Zobrazeno 1 - 10
of 14
pro vyhledávání: '"Philip T. L. C. Clausen"'
Autor:
Patrick Munk, Dongsheng Yang, Timo Röder, Leonie Maier, Thomas Nordahl Petersen, Ana Sofia Ribeiro Duarte, Philip T. L. C. Clausen, Christian Brinch, Liese Van Gompel, Roosmarijn Luiken, Jaap A. Wagenaar, Heike Schmitt, Dick J. J. Heederik, Dik J. Mevius, Lidwien A. M. Smit, Alex Bossers, Frank M. Aarestrup
Publikováno v:
mSystems, Vol 9, Iss 4 (2024)
ABSTRACTMetagenomic sequencing has proven to be a powerful tool in the monitoring of antimicrobial resistance (AMR). Here, we provide a comparative analysis of the resistome from pigs, poultry, veal calves, turkey, and rainbow trout, for a total of 5
Externí odkaz:
https://doaj.org/article/8c9e442d3be148e39a86a93eddf66e9e
Autor:
Derya Aytan-Aktug, Vladislav Grigorjev, Judit Szarvas, Philip T. L. C. Clausen, Patrick Munk, Marcus Nguyen, James J. Davis, Frank M. Aarestrup, Ole Lund
Publikováno v:
Microbiology Spectrum, Vol 10, Iss 6 (2022)
ABSTRACT High-throughput genome sequencing technologies enable the investigation of complex genetic interactions, including the horizontal gene transfer of plasmids and bacteriophages. However, identifying these elements from assembled reads remains
Externí odkaz:
https://doaj.org/article/4a2875f86c0a4300891ca90108be5927
Autor:
Derya Aytan-Aktug, Philip T. L. C. Clausen, Judit Szarvas, Patrick Munk, Saria Otani, Marcus Nguyen, James J. Davis, Ole Lund, Frank M. Aarestrup
Publikováno v:
mSystems, Vol 7, Iss 2 (2022)
ABSTRACT Plasmids play a major role facilitating the spread of antimicrobial resistance between bacteria. Understanding the host range and dissemination trajectories of plasmids is critical for surveillance and prevention of antimicrobial resistance.
Externí odkaz:
https://doaj.org/article/6edcfac552194615b133054c20338ae6
Autor:
Vanessa R. Marcelino, Philip T. L. C. Clausen, Jan P. Buchmann, Michelle Wille, Jonathan R. Iredell, Wieland Meyer, Ole Lund, Tania C. Sorrell, Edward C. Holmes
Publikováno v:
Genome Biology, Vol 21, Iss 1, Pp 1-15 (2020)
Abstract 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 used a recently developed concept in read mapping to develop a highly accurate metag
Externí odkaz:
https://doaj.org/article/603ad5e8d3794c12b57c37afbe8c7179
Publikováno v:
BMC Bioinformatics, Vol 19, Iss 1, Pp 1-8 (2018)
Abstract Background As the cost of sequencing has declined, clinical diagnostics based on next generation sequencing (NGS) have become reality. Diagnostics based on sequencing will require rapid and precise mapping against redundant databases because
Externí odkaz:
https://doaj.org/article/90d6362d17074d12909d8065e498f4c1
Publikováno v:
Frontiers in Microbiology, Vol 10 (2019)
Resistance in Mycobacterium tuberculosis is a major obstacle for effective treatment of tuberculosis. Multiple studies have shown promising results for predicting drug resistance in M. tuberculosis based on whole genome sequencing (WGS) data, however
Externí odkaz:
https://doaj.org/article/a3e4e3c5769b4f4c8d70ef24c02e2b3a
Autor:
Victoria A Janes, Sébastien Matamoros, Patrick Munk, Philip T L C Clausen, Sylvie M Koekkoek, Linda A M Koster, Marja E Jakobs, Bob de Wever, Caroline E Visser, Frank M Aarestrup, Ole Lund, Menno D de Jong, Patrick M M Bossuyt, Daniel R Mende, Constance Schultsz
Publikováno v:
Janes, V A, Matamoros, S B, Munk, P, Clausen, P T L C, Koekkoek, S M, Koster, L A M, Jakobs, M E, de Wever, B, Visser, C E, Aarestrup, F M, Lund, O, de Jong, M D, Bossuyt, P M M, Mende, D R & Schultsz, C 2022, ' Metagenomic DNA sequencing for semi-quantitative pathogen detection from urine : a prospective, laboratory-based, proof-of-concept study ', The Lancet Microbe, vol. 3, no. 8, pp. e588-e597 . https://doi.org/10.1016/S2666-5247(22)00088-X
Janes, V A, Matamoros, S, Munk, P, Clausen, P T L C, Koekkoek, S M, Koster, L A M, Jakobs, M E, de Wever, B, Visser, C E, Aarestrup, F M, Lund, O, de Jong, M D, Bossuyt, P M M, Mende, D R & Schultsz, C 2022, ' Metagenomic DNA sequencing for semi-quantitative pathogen detection from urine : a prospective, laboratory-based, proof-of-concept study ', Lancet. Microbe, vol. 3, no. 8, pp. e588-e597 . https://doi.org/10.1016/S2666-5247(22)00088-X
The Lancet. Microbe, 3(8), e588-e597. Elsevier Ltd
The Lancet Microbe, 3(8), e588-e597. Elsevier Ltd
Janes, V A, Matamoros, S, Munk, P, Clausen, P T L C, Koekkoek, S M, Koster, L A M, Jakobs, M E, de Wever, B, Visser, C E, Aarestrup, F M, Lund, O, de Jong, M D, Bossuyt, P M M, Mende, D R & Schultsz, C 2022, ' Metagenomic DNA sequencing for semi-quantitative pathogen detection from urine : a prospective, laboratory-based, proof-of-concept study ', Lancet. Microbe, vol. 3, no. 8, pp. e588-e597 . https://doi.org/10.1016/S2666-5247(22)00088-X
The Lancet. Microbe, 3(8), e588-e597. Elsevier Ltd
The Lancet Microbe, 3(8), e588-e597. Elsevier Ltd
BackgroundSemi-quantitative bacterial culture is the reference standard to diagnose urinary tract infection, but culture is time-consuming and can be unreliable if patients are receiving antibiotics. Metagenomics could increase diagnostic accuracy an
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c656416815f6e884a5d9cb570c878289
https://research.vumc.nl/en/publications/5752c867-80df-45eb-b348-08b4521fafeb
https://research.vumc.nl/en/publications/5752c867-80df-45eb-b348-08b4521fafeb
Autor:
Fernando Meyer, Adrian Fritz, Zhi-Luo Deng, David Koslicki, Till Robin Lesker, Alexey Gurevich, Gary Robertson, Mohammed Alser, Dmitry Antipov, Francesco Beghini, Denis Bertrand, Jaqueline J. Brito, C. Titus Brown, Jan Buchmann, Aydin Buluç, Bo Chen, Rayan Chikhi, Philip T. L. C. Clausen, Alexandru Cristian, Piotr Wojciech Dabrowski, Aaron E. Darling, Rob Egan, Eleazar Eskin, Evangelos Georganas, Eugene Goltsman, Melissa A. Gray, Lars Hestbjerg Hansen, Steven Hofmeyr, Pingqin Huang, Luiz Irber, Huijue Jia, Tue Sparholt Jørgensen, Silas D. Kieser, Terje Klemetsen, Axel Kola, Mikhail Kolmogorov, Anton Korobeynikov, Jason Kwan, Nathan LaPierre, Claire Lemaitre, Chenhao Li, Antoine Limasset, Fabio Malcher-Miranda, Serghei Mangul, Vanessa R. Marcelino, Camille Marchet, Pierre Marijon, Dmitry Meleshko, Daniel R. Mende, Alessio Milanese, Niranjan Nagarajan, Jakob Nissen, Sergey Nurk, Leonid Oliker, Lucas Paoli, Pierre Peterlongo, Vitor C. Piro, Jacob S. Porter, Simon Rasmussen, Evan R. Rees, Knut Reinert, Bernhard Renard, Espen Mikal Robertsen, Gail L. Rosen, Hans-Joachim Ruscheweyh, Varuni Sarwal, Nicola Segata, Enrico Seiler, Lizhen Shi, Fengzhu Sun, Shinichi Sunagawa, Søren Johannes Sørensen, Ashleigh Thomas, Chengxuan Tong, Mirko Trajkovski, Julien Tremblay, Gherman Uritskiy, Riccardo Vicedomini, Zhengyang Wang, Ziye Wang, Zhong Wang, Andrew Warren, Nils Peder Willassen, Katherine Yelick, Ronghui You, Georg Zeller, Zhengqiao Zhao, Shanfeng Zhu, Jie Zhu, Ruben Garrido-Oter, Petra Gastmeier, Stephane Hacquard, Susanne Häußler, Ariane Khaledi, Friederike Maechler, Fantin Mesny, Simona Radutoiu, Paul Schulze-Lefert, Nathiana Smit, Till Strowig, Andreas Bremges, Alexander Sczyrba, Alice Carolyn McHardy
Publikováno v:
Nature Methods
Meyer, F, Fritz, A, Deng, Z L, Koslicki, D, Lesker, T R, Gurevich, A, Robertson, G, Alser, M, Antipov, D, Beghini, F, Bertrand, D, Brito, J J, Brown, C T, Buchmann, J, Buluç, A, Chen, B, Chikhi, R, Clausen, P T L C, Cristian, A, Dabrowski, P W, Darling, A E, Egan, R, Eskin, E, Georganas, E, Goltsman, E, Gray, M A, Hansen, L H, Hofmeyr, S, Huang, P, Irber, L, Jia, H, Jørgensen, T S, Kieser, S D, Klemetsen, T, Kola, A, Kolmogorov, M, Korobeynikov, A, Kwan, J, LaPierre, N, Lemaitre, C, Li, C, Limasset, A, Malcher-Miranda, F, Mangul, S, Marcelino, V R, Marchet, C, Marijon, P, Meleshko, D, Mende, D R, Milanese, A, Nagarajan, N, Nissen, J, Nurk, S, Oliker, L, Paoli, L, Peterlongo, P, Piro, V C, Porter, J S, Rasmussen, S, Rees, E R, Reinert, K, Renard, B, Robertsen, E M, Rosen, G L, Ruscheweyh, H J, Sarwal, V, Segata, N, Seiler, E, Shi, L, Sun, F, Sunagawa, S, Sørensen, S J, Thomas, A, Tong, C, Trajkovski, M, Tremblay, J, Uritskiy, G, Vicedomini, R, Wang, Z, Wang, Z, Wang, Z, Warren, A, Willassen, N P, Yelick, K, You, R, Zeller, G, Zhao, Z, Zhu, S, Zhu, J, Garrido-Oter, R, Gastmeier, P, Hacquard, S, Häußler, S, Khaledi, A, Maechler, F, Mesny, F, Radutoiu, S, Schulze-Lefert, P, Smit, N, Strowig, T, Bremges, A, Sczyrba, A & McHardy, A C 2022, ' Critical Assessment of Metagenome Interpretation : the second round of challenges ', Nature Methods, vol. 19, no. 4, pp. 429-440 . https://doi.org/10.1038/s41592-022-01431-4
Nature Methods, 2022, 19 (4), pp.429-440. ⟨10.1038/s41592-022-01431-4⟩
Nature methods, 19(4), 429-440. Nature Publishing Group
Meyer, F, Fritz, A, Deng, Z-L, Koslicki, D, Lesker, T R, Gurevich, A, Robertson, G, Alser, M, Antipov, D, Beghini, F, Bertrand, D, Brito, J J, Brown, C T, Buchmann, J, Buluç, A, Chen, B, Chikhi, R, Clausen, P T L C, Cristian, A, Dabrowski, P W, Darling, A E, Egan, R, Eskin, E, Georganas, E, Goltsman, E, Gray, M A, Hansen, L H, Hofmeyr, S, Huang, P, Irber, L, Jia, H, Jørgensen, T S, Kieser, S D, Klemetsen, T, Kola, A, Kolmogorov, M, Korobeynikov, A, Kwan, J, LaPierre, N, Lemaitre, C, Li, C, Limasset, A, Malcher-Miranda, F, Mangul, S, Marcelino, V R, Marchet, C, Marijon, P, Meleshko, D, Mende, D R, Milanese, A, Nagarajan, N, Nissen, J, Nurk, S, Oliker, L, Paoli, L, Peterlongo, P, Piro, V C, Porter, J S, Rasmussen, S, Rees, E R, Reinert, K, Renard, B, Robertsen, E M, Rosen, G L, Ruscheweyh, H-J, Sarwal, V, Segata, N, Seiler, E, Shi, L, Sun, F, Sunagawa, S, Sørensen, S J, Thomas, A, Tong, C, Trajkovski, M, Tremblay, J, Uritskiy, G, Vicedomini, R, Wang, Z, Wang, Z, Wang, Z, Warren, A, Willassen, N P, Yelick, K, You, R, Zeller, G, Zhao, Z, Zhu, S, Zhu, J, Garrido-Oter, R, Gastmeier, P, Hacquard, S, Häußler, S, Khaledi, A, Maechler, F, Mesny, F, Radutoiu, S, Schulze-Lefert, P, Smit, N, Strowig, T, Bremges, A, Sczyrba, A & McHardy, A C 2022, ' Critical Assessment of Metagenome Interpretation : the second round of challenges ', Nature Methods, vol. 19, no. 4, pp. 429-440 . https://doi.org/10.1038/s41592-022-01431-4
Nature Methods, 19 (8)
Meyer, F, Fritz, A, Deng, Z L, Koslicki, D, Lesker, T R, Gurevich, A, Robertson, G, Alser, M, Antipov, D, Beghini, F, Bertrand, D, Brito, J J, Brown, C T, Buchmann, J, Buluç, A, Chen, B, Chikhi, R, Clausen, P T L C, Cristian, A, Dabrowski, P W, Darling, A E, Egan, R, Eskin, E, Georganas, E, Goltsman, E, Gray, M A, Hansen, L H, Hofmeyr, S, Huang, P, Irber, L, Jia, H, Jørgensen, T S, Kieser, S D, Klemetsen, T, Kola, A, Kolmogorov, M, Korobeynikov, A, Kwan, J, LaPierre, N, Lemaitre, C, Li, C, Limasset, A, Malcher-Miranda, F, Mangul, S, Marcelino, V R, Marchet, C, Marijon, P, Meleshko, D, Mende, D R, Milanese, A, Nagarajan, N, Nissen, J, Nurk, S, Oliker, L, Paoli, L, Peterlongo, P, Piro, V C, Porter, J S, Rasmussen, S, Rees, E R, Reinert, K, Renard, B, Robertsen, E M, Rosen, G L, Ruscheweyh, H J, Sarwal, V, Segata, N, Seiler, E, Shi, L, Sun, F, Sunagawa, S, Sørensen, S J, Thomas, A, Tong, C, Trajkovski, M, Tremblay, J, Uritskiy, G, Vicedomini, R, Wang, Z, Wang, Z, Wang, Z, Warren, A, Willassen, N P, Yelick, K, You, R, Zeller, G, Zhao, Z, Zhu, S, Zhu, J, Garrido-Oter, R, Gastmeier, P, Hacquard, S, Häußler, S, Khaledi, A, Maechler, F, Mesny, F, Radutoiu, S, Schulze-Lefert, P, Smit, N, Strowig, T, Bremges, A, Sczyrba, A & McHardy, A C 2022, ' Critical Assessment of Metagenome Interpretation : the second round of challenges ', Nature Methods, vol. 19, no. 4, pp. 429-440 . https://doi.org/10.1038/s41592-022-01431-4
Nature Methods, 2022, 19 (4), pp.429-440. ⟨10.1038/s41592-022-01431-4⟩
Nature methods, 19(4), 429-440. Nature Publishing Group
Meyer, F, Fritz, A, Deng, Z-L, Koslicki, D, Lesker, T R, Gurevich, A, Robertson, G, Alser, M, Antipov, D, Beghini, F, Bertrand, D, Brito, J J, Brown, C T, Buchmann, J, Buluç, A, Chen, B, Chikhi, R, Clausen, P T L C, Cristian, A, Dabrowski, P W, Darling, A E, Egan, R, Eskin, E, Georganas, E, Goltsman, E, Gray, M A, Hansen, L H, Hofmeyr, S, Huang, P, Irber, L, Jia, H, Jørgensen, T S, Kieser, S D, Klemetsen, T, Kola, A, Kolmogorov, M, Korobeynikov, A, Kwan, J, LaPierre, N, Lemaitre, C, Li, C, Limasset, A, Malcher-Miranda, F, Mangul, S, Marcelino, V R, Marchet, C, Marijon, P, Meleshko, D, Mende, D R, Milanese, A, Nagarajan, N, Nissen, J, Nurk, S, Oliker, L, Paoli, L, Peterlongo, P, Piro, V C, Porter, J S, Rasmussen, S, Rees, E R, Reinert, K, Renard, B, Robertsen, E M, Rosen, G L, Ruscheweyh, H-J, Sarwal, V, Segata, N, Seiler, E, Shi, L, Sun, F, Sunagawa, S, Sørensen, S J, Thomas, A, Tong, C, Trajkovski, M, Tremblay, J, Uritskiy, G, Vicedomini, R, Wang, Z, Wang, Z, Wang, Z, Warren, A, Willassen, N P, Yelick, K, You, R, Zeller, G, Zhao, Z, Zhu, S, Zhu, J, Garrido-Oter, R, Gastmeier, P, Hacquard, S, Häußler, S, Khaledi, A, Maechler, F, Mesny, F, Radutoiu, S, Schulze-Lefert, P, Smit, N, Strowig, T, Bremges, A, Sczyrba, A & McHardy, A C 2022, ' Critical Assessment of Metagenome Interpretation : the second round of challenges ', Nature Methods, vol. 19, no. 4, pp. 429-440 . https://doi.org/10.1038/s41592-022-01431-4
Nature Methods, 19 (8)
Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic an
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e6a457600da700f14909805684c3378a
https://hdl.handle.net/10453/163369
https://hdl.handle.net/10453/163369
Autor:
Derya Aytan-Aktug, Vladislav Grigorjev, Judit Szarvas, Philip T. L. C. Clausen, Patrick Munk, Marcus Nguyen, James J. Davis, Frank M. Aarestrup, Ole Lund
Publikováno v:
Aytan-Aktug, D, Grigorjev, V, Szarvas, J, Clausen, P T L C, Munk, P, Nguyen, M, Davis, J J, Aarestrup, F M & Lund, O 2022, ' SourceFinder : a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies ', Microbiology Spectrum, vol. 10, no. 6 . https://doi.org/10.1128/spectrum.02641-22
High-throughput genome sequencing technologies enable the investigation of complex genetic interactions, including the horizontal gene transfer of plasmids and bacteriophages. However, identifying these elements from assembled reads remains chal-leng
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7218628085131d0a30d20bb3b9c5104e
https://orbit.dtu.dk/en/publications/8a7854a6-0745-43c4-bdbe-43b6f2a270ab
https://orbit.dtu.dk/en/publications/8a7854a6-0745-43c4-bdbe-43b6f2a270ab
Autor:
Ole Lund, Frank Møller Aarestrup, James J. Davis, Marcus Nguyen, Judit Szarvas, Saria Otani, Derya Aytan-Aktug, Philip T. L. C. Clausen, Patrick Munk
Plasmids play a major role facilitating the spread of antimicrobial resistance between bacteria. Understanding the host range and dissemination trajectories of plasmids is critical for surveillance and prevention of antimicrobial resistance. Identifi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::a1bc9f63e2e38158cdffc3f8c3ec1463
https://doi.org/10.1101/2021.09.27.462084
https://doi.org/10.1101/2021.09.27.462084