as part of an NSF-funded expedition. In 2018, she worked for the US Geological Survey studying biological soil crusts in Moab, Utah, and she completed a research project examining benthic protozoa on the island of Mo’orea, French Polynesia. During the rest of her time as an undergraduate student she studied soil microbial ecology with the Firestone lab at UC Berkeley and completed an honors thesis focused on linking root exudate metabolites with fungal community composition in the rhizosphere. As a research associate in the Arkin lab, Madeline investigates mechanisms behind phage-host interactions as part of a COVID-19 related project. She plans to pursue a PhD in systems and quantitative biology. 


Alejandro Ramirez
Alejandro Ramirez
Affiliate
Projects: ENIGMA
AlejandroRamirez@lbl.gov  

Alejandro Ramirez is a Bioengineering Research Associate in the Arkin Laboratory at LBNL. He studied bioengineering, concentrating in synthetic biology and systems biology, and metabolic engineering at the University of California, Berkeley. In 2019 he interned at Amyris, Inc. as a fermentation operations associate for tanks sized 250 mL to 2.0 L before starting full-time at Endless West as a production associate in the creation of beverages and food from component chemicals. As his passion was still in synthetic biology, Alejandro returned to work for the Arkin Lab in 2020 joining the ENIGMA project under the supervision of Vivek Mutalik. His interests in science are in sustainable engineering, biological interactions, and genetic tools used in directed-evolution.


Undergraduate Students

Brooklyn Brace
Brooklyn Brace
Projects: CUBES
ogaloz@lbl.gov  

Brooklyn Brace is a fourth year undergraduate student at UC Berkeley studying Molecular and Cell Biology. She has an interest in microbiology and genomics and how they apply to bioengineering. Brooklyn joined the Arkin Lab in 2019, and she is currently working on the CUBES project in the MMFD division investigating genes important for nitrogen fixation. Previously, Brooklyn worked in a synthetic biology lab at Columbia University working on the development of a multiplexed drug screening platform for small molecule inhibitors of viral proteases.


Luis Ramirez Hernandez
Luis Ramirez Hernandez
Projects: BioDesign, Phage
luis.ramirezh@berkeley.edu  

Luis is a 4th year undergraduate and aspiring graduate student majoring in Molecular and Cell Biology. He joined the Arkin Lab in the summer of 2019 under the mentorship of Dr. Carim, with whom he studied phage-tail like bacteriocins, also known as tailocins. His first project encompassed designing vectors for the construction of recombinant tailocin proteins in order to investigate genetic determinants of killing specificity. More recently he’s helped conduct genome-wide fitness assays to elucidate genetic factors of bacterial resistance to tailocins in non-canonical organisms such as Pseudomonas fluorescens and Pseudomonas protegens. When not in the lab, you can catch him with a Nikon taking photos around the city, riding his bike along the marina, playing soccer at the park, or on a hiking trail. Outside of research, Luis is passionate about providing guidance, support, and information to aspiring and current students about the college application process and the college life, especially as it pertains to the experience of first-generation, low-income, undocumented/DACAmented, and LatinX students in higher education. To this end, he actively devotes his time to the Let’s Talk Universi-Tea Podcast – a project created alongside a group of his childhood friends and which is soon to be released.


Avery Hill
Avery Hill
Projects: CUBES
avery.hill@berkeley.edu  

Avery is a fourth year undergraduate student at UC Berkeley, currently working towards a double major in Economics and Molecular and Cell Biology with an emphasis in developmental genetics. She is interested in how the intersection of her two academic disciplines come together to further the research behind space exploration. In CUBES, Avery is working towards optimizing an elemental balance in a martian biomanufacturing system through the use of techno economic analysis. Outside of CUBES, Avery works at a biopharma consultancy and hopes to move into biotech in the future.


Davian Ho
Davian Ho
Projects: BioDesign, ENIGMA, CUBES
desireeho@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


Anderson Seamus Lee
Anderson Seamus Lee
Projects: CUBES
andersonlee@berkeley.edu  

Anderson Lee is a third-year undergraduate student at UC Berkeley studying Bioengineering with a focus on Synthetic and Computational Biology. He is currently optimizing the production of biopharmaceuticals to be utilized during space travel. In previous companies, he has developed an ELISA procedure to determine the concentration of a tumor-detecting drug in biological samples and enhanced a mobile, quick diagnostic machine that scans for viruses. Previous to the Arkin Lab, he worked in Mohammed Mofrad’s Cell and Biomechanics Laboratory at UC Berkeley where he used neural networks with backpropagation to predict a virus’ host based on the genome of the virus. In the future, he sees himself using synthetic biology to conquer problems inherent to the nature of space travel. He believes that technology already present in nature and perfected with evolution can be the key to send humans to other planets.


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.


Nick Nolan
Nick Nolan
Projects: BioDesign, Phage
nick.nolan@berkeley.edu  

Nick Nolan is a Bioengineering and EECS sophomore undergraduate student in the Arkin Laboratory at UC Berkeley; his current research topics are in viral engineering and control theory, though is always willing to delve into other topics of interest. As much as science is important to him, science education is equally so–thus he has organized the 2019 BioEHSC™, a Bioengineering High School Competition, the largest high school-specific competition of its kind in the world, as Junior Chair, and looks forward to serving as Senior Chair in the competition’s next annual iteration.


Will A Sharpless
Will A Sharpless
Projects: CUBES
willsharpless@berkeley.edu  

Will Sharpless has been an undergraduate researcher in the Arkin lab for 2 years. He works on the CUBES mission to design novel microbial communities for the rhizosphere of rice. Will is a math/bio double major at Cal and focuses on the dynamics and stability of biological systems, and the application of mathematics for nonlinear systems and networks to bioengineering. In the lab, Will works under the mentorship of postdoctoral researchers Kyle Sander and Fangchao Song.


Fengzhe Shi
Fengzhe Shi
Projects: CUBES
schweini@berkeley.edu  

Fengzhe Shi is an undergraduate at Beijing Jiaotong University and now an exchange student at UC Berkeley studying computer science. He joined Mesbah Lab during this period and took part in the CUBES project. In CUBES, Fengzhe mainly works on modeling deep learning based surrogate models in dynamic systems. Previously, he worked in a computer science lab at Peking University on an information retrieval and recommender system.