Scaling neighbor joining to one million taxa with dynamic and heuristic neighbor joining

por Clausen, Philip T L C
Publicado 2022

Rapid and precise alignment of raw reads against redundant databases with KMA

por Clausen, Philip T. L. C., Aarestrup, Frank M., Lund, Ole
Publicado 2018

Improved Resistance Prediction in Mycobacterium tuberculosis by Better Handling of Insertions and Deletions, Premature Stop Codons, and Filtering of Non-informative Sites

por Johnsen, Camilla Hundahl, Clausen, Philip T. L. C., Aarestrup, Frank M., Lund, Ole
Publicado 2019

MINTyper: an outbreak-detection method for accurate and rapid SNP typing of clonal clusters with noisy long reads

por Hallgren, Malte B, Overballe-Petersen, Søren, Lund, Ole, Hasman, Henrik, Clausen, Philip T L C
Publicado 2021

Metaphylogenetic analysis of global sewage reveals that bacterial strains associated with human disease show less degree of geographic clustering

por Ahrenfeldt, Johanne, Waisi, Madina, Loft, Isabella C., Clausen, Philip T. L. C., Allesøe, Rosa, Szarvas, Judit, Hendriksen, Rene S., Aarestrup, Frank M., Lund, Ole
Publicado 2020

PlasmidHostFinder: Prediction of Plasmid Hosts Using Random Forest

por Aytan-Aktug, Derya, Clausen, Philip T. L. C., Szarvas, Judit, Munk, Patrick, Otani, Saria, Nguyen, Marcus, Davis, James J., Lund, Ole, Aarestrup, Frank M.
Publicado 2022

SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies

por Aytan-Aktug, Derya, Grigorjev, Vladislav, Szarvas, Judit, Clausen, Philip T. L. C., Munk, Patrick, Nguyen, Marcus, Davis, James J., Aarestrup, Frank M., Lund, Ole
Publicado 2022

Automated download and clean-up of family-specific databases for kmer-based virus identification

por 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
Publicado 2020

CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data

por 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.
Publicado 2020

Nanopore sequencing technology for clinical diagnosis of infectious diseases where laboratory capacity is meager: A case report

por 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.
Publicado 2023

Critical Assessment of Metagenome Interpretation: the second round of challenges

por Meyer, Fernando, Fritz, Adrian, Deng, Zhi-Luo, Koslicki, David, Lesker, Till Robin, Gurevich, Alexey, Robertson, Gary, Alser, Mohammed, Antipov, Dmitry, Beghini, Francesco, Bertrand, Denis, Brito, Jaqueline J., Brown, C. Titus, Buchmann, Jan, Buluç, Aydin, Chen, Bo, Chikhi, Rayan, Clausen, Philip T. L. C., Cristian, Alexandru, Dabrowski, Piotr Wojciech, Darling, Aaron E., Egan, Rob, Eskin, Eleazar, Georganas, Evangelos, Goltsman, Eugene, Gray, Melissa A., Hansen, Lars Hestbjerg, Hofmeyr, Steven, Huang, Pingqin, Irber, Luiz, Jia, Huijue, Jørgensen, Tue Sparholt, Kieser, Silas D., Klemetsen, Terje, Kola, Axel, Kolmogorov, Mikhail, Korobeynikov, Anton, Kwan, Jason, LaPierre, Nathan, Lemaitre, Claire, Li, Chenhao, Limasset, Antoine, Malcher-Miranda, Fabio, Mangul, Serghei, Marcelino, Vanessa R., Marchet, Camille, Marijon, Pierre, Meleshko, Dmitry, Mende, Daniel R., Milanese, Alessio, Nagarajan, Niranjan, Nissen, Jakob, Nurk, Sergey, Oliker, Leonid, Paoli, Lucas, Peterlongo, Pierre, Piro, Vitor C., Porter, Jacob S., Rasmussen, Simon, Rees, Evan R., Reinert, Knut, Renard, Bernhard, Robertsen, Espen Mikal, Rosen, Gail L., Ruscheweyh, Hans-Joachim, Sarwal, Varuni, Segata, Nicola, Seiler, Enrico, Shi, Lizhen, Sun, Fengzhu, Sunagawa, Shinichi, Sørensen, Søren Johannes, Thomas, Ashleigh, Tong, Chengxuan, Trajkovski, Mirko, Tremblay, Julien, Uritskiy, Gherman, Vicedomini, Riccardo, Wang, Zhengyang, Wang, Ziye, Wang, Zhong, Warren, Andrew, Willassen, Nils Peder, Yelick, Katherine, You, Ronghui, Zeller, Georg, Zhao, Zhengqiao, Zhu, Shanfeng, Zhu, Jie, Garrido-Oter, Ruben, Gastmeier, Petra, Hacquard, Stephane, Häußler, Susanne, Khaledi, Ariane, Maechler, Friederike, Mesny, Fantin, Radutoiu, Simona, Schulze-Lefert, Paul, Smit, Nathiana, Strowig, Till, Bremges, Andreas, Sczyrba, Alexander, McHardy, Alice Carolyn
Publicado 2022