Welcome to the Baym Lab at Harvard Medical School, started in July 2017!

The lab The lab in November 2019

Antibiotic resistance is one of the defining public health threats of our time. Every time a new antibiotic has been introduced, resistance rapidly follows. We study how resistance evolves with the goal of making practical interventions that take into account, and even anticipates, pathogen evolution.

Our research ranges from basic evolutionary biology and bacteriology to analysis of clinical sequencing data to technology development.

Or, to describe what we do in Up Goer Five terms:

Very small living things that can not be killed hurt more and more people each year. People used to find many ways to kill them, but it is getting harder to find new ones that work. We study how the small things change over time to avoid being killed by us. We use this to find approaches to fighting the small things which expect these changes and change with them. We try to make approaches that can be used by doctors to keep killing the small things and to keep them from hurting people.

Our research is supported by the David and Lucile Packard Foundation, the Sloan Foundation, the Pew Charitable Trusts, and the NIH NIGMS.

Lab News

September 2021: Siân and Natalia's paper: Prophages encode phage-defense systems with cognate self-immunity, is published in Cell Host & Microbe!

September 2021: Jasmijn's paper Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification, is posted as a preprint

August 2021: Cristina Herren has started a new position as an Assistant Teaching Professor of Marine and Environmental Sciences at Northeastern University. Congratulations, Cristina!

August 2021: Jasmijn Baaijens has started a new position as an Assistant Professor of Computer Science at TU Delft. Congratulations, Jasmijn!

August 2021: Amy joined the lab as a PhD student!

June 2021: Indra joined the lab as a PhD student!

May 2021: Siân's collaboration with the Balskus lab, The gut bacterial natural product colibactin triggers induction of latent viruses in diverse bacteria, is posted as a preprint

April 2021: Karel's paper: Simplitigs as an efficient and scalable representation of de Bruijn graphs, is published in Genome Biology!

April 2021:Cristina's preprint posted: Decreased thermal tolerance as a trade-off of antibiotic resistance

March 2021: Michael's collaboration with Lee Kennedy-Shaffer and Bill Hanage, Perfect as the enemy of good: tracing transmissions with low-sensitivity tests to mitigate SARS-CoV-2 outbreaks, is published in The Lancet Microbe

March 2021: Michael has received a 2021 A. Clifford Barger Excellence in Mentoring Award from Harvard Medical School

February 2021: Ellie passed her qualifying exams. Way to be qualified, Ellie!

October 2020: Jasmijn is awarded the 2020 BioSB Young Investigator Award! Congratulations Jasmijn!!

October 2020: Arya joined the lab as a PhD student!

October 2020: Michael's collaboration with the Zhang Lab at Rice, Metastable hybridization-based DNA information storage to allow rapid and permanent erasure, is published in Nature Communications

August 2020: Ellie joined the lab as a PhD student!

July 2020:Siân and Natalia's preprint posted: Prophage-encoded phage defence proteins with cognate self-immunity

June 2020: The lab has been awarded a Pew Biomedical Scholarship for 2020-2024! 🎉🎉🎉

June 2020: Victoria and Siân's paper, Forensic microbial system for high-resolution object provenance, is published in Science!

May 9, 2020: Ellie helps the NC Dinos (NC 다이노스) throw out the first pitch.

February 2020: The lab has been awarded a Sloan Research Fellowship for 2020-2022! 🎉🎉🎉

February 2020: Karel's paper, Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing is published in Nature Microbiology!