Publications

Peer-reviewed research and preprint contributions in biochemistry, biophysics, and computational biology.

Google Scholar ORCID ID

FAIRer DNA sequence data with q2-ena-uploader: a QIIME 2 plugin for data deposition in the European Nucleotide Archive

Zuzana Sebechlebska, Michał Ziemski, Nicholas A. Bokulich

2026 • Microbiology Resource Announcements • Bioinformatics • DOI: 10.1128/mra.01155-25

ViromeXplore: integrative workflows for complete and reproducible virome characterization

Rodrigo Hernández-Velázquez, Michał Ziemski, Nicholas A. Bokulich

2025 • Briefings in Bioinformatics • Bioinformatics • DOI: 10.1093/bib/bbaf638

MOSHPIT: accessible, reproducible metagenome data science on the QIIME 2 framework

Michał Ziemski, Liz Gehret, Anthony Simard, Santiago Castro Dau, Vinzent Risch, Doriela Grabocka, Christos Matzoros, Colin Wood, Paula Momo Cabrera, Rodrigo Hernández-Velázquez, Chloe Herman, Keegan Evans, Michael S. Robeson, Evan Bolyen, J. Gregory Caporaso, Nicholas A. Bokulich

2025 • bioRxiv (Preprint) • Bioinformatics • DOI: 10.1101/2025.01.27.635007

Advancing FAIR meta-analyses of nucleotide sequence data with q2-fondue

A. Adamov, Michał Ziemski, Lina Kim, Lena Flörl, Nicholas A. Bokulich

2023 • F1000Research • Bioinformatics • DOI: 10.7490/f1000research.1119586.1

Reproducible acquisition, management and meta-analysis of nucleotide sequence (meta)data using q2-fondue

Michał Ziemski, A. Adamov, Lina Kim, Lena Flörl, Nicholas A. Bokulich

2022 • Bioinformatics • Bioinformatics • DOI: 10.1093/bioinformatics/btac639

RESCRIPt: Reproducible sequence taxonomy reference database management

Michael S. Robeson, Devon R. O’Rourke, Benjamin D. Kaehler, Michał Ziemski, Matthew R. Dillon, Jeffrey T. Foster, Nicholas A. Bokulich

2021 • PLOS Computational Biology • Bioinformatics • DOI: 10.1371/journal.pcbi.1009581

Beating Naive Bayes at Taxonomic Classification of 16S rRNA Gene Sequences

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

2021 • Frontiers in Microbiology • Bioinformatics • DOI: 10.3389/fmicb.2021.644487

Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops

Matthew R. Dillon, Evan Bolyen, A. Adamov, Aeriel D. Belk, Emily M. Borsom, Zachary M. Burcham, Justine W. Debelius, Heather L. Deel, Alexandra L. Emmons, Mehrbod Estaki, Chloe Herman, Christopher R. Keefe, Jamie Morton, Renato Oliveira, Andrew Sanchez, Anthony Simard, Yoshiki Vázquez‐Baeza, Michał Ziemski, Hazuki E. Miwa, Terry A. Kerere, Carline Coote, Richard Bonneau, Rob Knight, Guilherme Oliveira, Piraveen Gopalasingam, Benjamin D. Kaehler, Emily K. Cope, Jessica L. Metcalf, Michael S. Robeson, Nicholas A. Bokulich, J. Gregory Caporaso

2021 • PLOS Computational Biology • Bioinformatics • DOI: 10.1371/journal.pcbi.1009056

Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods

Nicholas A. Bokulich, Michał Ziemski, Michael S. Robeson, Benjamin D. Kaehler

2020 • Computational and Structural Biotechnology Journal • Bioinformatics • DOI: 10.1016/j.csbj.2020.11.049

Genome‐wide interaction screen for Mycobacterium tuberculosis ClpCP protease reveals toxin–antitoxin systems as a major substrate class

Michał Ziemski, Julia Leodolter, Gabrielle Taylor, Anne Kerschenmeyer, Eilika Weber‐Ban

2020 • FEBS Journal • Biochemistry • DOI: 10.1111/febs.15335

Publications

FAIRer DNA sequence data with q2-ena-uploader: a QIIME 2 plugin for data deposition in the European Nucleotide Archive

ViromeXplore: integrative workflows for complete and reproducible virome characterization

MOSHPIT: accessible, reproducible metagenome data science on the QIIME 2 framework

Advancing FAIR meta-analyses of nucleotide sequence data with q2-fondue

Reproducible acquisition, management and meta-analysis of nucleotide sequence (meta)data using q2-fondue

RESCRIPt: Reproducible sequence taxonomy reference database management

Beating Naive Bayes at Taxonomic Classification of 16S rRNA Gene Sequences

Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops

Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods

Genome‐wide interaction screen for Mycobacterium tuberculosis ClpCP protease reveals toxin–antitoxin systems as a major substrate class

Cdc48-like protein of actinobacteria (Cpa) is a novel proteasome interactor in mycobacteria and related organisms

Prokaryotic Ubiquitin-Like Protein and Its Ligase/Deligase Enzymes

Pupylation-dependent and -independent proteasomal degradation in mycobacteria

Bacterial Proteasome Activator Bpa (Rv3780) Is a Novel Ring-Shaped Interactor of the Mycobacterial Proteasome

Bacterial itaconate degradation promotes pathogenicity