Cameron Hearne
Cameron is a graduate student in Plant & Microbial Biology Dept and jointly advised by Drs. Mutalik and Arkin
Bradley Biggs
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.
Allison Hung
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.
Hanqiao Zhang
Han was an undergraduate in the Bioengineering Dept. He worked with Dr. Bernstein on mechanistic modeling and machine learning to monitor environmental contamination through genomics.
Jiaqi (Joshua) Huang
Joshua is a graduate student in the Dept. Comparative Biochemistry. He is working with Dr. Ruoshi Yuan on the time-lapse imaging project.
Sofia Milian
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
Adam Arkin
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.
Keith Keller
Keith Keller is a system administrator for KBase (https://kbase.us). He has been a member of the Arkin lab since 2002.
Marcin P. Joachimiak
Marcin Joachimiak is a Staff Researcher and Software Developer in the Environmental Genomics and Systems Biology Division at Lawrence Berkeley National Lab. He studied Mathematics at University of Chicago while creating transgenic yeast strains to enable high throughput herbicide screening for wheat. In 2002 he went West and studied Biophysics at UCSF where he implemented the Evolutionary Trace method and its variants (JEvTrace), identified novel targets and inhibitors for antimalarials, and performed the first genome annotation and contributed to the first gene expression analysis of the malaria parasite. After a year at Five Prime Therapeutics, where he founded the computational infrastructure and used the Riken mouse cDNA collection to discover novel human genes, he returned to academia as a postdoc in the Brenner Group at UC Berkeley. At UCB he developed a popular visualization tool (JColorGrid), performed key sequence and phylogeny analysis for the Global Ocean Survey, and published an affinity-based model for human branch point site prediction. Since 2006 he has been a member of the Arkin Laboratory, first as part of the ENIGMA project where he developed the gene expression analysis pipeline, functional genomics analysis tools in MicrobesOnline, and a novel machine learning algorithm for multi-data type biclustering. Since 2014 he has been part of the DOE KnowledgeBase where he designs and develops applications for statistical and visualization analysis and most recently on components of the system to enable rapid data type modeling, data science and machine learning, and integration with ontologies and knowledge graphs.
Morgan Price
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.
