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.
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:
Our research is supported by the David and Lucile Packard Foundation, the Pew Charitable Trusts, the NSF, and the NIH NIGMS.
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!
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-->