Welcome to the Baym Lab at Harvard Medical School! We are part of the Departments of Biomedical Informatics and Microbiology, the Harvard Program in Therapeutic Science, and the Broad Institute

The lab The lab in July 2022

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

November 2022: Jasmijn's paper Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques, is published in Genome Biology!

November 2022: Michael receives the Excellence in Mentoring Award from the Systems, Synthetic, and Quantitative Biology PhD program

August 2022: Anurag's paper Resolving deleterious and near-neutral effects requires different pooled fitness assay designs, is posted as a preprint

July 2022: Natalia won the best poster award in the Evolution and Ecology section at Viruses of Microbes 2022!

July 2022: Siân and Ellie's collaboration with Akos Nyerges and the Church Lab, Swapped genetic code blocks viral infections and gene transfer, is posted as a preprint

May 2022: Anurag's paper Parallel changes in gene essentiality over 50,000 generations of evolution, is posted as a preprint

April 2022: Cristina's paper: Decreased thermal niche breadth as a trade-off of antibiotic resistance, is published in The ISME Journal!

March 2022: Amy passed her qualifying exams. Way to be qualified, Amy!

March 2022: Indra has been recognized with a Certificate of Distinction in Teaching for the Fall 2021!

February 2022: Siân's collaboration with the Balskus lab, The bacterial toxin colibactin triggers prophage induction, is published in Nature!

January 2022: Célia joined the lab as a postdoc!

January 2022: Karel Brinda has started a new position as INRIA Starting Faculty, at INRIA, Rennes, France. Congratulations, Karel!

December 2021: Indra passed her qualifying exams. Way to be qualified, Indra!

November 2021: Siân and Natalia's paper appeared on the cover of Cell Host and Microbe!

October 2021: The NASEM consensus report Michael contributed to, Combating Antimicrobial Resistance and Protecting the Miracle of Modern Medicine, has been released

October 2021: Fernando joined the lab as a postdoc!

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

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!

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

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