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2025	Metagenomic co-assembly uncovers mobile antibiotic resistance genes in airborne microbiomes Communications Earth & Environment Burak Adnan Erkorkmaz, David Zeevi, Yinon Rudich
2025	Impact of simulation and reference catalogues on the evaluation of taxonomic profiling pipelines Microbial Genomics Vadim Puller, Florian Plaza Oñate, Edi Prifti, Raynald de Lahondès
2024	Insights into the seasonal changes in the taxonomic and functional diversity of bacteria in the eastern Arabian Sea: Shotgun metagenomics approach Marine Environmental Research Ashutosh Shankar Parab, Cathrine Sumathi Manohar
2024	Consumption of sucralose- and acesulfame-potassium-containing diet soda alters the relative abundance of microbial taxa at the species level: findings of two pilot studies Applied Physiology, Nutrition, and Metabolism Allison C. Sylvetsky, Rebecca A. Clement, Nathaniel Stearrett, Najy T. Issa, Fiona J. Dore, Raja Mazumder, Charles Hadley King, Monica J. Hubal, Peter J. Walter, Hongyi Cai, Sabyasachi Sen, Kristina I. Rother, Keith A. Crandall
2023	Conventional tobacco products harbor unique and heterogenous microbiomes Environmental Research Suhana Chattopadhyay, Padmini Ramachandran, Leena Malayil, Emmanuel F. Mongodin, Amy R. Sapkota
2023	Challenges and insights in the exploration of the low abundance human ocular surface microbiome Frontiers in Cellular and Infection Microbiology Elio L. Herzog, Marco Kreuzer, Martin S. Zinkernagel, Denise C. Zysset-Burri
2023	Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data Scientific Reports Aubrey R. Odom, Tyler Faits, Eduardo Castro-Nallar, Keith A. Crandall, W. Evan Johnson
2022	Comparative Analysis of Metagenomics and Metataxonomics for the Characterization of Vermicompost Microbiomes Frontiers in Microbiology Marcos Pérez-Losada, Dhatri Badri Narayanan, Allison R. Kolbe, Ignacio Ramos-Tapia, Eduardo Castro-Nallar, Keith A. Crandall, Jorge Domínguez
2022	SEQ2MGS: an effective tool for generating realistic artificial metagenomes from the existing sequencing data NAR Genomics and Bioinformatics Pieter-Jan Van Camp, Aleksey Porollo
2022	Viroscope: Plant viral diagnosis from high-throughput sequencing data using biologically-informed genome assembly coverage Frontiers in Microbiology Sandro L. Valenzuela, Tomás Norambuena, Verónica Morgante, Francisca García, Juan C. Jiménez, Carlos Núñez, Ignacia Fuentes, Bernardo Pollak
2022	Novel technologies to characterize and engineer the microbiome in inflammatory bowel disease Gut Microbes Alba Boix-Amorós, Hilary Monaco, Elisa Sambataro, Jose C. Clemente
2021	Whole-Genome Sequencing Analysis to Identify Infection with Multiple Species of Nontuberculous Mycobacteria Pathogens Visal Khieu, Pimjai Ananta, Orawee Kaewprasert, Marut Laohaviroj, Wises Namwat, Kiatichai Faksri
2021	A primer and discussion on DNA-based microbiome data and related bioinformatics analyses Peer Community Journal Gavin M. Douglas, Morgan G. I. Langille
2021	The oralome and its dysbiosis: New insights into oral microbiome-host interactions Computational and Structural Biotechnology Journal Allan Radaic, Yvonne L. Kapila
2020	Microbiome dynamics and genomic determinants of bovine mastitis Genomics M. Nazmul Hoque, Arif Istiaq, M. Shaminur Rahman, M. Rafiul Islam, Azraf Anwar, A.M.A.M. Zonaed Siddiki, Munawar Sultana, Keith A. Crandall, M. Anwar Hossain
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