Bondy-Denomy Lab Members

Joe is an Associate Professor at UCSF, in the Department of Microbiology & Immunology. Joe went to the University of Waterloo for his undergrad in Biology (Microbiology specialization) and spent time as a co-op student in labs at Western University (London, ON) and McGill University (Montreal, QC). Joe then attended the University of Toronto to complete his PhD in Alan Davidson’s Lab where he studied interactions between bacteriophages and the human pathogen Pseudomonas aeruginosa, focusing on the effects of lysogeny and the CRISPR-Cas immune system. In 2015, Joe started the lab at UCSF as a Sandler Fellow and in November of 2017, became an Assistant Professor. In July of 2020, he was promoted to Associate Professor with tenure. Joe also become an investigator with the UCB Innovative Genomics Institute in 2019. Alongside all of the exciting scientific endeavors Joe is involved with in lab, he is also a scientific advisory board member of SNIPR Biome and Excision Biotherapeutics and is a scientific advisory board member and co-founder of Acrigen Biosciences. Joe also has a long-standing love of baseball, Canada, and first and foremost, his wife and two sons. As a PI and UCSF Faculty member, Joe has completed Gilliam Mentorship Training, UCSF DEI Champion Training, and the following UCSF workshops: Acknowledging and Negotiating the Mentor-Mentee Tensions Inherent in the Research Lab, Career Conversations, and Three Truths and Three Tries: Facing and Overcoming Critical Social Justice Challenges at the Micro, Mezzo, and Macro Levels. The UCSF Graduate Faculty Development Program has a handy Faculty Participation Tracker and a comprehensive list of all faculty trainings.

Adolfo Cuesta is an Infectious Disease Fellow who joined the Bondy-Denomy lab in July 2024. He completed undergraduate training at Haverford College and then worked with Dr. Dan Littman at NYU studying Th17 cell regulation. He then migrated to the west coast to start in the UCSF MSTP. In 2019, he completed a PhD in Chemistry and Chemical Biology with Dr. Jack Taunton where he developed lysine-reactive aryl sulfonyl fluoride-based covalent inhibitors of Hsp90. He then completed his MD in 2021 and stayed at UCSF for Internal Medicine residency and Infectious Disease fellowship. He is excited about phage engineering and exploring the use of bacteriophage therapy to treat highly antibiotic resistant infections.

Alex is a postdoctoral scholar and joined the lab in October 2023. Alex grew up in the Bay Area in Daly City and obtained a degree in Molecular, Cell and Developmental Biology at UCLA. He completed his PhD at MIT in the Department of Biology where he conducted his research in the lab of Dr. Sebastian Lourido studying a single-cell eukaryotic pathogenic parasite called Toxoplasma gondii. His work focused on understanding the signaling events controlling virulence factor secretion that is required for infection. His work leveraged a combination of quantitative proteomics, biochemistry and light microscopy. In the Bondy-Denomy lab, Alex is now studying a more ancient battle between bacteria and the viruses that infect them. Alex is interested in developing genetic and biochemical approaches to identify new defense and anti-defense strategies used by these organisms. In his free time, Alex enjoys climbing, hiking, cooking, playing board games and learning about honey bees.

Alex Hong joined the Bondy-Denomy lab in July 2021 as a graduate student in the Tetrad program. Alex grew up in the suburbs of Dallas, Texas before attending MIT. There, he worked in Dr. Hazel Sive’s Lab on mapping cerebrospinal fluid directional flow in embryonic zebrafish. After graduating with a degree in Biology, Alex worked in Dr. Kevin Esvelt’s Sculpting Evolution Group on optimizing a high-throughput microinjection system for making transgenic C. elegans and establishing a CRISPR-Cas mediated daisy drive system in C. elegans. With his interests now directed towards new bacterial immune systems, Alex is working on studying the mechanism of the anti-phage system Gabija. Outside of research, Alex enjoys basketball/soccer, painting, singing, hiking, and biking.

Alexis Villani joined the Bondy-Denomy lab in July 2021 as a graduate student in the Tetrad program. Alexis grew up in sunny Orange County, CA; no sorry, it’s not like the show (The OC). She attended Orange Coast College where her incredible professors encouraged her to pursue research; then transferred to UC Irvine where she focused her degree in Immunology. During her undergrad, she spent a summer working on yeast prions in the Jarosz Lab at Stanford; which fueled her interest in protein biology. After graduating, she went on to do a Post-Baccalaureate program at Penn, working in James Shorter’s Lab; there she studied RNA and protein phase separation in the context of neurological disease. In the Bondy-Denomy lab, she is studying the mechanisms by which bacteria inactive their restriction-modification systems. Outside of research she enjoys spending time with her rambunctious toddler and partner, exploring museums, running, buying cute shoes, drinking LOTS of espresso, cooking, and making cocktails! She is funded by the iMicro T32 training grant (2021-2022) and received the NSF-GRFP Fellowship in 2022.

Claire Kokontis is a graduate student in the Tetrad program and joined the Bondy-Denomy lab in July 2021. Claire grew up in Chicago, IL and Palo Alto, CA, and attended the University of Chicago for undergrad. At UChicago Claire worked in the Ruthenberg Lab, where she studied chromatin biology and the role of epigenetic DNA modifications in gene regulation. In the Bondy-Denomy lab, Claire is now studying the mechanisms of anti-CRISPRs and the formation of jumbophage ΦKZ’s proteinaceous nucleus-like structure. In her free time, Claire enjoys painting, film photography and darkroom printing, knitting, and tending to her houseplants.

Daphne graduated from UCLA with a degree in Biophysics. As an undergraduate, she studied the effects of chaotropes and kosmotropes on protein hydration layers under the guidance of Dr. Giovanni Zocchi. She discovered her interest in structural biology when she spent a summer working under Dr. Kliment Verba at UCSF. As a graduate student, Daphne is characterizing anti-CRISPR proteins in collaboration with the Fraser Lab, as well as pursuing structural biology projects related to the phage-bacteria arms race. Outside of lab, Daphne enjoys birding, reading, and playing with her cat Lilly. Daphne is supported by a graduate fellowship from the UCSF Discovery Fellows Program.

Deepto joined the Bondy-Denomy Lab in September 2021 as a post-doctoral scholar. Prior to his post-doctoral adventures, Deepto was a Ruth L Kirschstein (NRSA) Graduate student in Prof. Alanna Schepartz’s lab at Yale/ UC Berkeley. Driven by his fascination with phages, bacteria, and their ever-inspiring time-immemorial battle for survival (read: treasure-trove of biotechnological application waiting to happen!), Deepto hopped across the pond for his post-doc research. At UCSF, Deepto is working with the Bondy-Denomy and David Agard labs to study the molecular underpinnings of THE MOST potent anti-immune mechanism used by jumbo-phages to thwart bacterial defenses. In his spare time, Deepto loves to write, photograph birds, host barbecues, dabble in trivia, play basketball, solve puzzles/ the NYT daily crossword and bake.

Esther is a postdoctoral researcher who joined the Bondy-Denomy lab in September 2024. Originally from Israel, she completed her graduate studies at Bar-Ilan University (BIU) in the Ehud Banin Lab, focusing on prophage-host interactions. During her time at BIU, Esther developed a passion for unraveling the complex dynamics between bacteria and phages. In the Bondy-Denomy lab, she is excited to explore bacterial immune system mechanisms and their regulation. Outside of research, Esther is the proud mother of twin boys, balancing her work as a dedicated scientist and parent. She enjoys supporting women in science and cherishing time with her family.

“Harshu Musunuri is an MD-PhD student in the biophysics program and is focused on synthetic bacteriophage engineering. Harshu grew up in Seattle and studied a combination of chemistry and computer science at Stanford, where she graduated from in 2022 with honors. During her undergrad, she worked in Dr. Peter Kim’s lab at the ChEM-H Institute, designing universal vaccines against SARS-CoV-2 and Influenza. She also spent summers at the Institute for Protein Design and at D.E. Shaw Research studying algorithms for protein design and molecular dynamics simulations. In the Bondy-Denomy lab, she will continue applying protein design to viruses (this time prokaryotic ones!) to enable generalizable retargeting of phage specificity, as well as custom payload delivery. She is excited to understand the molecular underpinnings of phage injection, and apply this towards new kinds of therapeutics for human disease. When she’s not at the bench or on her computer, Harshu loves to read, dance, bike around SF hills, and explore the outdoors.”

Iana joined the Bondy-Denomy Lab in November 2022 as a post-doctoral scholar. She completed her graduate work in Konstantin Severinov’s Lab at Skolkovo Institute of Science and Technology, Russia, where she studied CRISPR-Cas Type II effectors and their application in genome editing. In the Bondy-Denomy lab, Iana studies various Pseudomonas aeruginosa immune systems. She is also interested in the interplay between transposons and prokaryotic immune systems and the role of mobile genetic elements in the formation of defense islands. On weekends you can find Iana at the San Francisco Children’s Museums and playgrounds where she has fun with her family.

Miaoxi Liu is a Tetrad graduate student who joined the Bondy-Denomy lab in June 2024. Miaoxi grew up in Xi’an, the capital of thirteen dynasties of ancient China. She attended high school in Canada and pursued a bachelor’s degree in Immunology and Cell & Molecular Biology at the University of Toronto. During her undergraduate studies, she joined the Cowen Lab and used high-throughput screening methods to identify cell wall and cell wall organization genes of Candida albicans that are essential for cell growth. She also studied genes essential for Candida albicans pathogenic filamentation in anaerobic conditions. With an interest in immunology, she also worked in the Watts lab, studying the role of inflammatory monocytes in co-stimulating T cells during STING agonist immunotherapy. In the Bondy-Denomy lab, Miaoxi will continue studying immunology and host-pathogen interactions. She is excited to study new bacterial immune systems that could potentially target different families of phages. In her spare time, Miaoxi enjoys making crafts, drawing, and swimming.

“Michelle Grunberg is a Tetrad graduate student and joined the Bondy-Denomy lab in June 2024. She grew up in Los Angeles and graduated with a bachelors in biology from UC Santa Barbara in 2020. In undergrad, she studied a previously uncharacterized small open reading frame of the Kaposi’s sarcoma-associated herpesvirus in the lab of Dr. Carolina Arias and interned at UCSF and the Chan Zuckerberg Initiative Biohub, where she optimized metagenomic next-generation sequencing by harnessing CRISPR-Cas9 technology. After her bachelors, Michelle developed Cas13-based technologies to study viral and host RNA in the labs of Pardis Sabeti and Cameron Myhrvold at the Broad Institute and Princeton University. Later, she returned to the CZ Biohub, where she developed fluorescent reporters of viral infection in mammalian cell culture. As a graduate student in the Bondy-Denomy lab, she is excited to study novel phage inhibitors of nucleotide signaling immune systems such as Thoeris and CBASS. Outside of the lab, Michelle enjoys exploring the city, painting, reading, and getting out in nature.”

Tim is a post-doc in the Bondy-Denomy lab focused on characterizing the anti-phage systems of Gram-positive bacteria. He received his BSc in Biomedical Sciences from the University of Waterloo in Canada. He then did his PhD in the lab of Dr. John Whitney at McMaster University, studying how the type VII secretion system of Streptococcus intermedius exports toxic effectors. Tim spends his free time exploring the great city of San Francisco with his wife and dog and philosophizing over the finer points of Canadian vs. American culture (mostly in favour of Canada).

Wearn-Xin is a postdoc who joined the Bondy-Denomy lab in August 2023. Wearn-Xin grew up in the sunny island of Singapore and completed her graduate work in the Tang lab at the University of Oxford in the UK, where she finished her PhD with understanding movement of plasmids in Neisseria spp. After spending years deciding between researching on viruses or on bacteria, she has finally decided to do both. In the Bondy-Denomy lab, Wearn-Xin is working on understanding how conserved genes may inhibit phage replication in Pseudomonas aeruginosa. In her free time, Wearn-Xin enjoys a good hike, exploring new food places and petting dogs that come her way.