Team

Vivek Mutalik is a Staff Scientist and Principal Investigator at Environmental Genomics and Systems Biology Division and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; and Principal Investigator at Innovative Genomics Institute and ENIGMA a Science Focus Area program at LBNL. 

He is the lead PI at DOE BRaVE Phage Foundry, a unified platform for engineering phages. Previously, Mutalik lead the BIOFAB project, the world’s first biological design-build facility in Emeryville, CA, funded by NSF & directed by Drew Endy, Adam Arkin and Jay Keasling. Mutalik received his PhD in Chemical engineering from the Indian Institute of Technology Bombay, India in 2005 and was a Postdoctoral Fellow in Prof Carol Gross lab at University of California, San Francisco. Dr. Mutalik has three years of experience in the Biotechnology Industry in handling >150KL industrial fermentation units & bulk drug manufacturing. 

Denish is a project scientist in the Mutalik Lab and a member of the Phage Foundry initiative, funded by Dept of Energy Bioprepardeness program. Denish completed his PhD from Texas A&M University under the mentorship of Dr. Jason J Gill and Dr. 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). Denish did his postdoctoral training with Dr. Adam Arkin and Dr. Vivek Mutalik. During postdoctoral research, he applied CRISPRi technology to identify essential/non-essential regions in phage genomes. He 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.

Sarshad Koderi Valappil obtained his Ph.D. from the University of Szeged in Hungary, focusing on the fascinating field of Bacteria-phage coevolution. His research explored the impact of phage infection and phage resistance on the fitness of MDR Pseudomonas aeruginosa. Now, in the Mutalik lab, as a part of ENIGMA SFA project, Sarshad is developing advanced technologies to facilitate high-resolution lineage tracking of phages. This innovative approach explores beneficial mutations within both simple and complex microbial environments. By uncovering the mutations that promote positive outcomes, Sarshad's work will contribute to a deeper understanding of the intricate dynamics between bacteria and phages.

Lucas Morinière 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, 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 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 a joint postdoctoral researcher appointment between Arkin & Mutalik Labs, he focuses on uncovering the phage-host interaction determinants in hundreds of Escherichia coli and coliphages using high-genetic screens and a machine-learning-driven experimental workflow.

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 Virsoil2 funded 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 Selvakumar is a Postdoctoral Researcher in the Mutalik Lab and a member of the Phage Foundry initiative of the DOE BRaVE project focused on combating emerging drug-resistant pathogens. 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 Dr. Jennifer Curtis and Dr. Joshua Weitz. Prior to joining LBNL, Hemaa worked as a Scientist at Felix Biotechnology, where she advanced synthetic biology platforms for engineering therapeutic, non-model phages.

Mohamad earned his B.S. in Biotechnology and molecular biology from George Mason University, in Virginia, USA. And in December of 2023 he graduated from Johns Hopkins University, in Maryland, USA with a M.S. in Biotechnology. After Graduating from JHU he relocated to the Bay Area. As a Research Associate at Phage Foundry, Mohamad is working on developing automation methods to rapidly isolates phages and applying synthetic biology tools engineer and evolve phages with specific functional traits. In his previous career position he was working in a cancer therapeutic startup company in MD, and performed various high-throughput experiments to identify potent anticancer compounds. In his free time he enjoys performing DIY-Bio experiments such as genetically engineering yeast to produce beta-carotene and being involved in the DIY-Bio community. He also enjoys biking, hiking, boating, snowboarding, visiting museums and going to the beach. 

Melina Peña received her B.S. in Microbiology, Immunology, and Molecular Genetics from the University of California, Los Angeles. There she studied bacteriophages through the SEA-PHAGES program and also conducted research on indoor air quality in Los Angeles during the height of the COVID-19 pandemic. In the Arkin and Mutalik Labs, Melina is currently using high-throughput genomics and genetics to gain a better understanding of phage-host interactions in order to build predictive models linking bacterial genotype to bacteriophage susceptibility phenotype. When not conducting research, she likes to spend her free time reading books, hiking, and spending time with her family, friends, and her dogs.

Bhoomika completed her undergraduate degree in Biological Sciences from Columbia University. During undergrad, she worked to enrich and characterize the fitness of wild microbiomes when exposed to extreme environments. In the Mutalik Lab, Bhoomika is working on isolating and characterizing phages across various different bacterial strain isolates as part of the ENIGMA project. In her spare time, Bhoomika likes building rockets, going to hackathons, trying out new extreme adventure sports, and dancing.