Search

Your search keyword '"Gascuel, Olivier"' showing total 654 results
Start Over Author "Gascuel, Olivier"

Refine your results

more »

more »

more »

more »

more »
654 results on '"Gascuel, Olivier"'

1. Origin, evolution and global spread of SARS-CoV-2

Author

Zhukova, Anna, Blassel, Luc, Lemoine, Frédéric, Morel, Marie, Voznica, Jakub, and Gascuel, Olivier

Subjects
SARS-CoV-2, COVID19, Origin, Evolution, Transmission, Clusters, Biology (General), QH301-705.5
Abstract

SARS-CoV-2 is the virus responsible for the global COVID19 pandemic. We review what is known about the origin of this virus, detected in China at the end of December 2019. The genome of this virus mainly evolves under the effect of point mutations. These are generally neutral and have no impact on virulence and severity, but some appear to influence infectivity, notably the D614G mutation of the Spike protein. To date (30/09/2020) no recombination of the virus has been documented in the human host, and very few insertions and deletions. The worldwide spread of the virus was the subject of controversies that we summarize, before proposing a new approach free from the limitations of previous methods. The results show a complex scenario with, for example, numerous introductions to the USA and returns of the virus from the USA to certain countries including France.

Published
2020
Full Text
View/download PDF

4. The Bayesian Phylogenetic Bootstrap and its Application to Short Trees and Branches.

Author

Lemoine, Frédéric and Gascuel, Olivier

Abstract

Felsenstein's bootstrap is the most commonly used method to measure branch support in phylogenetics. Current sequencing technologies can result in massive sampling of taxa (e.g. SARS-CoV-2). In this case, the sequences are very similar, the trees are short, and the branches correspond to a small number of mutations (possibly 0). Nevertheless, these trees contain a strong signal, with unresolved parts but a low rate of false branches. With such data, Felsenstein's bootstrap is not satisfactory. Due to the frequentist nature of bootstrap sampling, the expected support of a branch corresponding to a single mutation is ∼63%, even though it is highly likely to be correct. Here, we propose a Bayesian version of the phylogenetic bootstrap in which sites are assigned uninformative prior probabilities. The branch support can then be interpreted as a posterior probability. We do not view the alignment as a small subsample of a large sample of sites, but rather as containing all available information (e.g. as with complete viral genomes, which are becoming routine). We give formulas for expected supports under the assumption of perfect phylogeny, in both the frequentist and Bayesian frameworks, where a branch corresponding to a single mutation now has an expected support of ∼90%. Simulations show that these theoretical results are robust to realistic data. Analyses on low-homoplasy viral and nonviral datasets show that Bayesian bootstrap support is easier to interpret, with high supports for branches very likely to be correct. As homoplasy increases, the two supports become closer and strongly correlated. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

5. Integrating Contact Tracing Data to Enhance Outbreak Phylodynamic Inference: A Deep Learning Approach.

Author

Xie, Ruopeng, Adam, Dillon C, Hu, Shu, Cowling, Benjamin J, Gascuel, Olivier, Zhukova, Anna, and Dhanasekaran, Vijaykrishna

Abstract

Phylodynamics is central to understanding infectious disease dynamics through the integration of genomic and epidemiological data. Despite advancements, including the application of deep learning to overcome computational limitations, significant challenges persist due to data inadequacies and statistical unidentifiability of key parameters. These issues are particularly pronounced in poorly resolved phylogenies, commonly observed in outbreaks such as SARS-CoV-2. In this study, we conducted a thorough evaluation of PhyloDeep, a deep learning inference tool for phylodynamics, assessing its performance on poorly resolved phylogenies. Our findings reveal the limited predictive accuracy of PhyloDeep (and other state-of-the-art approaches) in these scenarios. However, models trained on poorly resolved, realistically simulated trees demonstrate improved predictive power, despite not being infallible, especially in scenarios with superspreading dynamics, whose parameters are challenging to capture accurately. Notably, we observe markedly improved performance through the integration of minimal contact tracing data, which refines poorly resolved trees. Applying this approach to a sample of SARS-CoV-2 sequences partially matched to contact tracing from Hong Kong yields informative estimates of superspreading potential, extending beyond the scope of contact tracing data alone. Our findings demonstrate the potential for enhancing phylodynamic analysis through complementary data integration, ultimately increasing the precision of epidemiological predictions crucial for public health decision-making and outbreak control. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

9. Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable

Author

Mavian, Carla, Pond, Sergei Kosakovsky, Marini, Simone, Magalis, Brittany Rife, Vandamme, Anne-Mieke, Dellicour, Simon, Scarpino, Samuel V., Houldcroft, Charlotte, Villabona-Arenas, Julian, Paisie, Taylor K., Trovão, Nídia S., Boucher, Christina, Zhang, Yun, Scheuermann, Richard H., Gascuel, Olivier, Lam, Tommy Tsan-Yuk, Suchard, Marc A., Abecasis, Ana, Wilkinson, Eduan, de Oliveira, Tulio, Bento, Ana I., Schmidt, Heiko A., Martin, Darren, Hadfield, James, Faria, Nuno, Grubaugh, Nathan D., Neher, Richard A., Baele, Guy, Lemey, Philippe, Stadler, Tanja, Albert, Jan, Crandall, Keith A., Leitner, Thomas, Stamatakis, Alexandros, Prosperi, Mattia, and Salemi, Marco

Published
2020

10. The combinatorics of overlapping genes

Author

Lebre, Sophie and Gascuel, Olivier

Subjects
Quantitative Biology - Genomics
Abstract

Overlapping genes exist in all domains of life and are much more abundant than expected at their first discovery in the late 1970s. Assuming that the reference gene is read in frame +0, an overlapping gene can be encoded in two reading frames in the sense strand, denoted by +1 and +2, and in three reading frames in the opposite strand, denoted by -0, -1 and -2. This motivated numerous researchers to study the constraints induced by the genetic code on the various overlapping frames, mostly based on information theory. Our focus in this paper is on the constraints induced on two overlapping genes in terms of amino acids, as well as polypeptides. We show that simple linear constraints bind the amino acid composition of two proteins encoded by overlapping genes. Novel constraints are revealed when polypeptides are considered, and not just single amino acids. For example, in double-coding sequences with an overlapping reading frame -2, each Tyrosine (denoted as Tyr or Y) in the overlapping frame overlaps a Tyrosine in the reference frame +0 (and reciprocally), whereas specific words (e.g. YY) never occur. We thus distinguish between null constraints (YY = 0 in frame -2) and non-null constraints (Y in frame +0 <=> Y in frame -2). Our equivalence-based constraints are symmetrical and thus enable the characterization of the joint composition of overlapping proteins. We describe several formal frameworks and a graph algorithm to characterize and compute these constraints. These results yield support for understanding the mechanisms and evolution of overlapping genes, and for developing novel overlapping gene detection methods.

Published
2016

11. Numerical Optimization Techniques in Maximum Likelihood Tree Inference

Author

Guindon, Stéphane, Gascuel, Olivier, Crippen, Gordon, Advisory Editor, Dress, Andreas, Editor-in-Chief, Giegerich, Robert, Editorial Board Member, Kelso, Janet, Editorial Board Member, Linial, Michal, Editor-in-Chief, Felsenstein, Joe, Advisory Editor, Troyanskaya, Olga, Editor-in-Chief, Gusfield, Dan, Advisory Editor, Myers, Gene, Editorial Board Member, Istrail, Sorin, Advisory Editor, Pevzner, Pavel, Editorial Board Member, Vingron, Martin, Editor-in-Chief, Lengauer, Thomas, Advisory Editor, McClure, Marcella, Advisory Editor, Nowak, Martin, Advisory Editor, Sankoff, David, Advisory Editor, Shamir, Ron, Advisory Editor, Steel, Mike, Advisory Editor, Stormo, Gary, Advisory Editor, Tavaré, Simon, Advisory Editor, Warnow, Tandy, Advisory Editor, and Welch, Lonnie, Advisory Editor

Published
2019
Full Text
View/download PDF

12. A 'stochastic safety radius' for distance-based tree reconstruction

Author

Gascuel, Olivier and Steel, Mike

Subjects
Quantitative Biology - Populations and Evolution
Abstract

A variety of algorithms have been proposed for reconstructing trees that show the evolutionary relationships between species by comparing differences in genetic data across present-day taxa. If the leaf-to-leaf distances in a tree can be accurately estimated, then it is possible to reconstruct this tree from these estimated distances, using polynomial-time methods such as the popular `Neighbor-Joining' algorithm. There is a precise combinatorial condition under which distance-based methods are guaranteed to return a correct tree (in full or in part) based on the requirement that the input distances all lie within some `safety radius' of the true distances. Here, we explore a stochastic analogue of this condition, and mathematically establish upper and lower bounds on this `stochastic safety radius' for distance-based tree reconstruction methods. Using simulations, we show how this notion provides a new way to compare the performance of distance-based tree reconstruction methods. This may help explain why Neighbor-Joining performs so well, as its stochastic safety radius appears close to optimal (while its more classical safety radius is the same as many other less accurate methods)., Comment: 18 pages, 1 figure, 4 tables

Published
2014

13. Predicting the ancestral character changes in a tree is typically easier than predicting the root state

Author

Gascuel, Olivier and Steel, Mike

Subjects
Quantitative Biology - Populations and Evolution
Abstract

Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed to this purpose. Theoretical results are available that show that when the mutation rate become too large, reconstructing the ancestral state at the tree root is no longer feasible. Here, we also study the reconstruction of the ancestral changes that occurred along the tree edges. We show that, depending on the tree and branch length distribution, reconstructing these changes (i.e. reconstructing the ancestral state of all internal nodes in the tree) may be easier or harder than reconstructing the ancestral root state. However, results from information theory indicate that for the standard Yule tree, the task of reconstructing internal node states remains feasible, even for very high substitution rates. Moreover, computer simulations demonstrate that for more complex trees and scenarios, this result still holds. For a large variety of counting, parsimony-based and likelihood-based methods, the predictive accuracy of a randomly selected internal node in the tree is indeed much higher than the accuracy of the same method when applied to the tree root. Moreover, parsimony- and likelihood-based methods appear to be remarkably robust to sampling bias and model mis-specification., Comment: 58 pages, 4 figures

Published
2013

14. Branch lengths on Yule trees and the expected loss of phylogenetic diversity

Author

Mooers, Arne, Gascuel, Olivier, Stadler, Tanja, Li, Heyang, and Steel, Mike

Subjects
Quantitative Biology - Populations and Evolution
Abstract

Diversification is nested, and early models suggested this could lead to a great deal of evolutionary redundancy in the Tree of Life. This result is based on a particular set of branch lengths produced by the common coalescent, where pendant branches leading to tips can be very short compared to branches deeper in the tree. Here, we analyze alternative and more realistic Yule and birth-death models. We show how censoring at the present both makes average branches one half what we might expect and makes pendant and interior branches roughly equal in length. Although dependent on whether we condition on the size of the tree, its age, or both, these results hold both for the Yule model and for birth-death models with moderate extinction. Importantly, the rough equivalency in interior and exterior branch lengths means the loss of evolutionary history with loss of species can be roughly linear. Under these models, the Tree of Life may offer limited redundancy in the face of ongoing species loss., Comment: 3 figures

Published
2010

15. Inferring ancestral sequences in taxon-rich phylogenies

Author

Gascuel, Olivier and Steel, Mike

Subjects
Quantitative Biology - Populations and Evolution
Abstract

Statistical consistency in phylogenetics has traditionally referred to the accuracy of estimating phylogenetic parameters for a fixed number of species as we increase the number of characters. However, as sequences are often of fixed length (e.g. for a gene) although we are often able to sample more taxa, it is useful to consider a dual type of statistical consistency where we increase the number of species, rather than characters. This raises some basic questions: what can we learn about the evolutionary process as we increase the number of species? In particular, does having more species allow us to infer the ancestral state of characters accurately? This question is particularly relevant when sequence site evolution varies in a complex way from character to character, as well as for reconstructing ancestral sequences. In this paper, we assemble a collection of results to analyse various approaches for inferring ancestral information with increasing accuracy as the number of taxa increases., Comment: 32 pages, 5 figures, 1 table.

Published
2010

16. Accurate Detection of Convergent Mutations in Large Protein Alignments With ConDor.

Author

Morel, Marie, Zhukova, Anna, Lemoine, Frédéric, and Gascuel, Olivier

Subjects
REVERSE transcriptase, COMPARATIVE method, CONVERGENT evolution, AMINO acid sequence, PHENOTYPIC plasticity, PHENOTYPES
Abstract

Evolutionary convergences are observed at all levels, from phenotype to DNA and protein sequences, and changes at these different levels tend to be correlated. Notably, convergent mutations can lead to convergent changes in phenotype, such as changes in metabolism, drug resistance, and other adaptations to changing environments. We propose a two-component approach to detect mutations subject to convergent evolution in protein alignments. The "Emergence" component selects mutations that emerge more often than expected, while the "Correlation" component selects mutations that correlate with the convergent phenotype under study. With regard to Emergence, a phylogeny deduced from the alignment is provided by the user and is used to simulate the evolution of each alignment position. These simulations allow us to estimate the expected number of mutations in a neutral model, which is compared to the observed number of mutations in the data studied. In Correlation, a comparative phylogenetic approach, is used to measure whether the presence of each of the observed mutations is correlated with the convergent phenotype. Each component can be used on its own, for example Emergence when no phenotype is available. Our method is implemented in a standalone workflow and a webserver, called ConDor. We evaluate the properties of ConDor using simulated data, and we apply it to three real datasets: sedge PEPC proteins, HIV reverse transcriptase, and fish rhodopsin. The results show that the two components of ConDor complement each other, with an overall accuracy that compares favorably to other available tools, especially on large datasets. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

31. A Massively Parallel Exact Solution Algorithm for the Balanced Minimum Evolution Problem

Author

UCL - SSH/LIDAM/CORE - Center for operations research and econometrics, Catanzaro, Daniele, Frohn, Martin, Gascuel, Olivier, Pesenti, Raffaele, UCL - SSH/LIDAM/CORE - Center for operations research and econometrics, Catanzaro, Daniele, Frohn, Martin, Gascuel, Olivier, and Pesenti, Raffaele

Abstract

We build upon recent theoretical advances on the Balanced Minimum Evolution Problem (BMEP) to design a new massively parallel exact solution algorithm that proves to be up to one order of magnitude faster than the current state-of-the-art under the same computing settings and environment. We also investigate, for the first time, the theoretical connections between numerical stability and statistical consistency of the BMEP and we show that some rescaling techniques introduced to numerically stabilize the problem may affect negatively the statistical consistency of the optimal solution to the problem.

Published
2023

35. In-Depth Characterization of Full-Length Archived Viral Genomes after Nine Years of Posttreatment HIV Control

Author

Trémeaux, Pauline, primary, Lemoine, Frédéric, additional, Mélard, Adeline, additional, Gousset, Marine, additional, Boufassa, Faroudy, additional, Orr, Sylvie, additional, Monceaux, Valérie, additional, Gascuel, Olivier, additional, Lambotte, Olivier, additional, Hocqueloux, Laurent, additional, Saez-Cirion, Asier, additional, Rouzioux, Christine, additional, Avettand-Fenoel, Véronique, additional, Bani-Sadr, Firouzé, additional, Hentzien, Maxime, additional, Berger, Jean-Luc, additional, Kmiec, Isabelle, additional, Pichancourt, Gilles, additional, Nasri, Safa, additional, Hittinger, Gilles, additional, Lambry, Véronique, additional, Beaudrey, Anne-Cécile, additional, Pialoux, Gilles, additional, Chas, Julie, additional, Palacios, Christia, additional, Adda, Anne, additional, Viard, Jean Paul, additional, Dulucq, Marie-Josée, additional, Weiss, Laurence, additional, Karmochkine, Marina, additional, Meghadecha, Mohamed, additional, Salmon-Ceron, Dominique, additional, Piétri, Marie-Pierre, additional, Blanche, Philippe, additional, Molina, Jean-Michel, additional, Taulera, Olivier, additional, Ponscarme, Diane, additional, Delgado Bertaut, Jeannine, additional, Makhloufi, Djamila, additional, Godinot, Matthieu, additional, Artizzu, Valérie, additional, Miailhes, Patrick, additional, Cotte, Laurent, additional, Pailhes, Sophie, additional, Conrad, Anne, additional, Karkowski, Ludovic, additional, Ogoudjobi, Stanislas, additional, Yazdanpanah, Yazdan, additional, Matheron, Sophie, additional, Godard, Cindy, additional, Bernard, Louis, additional, Bastides, Frédéric, additional, Bourgault, Olivier, additional, Jacomet, Christine, additional, Goncalves, Emilie, additional, Chavanet, Pascal, additional, Piroth, Lionel, additional, Gohier, Sandrine, additional, Meybeck, Agnès, additional, Huleux, Thomas, additional, Cornavin, Pauline, additional, Debab, Yasmine, additional, Théron, David, additional, Prazuck, Thierry, additional, De Dieuleveult, Barbara, additional, Faller, Jean-Pierre, additional, Eglinger, Patricia, additional, Roblot, Pascal, additional, Plainchamp, David, additional, Aumaître, Hugues, additional, Malet, Martine, additional, Rouger, Christine, additional, Rémy, Gérard, additional, Isabelle, Melle Kmiec, additional, Delassus, Jean-Luc, additional, Devidas, Alain, additional, Froguel, Eric, additional, Tassi, Sylvie, additional, Genet, Philippe, additional, Gerbe, Juliette, additional, Patey, Olivier, additional, Laurent, Richier, additional, Drobacheff, Marie-Christine, additional, Proust, Aurélie, additional, Gil, Helder, additional, Gérard, Laurence, additional, Oksenhendler, Eric, additional, Lascoux, Caroline, additional, Parlier, Sylvie, additional, Lucht, Frédéric, additional, Ronat, Véronique, additional, Dupon, Michel, additional, Dutronc, Hervé, additional, Le Puil, Séverine, additional, Neau, Didier, additional, Mercié, Patrick, additional, Morlat, Philippe, additional, Caldato, Sabrina, additional, Schmit, Jean-Luc, additional, Decaux, Nathalie, additional, Bru, Jean-Pierre, additional, Clavere, Gaëlle, additional, Delfraissy, Jean-François, additional, Goujard, Cécile, additional, Bourdic, Katia, additional, Vittecoq, Daniel, additional, Bolliot, Claudine, additional, Lambert, Thierry, additional, Bergmann, Jean-François, additional, Parrinello, Maguy, additional, Welker, Yves, additional, Lafeuillade, Alain, additional, Philip, Gisèle, additional, Rapp, Christophe, additional, Lerondel, Melle, additional, de Truchis, Pierre, additional, Huguette, Berthe, additional, Jeantils, Vincent, additional, Mchangama, Fatouma, additional, Consigny, Paul Henri, additional, Touam, Fatima, additional, le Nagat, Sophie, additional, Bouchaud, Olivier, additional, Honoré, Patricia, additional, Boué, François, additional, Raho-Moussa, Mariem, additional, Viard, Jean-Paul, additional, Cros, Agnès, additional, Salmon-Céron, Dominique, additional, Pietri, Marie-Pierre, additional, Collias, Lio, additional, Zucman, David, additional, Blétry, Olivier, additional, Bornarel, Dominique, additional, Mortier, Emmanuel, additional, Feng, Zeng, additional, Lelièvre, Jean-Daniel, additional, Katlama, Christine, additional, Dudoit, Yasmine, additional, Simon, Anne, additional, Lupin, Catherine, additional, Girard, Pierre-Marie, additional, Pauchard, Michèle, additional, Abel, Sylvie, additional, Cabié, André, additional, Fialaire, Pascale, additional, Chennebault, Jean-Marie, additional, Rehaiem, Sami, additional, de Saint Martin, Luc, additional, Perfezou, ••••, additional, Duthe, Jean-Charles, additional, Weinbreck, Pierre, additional, Genet, Claire, additional, Garnier, Florence, additional, Poizot-Martin, Isabelle, additional, Fauche, Olivia, additional, Ivanova, Alena, additional, Philibert, Patrick, additional, Penda Sow, Mame, additional, Yeni, Patrick, additional, Godard, Cyndi, additional, Raffi, François, additional, Hüe, Hervé, additional, Perré, Philippe, additional, Roger, Pierre Marie, additional, Joulie, Aline, additional, Rosenthal, Éric, additional, Michelet, Christian, additional, Souala, Faouzi, additional, Ratajczak, Maja, additional, Partisani, Marialuisa, additional, Fischer, Patricia, additional, Nau, Pascale, additional, Delobel, Pierre, additional, Balsarin, Florence, additional, De Lavaissiere, Marc, additional, Verdon, Renaud, additional, Feret, Philippe, additional, Leclercq, Pascale, additional, Gerberon, ••••, additional, Meybeck, Agnés, additional, Biekre, Raphaël, additional, May, Thierry, additional, Bouillon, ••••, additional, Caron, François, additional, Theron, David, additional, Gatfosse, Marc, additional, Martinot, Martin, additional, Pachart, Anne, additional, Poubeau, Patrice, additional, Gaud, Catherine, additional, Uludag, Agnès, additional, Arsac, Philippe, additional, Bouaraba, Lydia, additional, de Dieulevault, Barbara, additional, De Lacroix Szmania, Isabelle, additional, Richier, Laurent, additional, Daneluzzi, Vincent, additional, Rouveix, Elisabeth, additional, Beck-Wirth, Geneviève, additional, Romand, Philippe, additional, Blum, Laurent, additional, Deschaud, Martine, additional, Michau, Christophe, additional, Bernard, Christian, additional, Salaun, Florence, additional, Muller, Philippe, additional, Poinsignon, Yves, additional, Lepretre, Annie, additional, Sotto, Albert, additional, Doncesco, ••••, additional, Perfezou, Pascale, additional, Duthe, Jean Charles, additional, Niault, Mathilde Aurore, additional, Mouton-Rioux, Virginie, additional, Talarmin, Jean-Philippe, additional, Duthé, Jean Charles, additional, Dupont, Mathilde, additional, Natur, Stéphane, additional, Hitoto, Hikombo, additional, and Ibrahim, Ali Mahamadou, additional

Published
2023
Full Text
View/download PDF

38. Inferring phylogenetic trees from intramolecular distances with Phylo-IMD

Author

Mansouri, Leila, Baltzis, Athanasios, Langer, Björn E, Magis, Cedrik, de Vienne, Damien M, Gascuel, Olivier, and Notredame, Cedric

Subjects
structure of protein, phylogeny, protein evolution, intramolecular distances
Abstract

Phylogenetic reconstruction is one of the most widely used modelling techniques in biology. While most available methods involve the use of sequence-based comparison it has long been discussed whether structural information could be used to further inform tree reconstruction. In this study, we explored the usability of intra molecular distances as a potential evolutionary character. Using multiple sequence alignment to identify homologous internal distances, we have defined a pairwise comparison metric, IMD, that can be used in combination with any distance-based phylogenetic method and lends itself to the measure of branch support values using a procedure similar to the Felsenstein bootstrap. The IMD metric was validated on a dataset of 508 protein families featuring a total of 10,668 protein sequences with known X-Ray structures. The benchmark was carried out using sequence-based maximum likelihood trees as references. Our most important finding is the observation that the IMD bootstrap support is a strong indicator of topological agreement between the structure-based IMD trees and their sequence-based maximum likelihood counterparts. We also developed a titration procedure that allowed us to determine that all things being equal, the evolutionary signal measured by IMD is roughly twice denser than the equivalent sequence-based signal. Altogether our results suggest the suitability of structure-based phylogeny for evolutionary analysis, but above all, they indicate structure-based phylogeny as a powerful means of providing new supporting evidence to protein phylogenetic tree reconstruction.&nbsp

Published
2022
Full Text
View/download PDF

39. Systematic use of orthologous information to improve the phylogeny of paralogous genes

Author

Baltzis, Athanasios, Mansouri, Leila, Magis, Cedrik, Gascuel, Olivier, and Notredame, Cedric

Abstract

Gene duplication is one of the main driving forces of evolution. Yet, establishing reliable phylogenetic relationships among paralogous genes remains a challenging task. Tree reconstruction can be significantly improved by increasing the amount of supporting data. In the case of paralogous gene reconstruction, it is, however, difficult to increase the amount of data without having to build extremely large gene trees in order to simultaneously infer orthologous and paralogous relationships. In this study, we focused on a specific scenario, in which one attempts to reconstruct a paralogous tree whose duplications took place before the last unique common ancestor of the considered genomes. In this precise situation, we show that the information across the sibling genomes can be combined either using a supermatrix or a supertree approach and that yields significant topological improvements. As a support to our claim, we constructed a simulated dataset featuring 500 families and complemented this analysis with 41 empirical datasets. The empirical validation was carried out by showing that when combining the information across genomes, one can increase the topological similarity between minimum evolution and maximum likelihood trees by enriching the genomic information. At a time when accurate orthologous assignments can be inferred using direct full genome alignments, our approach provides a new and efficient way to integrate large amounts of genomic data into accurate paralogous phylogenetic trees.&nbsp

Published
2022
Full Text
View/download PDF

40. Fast and accurate maximum-likelihood estimation of Birth-Death Exposed-Infectious epidemiological model from phylogenetic trees

Author

Zhukova, Anna, Hecht, Frédéric, Maday, Yvon, Gascuel, Olivier, Institut Pasteur [Paris] (IP), Laboratoire Jacques-Louis Lions (LJLL (UMR_7598)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), 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), O.G. was supported by PRAIRIE (ANR-19-P3IA-0001). Y.M. was supported by European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 810367), project EMC2, ANR-19-P3IA-0001,PRAIRIE,PaRis Artificial Intelligence Research InstitutE(2019), and European Project: 810367,EMC2(2019)

Subjects
[SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

Posté dans MedRxiv le 6 juillet 2023; The birth-death exposed-infectious (BDEI) model describes the transmission of pathogens featuring an incubation period (when the host is already infected but not yet infectious), for example Ebola and SARS-CoV-2. In a phylodynamics framework, it serves to infer such epidemiological parameters as the basic reproduction number R 0 , the incubation period and the infectious time from a phylogenetic tree (a genealogy of pathogen sequences). With constantly growing sequencing data, the BDEI model should be extremely useful for unravelling information on pathogen epidemics. However, existing implementations of this model in a phylodynamic framework have not yet caught up with the sequencing speed. While the accuracy of estimations should increase with data set size, existing BDEI implementations are limited to medium data sets of up to 500 samples, for both computing time and numerical instability reasons. We improve accuracy and drastically reduce computing time for the BDEI model by rewriting its differential equations in a highly parallelizable way, and by using a combination of numerical analysis methods for their efficient resolution. Our implementation takes one minute on a phylogenetic tree of 10 000 samples. We compare our parameter estimator to the existing implementations on simulated data. Results show that we are not only much faster (50 000 times), but also more accurate. An application of our method to the 2014 Ebola epidemic in Sierra-Leone is also convincing, with very fast calculation and precise estimates. Our BDEI estimator should become an important tool for routine epidemiological surveillance. It is available at github.com/evolbioinfo/BDEI . Significance Statement Phylodynamics uses pathogen genomes as a source of information for epidemiological parameter inference. With constantly growing genome sequence availability, phylodynamics has a high potential for shedding light on epidemics, especially in the beginning, when classical epidemiological data (e.g. incidence curves) are yet limited. However due to the high complexity of differential equations used in phylodynamic models, current implementations suffer from numerical instability and are only applicable to datasets of limited size (

Published
2022

42. Deciphering RNA G-quadruplex function during the early steps of HIV-1 infection

Author

Amrane, Samir, primary, Jaubert, Chloé, additional, Bedrat, Amina, additional, Rundstadler, Tiffany, additional, Recordon-Pinson, Patricia, additional, Aknin, Cindy, additional, Guédin, Aurore, additional, De Rache, Aurore, additional, Bartolucci, Laura, additional, Diene, Ibra, additional, Lemoine, Frédéric, additional, Gascuel, Olivier, additional, Pratviel, Geneviève, additional, Mergny, Jean-Louis, additional, and Andreola, Marie-Line, additional

Published
2022
Full Text
View/download PDF

45. Evolution of Tandemly Repeated Sequences Through Duplication and Inversion

Author

Bertrand, Denis, Lajoie, Mathieu, El-Mabrouk, Nadia, Gascuel, Olivier, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael, editor, Bourque, Guillaume, editor, and El-Mabrouk, Nadia, editor

Published
2006
Full Text
View/download PDF

46. Phylogénétique : quelles mesures de support pour les branches d’un arbre ?

Author

Gascuel, Olivier, Lemoine, Frédéric, 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), Bioinformatique évolutive - Evolutionary Bioinformatics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), O.G. is supported by PRAIRIE (ANR-19-P3IA-0001)., Gilles Didier, Stéphane Guindon, and ANR-19-P3IA-0001,PRAIRIE,PaRis Artificial Intelligence Research InstitutE(2019)

Subjects
bootstrap de transfert, bootstrap RELL, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Statistique, supports de branches, supports aLRT, bootstrap phylogénétique de Felsenstein, Phylogénétique
Abstract

International audience; Une fois une phylogénie estimée, se pose la question du support de ses branches et des inférences associées : Décrivent-elles la réalité du passé biologique ? Sontelles fiables, reproductibles, robustes ? Ou à l'inverse peut-on conclure que le signal contenu dans les données ne permet pas de trancher entre plusieurs hypothèses alternatives ? De nombreuses approches ont été proposées pour répondre à ces questions. Nous décrivons dans ce chapitre les principales méthodes utilisées aujourd'hui en phylogénétique. Certaines sont locales et demandent peu de temps calcul. D'autres comme le bootstrap requièrent à l'inverse des calculs lourds mais donnent une vision plus globale. On distingue les méthodes paramétriques qui font explicitement appel à un modèle de l'évolution des séquences et se basent sur la fonction de vraisemblance ou la distribution a posteriori dans un cadre Bayésien, et les approches non-paramétriques qui reposent sur moins d'hypothèses explicites. On trouvera quatre parties dans ce chapitre : (1) supports locaux ; (2) bootstrap phylogénétique de Felsenstein et bootstrap de transfert ; (3) supports Bayésiens basés sur les probabilités a posteriori; (4) comparaison de ces approches et discussion.

Published
2022
Full Text
View/download PDF

48. Markov Models in Molecular Evolution

Author

Galtier, Nicolas, Gascuel, Olivier, Jean-Marie, Alain, Dietz, K., editor, Gail, M., editor, Krickeberg, K., editor, Tsiatis, A., editor, Samet, J., editor, and Nielsen, Rasmus

Published
2005
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results