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 of Harvard and MIT.

The lab The lab in August 2023

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 Pew Charitable Trusts, the NSF, and the NIH NIGMS.

Lab News

April 2024: Natalia and Siân's paper, Diverse and abundant phages exploit conjugative plasmids, is published in Nature Communications!

March 2024: Shreyas passed his quals. Congratulations, Shreyas!

March 2024: Ellie was awarded an Kirschstein-NRSA/F31 fellowship from the NIH/NIAID for her work on phage discovery!

March 2024: Sophia passed her quals. Congratulations, Sophia!

March 2024: Tatiana joined the lab as a postdoc

March 2024: Michael was promoted to Associate Professor of Biomedical Informatics

February 2024: Natalia successfully defended her PhD thesis! Congratulations, Dr. Quinones-Olvera!! 🍾 🎉

February 2024: Kepler joined the lab as a PhD student

January 2024: Anurag's paper, Changing fitness effects of mutations through long-term bacterial evolution, is published in Science!

December 2023: Adele joined the lab as a Master's student

September 2023: Natalia, Fernando, and Celia give talks at the EMBO Plasmids as vehicles of AMR spread meeting

September 2023: Shreyas joined the lab as a PhD student

August 2023: Siân is awarded Best Talk at the Evergreen Phage Meeting!

August 2023: NSF awarded a grant for our work on plasmid-dependent phages!

May 2023: Anurag's paper, Resolving Deleterious and Near-Neutral Effects Requires Different Pooled Fitness Assay Designss, is published in the Journal of Molecular Evolution!

April 2023: Karel's paper with Simone and Natalia Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression, is posted as a preprint

April 2023: Anurag successfully defended his PhD thesis! Congratulations, Dr. Limdi!! 🍾 🎉

April 2023: Sophia joined the lab as a PhD student

March 2023: Natalia and Siân's paper Diverse and abundant viruses exploit conjugative plasmids, is posted as a preprint

March 2023: Siân and Ellie's collaboration with Akos Nyerges and the Church Lab, A swapped genetic code prevents viral infections and gene transfer, is published in Nature

February 2023: Siân's collaboration with Charlie Dulberger and the Rubin and Hatfull Labs, Mycobacterial nucleoid-associated protein Lsr2 is required for productive mycobacteriophage infection, is published in Nature Microbiology

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!

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

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 22, 2020:The wet lab has resumed limited activity with infection control measures.

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.

March 13, 2020:The wet lab closes for Covid-19.

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!

January 2020: Kaylee joined the lab as a research associate

November 2019: Elle is awarded a Rhodes Scholarship for 2020! Congratulations, Elle!

October 2019: Lucy and Jasmijn join the lab as postdocs

October 2019: Eve's Thesis wins "Best Master Thesis in Life Sciences and Technology" at EPFL! Congratulations, Eve!

September 2019: Siân and Natalia are contributing authors on The fitness landscape of the African Salmonella Typhimurium ST313 strain D23580 reveals unique properties of the pBT1 plasmid in PLOS Pathogens

July 2019: The lab has been awarded a MIRA/R35 Outstanding Early-Stage Investigator Award by NIH/NIGMS for 2019-2024! 🎉🎉🎉

July 2019: Michael contributes to Cell Host and Microbe's Voices on overcoming antibiotic resistance: Sustainable Stewardship Needs Evolution

July 2019: Eve presents a poster at the Microbial Population Biology Gordon Research Conference.

June 2019: Siân presents three talks and two posters at ASM Microbe, and wins a travel award! Wow.

June 2019: Mische joined the lab as a summer undergrad

May 2019: Elle joined the lab as a summer undergrad

March 2019: Natalia passed her quals. Congratulations, Natalia!

February 2019: Anurag passed his quals. Congratulations, Anurag!

February 2019: Cristina speaks at ASLO 2019 in Puerto Rico

October 2018: The lab has been awarded a 2018-2023 Packard Fellowship!

August 28, 2018: Karel's preprint posted: Lineage calling can identify antibiotic resistant clones within minutes

September 2018: Eve joined the lab as a master's student

September 2018: Michael speaks at the Southern California Microbiome Symposium

September 2018: Michael speaks at Lake Arrowhead Microbial Genomics, Siân and Karel present posters

September 2018: Cristina speaks at ISME in Germany

August 2018: Anurag joined the lab as a PhD student

July 2018: Natalia joined the lab as a PhD student

July 2018: Michael speaks at Microbial Stress Response GRC

May 2018: Isabel joined the lab as a summer undergrad

April 2018: Michael speaks at the Harvard MSI Symposium

April 2018: Simone joined the lab as a master's student

April 2018: Siân joined the lab as a postdoc

March 2018: Victoria joined the lab as a technician

February 2018: Scott joined the lab as a visiting postdoc

February 8, 2018: Cristina's preprint posted: Stronger connectivity of the resident gut microbiome lends resistance to invading bacteria

September 2017: Cristina joined the lab

August 2017: Michael speaks at the Microbial Darwinian Medicine Workshop

July 2017: The lab has started! Karel joins the lab as a joint postdoc with the Hanage Lab at HSPH