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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.

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 Ó³»­´«Ã½

Sosie was an associate computational biologist in the lab from 2021-2024. She was also part of the Ó³»­´«Ã½ 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 Ó³»­´«Ã½, 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 Ó³»­´«Ã½, 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 Ó³»­´«Ã½ 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 Ó³»­´«Ã½ 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 Ó³»­´«Ã½, 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 Ó³»­´«Ã½ 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 Ó³»­´«Ã½ 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 Ó³»­´«Ã½ 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 Ó³»­´«Ã½

Tim Straub worked at the Ó³»­´«Ã½ 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 Ó³»­´«Ã½, 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.