Microbial Phenomics & Systems Analyses Lab
LATEST NEWS
2026 APRIL - 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 MARCH - 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 FEBRUARY - 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 JANUARY - After years of work we have made one our largest projects available on the 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
2025 FALL UPDATE - Some beautiful new publications are available, for instance check out our latest genomics tool dualCRISPRi co-developed with the Veening lab in Lausanne and published in Cell Systems: https://doi.org/10.1016/j.cels.2025.101408
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).
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.
Microbial Phenomics & Systems Analyses Lab
LATEST NEWS
2026 APRIL - 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 MARCH - 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 FEBRUARY - 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 JANUARY - After years of work we have made one our largest projects available on the 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
2025 FALL UPDATE - Some beautiful new publications are available, for instance check out our latest genomics tool dualCRISPRi co-developed with the Veening lab in Lausanne and published in Cell Systems: https://doi.org/10.1016/j.cels.2025.101408
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).
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.
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
