Search

Your search keyword '"LOPEZ, PHILIPPE"' showing total 461 results
Start Over Author "LOPEZ, PHILIPPE"
461 results on '"LOPEZ, PHILIPPE"'

8. Read networks and k-laminar graphs

Author

Völkel, Finn, bapteste, Eric, Habib, Michel, Lopez, Philippe, and Vigliotti, Chloe

Subjects
Computer Science - Discrete Mathematics
Abstract

In this paper we introduce k-laminar graphs a new class of graphs which extends the idea of Asteroidal triple free graphs. Indeed a graph is k-laminar if it admits a diametral path that is k-dominating. This bio-inspired class of graphs was motivated by a biological application dealing with sequence similarity networks of reads (called hereafter read networks for short). We briefly develop the context of the biological application in which this graph class appeared and then we consider the relationships of this new graph class among known graph classes and then we study its recognition problem. For the recognition of k-laminar graphs, we develop polynomial algorithms when k is fixed. For k=1, our algorithm improves a Deogun and Krastch's algorithm (1999). We finish by an NP-completeness result when k is unbounded.

Published
2016

9. Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems

Author

Denoeud, France, Godfroy, Olivier, Cruaud, Corinne, Heesch, Svenja, Nehr, Zofia, Tadrent, Nachida, Couloux, Arnaud, Brillet-guéguen, Loraine, Delage, Ludovic, Mckeown, Dean, Motomura, Taizo, Sussfeld, Duncan, Fan, Xiao, Mazéas, Lisa, Terrapon, Nicolas, Barrera-redondo, Josué, Petroll, Romy, Reynes, Lauric, Choi, Seok-wan, Jo, Jihoon, Uthanumallian, Kavitha, Bogaert, Kenny, Duc, Céline, Ratchinski, Pélagie, Lipinska, Agnieszka, Noel, Benjamin, Murphy, Eleanor A., Lohr, Martin, Khatei, Ananya, Hamon-giraud, Pauline, Vieira, Christophe, Akerfors, Svea Sanja, Akita, Shingo, Avia, Komlan, Badis, Yacine, Barbeyron, Tristan, Belcour, Arnaud, Berrabah, Wahiba, Blanquart, Samuel, Bouguerba-collin, Ahlem, Bringloe, Trevor, Cattolico, Rose Ann, Cormier, Alexandre, Cruz De Carvalho, Helena, Dallet, Romain, De Clerck, Olivier, Debit, Ahmed, Denis, Erwan, Destombe, Christophe, Dinatale, Erica, Dittami, Simon, Drula, Elodie, Faugeron, Sylvain, Got, Jeanne, Graf, Louis, Groisillier, Agnès, Guillemin, Marie-laure, Harms, Lars, Hatchett, William John, Henrissat, Bernard, Hoarau, Galice, Jollivet, Chloé, Jueterbock, Alexander, Kayal, Ehsan, Kogame, Kazuhiro, Le Bars, Arthur, Leblanc, Catherine, Ley, Ronja, Liu, Xi, Lopez, Pascal Jean, Lopez, Philippe, Manirakiza, Eric, Massau, Karine, Mauger, Stéphane, Mest, Laetitia, Michel, Gurvan, Monteiro, Catia, Nagasato, Chikako, Nègre, Delphine, Pelletier, Eric, Phillips, Naomi, Potin, Philippe, Rensing, Stefan A., Rousselot, Ellyn, Rousvoal, Sylvie, Schroeder, Declan, Scornet, Delphine, Siegel, Anne, Tirichine, Leila, Tonon, Thierry, Valentin, Klaus, Verbruggen, Heroen, Weinberger, Florian, Wheeler, Glen, Kawai, Hiroshi, Peters, Akira F., Yoon, Hwan Su, Hervé, Cecile, Ye, Naihao, Bapteste, Eric, Valero, Myriam, Markov, Gabriel V., Corre, Erwan, Coelho, Susana M., Wincker, Patrick, Aury, Jean-marc, Cock, J. Mark, Denoeud, France, Godfroy, Olivier, Cruaud, Corinne, Heesch, Svenja, Nehr, Zofia, Tadrent, Nachida, Couloux, Arnaud, Brillet-guéguen, Loraine, Delage, Ludovic, Mckeown, Dean, Motomura, Taizo, Sussfeld, Duncan, Fan, Xiao, Mazéas, Lisa, Terrapon, Nicolas, Barrera-redondo, Josué, Petroll, Romy, Reynes, Lauric, Choi, Seok-wan, Jo, Jihoon, Uthanumallian, Kavitha, Bogaert, Kenny, Duc, Céline, Ratchinski, Pélagie, Lipinska, Agnieszka, Noel, Benjamin, Murphy, Eleanor A., Lohr, Martin, Khatei, Ananya, Hamon-giraud, Pauline, Vieira, Christophe, Akerfors, Svea Sanja, Akita, Shingo, Avia, Komlan, Badis, Yacine, Barbeyron, Tristan, Belcour, Arnaud, Berrabah, Wahiba, Blanquart, Samuel, Bouguerba-collin, Ahlem, Bringloe, Trevor, Cattolico, Rose Ann, Cormier, Alexandre, Cruz De Carvalho, Helena, Dallet, Romain, De Clerck, Olivier, Debit, Ahmed, Denis, Erwan, Destombe, Christophe, Dinatale, Erica, Dittami, Simon, Drula, Elodie, Faugeron, Sylvain, Got, Jeanne, Graf, Louis, Groisillier, Agnès, Guillemin, Marie-laure, Harms, Lars, Hatchett, William John, Henrissat, Bernard, Hoarau, Galice, Jollivet, Chloé, Jueterbock, Alexander, Kayal, Ehsan, Kogame, Kazuhiro, Le Bars, Arthur, Leblanc, Catherine, Ley, Ronja, Liu, Xi, Lopez, Pascal Jean, Lopez, Philippe, Manirakiza, Eric, Massau, Karine, Mauger, Stéphane, Mest, Laetitia, Michel, Gurvan, Monteiro, Catia, Nagasato, Chikako, Nègre, Delphine, Pelletier, Eric, Phillips, Naomi, Potin, Philippe, Rensing, Stefan A., Rousselot, Ellyn, Rousvoal, Sylvie, Schroeder, Declan, Scornet, Delphine, Siegel, Anne, Tirichine, Leila, Tonon, Thierry, Valentin, Klaus, Verbruggen, Heroen, Weinberger, Florian, Wheeler, Glen, Kawai, Hiroshi, Peters, Akira F., Yoon, Hwan Su, Hervé, Cecile, Ye, Naihao, Bapteste, Eric, Valero, Myriam, Markov, Gabriel V., Corre, Erwan, Coelho, Susana M., Wincker, Patrick, Aury, Jean-marc, and Cock, J. Mark

Abstract

Brown seaweeds are keystone species of coastal ecosystems, often forming extensive underwater forests, that are under considerable threat from climate change. Despite their ecological and evolutionary importance, this phylogenetic group, which is very distantly related to animals and land plants, is still poorly characterised at the genome level. Here we analyse 60 new genomes that include species from all the major brown algal orders. Comparative analysis of these genomes indicated the occurrence of several major events coinciding approximately with the emergence of the brown algal lineage. These included marked gain of new orthologous gene families, enhanced protein domain rearrangement, horizontal gene transfer events and the acquisition of novel signalling molecules and metabolic pathways. The latter include enzymes implicated in processes emblematic of the brown algae such as biosynthesis of the alginate-based extracellular matrix, and halogen and phlorotannin biosynthesis. These early genomic innovations enabled the adaptation of brown algae to their intertidal habitats. The subsequent diversification of the brown algal orders tended to involve loss of gene families, and genomic features were identified that correlated with the emergence of differences in life cycle strategy, flagellar structure and halogen metabolism. We show that integration of large viral genomes has had a significant impact on brown algal genome content and propose that this process has persisted throughout the evolutionary history of the lineage. Finally, analysis of microevolutionary patterns within the genusEctocarpusindicated that deep gene flow between species may be an important factor in genome evolution on more recent timescales.

Published
2024
Full Text
View/download PDF

10. Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems

Author

Denoeud, France, primary, Godfroy, Olivier, additional, Cruaud, Corinne, additional, Heesch, Svenja, additional, Nehr, Zofia, additional, Tadrent, Nachida, additional, Couloux, Arnaud, additional, Brillet-Guéguen, Loraine, additional, Delage, Ludovic, additional, Mckeown, Dean, additional, Motomura, Taizo, additional, Sussfeld, Duncan, additional, Fan, Xiao, additional, Mazéas, Lisa, additional, Terrapon, Nicolas, additional, Barrera-Redondo, Josué, additional, Petroll, Romy, additional, Reynes, Lauric, additional, Choi, Seok-Wan, additional, Jo, Jihoon, additional, Uthanumallian, Kavitha, additional, Bogaert, Kenny, additional, Duc, Céline, additional, Ratchinski, Pélagie, additional, Lipinska, Agnieszka, additional, Noel, Benjamin, additional, Murphy, Eleanor A., additional, Lohr, Martin, additional, Khatei, Ananya, additional, Hamon-Giraud, Pauline, additional, Vieira, Christophe, additional, Akerfors, Svea Sanja, additional, Akita, Shingo, additional, Avia, Komlan, additional, Badis, Yacine, additional, Barbeyron, Tristan, additional, Belcour, Arnaud, additional, Berrabah, Wahiba, additional, Blanquart, Samuel, additional, Bouguerba-Collin, Ahlem, additional, Bringloe, Trevor, additional, Cattolico, Rose Ann, additional, Cormier, Alexandre, additional, Cruz de Carvalho, Helena, additional, Dallet, Romain, additional, De Clerck, Olivier, additional, Debit, Ahmed, additional, Denis, Erwan, additional, Destombe, Christophe, additional, Dinatale, Erica, additional, Dittami, Simon, additional, Drula, Elodie, additional, Faugeron, Sylvain, additional, Got, Jeanne, additional, Graf, Louis, additional, Groisillier, Agnès, additional, Guillemin, Marie-Laure, additional, Harms, Lars, additional, Hatchett, William John, additional, Henrissat, Bernard, additional, Hoarau, Galice, additional, Jollivet, Chloé, additional, Jueterbock, Alexander, additional, Kayal, Ehsan, additional, Kogame, Kazuhiro, additional, Bars, Arthur Le, additional, Leblanc, Catherine, additional, Ley, Ronja, additional, Liu, Xi, additional, Lopez, Pascal Jean, additional, Lopez, Philippe, additional, Manirakiza, Eric, additional, Massau, Karine, additional, Mauger, Stéphane, additional, Mest, Laetitia, additional, Michel, Gurvan, additional, Monteiro, Catia, additional, Nagasato, Chikako, additional, Nègre, Delphine, additional, Pelletier, Eric, additional, Phillips, Naomi, additional, Potin, Philippe, additional, Rensing, Stefan A., additional, Rousselot, Ellyn, additional, Rousvoal, Sylvie, additional, Schroeder, Declan, additional, Scornet, Delphine, additional, Siegel, Anne, additional, Tirichine, Leila, additional, Tonon, Thierry, additional, Valentin, Klaus, additional, Verbruggen, Heroen, additional, Weinberger, Florian, additional, Wheeler, Glen, additional, Kawai, Hiroshi, additional, Peters, Akira F., additional, Yoon, Hwan Su, additional, Hervé, Cécile, additional, Ye, Naihao, additional, Bapteste, Eric, additional, Valero, Myriam, additional, Markov, Gabriel V., additional, Corre, Erwan, additional, Coelho, Susana M., additional, Wincker, Patrick, additional, Aury, Jean-Marc, additional, and Cock, J. Mark, additional

Published
2024
Full Text
View/download PDF

24. List of Authors

Author

Achaz, Guillaume, primary, Bapteste, Eric, additional, Berthier, Serge, additional, Blandin, Patrick, additional, Chazot, Nicolas, additional, Cohen, Claudine, additional, De Wever, Patrick, additional, Debat, Vincent, additional, Dutertre, Sébastien, additional, Elias, Marianne, additional, Finney, Stan, additional, Grandcolas, Philippe, additional, Gomez, Doris, additional, Heams, Thomas, additional, Hugot, Jean-Pierre, additional, Lalis, Aude, additional, Lehmann, Jean, additional, Llaurens, Violaine, additional, Lopez, Philippe, additional, Martinez-Vargas, Jessica, additional, Maurel, Marie-Christine, additional, Nattier, Romain, additional, Nicolas, Violaine, additional, Puillandre, Nicolas, additional, Saintomé, Carole, additional, Vigliotti, Chloé, additional, and Wirth, Thierry, additional

Published
2018
Full Text
View/download PDF

37. CHARACTERISTICS OF OCCASIONAL POOR MEDIUM-RANGE WEATHER FORECASTS FOR EUROPE

Author

Rodwell, Mark J, Magnusson, Linus, Bauer, Peter, Bechtold, Peter, Bonavita, Massimo, Cardinali, Carla, Diamantakis, Michail, Earnshaw, Paul, Garcia-Mendez, Antonio, Isaksen, Lars, Källén, Erland, Klocke, Daniel, Lopez, Philippe, McNally, Tony, Persson, Anders, Prates, Fernando, and Wedi, Nils

Published
2013

45. Hundreds of out-of-frame remodelled gene families in the E. coli pangenome

Author

Watson, Andrew, Lopez, Philippe, Bapteste, Eric, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)

Subjects
[SDV]Life Sciences [q-bio]
Abstract

International audience; All genomes include gene families with very limited taxonomic distributions that potentially represent new genes and innovations in protein-coding sequence, raising questions on the origins of such genes. Some of these genes are hypothesised to have formed de novo, from non-coding sequences, and recent work has begun to elucidate the processes by which de novo gene formation can occur. A special case of de novo gene formation, overprinting, describes the origin of new genes from non-coding alternative reading frames of existing open reading frames (ORFs). We argue that additionally, out-of-frame gene fission/fusion events of alternative reading frames of ORFs and out-of-frame lateral gene transfers could contribute to the origin of new gene families. To demonstrate this, we developed an original pattern-search in sequence similarity networks, enhancing the use of these graphs, commonly used to detect in-frame remodelled genes. We applied this approach to gene families in 524 complete genomes of Escherichia coli. We identified 767 gene families whose evolutionary history likely included at least one out-of-frame remodelling event. These genes with out-of-frame components represent 2.5% of all genes in the E. coli pangenome, suggesting that alternative reading frames of existing ORFs can contribute to a significant proportion of de novo genes in bacteria.

Published
2021

46. Aging at Evolutionary Crossroads: Longitudinal Gene Co-expression Network Analyses of Proximal and Ultimate Causes of Aging in Bats

Author

Teulière Jérôme, Lapointe François-Joseph, Lopez Philippe, Bapteste Eric, Corel Eduardo, Bernard Guillaume, Laboratoire National de Métrologie et d’Essais (LNE), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), and Université de Montréal (UdeM)

Subjects
longitudinal transcriptomics, [SDV]Life Sciences [q-bio], evolution of aging, antagonistic pleiotropy theory, Myotis myotis, AcademicSubjects/SCI01180, Genetics, disposable soma theory, Selection, Genetic, Molecular Biology, Gene, Ecology, Evolution, Behavior and Systematics, Selection (genetic algorithm), Discoveries, Natural selection, biology, AcademicSubjects/SCI01130, biology.organism_classification, Phenotype, Biological Evolution, Natural population growth, Evolutionary biology, Homogeneous, mutation accumulation theory, Gene co-expression network, Transcriptome
Abstract

How, when, and why do organisms, their tissues, and their cells age remain challenging issues, although researchers have identified multiple mechanistic causes of aging, and three major evolutionary theories have been developed to unravel the ultimate causes of organismal aging. A central hypothesis of these theories is that the strength of natural selection decreases with age. However, empirical evidence on when, why, and how organisms age is phylogenetically limited, especially in natural populations. Here, we developed generic comparisons of gene co-expression networks that quantify and dissect the heterogeneity of gene co-expression in conspecific individuals from different age-classes to provide topological evidence about some mechanical and fundamental causes of organismal aging. We applied this approach to investigate the complexity of some proximal and ultimate causes of aging phenotypes in a natural population of the greater mouse-eared bat Myotis myotis, a remarkably long-lived species given its body size and metabolic rate, with available longitudinal blood transcriptomes. M. myotis gene co-expression networks become increasingly fragmented with age, suggesting an erosion of the strength of natural selection and a general dysregulation of gene co-expression in aging bats. However, selective pressures remain sufficiently strong to allow successive emergence of homogeneous age-specific gene co-expression patterns, for at least 7 years. Thus, older individuals from long-lived species appear to sit at an evolutionary crossroad: as they age, they experience both a decrease in the strength of natural selection and a targeted selection for very specific biological processes, further inviting to refine a central hypothesis in evolutionary aging theories.

Published
2021

Catalog

Books, media, physical & digital resources
See catalog results