At the van Opijnen Lab, we are dedicated to tackling one of the most pressing challenges in global health today: the rise and spread of drug-resistant infectious diseases. With over 2.8 million antibiotic-resistant infections occurring annually in the U.S. alone, traditional treatments are becoming less effective, resulting in increased fatalities and more complex cases of infection. Our innovative approaches harness both experimental and computational strategies to develop new antimicrobial therapies, enhancing our understanding of how pathogens interact with their environments and available drugs.
Microbial Phenomics & Systems Analyses Lab
LATEST NEWS
2025 SPRING UPDATE - The lab has been extremely hard at work, with projects focused on developing computational AI-mediated tools to predict drug-interactions and efficacy, mapping out bacterial immune evasion strategies, and develop data-driven antigen discovery approaches to design immune and drug potentiating antimicrobial strategies. For those interested in this work, to join the lab as a graduate student or postdoc, or for collaboration opportunities, please do not hesitate to reach out.
2024 SUMMER UPDATE V - “To stave off the evolution of antibiotic resistance there is no such thing as excess when it comes to genomics tools.” Charles Darwin is rumored to have said to Alfred Russel Wallace while hunting dodo’s in the Australian outback. Which is why we believe so strongly in developing increasing options to explore the genomics of bacterial pathogens in ever more complexity. Our newest tool editions are ‘CRISPRi-TnSeq’ developed by former postdoctoral fellow Dr. Bimal Jana. You can read all about this new approach to uncover genetic interactions between essential genes and the rest of the genome in Nature Microbiology (doi.org/10.1038/s41564-024-01759-x). Also with the lab of Jan-Willem Veening in Lausanne we helped develop ‘dualCRISPRi’, another approach to uncover genetic interactions, using two guide RNA’s, simultaneously targeting two different genes on a genome-wide scale. This manuscript is under review and you can knock yourself out with it on bioRxiv (doi.org/10.1101/2024.08.14.607739).
2024 SUMMER UPDATE IV - We had our new Element Biosciences AVITI Sequencer installed and are extremely excited to start generating lots of sequencing data using Tn-Seq, (sc & dual)RNA-Seq, (sc)WGS, CRISPRi-Seq and using our newest tools CRISPRi-TnSeq and dualCRISPRi-Seq (also see above)! In the last couple of days we completed our first Tn-Seq runs on the sequencer with an overall Q43 quality score, and close to a billion reads! Truly amazing! Let us know if you want to learn more about the AVITI and want us to help you with a sequencing run of your own!
2024 SUMMER UPDATE III - We have made a full transition to Boston Children’s Hospital and the lab is slowly but surely getting back into gear! Instruments are being actively installed, old lab members are getting used to the new surroundings and 3 new lab members have joined and are getting familiar with all the ongoing projects in the lab. The Spring & Summer have been extremely hectic, but we’re all starting the feel like things are getting back to ‘normal’ and ideas and data are finally starting to flow freely!
2024 SPRING UPDATE II - As you can see the lab is in transition and this website is actively being updated to reflect current research and the move to Boston Children’s Hospital. So stay tuned and come back soon!
2024 SPRING UPDATE I - The Lab is MOVING to Boston Children’s Hospital at Harvard Medical School! To enable this the labs at the Broad Institute and Boston College are fusing into one super lab at the #1 Children’s Hospital in the US, located in the heart of Boston! The lab is also looking to hire amazing scientists at all levels! This means we’re looking for multiple postdocs, undergraduates are welcome again to apply to the lab and (prospective) HMS graduate students are encouraged to contact Dr. van Opijnen to inquire about the lab and any opportunities.
LAB STATEMENT
Our lab stands for a collaborative culture that embraces equity, diversity, and inclusion as a source of strength. We reject systemic discrimination, exclusion or hatred that promotes a narrow, exclusionary vision for our society.