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Microbial Phenomics & Systems Analyses Lab


LATEST NEWS

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.

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Microbial Phenomics & Systems Analyses Lab


LATEST NEWS

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.

The van Opijnen Lab practices microbial systems biology which basically means that we try to understand a bacterium as a complete system. So instead of carefully studying the organism one component at the time we build networks of all the genetic elements that drive a bacterium's behavior. Thereby we rapidly develop a real good understanding of how a bacterium does its thing, for instance trigger disease.

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Our work


We mainly focus on pathogenic bacteria and apply a combination of high-throughput robotics, next generation sequencing and computational biology to discover what makes them tick.

Our work


We mainly focus on pathogenic bacteria and apply a combination of high-throughput robotics, next generation sequencing and computational biology to discover what makes them tick.

The van Opijnen Lab focuses on projects to determine how bacteria trigger disease on a genome-wide level and species-wide scale, we elucidate the fine inner workings of antibiotics and we develop new genome-wide tools and screens to identify novel antimicrobial compounds.

More research

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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 between 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 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 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