Zobrazeno 1 - 10
of 21
pro vyhledávání: '"Antoine Limasset"'
Autor:
Christopher Quince, Sergey Nurk, Sebastien Raguideau, Robert James, Orkun S. Soyer, J. Kimberly Summers, Antoine Limasset, A. Murat Eren, Rayan Chikhi, Aaron E. Darling
Publikováno v:
Genome Biology, Vol 22, Iss 1, Pp 1-34 (2021)
Abstract We introduce STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, from multiple metagenome samples. STRONG performs coassembly, and binning into metagenome assembled genomes (MAGs), and stores the coassembly graph
Externí odkaz:
https://doaj.org/article/c74ea889eddf4483a41b363af8e7877a
Publikováno v:
Scientific Reports, Vol 11, Iss 1, Pp 1-13 (2021)
Abstract Third-generation sequencing technologies allow to sequence long reads of tens of kbp, that are expected to solve various problems. However, they display high error rates, currently capped around 10%. Self-correction is thus regularly used in
Externí odkaz:
https://doaj.org/article/fcd66fffea6c4c26a56a20d13c28f227
Autor:
Camille Marchet, Antoine Limasset
Publikováno v:
Recomb 2022-26th Annual International Conference on Research in Computational Molecular Biology
Recomb 2022-26th Annual International Conference on Research in Computational Molecular Biology, May 2022, La jolla, United States
Recomb 2022-26th Annual International Conference on Research in Computational Molecular Biology, May 2022, La jolla, United States
International audience; A public database such as the SRA (Sequence Read Archive) has reached 30 peta-bases of raw sequences and doubles its nucleotide content every two years. While BLAST-like methods can routinely search a sequence in a single geno
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::97685c3a2c73a6da26caa721271c1560
https://hal.science/hal-03871213
https://hal.science/hal-03871213
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
Publikováno v:
22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
22nd International Workshop on Algorithms in Bioinformatics (WABI 2022), Sep 2022, Postdam, Germany. ⟨10.1101/2021.11.04.467355v1⟩
WABI 2022-22nd International Workshop on Algorithms in Bioinformatics
WABI 2022-22nd International Workshop on Algorithms in Bioinformatics, Sep 2022, Postdam, Germany. pp.25:1-25:15, ⟨10.4230/LIPIcs.WABI.2022.25⟩
22nd International Workshop on Algorithms in Bioinformatics (WABI 2022), Sep 2022, Postdam, Germany. ⟨10.1101/2021.11.04.467355v1⟩
WABI 2022-22nd International Workshop on Algorithms in Bioinformatics
WABI 2022-22nd International Workshop on Algorithms in Bioinformatics, Sep 2022, Postdam, Germany. pp.25:1-25:15, ⟨10.4230/LIPIcs.WABI.2022.25⟩
Motivation. To keep up with the scale of genomic databases, several methods rely on local sensitive hashing methods to efficiently find potential matches within large genome collections. Existing solutions rely on Minhash or Hyperloglog fingerprints
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::45b3e19ddae2fd221c552dc0cc4e84d2
https://doi.org/10.1101/2021.11.04.467355
https://doi.org/10.1101/2021.11.04.467355
Autor:
Karine Van Doninck, Richard Cordaux, Thomas Lenormand, Clément Gilbert, Karine Labadie, Lyam Baudry, Julie Virgo, Boris Hespeels, Djampa K. L. Kozlowski, Jitendra Narayan, Alessandro Derzelle, Marie Cariou, Antoine Limasset, Florence Gaudray, Bernard Hallet, Martial Marbouty, Etienne Danchin, Antoine Houtain, Rohan Arora, Matthieu Terwagne, Corinne Cruaud, Nadège Guiglielmoni, Jean-François Flot, Romain Koszul, Paul Simion, Emilien Nicolas, Marc Llirós
Publikováno v:
Science Advances
Science Advances, 2021, 7 (41), pp.eabg4216. ⟨10.1126/sciadv.abg4216⟩
Science advances, 7 (41
Science Advances, American Association for the Advancement of Science (AAAS), 2021, 7 (41), pp.eabg4216. ⟨10.1126/sciadv.abg4216⟩
Science Advances, 2021, 7 (41), pp.eabg4216. ⟨10.1126/sciadv.abg4216⟩
Science advances, 7 (41
Science Advances, American Association for the Advancement of Science (AAAS), 2021, 7 (41), pp.eabg4216. ⟨10.1126/sciadv.abg4216⟩
Bdelloid rotifers are notorious as a speciose ancient clade comprising only asexual lineages. Thanks to their ability to repair highly fragmented DNA, most bdelloid species also withstand complete desiccation and ionizing radiation. Producing a well-
Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer
Autor:
Paul, Simion, Jitendra, Narayan, Antoine, Houtain, Alessandro, Derzelle, Lyam, Baudry, Emilien, Nicolas, Rohan, Arora, Marie, Cariou, Corinne, Cruaud, Florence Rodriguez, Gaudray, Clément, Gilbert, Nadège, Guiglielmoni, Boris, Hespeels, Djampa K L, Kozlowski, Karine, Labadie, Antoine, Limasset, Marc, Llirós, Martial, Marbouty, Matthieu, Terwagne, Julie, Virgo, Richard, Cordaux, Etienne G J, Danchin, Bernard, Hallet, Romain, Koszul, Thomas, Lenormand, Jean-Francois, Flot, Karine, Van Doninck
Publikováno v:
Science Advances
Description
High-quality genome assembly of ancient asexual rotifer reveals homologous chromosomes that frequently recombine.
Bdelloid rotifers are notorious as a speciose ancient clade comprising only asexual lineages. Thanks to their abil
High-quality genome assembly of ancient asexual rotifer reveals homologous chromosomes that frequently recombine.
Bdelloid rotifers are notorious as a speciose ancient clade comprising only asexual lineages. Thanks to their abil
Autor:
Sergey Nurk, J. Kimberly Summers, Robert James, Rayan Chikhi, Christopher Quince, A. Murat Eren, Antoine Limasset, Orkun S. Soyer, Aaron E. Darling, Sebastien Raguideau
Publikováno v:
Genome Biology
Genome Biology, Vol 22, Iss 1, Pp 1-34 (2021)
Genome Biology, 2021, 22 (1), ⟨10.1186/s13059-021-02419-7⟩
Genome Biology, BioMed Central, 2021, 22 (1), ⟨10.1186/s13059-021-02419-7⟩
Genome Biology, Vol 22, Iss 1, Pp 1-34 (2021)
Genome Biology, 2021, 22 (1), ⟨10.1186/s13059-021-02419-7⟩
Genome Biology, BioMed Central, 2021, 22 (1), ⟨10.1186/s13059-021-02419-7⟩
We introduce STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, from multiple metagenome samples. STRONG performs coassembly, and binning into metagenome assembled genomes (MAGs), and stores the coassembly graph prior to
Autor:
Zho. Wang, Ariane Khaledi, Alice C. McHardy, Anton Korobeynikov, A. Cristian, Gherman Uritskiy, Huijue Jia, Philip Thomas Lanken Conradsen Clausen, Till Strowig, Denis Bertrand, N. Smit, Niranjan Nagarajan, Enrico Seiler, Adam G. Thomas, David Koslicki, Piotr Wojtek Dabrowski, Vitor C. Piro, Andreas Bremges, L. Oliker, Petra Gastmeier, Steven Hofmeyr, Zhe Wang, Jason C. Kwan, Alessio Milanese, Tue Sparholt Jørgensen, Mohammed Alser, J. S. Porter, Alexander Sczyrba, Georg Zeller, Bernhard Y. Renard, Chenhao Li, Riccardo Vicedomini, Chengxuan Tong, Andrew S. Warren, Jaqueline J. Brito, Alexey Gurevich, Axel Kola, C.T. Brown, Julien Tremblay, Shinichi Sunagawa, F. Maechler, G. Robertson, Jakob Nybo Nissen, Ruben Garrido-Oter, Rob Egan, Simon Rasmussen, Katherine Yelick, Fernando Meyer, Zhengqiao Zhao, Daniel R Mende, Shanfeng Zhu, Lizhen Shi, F. Malcher-Miranda, Fengzhu Sun, Zi. Wang, Lars Hestbjerg Hansen, J. Buchmann, S. D. Kieser, Jie Zhu, E. M. Robertsen, Fantin Mesny, Sergey Nurk, Pierre Marijon, Dmitry Meleshko, Gail L. Rosen, Nicola Segata, Nathan LaPierre, Eugene Goltsman, Varuni Sarwal, Mirko Trajkovski, Dmitry Antipov, P. Huang, Vanesa R. Marcelino, Francesco Beghini, Antoine Limasset, Rayan Chikhi, Eleazar Eskin, M. A. Gray, Camille Marchet, Lucas Paoli, Adrian Fritz, Evangelos Georganas, Zhi-Luo Deng, T. Klemetsen, Hans-Joachim Ruscheweyh, Evan R. Rees, S. Häußler, Simona Radutoiu, Stéphane Hacquard, Paul Schulze-Lefert, Mikhail Kolmogorov, N. P. Willassen, Pierre Peterlongo, Knut Reinert, Claire Lemaitre, Ronghui You, Søren J. Sørensen, Aydin Buluc, Luiz Irber, Serghei Mangul, B. Chen, Aaron E. Darling
Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the community-driven initiative for the Critical Assessment of Metagenome Interpretation (CAMI). In its second challenge, CAMI engaged the community to asses
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::30f2c611599ba0fd5421c09bf5485486
https://doi.org/10.1101/2021.07.12.451567
https://doi.org/10.1101/2021.07.12.451567
Publikováno v:
Bioinformatics
Bioinformatics, 2021, 37 (18), pp.2858-2865. ⟨10.1093/bioinformatics/btab217⟩
Bioinformatics, Oxford University Press (OUP), 2021, 37 (18), pp.2858-2865. ⟨10.1093/bioinformatics/btab217⟩
Bioinformatics, 2021, 37 (18), pp.2858-2865. ⟨10.1093/bioinformatics/btab217⟩
Bioinformatics, Oxford University Press (OUP), 2021, 37 (18), pp.2858-2865. ⟨10.1093/bioinformatics/btab217⟩
Motivation A plethora of methods and applications share the fundamental need to associate information to words for high-throughput sequence analysis. Doing so for billions of k-mers is commonly a scalability problem, as exact associative indexes can
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::20ba433a795c948b78c8cd9dfc53f335
https://hal.science/hal-03443183
https://hal.science/hal-03443183