Søren M. Karst
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Back to basics–the influence of DNA extraction and primer choice on phylogenetic analysis of activated sludge communities
M Albertsen, SM Karst, AS Ziegler, RH Kirkegaard, PH Nielsen
PloS one 10 (7), e0132783, 2015
ampvis2: an R package to analyse and visualise 16S rRNA amplicon data
KS Andersen, RH Kirkegaard, SM Karst, M Albertsen
BioRxiv, 299537, 2018
Low temperature partial nitritation/anammox in a moving bed biofilm reactor treating low strength wastewater
EM Gilbert, S Agrawal, SM Karst, H Horn, PH Nielsen, S Lackner
Environmental science & technology 48 (15), 8784-8792, 2014
MiDAS: the field guide to the microbes of activated sludge
SJ McIlroy, AM Saunders, M Albertsen, M Nierychlo, B McIlroy, ...
Database 2015, bav062, 2015
High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing
SM Karst, RM Ziels, RH Kirkegaard, EA Sørensen, D McDonald, Q Zhu, ...
Nature methods 18 (2), 165-169, 2021
Cyanate as an energy source for nitrifiers
M Palatinszky, C Herbold, N Jehmlich, M Pogoda, P Han, M von Bergen, ...
Nature 524 (7563), 105-108, 2015
A critical assessment of the microorganisms proposed to be important to enhanced biological phosphorus removal in full-scale wastewater treatment systems
M Stokholm-Bjerregaard, SJ McIlroy, M Nierychlo, SM Karst, M Albertsen, ...
Frontiers in microbiology 8, 247313, 2017
Oxford Nanopore R10. 4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing
M Sereika, RH Kirkegaard, SM Karst, TY Michaelsen, EA Sørensen, ...
Nature methods 19 (7), 823-826, 2022
Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias
SM Karst, MS Dueholm, SJ McIlroy, RH Kirkegaard, PH Nielsen, ...
Nature biotechnology 36 (2), 190-195, 2018
Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing
CM Singleton, F Petriglieri, JM Kristensen, RH Kirkegaard, TY Michaelsen, ...
Nature communications 12 (1), 2009, 2021
Culture-independent analyses reveal novel anaerolineaceae as abundant primary fermenters in anaerobic digesters treating waste activated sludge
SJ McIlroy, RH Kirkegaard, MS Dueholm, E Fernando, SM Karst, ...
Frontiers in microbiology 8, 1134, 2017
MiDAS 2.0: an ecosystem-specific taxonomy and online database for the organisms of wastewater treatment systems expanded for anaerobic digester groups
SJ McIlroy, RH Kirkegaard, B McIlroy, M Nierychlo, JM Kristensen, ...
Database 2017, bax016, 2017
The impact of immigration on microbial community composition in full-scale anaerobic digesters
RH Kirkegaard, SJ McIlroy, JM Kristensen, M Nierychlo, SM Karst, ...
Scientific reports 7 (1), 9343, 2017
Characterization of the First “Candidatus Nitrotoga” Isolate Reveals Metabolic Versatility and Separate Evolution of Widespread Nitrite-Oxidizing Bacteria
K Kitzinger, H Koch, S Lücker, CJ Sedlacek, C Herbold, J Schwarz, ...
MBio 9 (4), 10.1128/mbio. 01186-18, 2018
“Candidatus Propionivibrio aalborgensis”: a novel glycogen accumulating organism abundant in full-scale enhanced biological phosphorus removal plants
M Albertsen, SJ McIlroy, M Stokholm-Bjerregaard, SM Karst, PH Nielsen
Frontiers in Microbiology 7, 191473, 2016
Metabolic model for the filamentous ‘Candidatus Microthrix parvicella’ based on genomic and metagenomic analyses
S Jon McIlroy, R Kristiansen, M Albertsen, S Michael Karst, S Rossetti, ...
The ISME journal 7 (6), 1161-1172, 2013
Generation of comprehensive ecosystem-specific reference databases with species-level resolution by high-throughput full-length 16S rRNA gene sequencing and automated taxonomy …
MS Dueholm, KS Andersen, SJ McIlroy, JM Kristensen, E Yashiro, ...
MBio 11 (5), 10.1128/mbio. 01557-20, 2020
Mmgenome: a toolbox for reproducible genome extraction from metagenomes
SM Karst, RH Kirkegaard, M Albertsen
BioRxiv, 059121, 2016
Genomic and in situ investigations of the novel uncultured Chloroflexi associated with 0092 morphotype filamentous bulking in activated sludge
SJ McIlroy, SM Karst, M Nierychlo, MS Dueholm, M Albertsen, ...
The ISME Journal 10 (9), 2223-2234, 2016
Survival and activity of individual bioaugmentation strains
MS Dueholm, IG Marques, SM Karst, S D’Imperio, VP Tale, D Lewis, ...
Bioresource Technology 186, 192-199, 2015
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