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

Microbiology Resource Announcements

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

ViromeXplore: integrative workflows for complete and reproducible virome characterization

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

Briefings in Bioinformatics

2025 • 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

bioRxiv (Preprint)

2025 • 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

F1000Research

2023 • 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

Bioinformatics

2022 • 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

PLOS Computational Biology

2021 • 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

Frontiers in Microbiology

2021 • 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

PLOS Computational Biology

2021 • 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

Computational and Structural Biotechnology Journal

2020 • 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

FEBS Journal

2020 • Biochemistry • DOI: 10.1111/febs.15335

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

Michał Ziemski, Ahmad Jomaa, Daniel Mayer, Sonja Rutz, Christoph Giese, Dmitry B. Veprintsev, Eilika Weber‐Ban

eLife

2018 • Biochemistry • DOI: 10.7554/eLife.34055

Prokaryotic Ubiquitin-Like Protein and Its Ligase/Deligase Enzymes

Cyrille L. Delley, Andreas U. Müller, Michał Ziemski, Eilika Weber‐Ban

Journal of Molecular Biology

2017 • Biochemistry • DOI: 10.1016/j.jmb.2017.04.020

Pupylation-dependent and -independent proteasomal degradation in mycobacteria

Frank Imkamp, Michał Ziemski, Eilika Weber‐Ban

Biomolecular Concepts

2015 • Biochemistry • DOI: 10.1515/bmc-2015-0017

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

Cyrille L. Delley, Juerg Laederach, Michał Ziemski, Marcel Bolten, Daniel Boehringer, Eilika Weber‐Ban

PLoS ONE

2014 • Biochemistry • DOI: 10.1371/journal.pone.0114348

Bacterial itaconate degradation promotes pathogenicity

Jahminy Sasikaran, Michał Ziemski, Piotr K. Zadora, Angela Fleig, Ivan A. Berg

Nature Chemical Biology

2014 • Biochemistry • DOI: 10.1038/nchembio.1482