Team

Vivek Mutalik is a staff scientist at the Environmental Genomics and Systems Biology (EGSB) and the Biological Systems and Engineering (BSE) divisions at Lawrence Berkeley National Laboratory located in Berkeley, CA. Mutalik is principal investigator at the BRaVE (Biopreparedness Research Virtual Environment) Phage Foundry and at ENIGMA (Ecosystems & Networks Integrated with Genes & Molecular Assemblies), a Science Focus Area program at Berkeley Lab.

The Mutalik Lab leads diverse aspects of phage isolation, evolution and engineering, and generates datasets for predictive modeling.

Simon’s research interests revolve around viral diversity in the environment and the impacts of virus-host interactions on individual microbes and on ecosystems. His current work includes the development of bioinformatics tools for viral datasets, the analysis and meta-analysis of viral genomes assembled from metagenomes, and the design of new approaches to investigate virus-host interactions in nature.

Roux will contribute to the phage genomics analysis and the design and analysis of metagenomic exploration of phages in wastewater samples.

The Arkin Lab has been involved in Synthetic Biology since its inception developing fundamental genetic technologies for precise and predictable control of gene expression, uniform design of gene expression networks, technologies for genome-scale manipulation and characterization of gene function; the design of host strains optimized for engineering for different applications; and foundational genetic and computational/data science technologies that support the creation of biofoundries.

The Arkin Lab will aid in the computational analysis and phage design aspects of the proposal. Responsibilities include collaborating on design of experiments, data analysis and interpretation, drafting and dissemination of results, designing course material based on the techniques and results from the research project.

Archana is an engineer and marine biologist. She primarily works on the interface between environmental engineering and coastal marine microbiology. Anand is intrigued by microbes that drive several vital biogeochemical processes in the land and ocean. Today, she researches microbes in wastewater while developing and applying bioinformatics techniques to understand the mixed microbial communities involved in nutrient removal and cycling as well as emerging infectious disease pathogens. She obtained her PhD in Ecology & Biodiversity from the University of Hong Kong and her B.Eng from the National University of Singapore.

Coming soon.

The Cress Lab at UC Berkeley’s Innovative Genomics Institute develops targeted microbiome editing and phage engineering technologies. A major objective of the lab involves characterizing and repurposing natural phages and plasmids as DNA delivery devices for microbiome editing to solve challenges environmental and human health challenges. Towards this goal, they have established phage functional genomics approaches that will help guide therapeutic phage engineering in the Phage Foundry.

The Cress Lab will perform genome-scale phage functional genomics of diverse phages infecting ESKAPE pathogens. They will also engineer therapeutic phages with enhanced host-range and infectivity against priority strains.

Coming soon.

Catherine is a staff scientist in bioengineering and biotechnology at Sandia National Laboratories. Mageeney’s previous work has focused on phage isolation and characterization, computation genomic island prediction, phage engineering, and prophage-mediate defense mechanisms.

Sandia’s team will leverage our genomic island prediction software to predict prophages integrated into bacterial genomes. We will use this information to engineer and reboot these prophages for bacterial strain where environmental phages are hard to isolate.

Coming soon.

Coming soon.

Jamie is a biologist research scientist in the Biological Systems and Engineering Division. She is a developmental and cancer biologist and her research interests include biological responses to environmental and radiological insults. She studies mixed radiological exposures, ultra high dose radiotherapy and the impact of thirdhand tobacco and cannabis smoke exposure in vitro and in vivo.

Inman is establishing a reproducible superficial murine skin bacterial infection model and evaluating topical phage treatment in the model. She is also investigating the role of host genetics on phage composition and abundance.

Mark’s interest in microbial life began in Montreal, Canada, where he completed his BSc. in microbiology and immunology at McGill University. Inspired by the nascent field of synthetic biology, Mimee pursued studies at the Massachusetts Institute of Technology, completing his PhD in microbiology and postdoctoral training in the Synthetic Biology Group. Mimee joined the University of Chicago as an assistant professor in the Department of Microbiology and the Pritzker School of Molecular Engineering in 2019 where he develops strategies to engineer the gut microbiome.

The Mimee Lab is leading efforts to engineer and evolve bacteriophage that target multi-drug resistant Klebsiella pneumoniae.

Petr received his PhD in Structural Biology at Purdue University, under mentorship of Michael Rossmann. Leiman is an Assistant Professor at École Polytechnique Fédérale de Lausanne (Swiss Federal Institute of Technology Lausanne) in Lausanne, Switzerland, and an Associate Professor at the University of Texas Medical Branch in Galveston, Texas.

The Leiman Lab is contributing to the structure and function of multivalent phage baseplate and structural and functional aspects of tail fiber-lipopolysaccharide interaction.

Denish Piya joined the Mutalik Lab as a project scientist for the Phage Foundry initiative. He completed his PhD from Texas A&M University under the mentorship of Jason J. Gill and Ry Young. His dissertation work involved investigation of the antirestriction component of bacteriophage P1 and high-throughput screen of host factors required for propagation of phages LL5 and LL12 (components of prebiotic formulation). Piya did his postdoctoral training with Adam Arkin and Vivek Mutalik. During his postdoctoral research, he applied CRISPRi technology to identify essential/non-essential regions in phage genomes.

Piya is currently interested in identifying factors that modulate interactions between phages and pathogenic bacteria so that machine learning tools can be employed to predict interaction between novel phages and their bacterial hosts.

Ella is a research specialist in the Mimee Lab at the University of Chicago. She has worked on DNA damage avoidance mechanisms in E. coli (Kuzminov Lab, University of Illinois Urbana-Champaign), pilin antigenic variation in N. gonorrhoeae (Seifert Lab, Northwestern University), and the Vibrio fischeri colonization of the Hawaiian bobtail squid (Mandel Lab, now University of Wisconsin-Madison). Ella enjoys bacterial genetics and creating agar art.

Ella works on isolating, characterizing, and engineering bacteriophages that infect Klebsiella pneumoniae that cause recurrent urinary tract infections.

Ryan is a project scientist at the Phage Foundry. He received his PhD in Microbiology from University of California, Berkeley. He has also performed postdoctoral research in host-microbe interactions and has held multiple industry roles as a bioinformatician.

Melnyk will be working to develop barcoded transposon libraries in model host strains and to do high-throughput screening of carbon sources, antibiotics, and stressors.

Avery is a postdoctoral researcher in the Environmental Genomics and Systems Biology division at Berkeley Lab. Avery completed his BSc at the University of Toronto in Genetics and Geosciences in 2015 and his PhD at the University of British Columbia in the Genome Sciences and Technology program in 2023. His doctoral research related to the development of high-throughput screening paradigms for the study of photosynthetic microorganisms, as well as the application of computational tools to investigate microbial community structure and dynamics in natural and engineered environments, including photobioreactors and the human lung.

Noonan is using statistical and machine learning approaches to predict phage-host interactions with the goal of selecting or engineering phages to target specific human pathogens.

Flavien Maucourt earned his PhD from the University Claude Bernard Lyon 1 in France at the Microbial Ecology Lab of Lyon (UMR 5557). His thesis research was focused on the ecology, interaction and depollution capabilities of bacterial and fungal microbes from historically Polychlorinated Biphenyls (PCB) polluted soils.

At the Mutalik Lab, as part of the Phage Foundry project, his present research focuses on developing methods to engineer the bacterial host to build loss-of-function libraries and to develop new technologies to study phage-host interactions and other microbial interaction determinants.

Hemaa is a postdoctoral researcher in the Mutalik Lab and a member of the Phage Foundry. She is interested in developing next-generation approaches to characterize phage-host interactions and building novel machine learning approaches to predict phage susceptibility. She is an alumnus of Georgia Tech (PhD, Physics) and IISc, Bangalore (BS, Physics). During her doctoral studies, she contributed to the development of self-regenerating, biocompatible polymer brushes with anti-biofilm properties and studied the spatiotemporal dynamics of phage-biofilm-immune cell interactions with the guidance of Jennifer Curtis and Joshua Weitz. Prior to joining Berkeley Lab, Hemaa worked as a Scientist at Felix Biotechnology, where she advanced synthetic biology platforms for engineering therapeutic, non-model phages.

Jessica is a postdoctoral appointee at Sandia National Laboratories in biotechnology and bioengineering. She obtained her PhD in Microbiology from the University of California, Davis, in Winter 2023. Throughout her career, she has worked on a number of different topics throughout her career in Microbiology, such as soil microbial ecology and plant-microbe interactions.

Trinh’s contribution to the Phage Foundry involves developing a workflow for the engineering of phages from pathogens of interest and rebooting them to potentially be used to combat these pathogens.

Milo Johnson is a postdoc broadly interested in genotype->phenotype maps and predictability in evolution. He completed his PhD in Michael Desai’s lab at Harvard, where he studied the determinants of fitness effects and evolutionary dynamics in budding yeast. He now works at UC Berkeley and LBNL in the Koskella and Deutschbauer labs, respectively. He is currently working to understand how the effects of mutations and patterns of epistasis change as we move from a lab environment to an organism’s natural environment.

For the Phage Foundry project, Milo is helping analyze, interpret, and visualize data from high-throughput barcode-based assays in both phage and bacterial hosts. He hopes that this data will allow us to build predictive models of phage host range and to learn something about the phage genotype->phenotype map in the process.

Darian is a microbial ecology PhD student at the University of California, Berkeley.

Doakes conducts research at the Koskella Lab.

Coming soon.

Angela is a Staff Research Associate focusing on all things phage related in the Cress Lab at the Innovative Genomics Institute. Angela’s research focus within the Phage Foundry will be on phage functional genomics. She is incredibly excited about the application of phage functional genomics to help guide therapeutic phage engineering. 

Angela received her BS in Molecular Environmental Biology from University of California, Berkeley. While at Cal, Angela was able to develop a diverse academic and research background in freshwater ecology, plant genetics, and now microbiology. In her previous position with the USDA, Angela’s work focused on characterizing phage targeting Shiga Toxin human pathogens for the development of phage cocktails. Outside of work, you can find Angela climbing, backpacking, and reading sci-fi novels.

Mohamad earned his B.S. in Biotechnology and molecular biology from George Mason University, in Virginia, and he graduated from Johns Hopkins University, in Maryland, with a M.S. in Biotechnology. During his undergraduate he participated in the SEA-PHAGES program, where he isolated and published his phage on PhagesDB.org. In his previous career position he was working in a cancer therapeutic startup company in Maryland, and performed various high-throughput experiments to identify potent anticancer compounds.

Mohamad is working on supporting the goals of the Phage Foundry by ensuring phages of different ESKAPE pathogens are discovered and isolated from diverse environmental samples, performing experiments to elucidate phage-host interactions, validating and optimizing workflows for assaying phage-antimicrobial combinations, and applying synthetic biology to evolve phages with specific functional traits.

Isabella Murray is studying for her undergraduate degree at the University of California, Berkeley in biochemistry and microbiology while working as an undergraduate researcher with the Phage Foundry. Her research interests revolve around viral and microbial diversity, and the interactions between microbes and their viruses.

With the Phage Foundry in the Mutalik Lab, Isabella is helping to investigate the genetic factors involved in bacteria-phage interactions, bacterial conjugation, and the use of high throughput technologies. 

Gwyneth is a senior administrator supporting Adam Arkin and his laboratory at Berkeley Lab and University of California, Berkeley. She helps move science forward in the administrative realm.

Gwyneth supports Adam Arkin with his Phage Foundry commitments.

Caitlin is a program manager supporting the Phage Foundry.