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.

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.

Erin Huiting is a Biomedical Sciencesgraduate student and joined the Bondy-Denomy lab in July 2020. Erin grew up in the mountains of Evergreen, Colorado and pursued a degree in Molecular Biology at Colgate University (sadly, she did not receive any free toothpaste). Prior to and following graduation, she worked at the NIH studying the persistence of HIV reservoirs and anti-viral host immunity, as well as the efficacy of HIV cure strategies in human clinical trials, within the lab of Drs. Tae-Wook Chun and Anthony Fauci. As an NSF Fellow in the Bondy-Denomy lab, Erin will continue studying immunology and host-pathogen interactions. She is excited to study new bacterial immune systems within native host organisms, especially uncovering how the cyclic oligonucleotide-based anti-phage signaling system (CBASS) works in Pseudomonas. In her spare time, Erin is involved in gender equity advocacy, exploring the outdoors, or playing/watching soccer.

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.

Sukrit is a Damon Runyon Fellow in the Bondy-Denomy lab. Sukrit is developing a computational and experimental platform to systematically explore phage-encoded strategies for interfering with bacterial cells. Complex interactions in prokaryotic communities (such as the gut microbiome) can often lead to genetic information being exchanged, modified, and reused by competing species. Using comparative genomics he hopes to discover new biological processes that might have been missed by classical approaches. Prior to the Bondy-Denomy lab, he was a postdoc in Jonathan Weissman’s lab at UCSF, where he worked on pooled CRISPRi screening methods to investigate dengue-virus infections in monocyte derived dendritic cells, and led an oceanic viral survey that doubled the number of known RNA viruses in the biosphere. Sukrit obtained his PhD in Andy Fire’s Lab at Stanford where he discovered CRISPR adaptation to RNA, a novel mode among the handful of known mechanisms for reverse flow of genetic information from RNA into DNA genomes, including those employed by retroviruses, telomeres, retrotransposons, mobile group II introns, and phage diversity generating elements. A PCR standardization method he developed during his PhD also formed the basis of a new Non-Invasive Prenatal Test (NIPT) for monogenic disorders such as thalassemias, cystic fibrosis, and spinal muscular atrophy. Prior to his fellowship at UCSF, he was co-founder and chief scientific officer of BillionToOne Inc., where he designed and led two clinical trials for determining the efficacy of this NIPT method for ß-thalassemia and Down’s syndrome. BillionToOne currently markets this test worldwide, and is on the Y-Combinator Top Companies List. Sukrit was an undergraduate at Princeton, and a obtained an MPhil as a Gates Scholar at Trinity College, Cambridge.

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.

Ying is a lab manager in the Bondy-Denomy lab. She obtained her undergraduate degree in Life Science at Huazhong Agriculture University in Wuhan, China. She completed her graduate work at the National Key Laboratory of Crop Genetic Improvement at Huazhong Agricultural University, where she studied Mutant library construction, Genetics, and Gene function research. Then she completed her post-doc research training, in Sainsbury lab and the University of Nebraska-Lincoln, where she researched about Gene-editing in plants, the interaction of plants and microbes, and next-generation sequencing. During the pandemic, she joined in the Covid IgG and IgM test kit R&D. In her free time, she enjoys hiking, swimming, and story time with kids.

Yuping joined the Bondy-Denomy lab in October, 2019 as a postdoctoral scholar. Yuping was a graduate student in the Sherlock Lab and Petrov Lab at Stanford University. Her Ph.D. work focused on understanding evolutionary processes quantitatively using S. cerevisiae. Originally from China, Yuping got her undergraduate degree in Bioinformatics at Huazhong University of Sci. & Tech., China, where she worked with Dr. Yu Xue on the computational construction of the lysine acetylation network. After her undergraduate, Yuping was interested in learning how to conduct biological experiments and worked as a research technician with Dr. Hong Zhang at National Institute of Biological Sciences, China, to study developmental biology in C. elegans. In the Bondy-Denomy lab, Yuping is working on discovering new bacterial immune systems against a special group of phages – the jumbophages – and understanding the mechanisms of such immune systems. Outside the lab, Yuping likes climbing rocks, running trails, hiking the wilderness and looking funny in her VR headset trying to master VR games.