| 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 | 806 | 2019 |
| Rapid and precise alignment of raw reads against redundant databases with KMA PTLC Clausen, FM Aarestrup, O Lund BMC bioinformatics 19, 1-8, 2018 | 627 | 2018 |
| 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 | 367 | 2022 |
| 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 | 249 | 2022 |
| 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 | 190 | 2016 |
| 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 | 138 | 2020 |
| 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 | 76 | 2019 |
| 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 | 42 | 2020 |
| P., van de Schans RS Hendriksen, P Munk, P Njage, B van Bunnik, L McNally, ... MGM, Zuidema, T., de Roda Husman, AM, Rasmussen, S., Petersen, B., et al, 2019 | 17 | 2019 |
| 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 | 14 | 2022 |
| 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 | 14 | 2021 |
| 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 | 13 | 2022 |
| 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 | 13 | 2021 |
| 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 | 11 | 2019 |
| Scaling neighbor joining to one million taxa with dynamic and heuristic neighbor joining PTLC Clausen Bioinformatics 39 (1), btac774, 2023 | 10 | 2023 |
| 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 | 10 | 2022 |
| Improved ontology for eukaryotic single-exon coding sequences in biological databases R Jorquera, C González, P Clausen, B Petersen, DS Holmes Database 2018, bay089, 2018 | 9 | 2018 |
| 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 | 7 | 2020 |
| 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 | 6 | 2020 |
| 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 | 4 | 2021 |
Frank AarestrupTechnical University of Denmark, DTUVerificeret mail på food.dtu.dk