Michal Ziemski
Overview
Explore the profile of Michal Ziemski including associated specialties, affiliations and a list of published articles.
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11
Citations
476
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Recent Articles
1.
Ziemski M, Gehret L, Simard A, Dau S, Risch V, Grabocka D, et al.
bioRxiv
. 2025 Feb;
PMID: 39975011
Metagenome sequencing has revolutionized functional microbiome analysis across diverse ecosystems, but is fraught with technical hurdles. We introduce MOSHPIT (https://moshpit.readthedocs.io), software built on the QIIME 2 framework (Q2F) that integrates...
2.
Ziemski M, Adamov A, Kim L, Florl L, Bokulich N
Bioinformatics
. 2022 Sep;
38(22):5081-5091.
PMID: 36130056
Motivation: The volume of public nucleotide sequence data has blossomed over the past two decades and is ripe for re- and meta-analyses to enable novel discoveries. However, reproducible re-use and...
3.
Robeson 2nd M, ORourke D, Kaehler B, Ziemski M, Dillon M, Foster J, et al.
PLoS Comput Biol
. 2021 Nov;
17(11):e1009581.
PMID: 34748542
Nucleotide sequence and taxonomy reference databases are critical resources for widespread applications including marker-gene and metagenome sequencing for microbiome analysis, diet metabarcoding, and environmental DNA (eDNA) surveys. Reproducibly generating, managing,...
4.
Ziemski M, Wisanwanichthan T, Bokulich N, Kaehler B
Front Microbiol
. 2021 Jul;
12:644487.
PMID: 34220738
Naive Bayes classifiers (NBC) have dominated the field of taxonomic classification of amplicon sequences for over a decade. Apart from having runtime requirements that allow them to be trained and...
5.
Dillon M, Bolyen E, Adamov A, Belk A, Borsom E, Burcham Z, et al.
PLoS Comput Biol
. 2021 Jun;
17(6):e1009056.
PMID: 34166363
In October of 2020, in response to the Coronavirus Disease 2019 (COVID-19) pandemic, our team hosted our first fully online workshop teaching the QIIME 2 microbiome bioinformatics platform. We had...
6.
Bokulich N, Ziemski M, Robeson 2nd M, Kaehler B
Comput Struct Biotechnol J
. 2020 Dec;
18:4048-4062.
PMID: 33363701
Microbiomes are integral components of diverse ecosystems, and increasingly recognized for their roles in the health of humans, animals, plants, and other hosts. Given their complexity (both in composition and...
7.
Ziemski M, Leodolter J, Taylor G, Kerschenmeyer A, Weber-Ban E
FEBS J
. 2020 Apr;
288(1):111-126.
PMID: 32301575
In Mycobacterium tuberculosis (Mtb), the Clp protease degradation pathway, mediated by the modular ClpCP and ClpXP protease complexes, is essential for growth and presents an attractive drug target. Employing a...
8.
Ziemski M, Jomaa A, Mayer D, Rutz S, Giese C, Veprintsev D, et al.
Elife
. 2018 May;
7.
PMID: 29809155
Cdc48 is a AAA+ ATPase that plays an essential role for many cellular processes in eukaryotic cells. An archaeal homologue of this highly conserved enzyme was shown to directly interact...
9.
Delley C, Muller A, Ziemski M, Weber-Ban E
J Mol Biol
. 2017 May;
429(22):3486-3499.
PMID: 28478282
Prokaryotic ubiquitin-like protein (Pup) and the modification enzymes involved in attaching Pup to or removing it from target proteins present a fascinating example of convergent evolution with respect to eukaryotic...
10.
Imkamp F, Ziemski M, Weber-Ban E
Biomol Concepts
. 2015 Sep;
6(4):285-301.
PMID: 26352358
Bacteria make use of compartmentalizing protease complexes, similar in architecture but not homologous to the eukaryotic proteasome, for the selective and processive removal of proteins. Mycobacteria as members of the...