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Romulo A. dos Santos, Petr Blabolil

Alejandro De Santiago, Tiago José Pereira, Timothy John Ferrero, Natalie Barnes, Delphine Lallias, Simon Creer, Holly M. Bik

Philipp E. Bayer, Adam Bennett, Georgia Nester, Shannon Corrigan, Eric J. Raes, Madalyn Cooper, Marcelle E. Ayad, Philip McVey, Anya Kardailsky, Jessica Pearce, Matthew W. Fraser, Priscila Goncalves, Stephen Burnell, Sebastian Rauschert

Lenore Pipes, Rasmus Nielsen

Zhuoying Li, Wencheng Zhao, Yun Jiang, Yongjing Wen, Min Li, Li Liu, Keshu Zou

Ingrid V. Bunholi, Nicole R. Foster, Jordan M. Casey

Jillian Rumore, Matthew Walker, Franco Pagotto, Jessica D. Forbes, Christy-Lynn Peterson, Andrea D. Tyler, Morag Graham, Gary Van Domselaar, Celine Nadon, Aleisha Reimer, Natalie Knox

Melissa Gray, Zhengqiao Zhao, Gail L. Rosen

Christina Nießl, Moritz Herrmann, Chiara Wiedemann, Giuseppe Casalicchio, Anne‐Laure Boulesteix

Marlène Chiarello, Mark McCauley, Sébastien Villéger, Colin R. Jackson

Lidia Garrido-Sanz, Miquel Àngel Senar, Josep Piñol

Carine Poussin, Lusine Khachatryan, Nicolas Sierro, Vijay Kumar Narsapuram, Fernando Meyer, Vinay Kaikala, Vandna Chawla, Usha Muppirala, Sunil Kumar, Vincenzo Belcastro, James N. D. Battey, Elena Scotti, Stéphanie Boué, Alice C. McHardy, Manuel C. Peitsch, Nikolai V. Ivanov, Julia Hoeng

Kodjovi D. Mlaga, Alban Mathieu, Charles Joly Beauparlant, Alban Ott, Ahmad Khodr, Olivier Perin, Arnaud Droit

Stefan Buchka, Alexander Hapfelmeier, Paul P. Gardner, Rory Wilson, Anne-Laure Boulesteix

Jose S. Hleap, Joanne E. Littlefair, Dirk Steinke, Paul D. N. Hebert, Melania E. Cristescu

Laetitia Mathon, Alice Valentini, Pierre‐Edouard Guérin, Eric Normandeau, Cyril Noel, Clément Lionnet, Emilie Boulanger, Wilfried Thuiller, Louis Bernatchez, David Mouillot, Tony Dejean, Stéphanie Manel

Michal Ziemski, Treepop Wisanwanichthan, Nicholas A. Bokulich, Benjamin D. Kaehler

Pei-Ying Hong, David Mantilla-Calderon, Changzhi Wang

Stephanie N. Kivlin, Christine V. Hawkes

Karen W. Hughes, Alexis Case, P. Brandon Matheny, Stephanie Kivlin, Ronald H. Petersen, Andrew N. Miller, Teresa Iturriaga

Mathieu Seppey, Mosè Manni, Evgeny M. Zdobnov

Daniel Straub, Nia Blackwell, Adrian Langarica-Fuentes, Alexander Peltzer, Sven Nahnsen, Sara Kleindienst

Mikang Sim, Jongin Lee, Daehwan Lee, Daehong Kwon, Jaebum Kim

Devon R. O'Rourke, Nicholas A. Bokulich, Michelle A. Jusino, Matthew D. MacManes, Jeffrey T. Foster

Lukas M. Weber, Wouter Saelens, Robrecht Cannoodt, Charlotte Soneson, Alexander Hapfelmeier, Paul P. Gardner, Anne-Laure Boulesteix, Yvan Saeys, Mark D. Robinson

Enrique Doster, Pablo Rovira, Noelle R. Noyes, Brandy A. Burgess, Xiang Yang, Margaret D. Weinroth, Lyndsey Linke, Roberta Magnuson, Christina Boucher, Keith E. Belk, Paul S. Morley

Alexander M Piper, Jana Batovska, Noel O I Cogan, John Weiss, John Paul Cunningham, Brendan C Rodoni, Mark J Blacket

2025	Comparison of Bioinformatic Pipelines for eDNA Metabarcoding Data Analysis of Fish Populations Fishes Romulo A. dos Santos, Petr Blabolil
2025	Persistent Gaps and Errors in Reference Databases Impede Ecologically Meaningful Taxonomy Assignments in 18S rRNA Studies: A Case Study of Terrestrial and Marine Nematodes Environmental DNA Alejandro De Santiago, Tiago José Pereira, Timothy John Ferrero, Natalie Barnes, Delphine Lallias, Simon Creer, Holly M. Bik
2025	A Comprehensive Evaluation of Taxonomic Classifiers in Marine Vertebrate eDNA Studies Molecular Ecology Resources Philipp E. Bayer, Adam Bennett, Georgia Nester, Shannon Corrigan, Eric J. Raes, Madalyn Cooper, Marcelle E. Ayad, Philip McVey, Anya Kardailsky, Jessica Pearce, Matthew W. Fraser, Priscila Goncalves, Stephen Burnell, Sebastian Rauschert
2024	A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets eLife Lenore Pipes, Rasmus Nielsen
2024	New insights into biologic interpretation of bioinformatic pipelines for fish eDNA metabarcoding: A case study in Pearl River estuary Journal of Environmental Management Zhuoying Li, Wencheng Zhao, Yun Jiang, Yongjing Wen, Min Li, Li Liu, Keshu Zou
2023	Environmental DNA and RNA in aquatic community ecology: Toward methodological standardization Environmental DNA Ingrid V. Bunholi, Nicole R. Foster, Jordan M. Casey
2023	Use of a taxon-specific reference database for accurate metagenomics-based pathogen detection of Listeria monocytogenes in turkey deli meat and spinach BMC Genomics Jillian Rumore, Matthew Walker, Franco Pagotto, Jessica D. Forbes, Christy-Lynn Peterson, Andrea D. Tyler, Morag Graham, Gary Van Domselaar, Celine Nadon, Aleisha Reimer, Natalie Knox
2022	How Scalable Are Clade-Specific Marker K-Mer Based Hash Methods for Metagenomic Taxonomic Classification? Frontiers in Signal Processing Melissa Gray, Zhengqiao Zhao, Gail L. Rosen
2022	Over‐optimism in benchmark studies and the multiplicity of design and analysis options when interpreting their results WIREs Data Mining and Knowledge Discovery Christina Nießl, Moritz Herrmann, Chiara Wiedemann, Giuseppe Casalicchio, Anne‐Laure Boulesteix
2022	Ranking the biases: The choice of OTUs vs. ASVs in 16S rRNA amplicon data analysis has stronger effects on diversity measures than rarefaction and OTU identity threshold PLOS ONE Marlène Chiarello, Mark McCauley, Sébastien Villéger, Colin R. Jackson
2022	Drastic reduction of false positive species in samples of insects by intersecting the default output of two popular metagenomic classifiers PLOS ONE Lidia Garrido-Sanz, Miquel Àngel Senar, Josep Piñol
2022	Crowdsourced benchmarking of taxonomic metagenome profilers: lessons learned from the sbv IMPROVER Microbiomics challenge BMC Genomics Carine Poussin, Lusine Khachatryan, Nicolas Sierro, Vijay Kumar Narsapuram, Fernando Meyer, Vinay Kaikala, Vandna Chawla, Usha Muppirala, Sunil Kumar, Vincenzo Belcastro, James N. D. Battey, Elena Scotti, Stéphanie Boué, Alice C. McHardy, Manuel C. Peitsch, Nikolai V. Ivanov, Julia Hoeng
2021	Soil Biology Kalaivani Nadarajah
2021	HCK and ABAA: A Newly Designed Pipeline to Improve Fungi Metabarcoding Analysis Frontiers in Microbiology Kodjovi D. Mlaga, Alban Mathieu, Charles Joly Beauparlant, Alban Ott, Ahmad Khodr, Olivier Perin, Arnaud Droit
2021	On the optimistic performance evaluation of newly introduced bioinformatic methods Genome Biology Stefan Buchka, Alexander Hapfelmeier, Paul P. Gardner, Rory Wilson, Anne-Laure Boulesteix
2021	Assessment of current taxonomic assignment strategies for metabarcoding eukaryotes Molecular Ecology Resources Jose S. Hleap, Joanne E. Littlefair, Dirk Steinke, Paul D. N. Hebert, Melania E. Cristescu
2021	Benchmarking bioinformatic tools for fast and accurate eDNA metabarcoding species identification Molecular Ecology Resources Laetitia Mathon, Alice Valentini, Pierre‐Edouard Guérin, Eric Normandeau, Cyril Noel, Clément Lionnet, Emilie Boulanger, Wilfried Thuiller, Louis Bernatchez, David Mouillot, Tony Dejean, Stéphanie Manel
2021	Beating Naive Bayes at Taxonomic Classification of 16S rRNA Gene Sequences Frontiers in Microbiology Michal Ziemski, Treepop Wisanwanichthan, Nicholas A. Bokulich, Benjamin D. Kaehler
2020	Metagenomics as a Tool To Monitor Reclaimed-Water Quality Applied and Environmental Microbiology Pei-Ying Hong, David Mantilla-Calderon, Changzhi Wang
2020	Spatial and temporal turnover of soil microbial communities is not linked to function in a primary tropical forest Ecology Stephanie N. Kivlin, Christine V. Hawkes
2020	Secret lifestyles of pyrophilous fungi in the genus Sphaerosporella American Journal of Botany Karen W. Hughes, Alexis Case, P. Brandon Matheny, Stephanie Kivlin, Ronald H. Petersen, Andrew N. Miller, Teresa Iturriaga
2020	LEMMI: a continuous benchmarking platform for metagenomics classifiers Genome Research Mathieu Seppey, Mosè Manni, Evgeny M. Zdobnov
2020	Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline Frontiers in Microbiology Daniel Straub, Nia Blackwell, Adrian Langarica-Fuentes, Alexander Peltzer, Sven Nahnsen, Sara Kleindienst
2020	TAMA: improved metagenomic sequence classification through meta-analysis BMC Bioinformatics Mikang Sim, Jongin Lee, Daehwan Lee, Daehong Kwon, Jaebum Kim
2020	A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses Ecology and Evolution Devon R. O'Rourke, Nicholas A. Bokulich, Michelle A. Jusino, Matthew D. MacManes, Jeffrey T. Foster
2019	Essential guidelines for computational method benchmarking Genome Biology Lukas M. Weber, Wouter Saelens, Robrecht Cannoodt, Charlotte Soneson, Alexander Hapfelmeier, Paul P. Gardner, Anne-Laure Boulesteix, Yvan Saeys, Mark D. Robinson
2019	A Cautionary Report for Pathogen Identification Using Shotgun Metagenomics; A Comparison to Aerobic Culture and Polymerase Chain Reaction for Salmonella enterica Identification Frontiers in Microbiology Enrique Doster, Pablo Rovira, Noelle R. Noyes, Brandy A. Burgess, Xiang Yang, Margaret D. Weinroth, Lyndsey Linke, Roberta Magnuson, Christina Boucher, Keith E. Belk, Paul S. Morley
2019	Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance GigaScience Alexander M Piper, Jana Batovska, Noel O I Cogan, John Weiss, John Paul Cunningham, Brendan C Rodoni, Mark J Blacket
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