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Muhammad Farooq, Ifra Siddique, Amina Nabi, Muhammad Naseer, Ayesha Younis, Sadia Siddique

Dana Bludau, Guido Sieber, Manan Shah, Aman Deep, Jens Boenigk, Daniela Beisser

Inès Barrenechea Angeles, Ngoc-Loi Nguyen, Mattia Greco, Koh Siang Tan, Jan Pawlowski

Yinglin Xia, Jun Sun

Ze-Gang Wei, Xu Chen, Xiao-Dan Zhang, Hao Zhang, Xing-Guo Fan, Hong-Yan Gao, Fei Liu, Yu Qian

Jiahui Xu, Jianlin Han, Hua Su, Changyu Zhu, Zijing Quan, Lei Wu, Zhenzhen Yi

Antonija Kulaš, Vesna Gulin, Renata Matoničkin Kepčija, Petar Žutinić, Mirela Sertić Perić, Sandi Orlić, Katarina Kajan, Thorsten Stoeck, Guillaume Lentendu, Ivan Čanjevac, Ivan Martinić, Marija Gligora Udovič

Ze-Gang Wei, Xiao-Dan Zhang, Ming Cao, Fei Liu, Yu Qian, Shao-Wu Zhang

Yuchun Yang, Jie Pan, Zhichao Zhou, Jiapeng Wu, Yang Liu, Jih-Gaw Lin, Yiguo Hong, Xiaoyan Li, Meng Li, Ji-Dong Gu

M.G Kelly, S Juggins, D.G Mann, S Sato, R Glover, N Boonham, M Sapp, E Lewis, U Hany, P Kille, T Jones, K Walsh

Sébastien Terrat, Christophe Djemiel, Corentin Journay, Battle Karimi, Samuel Dequiedt, Walid Horrigue, Pierre‐Alain Maron, Nicolas Chemidlin Prévost‐Bouré, Lionel Ranjard

Kathleen J. Pitz, Jinchen Guo, Shannon B. Johnson, Tracy L. Campbell, Haibin Zhang, Robert C. Vrijenhoek, Francisco P. Chavez, Jonathan Geller

Yoann Dufresne, Franck Lejzerowicz, Laure Apotheloz Perret-Gentil, Jan Pawlowski, Tristan Cordier

Sabine Filker, Steffen Kühner, Melanie Heckwolf, Jan Dierking, Thorsten Stoeck

Gianna Pitsch, Estelle Patricia Bruni, Dominik Forster, Zhishuai Qu, Bettina Sonntag, Thorsten Stoeck, Thomas Posch

Dominik Forster, Guillaume Lentendu, Sabine Filker, Elyssa Dubois, Thomas A. Wilding, Thorsten Stoeck

David A. Caron, Sarah K. Hu

Wei Xiong, Aibin Zhan

Martin Rippin, Sebastian Lange, Nicole Sausen, Burkhard Becker

Bharat Mishra, Yali Sun, Hadia Ahmed, Xiaoyu Liu, M. Shahid Mukhtar

Frédéric Mahé, Colomban de Vargas, David Bass, Lucas Czech, Alexandros Stamatakis, Enrique Lara, David Singer, Jordan Mayor, John Bunge, Sarah Sernaker, Tobias Siemensmeyer, Isabelle Trautmann, Sarah Romac, Cédric Berney, Alexey Kozlov, Edward A. D. Mitchell, Christophe V. W. Seppey, Elianne Egge, Guillaume Lentendu, Rainer Wirth, Gabriel Trueba, Micah Dunthorn

Cecilia Noecker, Colin P. McNally, Alexander Eng, Elhanan Borenstein

Sten Anslan, Mohammad Bahram, Indrek Hiiesalu, Leho Tedersoo

Patrick J. Keeling, Javier del Campo

2025	Methods and Protocols in Food Science Muhammad Farooq, Ifra Siddique, Amina Nabi, Muhammad Naseer, Ayesha Younis, Sadia Siddique
2025	Breaking the Standard: Can Oxford Nanopore Technologies Sequencing Compete With Illumina in Protistan Amplicon Studies? Environmental DNA Dana Bludau, Guido Sieber, Manan Shah, Aman Deep, Jens Boenigk, Daniela Beisser
2024	Assigning the unassigned: A signature-based classification of rDNA metabarcodes reveals new deep-sea diversity PLOS ONE Inès Barrenechea Angeles, Ngoc-Loi Nguyen, Mattia Greco, Koh Siang Tan, Jan Pawlowski
2023	Bioinformatic and Statistical Analysis of Microbiome Data Yinglin Xia, Jun Sun
2023	Comparison of Methods for Biological Sequence Clustering IEEE/ACM Transactions on Computational Biology and Bioinformatics Ze-Gang Wei, Xu Chen, Xiao-Dan Zhang, Hao Zhang, Xing-Guo Fan, Hong-Yan Gao, Fei Liu, Yu Qian
2022	Diversity Patterns of Protists Are Highly Affected by Methods Disentangling Biological Variants: A Case Study in Oligotrich (s.l.) Ciliates Microorganisms Jiahui Xu, Jianlin Han, Hua Su, Changyu Zhu, Zijing Quan, Lei Wu, Zhenzhen Yi
2022	ACS In Focus
2021	Ciliates (Alveolata, Ciliophora) as bioindicators of environmental pressure: A karstic river case Ecological Indicators Antonija Kulaš, Vesna Gulin, Renata Matoničkin Kepčija, Petar Žutinić, Mirela Sertić Perić, Sandi Orlić, Katarina Kajan, Thorsten Stoeck, Guillaume Lentendu, Ivan Čanjevac, Ivan Martinić, Marija Gligora Udovič
2021	Comparison of Methods for Picking the Operational Taxonomic Units From Amplicon Sequences Frontiers in Microbiology Ze-Gang Wei, Xiao-Dan Zhang, Ming Cao, Fei Liu, Yu Qian, Shao-Wu Zhang
2020	Complex microbial nitrogen-cycling networks in three distinct anammox-inoculated wastewater treatment systems Water Research Yuchun Yang, Jie Pan, Zhichao Zhou, Jiapeng Wu, Yang Liu, Jih-Gaw Lin, Yiguo Hong, Xiaoyan Li, Meng Li, Ji-Dong Gu
2020	Development of a novel metric for evaluating diatom assemblages in rivers using DNA metabarcoding Ecological Indicators M.G Kelly, S Juggins, D.G Mann, S Sato, R Glover, N Boonham, M Sapp, E Lewis, U Hany, P Kille, T Jones, K Walsh
2020	ReClustOR: a re‐clustering tool using an open‐reference method that improves operational taxonomic unit definition Methods in Ecology and Evolution Sébastien Terrat, Christophe Djemiel, Corentin Journay, Battle Karimi, Samuel Dequiedt, Walid Horrigue, Pierre‐Alain Maron, Nicolas Chemidlin Prévost‐Bouré, Lionel Ranjard
2020	Zooplankton biogeographic boundaries in the California Current System as determined from metabarcoding PLOS ONE Kathleen J. Pitz, Jinchen Guo, Shannon B. Johnson, Tracy L. Campbell, Haibin Zhang, Robert C. Vrijenhoek, Francisco P. Chavez, Jonathan Geller
2019	SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data BMC Bioinformatics Yoann Dufresne, Franck Lejzerowicz, Laure Apotheloz Perret-Gentil, Jan Pawlowski, Tristan Cordier
2019	A fundamental difference between macrobiota and microbial eukaryotes: protistan plankton has a species maximum in the freshwater‐marine transition zone of the Baltic Sea Environmental Microbiology Sabine Filker, Steffen Kühner, Melanie Heckwolf, Jan Dierking, Thorsten Stoeck
2019	Seasonality of Planktonic Freshwater Ciliates: Are Analyses Based on V9 Regions of the 18S rRNA Gene Correlated With Morphospecies Counts? Frontiers in Microbiology Gianna Pitsch, Estelle Patricia Bruni, Dominik Forster, Zhishuai Qu, Bettina Sonntag, Thorsten Stoeck, Thomas Posch
2019	Improving eDNA‐based protist diversity assessments using networks of amplicon sequence variants Environmental Microbiology Dominik Forster, Guillaume Lentendu, Sabine Filker, Elyssa Dubois, Thomas A. Wilding, Thorsten Stoeck
2019	Are We Overestimating Protistan Diversity in Nature? Trends in Microbiology David A. Caron, Sarah K. Hu
2018	Testing clustering strategies for metabarcoding‐based investigation of community–environment interactions Molecular Ecology Resources Wei Xiong, Aibin Zhan
2018	Biodiversity of biological soil crusts from the Polar Regions revealed by metabarcoding FEMS Microbiology Ecology Martin Rippin, Sebastian Lange, Nicole Sausen, Burkhard Becker
2017	Global temporal dynamic landscape of pathogen-mediated subversion of Arabidopsis innate immunity Scientific Reports Bharat Mishra, Yali Sun, Hadia Ahmed, Xiaoyu Liu, M. Shahid Mukhtar
2017	Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests Nature Ecology & Evolution Frédéric Mahé, Colomban de Vargas, David Bass, Lucas Czech, Alexandros Stamatakis, Enrique Lara, David Singer, Jordan Mayor, John Bunge, Sarah Sernaker, Tobias Siemensmeyer, Isabelle Trautmann, Sarah Romac, Cédric Berney, Alexey Kozlov, Edward A. D. Mitchell, Christophe V. W. Seppey, Elianne Egge, Guillaume Lentendu, Rainer Wirth, Gabriel Trueba, Micah Dunthorn
2017	High-resolution characterization of the human microbiome Translational Research Cecilia Noecker, Colin P. McNally, Alexander Eng, Elhanan Borenstein
2017	PipeCraft: Flexible open‐source toolkit for bioinformatics analysis of custom high‐throughput amplicon sequencing data Molecular Ecology Resources Sten Anslan, Mohammad Bahram, Indrek Hiiesalu, Leho Tedersoo
2017	Marine Protists Are Not Just Big Bacteria Current Biology Patrick J. Keeling, Javier del Campo
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