Bacterial Genomics Group people

Ashlee M. Earl
Senior Group Leader, Bacterial Genomics
617-714-7927
 
 
Abigail Manson
Group Leader, Bacterial Computatlonal Genomics

Abby is working 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

Bruce Walker
Bruce Walker
Visiting Scientist

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.

Colin Worby
Colin Worby
Computational Biologist

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.

Alejandro Pironti
Alejandro Pironti
Postdoctoral Associate

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).

Wen-Chi Chou
Wen-Chi Chou
Postdoctoral Associate

Wen-Chi is interested in human gut microbiome and its relationship to diseases. He is studying 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.

Tim Straub
Tim Straub
Associate Computational Biologist

Tim Straub joined the Broad Institute in 2015 where he works mainly in the realm of microbial genomics and evolution, with a strong focus on bacteria. He splits 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. Current projects include 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.

Rauf Salamzade
Rauf Salamzade
Associate Computational Biologist
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Lucas Van Dijk
Associate Computational biologist

Lucas joined our group as computational associate after finishing his M.Sc. in bioinformatics at Delft University of Technology. He has several years of software engineering experience, obtained at small companies, large companies and as Google Summer of Code student. Lucas focusses mainly on designing mathematical models, algorithms and data structures to analyse bacterial genomic data, to support our projects like understanding Enterococcus antibiotic resistance. His work also contributes to his PhD thesis which he pursues at Delft University of Technology.

Christophe Georgescu
Christophe Georgescu
Associate Computational Biologist

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 TUDelft in Thomas Abeel’s group where he worked on large structural variability in Mycobacterium tuberculosis. His focus is mainly to develop new bioinformatic algorithms.

Thomas Abeel
Visiting Scientist

Thomas Abeel is an Assistant 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

Keira Cohen
Visiting Scientist
 
 
Sr. Research Scientist
 
 

 

Previous Group Members

Gustavo C. Cerqueira
Senior Computational Scientist


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.  

 

Senior Computational Biologist


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.