Karel Brinda

Karel Brinda, PhD

Former Research Associate in Biomedical Informatics, Harvard Medical School
Baym Lab

Karel Brinda was a postdoctoral research associate, working with Bill Hanage in the Center for Communicable Disease Dynamics at Harvard T.H. Chan School of Public Health and Michael Baym in the Department of Biomedical Informatics at Harvard Medical School. His research focused on methods for rapid antibiotic resistance detection from point-of-care sequencing data obtained by mobile sequencing technologies.

Karel is the lead developer of RASE, ProPhyle, Ococo, RNFtools, SAMsift, ProphAsm, DyMas, and Disty McMatrixFace. He was also involved in the development of Blind Friendly Maps, ProPhex, Seed-Kraken, Seed-Jellyfish, and NanoSim-H.

Prior to joining Harvard, Karel received his PhD in computer science at Université Paris-Est and a master degree in mathematical computer science at the Czech Technical University in Prague.

SARS-CoV-2 epidemic after social and economic reopening in three U.S. states reveals shifts in age structure and clinical characteristics.
Authors: Wikle NB, Tran TN, Gentilesco B, Leighow SM, Albert E, Strong ER, Brinda K, Inam H, Yang F, Hossain S, Chan P, Hanage WP, Messick M, Pritchard JR, Hanks EM, Boni MF.
Sci Adv
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High-resolution genomic surveillance elucidates a multilayered hierarchical transfer of resistance between WWTP- and human/animal-associated bacteria.
Authors: Che Y, Xu X, Yang Y, Brinda K, Hanage W, Yang C, Zhang T.
Microbiome
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SARS-CoV-2 epidemic after social and economic reopening in three US states reveals shifts in age structure and clinical characteristics.
Authors: Wikle N, Tran TN, Gentilesco B, Leighow SM, Albert J, Strong ER, Brinda K, Inam H, Yang F, Hossain S, Chan P, Hanage WP, Messick M, Pritchard JR, Hanks EM, Boni MF.
medRxiv
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Reply to Partridge et al.: Complementary bioinformatics and experimental approaches to investigate the transfer of AMR genes.
Authors: Che Y, Yang Y, Xu X, Brinda K, Polz MF, Hanage WP, Zhang T.
Proc Natl Acad Sci U S A
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Optimal SARS-CoV-2 vaccine allocation using real-time attack-rate estimates in Rhode Island and Massachusetts.
Authors: Tran TN, Wikle NB, Albert E, Inam H, Strong E, Brinda K, Leighow SM, Yang F, Hossain S, Pritchard JR, Chan P, Hanage WP, Hanks EM, Boni MF.
BMC Med
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Reply to Shaw: Challenges for enrichment analysis of AMR gene-bearing plasmids.
Authors: Che Y, Yang Y, Xu X, Brinda K, Polz MF, Hanage WP, Zhang T.
Proc Natl Acad Sci U S A
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Simplitigs as an efficient and scalable representation of de Bruijn graphs.
Authors: Brinda K, Baym M, Kucherov G.
Genome Biol
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Conjugative plasmids interact with insertion sequences to shape the horizontal transfer of antimicrobial resistance genes.
Authors: Che Y, Yang Y, Xu X, Brinda K, Polz MF, Hanage WP, Zhang T.
Proc Natl Acad Sci U S A
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Optimal SARS-CoV-2 vaccine allocation using real-time seroprevalence estimates in Rhode Island and Massachusetts.
Authors: Tran TN, Wikle N, Albert J, Inam H, Strong E, Brinda K, Leighow SM, Yang F, Hossain S, Pritchard JR, Chan P, Hanage WP, Hanks EM, Boni MF.
medRxiv
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Using Genetic Distance from Archived Samples for the Prediction of Antibiotic Resistance in Escherichia coli.
Authors: MacFadden DR, Coburn B, Brinda K, Corbeil A, Daneman N, Fisman D, Lee RS, Lipsitch M, McGeer A, Melano RG, Mubareka S, Hanage WP.
Antimicrob Agents Chemother
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