Articles with public access mandates - Philip ClausenLearn more
Available somewhere: 20
Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage
RS Hendriksen, P Munk, P Njage, B Van Bunnik, L McNally, ...
Nature communications 10 (1), 1124, 2019
Mandates: Villum Foundation, European Commission
Rapid and precise alignment of raw reads against redundant databases with KMA
PTLC Clausen, FM Aarestrup, O Lund
BMC bioinformatics 19, 1-8, 2018
Mandates: European Commission
ResFinder–an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes
AF Florensa, RS Kaas, PTLC Clausen, D Aytan-Aktug, FM Aarestrup
Microbial Genomics 8 (1), 000748, 2022
Mandates: European Commission
Critical assessment of metagenome interpretation: the second round of challenges
F Meyer, A Fritz, ZL Deng, D Koslicki, TR Lesker, A Gurevich, G Robertson, ...
Nature methods 19 (4), 429-440, 2022
Mandates: US National Science Foundation, US Department of Energy, Swiss National …
Benchmarking of methods for identification of antimicrobial resistance genes in bacterial whole genome data
PTLC Clausen, E Zankari, FM Aarestrup, O Lund
Journal of Antimicrobial Chemotherapy 71 (9), 2484-2488, 2016
Mandates: European Commission
CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data
VR Marcelino, PTLC Clausen, JP Buchmann, M Wille, JR Iredell, W Meyer, ...
Genome biology 21, 1-15, 2020
Mandates: National Health and Medical Research Council, Australia, European Commission
LRE-Finder, a Web tool for detection of the 23S rRNA mutations and the optrA, cfr, cfr(B) and poxtA genes encoding linezolid resistance in enterococci from …
H Hasman, PTLC Clausen, H Kaya, F Hansen, JD Knudsen, M Wang, ...
Journal of Antimicrobial Chemotherapy 74 (6), 1473-1476, 2019
Mandates: European Commission
Prediction of acquired antimicrobial resistance for multiple bacterial species using neural networks
D Aytan-Aktug, PTLC Clausen, V Bortolaia, FM Aarestrup, O Lund
Msystems 5 (1), 10.1128/msystems. 00774-19, 2020
Mandates: European Commission
MINTyper: an outbreak-detection method for accurate and rapid SNP typing of clonal clusters with noisy long reads
MB Hallgren, S Overballe-Petersen, O Lund, H Hasman, PTLC Clausen
Biology Methods and Protocols 6 (1), bpab008, 2021
Mandates: European Commission
Metagenomic DNA sequencing for semi-quantitative pathogen detection from urine: a prospective, laboratory-based, proof-of-concept study
VA Janes, S Matamoros, P Munk, PTLC Clausen, SM Koekkoek, ...
The Lancet Microbe 3 (8), e588-e597, 2022
Mandates: European Commission
Predicting antimicrobial resistance using partial genome alignments
D Aytan-Aktug, M Nguyen, PTLC Clausen, RL Stevens, FM Aarestrup, ...
Msystems 6 (3), 10.1128/msystems. 00185-21, 2021
Mandates: US Department of Energy, US Department of Defense, US National Institutes of …
Improved Resistance Prediction in Mycobacterium tuberculosis by Better Handling of Insertions and Deletions, Premature Stop Codons, and Filtering of Non …
CH Johnsen, PTLC Clausen, FM Aarestrup, O Lund
Frontiers in microbiology 10, 2464, 2019
Mandates: European Commission
PlasmidHostFinder: prediction of plasmid hosts using random forest
D Aytan-Aktug, PTLC Clausen, J Szarvas, P Munk, S Otani, M Nguyen, ...
Msystems 7 (2), e01180-21, 2022
Mandates: US Department of Energy, US National Institutes of Health
SourceFinder: A machine-learning-based tool for identification of chromosomal, plasmid, and bacteriophage sequences from assemblies
D Aytan-Aktug, V Grigorjev, J Szarvas, PTLC Clausen, P Munk, M Nguyen, ...
Microbiology Spectrum 10 (6), e02641-22, 2022
Mandates: US Department of Energy, US National Institutes of Health
CRHP Finder, a webtool for the detection of clarithromycin resistance in Helicobacter pylori from whole‐genome sequencing data
M Yusibova, H Hasman, PTLC Clausen, F Imkamp, K Wagner, ...
Helicobacter 25 (6), e12752, 2020
Mandates: European Commission
Scaling neighbor joining to one million taxa with dynamic and heuristic neighbor joining
PTLC Clausen
Bioinformatics 39 (1), btac774, 2023
Mandates: European Commission
Metaphylogenetic analysis of global sewage reveals that bacterial strains associated with human disease show less degree of geographic clustering
J Ahrenfeldt, M Waisi, IC Loft, PTLC Clausen, R Allesøe, J Szarvas, ...
Scientific reports 10 (1), 3033, 2020
Mandates: European Commission
Automated download and clean-up of family-specific databases for kmer-based virus identification
RL Allesøe, CK Lemvigh, MVT Phan, PTLC Clausen, AF Florensa, ...
Bioinformatics 37 (5), 705-710, 2021
Mandates: UK Medical Research Council, European Commission
SpanSeq: similarity-based sequence data splitting method for improved development and assessment of deep learning projects
A Ferrer Florensa, JJ Almagro Armenteros, H Nielsen, FM Aarestrup, ...
NAR Genomics and Bioinformatics 6 (3), lqae106, 2024
Mandates: European Commission
ARGprofiler—a pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets
HM Martiny, N Pyrounakis, TN Petersen, O Lukjančenko, FM Aarestrup, ...
Bioinformatics 40 (3), btae086, 2024
Mandates: European Commission
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