Search Results - "Clausen, C L"

Rapid and precise alignment of raw reads against redundant databases with KMA by Clausen, Philip T L C, Aarestrup, Frank M, Lund, Ole

“…As the cost of sequencing has declined, clinical diagnostics based on next generation sequencing (NGS) have become reality. Diagnostics based on sequencing…”
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CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data by Marcelino, Vanessa R, Clausen, Philip T L C, Buchmann, Jan P, Wille, Michelle, Iredell, Jonathan R, Meyer, Wieland, Lund, Ole, Sorrell, Tania C, Holmes, Edward C

“…There is an increasing demand for accurate and fast metagenome classifiers that can not only identify bacteria, but all members of a microbial community. We…”
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Prediction of Acquired Antimicrobial Resistance for Multiple Bacterial Species Using Neural Networks by Aytan-Aktug, D, Clausen, P T L C, Bortolaia, V, Aarestrup, F M, Lund, O

“…Machine learning has proven to be a powerful method to predict antimicrobial resistance (AMR) without using prior knowledge for selected bacterial…”
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PlasmidHostFinder: Prediction of Plasmid Hosts Using Random Forest by Aytan-Aktug, Derya, Clausen, Philip T L C, Szarvas, Judit, Munk, Patrick, Otani, Saria, Nguyen, Marcus, Davis, James J, Lund, Ole, Aarestrup, Frank M

“…Plasmids play a major role facilitating the spread of antimicrobial resistance between bacteria. Understanding the host range and dissemination trajectories of…”
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Predicting Antimicrobial Resistance Using Partial Genome Alignments by Aytan-Aktug, D, Nguyen, M, Clausen, P. T. L. C, Stevens, R. L, Aarestrup, F. M, Lund, O, Davis, J. J

“…Antimicrobial resistance (AMR) is an important global health threat that impacts millions of people worldwide each year. Developing methods that can detect and…”
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Improved Resistance Prediction in Mycobacterium tuberculosis by Better Handling of Insertions and Deletions, Premature Stop Codons, and Filtering of Non-informative Sites by Johnsen, Camilla Hundahl, Clausen, Philip T. L. C., Aarestrup, Frank M., Lund, Ole

“…Resistance in Mycobacterium tuberculosis is a major obstacle for effective treatment of tuberculosis. Multiple studies have shown promising results for…”
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SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies by Aytan-Aktug, Derya, Grigorjev, Vladislav, Szarvas, Judit, Clausen, Philip T L C, Munk, Patrick, Nguyen, Marcus, Davis, James J, Aarestrup, Frank M, Lund, Ole

“…High-throughput genome sequencing technologies enable the investigation of complex genetic interactions, including the horizontal gene transfer of plasmids and…”
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Metaphylogenetic analysis of global sewage reveals that bacterial strains associated with human disease show less degree of geographic clustering by Ahrenfeldt, Johanne, Waisi, Madina, Loft, Isabella C., Clausen, Philip T. L. C., Allesøe, Rosa, Szarvas, Judit, Hendriksen, Rene S., Aarestrup, Frank M., Lund, Ole

“…Knowledge about the difference in the global distribution of pathogens and non-pathogens is limited. Here, we investigate it using a multi-sample metagenomics…”
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Scaling neighbor joining to one million taxa with dynamic and heuristic neighbor joining by Clausen, Philip T L C

“…Abstract Motivation The neighbor-joining (NJ) algorithm is a widely used method to perform iterative clustering and forms the basis for phylogenetic…”
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Benchmarking of methods for identification of antimicrobial resistance genes in bacterial whole genome data by Clausen, Philip T L C, Zankari, Ea, Aarestrup, Frank M, Lund, Ole

“…Next generation sequencing (NGS) may be an alternative to phenotypic susceptibility testing for surveillance and clinical diagnosis. However, current…”
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The European livestock resistome by Munk, Patrick, Yang, Dongsheng, Röder, Timo, Maier, Leonie, Petersen, Thomas Nordahl, Duarte, Ana Sofia Ribeiro, Clausen, Philip T L C, Brinch, Christian, Van Gompel, Liese, Luiken, Roosmarijn, Wagenaar, Jaap A, Schmitt, Heike, Heederik, Dick J J, Mevius, Dik J, Smit, Lidwien A M, Bossers, Alex, Aarestrup, Frank M

“…Metagenomic sequencing has proven to be a powerful tool in the monitoring of antimicrobial resistance (AMR). Here, we provide a comparative analysis of the…”
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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 whole-genome sequences by Hasman, Henrik, Clausen, Philip T L C, Kaya, Hülya, Hansen, Frank, Knudsen, Jenny Dahl, Wang, Mikala, Holzknecht, Barbara Juliane, Samulioniené, Jurgita, Røder, Bent L, Frimodt-Møller, Niels, Lund, Ole, Hammerum, Anette M

“…In enterococci, resistance to linezolid is often mediated by mutations in the V domain of the 23S rRNA gene (G2576T or G2505A). Furthermore, four genes [optrA,…”
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ARGprofiler—a pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets by Martiny, Hannah-Marie, Pyrounakis, Nikiforos, Petersen, Thomas N, Lukjančenko, Oksana, Aarestrup, Frank M, Clausen, Philip T L C, Munk, Patrick

“…Abstract Motivation Analyzing metagenomic data can be highly valuable for understanding the function and distribution of antimicrobial resistance genes (ARGs)…”
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Automated download and clean-up of family-specific databases for kmer-based virus identification by Allesøe, Rosa L, Lemvigh, Camilla K, Phan, My V T, Clausen, Philip T L C, Florensa, Alfred F, Koopmans, Marion P G, Lund, Ole, Cotten, Matthew

“…Abstract Summary Here, we present an automated pipeline for Download Of NCBI Entries (DONE) and continuous updating of a local sequence database based on…”
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NanoMGT: Marker gene typing of low complexity mono-species metagenomic samples using noisy long reads by Hallgren, Malte B, Clausen, Philip T L C, Aarestrup, Frank M

“…Rapid advancements in sequencing technologies have led to significant progress in microbial genomics, yet challenges persist in accurately identifying…”
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Hyperimmune immunoglobulin for hospitalised patients with COVID-19 (ITAC): a double-blind, placebo-controlled, phase 3, randomised trial by Polizzotto, Mark N., Nordwall, Jacqueline, Babiker, Abdel G., Phillips, Andrew, Vock, David M., Eriobu, Nnakelu, Kwaghe, Vivian, Paredes, Roger, Mateu, Lourdes, Ramachandruni, Srikanth, Narang, Rajeev, Jain, Mamta K., Lazarte, Susana M., Baker, Jason V., Frosch, Anne E.P., Poulakou, Garyfallia, Syrigos, Konstantinos N., Arnoczy, Gretchen S., McBride, Natalie A., Robinson, Philip A., Sarafian, Farjad, Bhagani, Sanjay, Taha, Hassan S., Benfield, Thomas, Liu, Sean T.H., Antoniadou, Anastasia, Jensen, Jens Ulrik Stæhr, Kalomenidis, Ioannis, Susilo, Adityo, Hariadi, Prasetyo, Jensen MD, Tomas O., Morales-Rull, Jose Luis, Helleberg, Marie, Meegada, Sreenath, Johansen, Isik S., Canario, Daniel, Fernández-Cruz, Eduardo, Metallidis, Simeon, Shah, Amish, Sakurai, Aki, Koulouris, Nikolaos G., Trotman, Robin, Weintrob, Amy C., Podlekareva, Daria, Hadi, Usman, Lloyd, Kathryn M., Røge, Birgit Thorup, Saito, Sho, Sweerus, Kelly, Malin, Jakob J., Lübbert, Christoph, Muñoz, Jose, Cummings, Matthew J., Losso, Marcelo H., Turner, Dan, Shaw-Saliba, Kathryn, Dewar, Robin, Highbarger, Helene, Lallemand, Perrine, Rehman, Tauseef, Gerry, Norman, Arlinda, Dona, Chang, Christina C., Grund, Birgit, Holbrook, Michael R., Holley, Horace P., Hudson, Fleur, McNay, Laura A., Murray, Daniel D., Pett, Sarah L., Shaughnessy, Megan, Smolskis, Mary C., Touloumi, Giota, Wright, Mary E., Doyle, Mittie K., Popik, Sharon, Hall, Christine, Ramanathan, Roshan, Cao, Huyen, Mondou, Elsa, Willis, Todd, Thakuria, Joseph V., Yel, Leman, Higgs, Elizabeth, Kan, Virginia L., Lundgren, Jens D., Neaton, James D., Lane, H. Clifford

“…Passive immunotherapy using hyperimmune intravenous immunoglobulin (hIVIG) to SARS-CoV-2, derived from recovered donors, is a potential rapidly available,…”
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SinEx DB 2.0 update 2020: database for eukaryotic single-exon coding sequences by Jorquera, R, González, C, Clausen, P T L C, Petersen, B, Holmes, D S

“…Single-exon coding sequences (CDSs), also known as 'single-exon genes' (SEGs), are defined as nuclear, protein-coding genes that lack introns in their CDSs…”
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MINTyper: an outbreak-detection method for accurate and rapid SNP typing of clonal clusters with noisy long reads by Hallgren, Malte B, Overballe-Petersen, Søren, Lund, Ole, Hasman, Henrik, Clausen, Philip T L C

“…Abstract For detection of clonal outbreaks in clinical settings, we present a complete pipeline that generates a single-nucleotide polymorphisms-distance…”
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Nanopore sequencing technology for clinical diagnosis of infectious diseases where laboratory capacity is meager: A case report by Kumburu, Happiness H., Shayo, Mariana, van Zwetslaar, Marco, Njau, Judith, Kuchaka, Davis J., Ignas, Ignas P., Wadugu, Boaz, Kasworm, Robert, Masaki, Lazaro J., Hallgren, Malte B., Clausen, Philip T.L.C., Mmbaga, Blandina Theophil, Aarestrup, Frank M., Sonda, Tolbert B.

“…In resource-limited settings, patients are often first presented to clinical settings when seriously ill and access to proper clinical microbial diagnostics is…”
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Metagenomic DNA sequencing for semi-quantitative pathogen detection from urine: a prospective, laboratory-based, proof-of-concept study by Janes, Victoria A, Matamoros, Sébastien, Munk, Patrick, Clausen, Philip T L C, Koekkoek, Sylvie M, Koster, Linda A M, Jakobs, Marja E, de Wever, Bob, Visser, Caroline E, Aarestrup, Frank M, Lund, Ole, de Jong, Menno D, Bossuyt, Patrick M M, Mende, Daniel R, Schultsz, Constance

“…Semi-quantitative bacterial culture is the reference standard to diagnose urinary tract infection, but culture is time-consuming and can be unreliable if…”
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