Publications by authors named "Benjamin Sobkowiak"

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The resistance trends in Mycobacterium kansasii pulmonary isolates and identification of risk factors for drug resistance in Taiwan.
Sheng-Bin Fan, Hung-Ling Huang, Hung-Pin Tu, Benjamin Sobkowiak, Meng-Hsuan Cheng

J Glob Antimicrob Resist· November 2025

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Integrating genomic and spatial analyses to describe tuberculosis transmission: a scoping review.
Yu Lan, Isabel Rancu, Melanie H Chitwood, Benjamin Sobkowiak, Kate Nyhan

Lancet Microbe· August 2025

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Classification of unsequenced Mycobacterium tuberculosis strains in a high-burden setting using a pairwise logistic regression approach.
Isabel Rancu, Benjamin Sobkowiak, Joshua L Warren, Nelly Ciobanu, Alexandru Codreanu

Access Microbiol· May 2025

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Distribution and transmission of M. tuberculosis in a high-HIV prevalence city in Malawi: A genomic and spatial analysis.
Melanie H Chitwood, Elizabeth L Corbett, Victor Ndhlovu, Benjamin Sobkowiak, Caroline Colijn

PLOS Glob Public Health· April 2025

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Signatures of transmission in within-host Mycobacterium tuberculosis complex variation: a retrospective genomic epidemiology study.
Katharine S Walter, Ted Cohen, Barun Mathema, Caroline Colijn, Benjamin Sobkowiak

Lancet Microbe· January 2025

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A new method for detecting mixed Mycobacterium tuberculosis infection and reconstructing constituent strains provides insights into transmission.
Benjamin Sobkowiak, Patrick Cudahy, Melanie H Chitwood, Taane G Clark, Caroline Colijn

Genome Med· January 2025

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TGV: suite of tools to visualize transmission graphs.
Jody E Phelan, Fatima Niazi, Linfeng Wang, Gabrielle C Ngwana-Joseph, Benjamin Sobkowiak

NAR Genom Bioinform· December 2024

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Tiled Amplicon Sequencing Enables Culture-free Whole-Genome Sequencing of Pathogenic Bacteria From Clinical Specimens.
Chaney C Kalinich, Freddy L Gonzalez, Alice Osmaston, Mallery I Breban, Isabel Distefano, Benjamin Sobkowiak

bioRxiv· December 2024

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Early prediction of Mycobacterium tuberculosis transmission clusters using supervised learning models.
Omid Gheysar Gharamaleki, Caroline Colijn, Inna Sekirov, James C Johnston, Benjamin Sobkowiak

Sci Rep· November 2024

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Author Correction: The recent rapid expansion of multidrug resistant Ural lineage Mycobacterium tuberculosis in Moldova.
Melanie H Chitwood, Caroline Colijn, Chongguang Yang, Valeriu Crudu, Nelly Ciobanu, Benjamin Sobkowiak

Nat Commun· October 2024

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Phylogeographic Analysis of Mycobacterium kansasii Isolates from Patients with M. kansasii Lung Disease in Industrialized City, Taiwan.
Patrick George Tobias Cudahy, Po-Chen Liu, Joshua L Warren, Benjamin Sobkowiak, Chongguang Yang

Emerg Infect Dis· August 2024

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Corrigendum to-"Identifying local foci of tuberculosis transmission in Moldova using a spatial multinomial logistic regression model" [eBioMedicine 102(2024) 105085].
Yu Lan, Valeriu Crudu, Nelly Ciobanu, Alexandru Codreanu, Melanie H Chitwood, Benjamin Sobkowiak

EBioMedicine· July 2024

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e3SIM: epidemiological-ecological-evolutionary simulation framework for genomic epidemiology.
Peiyu Xu, Shenni Liang, Andrew Hahn, Vivian Zhao, Wai Tung 'Jack' Lo, Benjamin Sobkowiak

bioRxiv· July 2024

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Identifying local foci of tuberculosis transmission in Moldova using a spatial multinomial logistic regression model.
Yu Lan, Valeriu Crudu, Nelly Ciobanu, Alexandru Codreanu, Melanie H Chitwood, Benjamin Sobkowiak

EBioMedicine· April 2024

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The recent rapid expansion of multidrug resistant Ural lineage Mycobacterium tuberculosis in Moldova.
Melanie H Chitwood, Caroline Colijn, Chongguang Yang, Valeriu Crudu, Nelly Ciobanu, Benjamin Sobkowiak

Nat Commun· April 2024

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Spatial modeling of Mycobacterium tuberculosis transmission with dyadic genetic relatedness data.
Joshua L Warren, Melanie H Chitwood, Benjamin Sobkowiak, Caroline Colijn, Ted Cohen

Biometrics· December 2023

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Signatures of transmission in within-host variation.
Katharine S Walter, Ted Cohen, Barun Mathema, Caroline Colijn, Benjamin Sobkowiak

medRxiv· December 2023

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Phylogenetic identification of influenza virus candidates for seasonal vaccines.
Maryam Hayati, Benjamin Sobkowiak, Jessica E Stockdale, Caroline Colijn

Sci Adv· November 2023

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The utility of SARS-CoV-2 genomic data for informative clustering under different epidemiological scenarios and sampling.
Benjamin Sobkowiak, Pouya Haghmaram, Natalie Prystajecky, James E A Zlosnik, John Tyson

Infect Genet Evol· September 2023

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Genomic epidemiology offers high resolution estimates of serial intervals for COVID-19.
Jessica E Stockdale, Kurnia Susvitasari, Paul Tupper, Benjamin Sobkowiak, Nicola Mulberry

Nat Commun· August 2023

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Comparing transmission reconstruction models from whole genome sequence data.
Benjamin Sobkowiak, Kamila Romanowski, Inna Sekirov, Jennifer L Gardy, James C Johnston

Epidemiol Infect· June 2023

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Genome-Wide Association with Uncertainty in the Genetic Similarity Matrix.
Shijia Wang, Shufei Ge, Benjamin Sobkowiak, Liangliang Wang, Louis Grandjean

J Comput Biol· February 2023

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Cov2clusters: genomic clustering of SARS-CoV-2 sequences.
Benjamin Sobkowiak, Kimia Kamelian, James E A Zlosnik, John Tyson, Anders Gonçalves da Silva

BMC Genomics· October 2022

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Phylogeography and transmission of M. tuberculosis in Moldova: A prospective genomic analysis.
Chongguang Yang, Benjamin Sobkowiak, Vijay Naidu, Alexandru Codreanu, Nelly Ciobanu

PLoS Med· February 2022

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Using Whole-genome Sequencing to Determine the Timing of Secondary Tuberculosis in British Columbia, Canada.
Kamila Romanowski, Benjamin Sobkowiak, Jennifer L Guthrie, Victoria J Cook, Jennifer L Gardy

Clin Infect Dis· August 2021

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