Team - PROTECT

The PROTECT team spans experts across multiple backgrounds, institutions, and career stages.

Investigators

Adam Arkin

Principal InvestigatorUniversity of California, Berkeley

Adam Arkin is a distinguished researcher specializing in microbiology and bioengineering,
with extensive experience leading multidisciplinary teams.

Karstn B. Zengler

Karsten B. Zengler

Co-investigatorUniversity of California, San Diego

Karsten Zengler, a Professor at UC San Diego with over 20 years of experience in microbiology and systems biology, is a pioneer in community systems biology and high-throughput microbial cultivation, with a focus on host–microbe interactions, quantitative omics, and microbiome roles in health and disease.

Victor Nizet

Co-investigatorUniversity of California, San Diego

Victor Nizet, a Distinguished Professor of Pediatrics, focuses on bacterial pathogenesis and the innate immune system—particularly streptococcal and staphylococcal infections—and collaborates with biotech partners to develop novel antibiotic and immune-based therapies.

Douglas Conrad

Co-investigatorCleveland Clinic, Cleveland

Douglas Conrad, Professor of Medicine and Director of Adult Cystic Fibrosis, specializes in airway microbiome research, focusing on the integration of metagenomic, metabolomic, and genomic data with clinical phenotypes in cystic fibrosis.

Fatemah Askarian

Co-investigatorUniversity of California, San Diego

Fatemeh Askarian’s research focuses on host–pathogen interactions, combining microbial and host-based approaches to study the molecular pathogenesis of multi-drug resistant infections. In the PROTECT project, she leads in vivo translational efforts to advance clinical applications.

Jacob Hilzinger

Co-investigatorUniversity of California, San Diego

Jacob Hilzinger, an expert in microbial physiology, systems biology, and synthetic biology, applies genetic and systems-level tools to understand and engineer microbes while overseeing probiotic formulation, tissue-culture platform development, translational scoring of synbiotic products, and related business development efforts.

Kelsey Hern

Co-investigatorNorthwestern University, Chicago

Kelsey Hern, who holds a PhD in Microbiology from UC Berkeley, is a co-investigator on PROTECT, where she leads efforts in non-invasive engraftment monitoring and oversees scaling and early manufacturing to support therapeutic development for respiratory conditions.

Patricia Lenhart-Pendergrass

Co-investigatorUniversity of California, San Diego

Patricia M. Lenhart-Pendergrass, an Assistant Adjunct Professor specializing in pediatric pulmonology, researches infections in cystic fibrosis and leads patient sampling efforts for the PROTECT project.

Chantal Darquenne

Co-investigatorUniversity of California, San Diego

Chantal Darquenne is a Professor of Medicine and the former ISAM President, specializing in aerosol dynamics in the human lung, with research spanning inhaled therapeutics, toxicology, and respiratory physiology; and currently advise on mouse aerosol exposure systems and dosimetry to translate findings to human contexts.

Praveen Akuthota

Co-investigatorUniversity of California, San Diego

Praveen Akuthota, MD, is a board-certified pulmonologist who treats all types of asthma as well as eosinophilic pulmonary disease, including eosinophilic granulomatosis with polyangiitis. As a professor in the Department of Medicine, Dr. Akuthota conducts research on asthma and eosinophilic disease, which includes clinical trials.

Scientists

Spencer Long

Data ScientistUniversity of California, Berkeley

Spencer Long is a data scientist with a multidisciplinary background who specializes in bioinformatics, machine learning, and multi-omic data integration, supporting microbiome-based respiratory research within PROTECT while building scalable scientific platforms and infrastructure.

Postdoctoral Researchers

Alex Styer

Postdoctoral ResearcherUniversity of California, Berkeley

Alex is a computational biologist who applies experimental design, sequencing, and bioinformatics to study diverse microbial systems, and on the PROTECT team, he analyzes isolate genomes and models probiotic formulations aimed at protecting cystic fibrosis patients from Pseudomonas aeruginosa.

Sun-Young Kim

Postdoctoral ResearcherUniversity of California, Berkeley

Sun-young has a background in microbiology with research experience in bacterial secretion systems and microcins; in the PROTECT project focuses on isolating commensals and pathogens while profiling antibiotic resistance and carbon metabolism.

Ka Pui Sharon Yau

Postdoctoral ResearcherUniversity of California, San Dieogo

Sharon Yau is trained in immunology with a research focus on host–pathogen interactions, particularly innate immune responses to fungal pathogens. Her interest lies in how macrophages and neutrophils sense infection and activate inflammasome pathways, cytokine signaling, and regulated cell death to shape disease outcomes. Within the PROTECT team, she will assist in optimizing animal models of pulmonary infection to support in vivo studies.

Graduate Researchers

Gwyneth Hutchinson-Ramirez

Graduate ResearcherUniversity of California, Berkeley

Gwyneth’s research career in cell biology and tissue engineering has spanned academia, industry, and federal institutions. She leads the tissue engineering efforts for PROTECT, developing advanced organotypic lung tissue models to study microbial interactions.

Sherlyn Weng

Graduate ResearcherUniversity of California, San Diego

Sherlyn Weng’s focus is in Bioinformatics & Systems Biology, she is studying the human microbiome’s role in disease using multi-omics approaches, focusing on processing metaRibo-Seq data to generate compositional-functional profiles for downstream analysis.

Vishant Gandhi

Graduate ResearcherUniversity of California, San Diego

Vishant Gandhi, has a bioengineering background where he studied host-microbe and microbe-microbe interactions, in the PROTECT project, he is focusing on isolating rare commensal and pathogenic strains and contributing to large-scale multi-omics efforts to develop targeted microbial therapeutics.

Emma Rooholfada

Graduate ResearcherUniversity of California, San Diego

Emma Rooholfada investigates how microbial communities impact human health and disease, and in the PROTECT project, she uses multi-omics analyses of patient samples to identify prebiotic substrates that could help target Pseudomonas aeruginosa infections.

Rita Achour

Graduate Researcher University of California, Berkeley

Rita, a bioengineering master’s student from TU Delft and Leiden University, focuses on personalized medicine and immunology, with a specific interest in leveraging the gut microbiome for therapies and modeling commensal interactions in the respiratory tract.

Research Associates

Corinn Walker

Staff Research AssociateUniversity of California, San Diego

Corinn Walker has a background in biology, she is passionate about host–bacteria interactions and disease mechanisms, and as part of the PROTECT team, she processes biological samples and conduct metaDNA-Seq, metaRNA-Seq, and metaRibo-Seq analyses.

Armin Kousha

Staff Research AssociateUniversity of California, San Diego

Armin Kousha specializes in bacterial pathogenesis and translational in vivo analysis, conducting experiments to develop innovative treatment strategies for improving the clinical management of infectious diseases.

Chloe Lieng

Staff Research AssociateUniversity of California, San Diego

Chloe Lieng is a molecular biologist with a BSc in Marine Biology and an MRes in Molecular and Cellular Biosciences, with focus on microbiome science. In the PROTECT project, Chloe leads experimental efforts focusing on next-generation sequencing and multi-omics approaches.

John Hiedo

Staff Research AssociateUniversity of California, San Diego

John Hiedo holds a bachelor’s degree in Biology with a minor in Computer Science and is currently pursuing a Master’s in CS/ML at Georgia Tech. With five years of experience in biotech and academia, he specializes in processing human sputum samples for functional protein data in cystic fibrosis and optimizing omics experiments for mice infected with PA/ASMA strains.

Undergraduate Researchers

Allie (Sarah) Cabiles

Undergraduate ResearcherUniversity of California, Berkeley

Allie (Sarah) Cabiles is an undergraduate at UC Berkeley studying bioengineering. Her interests lie at the intersection of biochemistry and synthetic biology, and she hopes to pursue a career in the biotech industry focused on harnessing these fields within translational medicine to develop accessible solutions to global challenges such as healthcare equity and sustainability.

Pranav Chigullapalli

Undergraduate ResearcherUniversity of California, San Diego

Pranav is an undergraduate student studying Bioengineering. As part of the PROTECT team, he contributes to processing biological samples for omics analysis.

Anisha Pallikonda

Undergraduate ResearcherUniversity of California, Berkeley

Anisha Pallikonda is a sophomore at UC Berkeley, studying Bioengineering and Data Science. She is interested in synthetic biology and genetic engineering for healthcare applications. She is working with Dr. Sun-Young Kim on the PROTECT project.

Tony Zhong

Undergraduate ResearcherUniversity of California, Berkeley

Tony Zhong is a Microbial Biology undergraduate at UC Berkeley with academic interests in synthetic biology and microbial pathogenesis. He is particularly interested in how engineered microbial systems can be applied to prevent infection, enhance microbiome stability, and support translational medicine.

Kit Bailey

Undergraduate ResearcherUniversity of California, San Diego

Kit Bailey is an undergraduate bioengineering student. He contributes to the PROTECT project by assisting in multi-omics sample processing and analysis.

Ritushree Ganguli

Undergraduate ResearcherUniversity of California, Berkeley

Ritu is currently a Berkeley undergraduate studying Molecular & Cell Biology on the Molecular Therapeutics track, with strong interests in drug development and design, infectious diseases, and the intersection of biotechnology and global health. She will be working with Gwyneth Hutchinson-Ramirez to support research regarding tissue engineering and studying microbial interactions.

Erin Song

Undergraduate ResearcherUniversity of California, Berkeley

Erin is an undergraduate in the Bioengineering Department mentored by Gwyneth Hutchinson-Ramirez. Previously worked with data collection/analysis, research methodology, and medical devices like fMRI as an undergraduate researcher at the Psychology Department Computational Neuroscience Lab. She is gaining experience in mammalian tissue culture and other molecular biology techniques/skills. She is growing her skill set as a bioengineer. She is expanding her expertise in lab techniques/technologies and contribute to the lab’s pioneering work in tissue culture and engineering!

Srishti Vadya

Undergraduate ResearcherUniversity of California, Berkeley

Srishti is a sophomore at UC Berkeley. She is working with Gwyneth Hutchinson on PROTECT because of their work with infections and human lung tissue. She is studying Molecular and Cell Biology. Her interests lie in healthcare and genetic engineering, specifically how advances in biotechnology can be translated into innovative therapies that improve patient outcomes.

Sreshta Yelisetti

Undergraduate ResearcherUniversity of California, Berkeley

Sreshta is a sophomore at UC Berkeley studying Bioengineering and EECS. She is working with Dr. Jacob Hilzinger on Project PROTECT to genetically engineer P. Aeruginosa for antibiotic screening. Her interests lie in genetic engineering and computational biology.

Alisa Koltsova

Undergraduate ResearcherUniversity of California, Berkeley

Alisa is an undergraduate pursuing a dual focus in Bioengineering and Molecular and Cell Biology. Her research interests center on understanding biological systems at the cellular and molecular level, with a particular emphasis on leveraging microbiology and synthetic biology to advance the development of novel medical technologies. She contributes to the ARPA-H PROTECT project, where she prepares bacterial samples to investigate microbial interactions within the lower respiratory tract.

Administrators

Gwyneth Terry

Senior Administrator

University of California, Berkeley

Gwyneth Terry is a senior administrator with a geology background who supports Adam Arkin’s lab at Berkeley Lab and UC Berkeley by navigating institutional processes and enabling scientific progress through administrative coordination.

Ezgi Booth

Project CoordinatorUniversity of California, Berkeley

Ezgi Booth, with a background in genetics and computational biology, brings experience in scientific project management and supports PROTECT by coordinating administrative, reporting, procedural, and legal processes while fostering communication across multidisciplinary teams.

Dahen Ibarra Munoz

Clinical Research CoordinatorUniversity of California, San Diego

Dahen Ibarra Munoz is an an ECFMG-certified medical doctor with a background in public health and medical research, specializing in pulmonary and psychiatric medicine, and currently support the PROTECT project through participant recruitment, sample and data collection, and IRB-related processes.

Melissa Suarez

Clinical Research CoordinatorUniversity of California, San Diego

Melissa is a foreign-trained physician (MD) from Bogotá, Colombia. She has 5 years of clinical trials experience at UCSD, working in interventional Cardiology, Urology, and Pulmonology. Melissa is passionate about improving healthcare outcomes through collaboration and innovation. As a Clinical Research Coordinator for the PROTECT study, she obtains informed consent from eligible patients, collects specimens, and ensures regulatory compliance.