Bacterial Genomics Group people
Abby has worked on comparative genomics projects of many different bacteria, including analyses of whole genome sequences of M. tuberculosis, Enterococcus, Fusobacterium, E. coli, and other microbes, with particular emphasis on the evolution of drug resistance and virulence factors. Read more
Colin Worby is interested in bacterial transmission dynamics and the spread of antimicrobial resistance. He is currently exploring the impact of antibiotic use on the human gut resistome and the acquisition of antibiotic resistance elements during international travel. Before joining the Broad Institute, he received his PhD in statistics from the University of Nottingham, and was a postdoctoral research fellow at Harvard School of Public Health and in the Department of Ecology and Evolutionary Biology at Princeton University.
Alex is a molecular biologist seeking to incorporate computational biology into the study of infectious disease and host-pathogen interactions. She is currently using comparative genomics and transcriptomics to identify bacterial and host factors that govern Salmonella persistence. Before joining the Broad Institute, she received her PhD in biology from New York University where she studied the endosymbiotic relationship that parasitic nematodes have with the bacteria Wolbachia.
Josh is a microbiologist interested in the ecological and evolutionary processes that drive the development and spread of antimicrobial-resistant superbugs. Currently, he is using large genomic datasets to understand the emergence of multidrug-resistant Enterobacteriaceae in vulnerable human populations, with the goal of informing health professionals of mitigation strategies. Before joining the Broad Institute, he received his PhD in Molecular and Evolutionary Systems Biology from the University of New Hampshire where he studied genome evolution and population dynamics of Staphylococcus species.
Veda is a microbiologist interested in using computational approaches to study the epidemiology and evolution of pathogens in healthcare settings. Currently, she is using a large collection of microbial genomes to understand the transmission of multidrug-resistant organisms in long term care facilities and the impact of decolonisation interventions on the spread of infections. Before joining the Broad Institute, she received her PhD in microbiology from MIT where studied host-microbe interactions in the skin microbiome during health and disease.
Miranda joined our group as a Postdoctoral Fellow after completing her PhD at the Karolinska Institute in Sweden, where she focused on the microbiome's role in psychiatric disorders. Currently, she is analyzing omics data, including metabolomics and metagenomics, from longitudinal studies in women with recurrent urinary tract infections (rUTI). The goal is to map the interactions between host, pathogen, and microbiota factors that contribute to rUTI.
Arjun joined the group after graduating from Dartmouth College with a B.A. in Biology and Mathematics. His previous research focused on searching for genes associated with hyperthermophily in the bacterial phylum Thermotogota. Currently, Arjun is working to track bacterial strain dynamics in the microbiota of international travelers and to determine the best methods for identifying cases of strain sharing between individuals.
Marco is a Computational Associate and a PhD student at Delft University of Technology. He is interested in using genomics to understand how resistant bacteria spread and evolve. Before joining the group, Marco earned his bachelor's and master's degrees in Bioengineering, specializing in Biomedical Engineering, at the University of Porto. His previous work included the development of computational approaches to analyze plasmid evolution, studying the association between cancer and the human microbiome, and developing Machine Learning models for biomedical applications.
Srujana is a Computational Associate in the Bacterial Genomics Group. She graduated from Carnegie Mellon University with an MS in Computational Biology, where her thesis examined allelic variation in receptor-peptide cell-cell signaling systems in Streptococcus pneumoniae. At the Broad Institute, her research investigates epidemiological patterns, antimicrobial resistance mechanisms, and within-host diversity of Neisseria gonorrhoeae, focusing on its adaptation to host niches and immune pressures through antigenic and transcriptional variation.
Joseph joined the group after graduating from Northeastern University with a B.S. in Data Science and Biology, where he applied computational methods to explore shared molecular signatures among autoimmune diseases. His current research focuses on understanding the role of the gut microbiome in women with a history of recurrent urinary tract infections, aiming to uncover microbial patterns that may contribute to infection susceptibility.
Bruce is VP of Technology at Applied Invention. He is working with the Broad's Bacterial Genomics Group on development of new computational algorithms and application of new technologies to bacterial genomics and microbiome analysis. Bruce has spent most of his career developing high-performance computing solutions for scientific and commercial applications. He worked in the computer industry for over 15 years at Sun Microsystems and Thinking Machines, where he was part of the core design team for the Connection Machine series of massively parallel supercomputers. Prior to joining Applied Invention, he worked at the Broad Institute for over 10 years as Director of Advanced IT, designing and managing the Broad's computing environment, and as Director of Genome Assembly and Analysis, leading a team developing algorithms and high-throughput pipelines for putting together high-quality genomes from viruses to mammals. Bruce has a B.S. in Physics from MIT
Thomas Abeel is an Associate Professor at the Department of Intelligent Systems of the Faculty of Electrical Engineering, Mathematics and Computer Science at the TU Delft. He is working with the Broad Bacterial Genomics group on several projects, including methods development projects. Read more
Previous Group Members
Lucas joined our group as computational associate after finishing his M.Sc. in bioinformatics at Delft University of Technology, after several years of software engineering experience, obtained at small companies, large companies and as Google Summer of Code student. Lucas focuses mon designing mathematical models, algorithms and data structures to analyse bacterial genomic data, to support our projects like understanding Enterococcus antibiotic resistance. His work also contributed to his PhD thesis, which he pursued at Delft University of Technology. Lucas currently works in the Data Sciences Platform at the Broad Institute
Sosie was an associate computational biologist in the lab from 2021-2024. She was also part of the Broad Biomedical Post-Baccalaureate Scholars Program. She completed her B.S. in Chemical Engineering at Stanford University, and her previous work includes cloning, drug design and testing, and data visualization. At the Broad, she worked on metagenomic assembly. She is currently pursuing a Ph.D. at Brown University.
Mark was an associate computational biologist in the lab from 2021-2024, interested in the relationship between host and microbiome. He used metatranscriptomics to profile the activity of the gut microbiome of women suffering from recurrent UTIs. Before joining the group, Mark received a B.A. in Statistics and Computational Biology from Colby College. At Colby, he studied the gut microbiome communities of wild bumblebees. He is currently pursuing a Ph.D. at the University of California, Berkeley.
Aysun is a visiting PhD student, currently working on the EnteroGenome project. She is doing her PhD thesis at Delft University of Technology in Thomas Abeel's group, exploring antimicrobial resistance in pathogenic bacteria. She is interested in comparative genomics using pan-genome graphs. Before joining the group, Aysun has received a B.Sc. and M.Sc. in chemical engineering at Bogazici University in Istanbul.
Evelyn Madoroba was visiting the Bacterial Genomics Group from January -June 2023. She is a Full Professor of Microbiology at University of Zululand, South Africa. She holds a PhD in Microbiology, an MSc in Biotechnology degree obtained with University Book Prize for best student in class. Furthermore, she holds a Masters in Business Leadership degree. In addition, she completed a Postgraduate Diploma in Higher Education, and was awarded the Student Excellence Award for the module on ‘Diversity and the Student in Higher Education’. She is rated by the National Research Foundation, South Africa as a researcher in category C2. She is passionate about understanding antimicrobial resistance, microbial genomics and characterization of bacterial pathogens including but not limited to Salmonella, Campylobacter, Staphylococcus, Listeria and Escherichia coli. Furthermore, her research interests include bioprospecting for new antimicrobial compounds produced by microorganisms that reside in marine environments. Evelyn is interested in microbial food safety, specifically rapid and accurate diagnosis of bacterial foodborne pathogens and is well-versed with the ISO17025 Quality Management System. She is passionate about capacity building, skills development, and academic entrepreneurship. Evelyn has trained several PhD and Masters students, and has published many peer-reviewed manuscripts.
Gracie was an associate computational biologist who joined the group after obtaining a B.A. in Molecular and Cell Biology and a minor in Computer Science from the University of California, Berkeley. Her previous research compared the vaginal, endocervical, and rectal microbiomes of Fijian women. She is currently pursuing a Master's degree in computer science at Northeastern University.
Sushmita Sridhar is a microbiologist studying antimicrobial resistance in enteric bacteria using a combination of computational and laboratory approaches. Her projects focus on the acquisition and carriage of drug-resistant organisms in international travelers and genomic and phenotypic characterization of drug-resistant Klebsiella pneumoniae from Bangladesh. Before her postdoc, she received her PhD from the University of Cambridge/Wellcome Sanger Institute, where she investigated the bacterial resistance to ciprofloxacin.
Andrew is interested in microbial ecology and the evolution of antibiotic resistance. He worked on the EnteroGenome project in collaboration with the Gilmore Lab. He studied Applied Math as an undergraduate at Harvard.
Ryan's research in the bacterial genomics group involved studying the evolution of drug resistance and microbial population genetics. She worked on comparative genomics projects to examine determinants of drug resistance in bacteria. Before joining the group, Ryan received a B.S. in Applied Mathematics-Biology from Brown University.
Wen-Chi's research in the bacterial genomics group was involved with human gut microbiome and its relationship to diseases. He studied the effects of cranberry juice on the gut microbiome of patients with a history of recurrent urinary tract infections. Before joining the Broad Institute, he received his Ph.D. in Bioinformatics from the University of Georgia, and he worked as a postdoctoral research fellow in genetic epidemiology at Harvard Medical School.
Gustavo's research in the bacterial genomics group involved the identification of the genetic causes of infectivity, pathogenicity and resistance to drugs and antibiotics in human and livestock pathogens. He used genotype-phenotype association methods based on gene content difference, single nucleotide polymorphisms and genome structural variants to accomplish that. Gustavo has a Ph.D. in Bioinformatics from the Universidade Federal de Minas Gerais (Brazil) and held positions at The Institute for Genomic Research (TIGR, currently JCVI) and the Institute for Genome Sciences (IGS, University of Maryland School of Medicine), before working at the Broad institute from 2011-2017.
Chris is interested in the genetic basis of pathogenicity and drug resistance in bacteria and fungi, and exploring phylogenetic and other evolutionary methods to uncover these relationships. His recent work focused on the evolution of drug resistance in Mycobacterium tuberculosis and virulence in Cryptococcus neoformans. Chris has a Ph.D. in Entomology from the University of Maryland, College Park and held postdoctoral positions at The Institute for Genomic Research (TIGR, currently JCVI) and the University of Rochester, before working at the Broad institute from 2010-2017.
Alejandro is interested in precision medicine for infectious disease. He analyses bacterial genomes in order to identify and track the genetic elements that make bacteria resistant or susceptible to antibiotics. Alejandro's current projects focus on the spread of carbapenem resistance in nosocomial Enterobacteriaceae and on the determinants of synergistic effects in antibiotic combinations. Before joining the Broad Institute, Alejandro performed research in the field of antiretroviral combination therapy. He earned his Ph.D. in Computational Biology at the Max Planck Institute for Informatics (Germany), before working at the Broad Institute from 2016-2021.
Rauf is an associate computational biologist in the group primarily interested in comparative genomics and evolutionary analysis of diverse bacterial clades. Currently, he provides support for projects focusing on the emergence of antibiotic resistant Enterococcus which are part of an ongoing collaboration with the Gilmore lab. Prior to joining the group, he received his Bachelor’s degree in Bioinformatics at the University of California, Santa Cruz. He worked at the Broad Institute from 2017-2020, before moving on to the University of Wisconsin-Madison to work on his Ph.D.
Christophe finished his M.Sc. in Bioinformatics at the Université Paris Diderot (France) doing an internship at the Broad Institute in Ashlee Earl’s group, working on a scalable orthogroup clustering algorithm. During his first year of M.Sc., he also did an internship at the T.U. Delft in Thomas Abeel’s group where he worked on large structural variability in Mycobacterium tuberculosis. He is currently working in the Data Sciences Platform at the Broad Institute
Tim Straub worked at the Broad institute from 2015-2021. He worked mainly in the realm of microbial genomics and evolution, with a strong focus on bacteria. He split his time between the bacterial and the malarial genomics groups at the GCID, assisting on multiple fronts studying the genomics of infectious diseases and collaborating with other research groups across the Harvard and MIT community. Project included the EnteroGenome project (collaborating with the Gilmore lab) and the genomics of Wolbachia parasite in Anopheles gambiae mosquitoes (Catteruccia lab). Before joining the Broad, he received his Bachelor's of Science from Tufts University as well as his Master's of Science from Dartmouth College.
Sophia Green was a visiting student in the bacterial genomics group in the spring of 2021. She is now attending MIT as a freshman. She is passionate about programming and its application in a variety of fields, especially life sciences. In the group, she worked on creating truth data sets for a bacterial genomics project.
