Microbial Phenomics & Systems Analyses Lab
LATEST NEWS
2026 FALL UPDATE II - We welcomed Jacob Bradley and Abigail Thomas to the lab. Jacob and Abigail will be dividing their time, hands and their incredible brains between our Microbial Systems Sequencing and Analysis Core and the lab!
2026 FALL UPDATE I - We welcomed Sally Song, a HMS graduate student to the lab! Sally will be working on drug persisters and developing a new genomics tools!
2026 SUMMER UPDATE - Check out our PUBLICATIONS page for some of our latest work in Cell Host & Microbe and mBio.
2026 OPEN POSITIONS - We have positions open for new HMS graduate students! If you are thinking about applying to HMS and are interested in Microbial Genomics, the Host Immune System and the Integration of AI to develop new antimicrobial strategies then send us a message!
2026 SEQUENCING CORE NEWS! - We have officially founded our Microbial Systems Sequencing and Analysis Core (MSSAC) at Boston Children’s hospital. We can now take care of all of your sequencing, sample preparation and analysis needs. Whether you are at BCH, HMS, external Academic or Industry we gladly work with anyone. Check out our dedicated SEQUENCING page and send us an email if you want more information.
2026 SPRING UPDATE - With the Chatterjee lab we developed a new proteome profiling tool enabled by bioorthogonal noncanonical amino acid tagging, you can find it at Nature Chemical Biology: https://www.nature.com/articles/s41589-025-02039-3
2026 WINTER UPDATE - After years of work we have made one our largest projects available on bioRxiv, it describes how drug tolerant bacteria, instead of resistant bacteria, preferentially evolve in vivo. Moreover, it describes a new general drug and stress response that works by controlling RNA quantity and quality during stress, and a ribosomal reboot mechanism when stress is removed. You can read it here: https://doi.org/10.64898/2026.02.02.703294
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.
Microbial Phenomics & Systems Analyses Lab
LATEST NEWS
2026 FALL UPDATE II - We welcomed Jacob Bradley and Abigail Thomas to the lab. Jacob and Abigail will be dividing their time, hands and their incredible brains between our Microbial Systems Sequencing and Analysis Core and the lab!
2026 FALL UPDATE I - We welcomed Sally Song, a HMS graduate student to the lab! Sally will be working on drug persisters and developing a new genomics tools!
2026 SUMMER UPDATE - Check out our PUBLICATIONS page for some of our latest work in Cell Host & Microbe and mBio.
2026 OPEN POSITIONS - We have positions open for new HMS graduate students! If you are thinking about applying to HMS and are interested in Microbial Genomics, the Host Immune System and the Integration of AI to develop new antimicrobial strategies then send us a message!
2026 SEQUENCING CORE NEWS! - We have officially founded our Microbial Systems Sequencing and Analysis Core (MSSAC) at Boston Children’s hospital. We can now take care of all of your sequencing, sample preparation and analysis needs. Whether you are at BCH, HMS, external Academic or Industry we gladly work with anyone. Check out our dedicated SEQUENCING page and send us an email if you want more information.
2026 SPRING UPDATE - With the Chatterjee lab we developed a new proteome profiling tool enabled by bioorthogonal noncanonical amino acid tagging, you can find it at Nature Chemical Biology: https://www.nature.com/articles/s41589-025-02039-3
2026 WINTER UPDATE - After years of work we have made one our largest projects available on bioRxiv, it describes how drug tolerant bacteria, instead of resistant bacteria, preferentially evolve in vivo. Moreover, it describes a new general drug and stress response that works by controlling RNA quantity and quality during stress, and a ribosomal reboot mechanism when stress is removed. You can read it here: https://doi.org/10.64898/2026.02.02.703294
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.
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.
Our MISSION
Our mission is to fuel the development of advanced antimicrobial strategies by integrating cutting-edge technology with detailed biological research. We believe that by systematically mapping the mechanisms of bacterial immune evasion and drug resistance, we can identify novel targets for therapies that can improve treatment outcomes and mitigate the effects of antibiotic resistance.
Our MISSION
Our mission is to fuel the development of advanced antimicrobial strategies by integrating cutting-edge technology with detailed biological research. We believe that by systematically mapping the mechanisms of bacterial immune evasion and drug resistance, we can identify novel targets for therapies that can improve treatment outcomes and mitigate the effects of antibiotic resistance.
We engage extensively in interdisciplinary collaborations, integrating ideas from biology, chemistry, physics, and computer science to solve complex infectious disease challenges. Our work is not only innovative—it is essential. With partnerships at academic institutions and biotech companies, we are expanding the realms of possibility in infectious disease research.
More research
The Lab
The Lab
Tim van opijnen
Principal Investigator
Dr. Tim van Opijnen received his Masters in evolutionary genetics from the University of Amsterdam, and as a graduate student he worked on the evolution of HIV at the Medical School of the University of Amsterdam. As a postdoctoral fellow in the lab of Dr. Andrew Camilli at Tufts University in Boston his interests shifted to bacterial pathogens and systems biology. He was a Professor of Microbial Systems Biology at Boston College (2013-2022), the Director of the Microbial Innovation lab at the Broad Institute of MIT and Harvard (2022-2024), and since 2024 a member of the Faculty and Associate Professor at Boston Children’s Hospital and Harvard Medical School.
The workers
Postdocs & Grad students
Check out the PEOPLE page for more information on who's who in the lab.
Please contact us if you are a (prospective) graduate student at HMS and you want to learn more about and/or join the lab.
Additionally, we are always interested to meet new talent and explore possible opportunities to join the lab. Just send an email and a CV to tim.vanopijnen@childrens.harvard.edu
The Rookies
Undergraduates
Undergraduates work in close collaboration with a postdoc or graduate student. And yes, there are openings!
If you are an undergraduate at Harvard, MIT, Tufts, Northeastern, BU, BC, or any other great school, and you’re passionate about research and can’t wait to get your hands dirty then send an email describing who you are, what you’re interested in, and why you are contacting us. Include your CV and send it to: tim.vanopijnen@childrens.harvard.edu
