Search Results - "GOUY, Manolo"

Genome-scale coestimation of species and gene trees by Boussau, Bastien, Szöllosi, Gergely J, Duret, Laurent, Gouy, Manolo, Tannier, Eric, Daubin, Vincent

“…Comparisons of gene trees and species trees are key to understanding major processes of genome evolution such as gene duplication and loss. Because current…”
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leBIBIQBPP: a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences by Flandrois, Jean-Pierre, Perrière, Guy, Gouy, Manolo

“…Estimating the phylogenetic position of bacterial and archaeal organisms by genetic sequence comparisons is considered as the gold-standard in taxonomy. This…”
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Parallel adaptations to high temperatures in the Archaean eon by Gouy, Manolo, Boussau, Bastien, Blanquart, Samuel, Necsulea, Anamaria, Lartillot, Nicolas

“…Fossils of organisms dating from the origin and diversification of cellular life are scant and difficult to interpret, for this reason alternative means to…”
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Lateral gene transfer as a support for the tree of life by Abby, Sophie S., Tannier, Eric, Gouy, Manolo, Daubin, Vincent

“…Lateral gene transfer (LGT), the acquisition of genes from other species, is a major evolutionary force. However, its success as an adaptive process makes the…”
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Treerecs: an integrated phylogenetic tool, from sequences to reconciliations by Comte, Nicolas, Morel, Benoit, Hasić, Damir, Guéguen, Laurent, Boussau, Bastien, Daubin, Vincent, Penel, Simon, Scornavacca, Celine, Gouy, Manolo, Stamatakis, Alexandros, Tannier, Eric, Parsons, David P

“…Abstract Motivation Gene and species tree reconciliation methods are used to interpret gene trees, root them and correct uncertainties that are due to scarcity…”
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Resurrection of Ancestral Malate Dehydrogenases Reveals the Evolutionary History of Halobacterial Proteins: Deciphering Gene Trajectories and Changes in Biochemical Properties by Blanquart, Samuel, Groussin, Mathieu, Le Roy, Aline, Szöllosi, Gergely J, Girard, Eric, Franzetti, Bruno, Gouy, Manolo, Madern, Dominique

“…Abstract Extreme halophilic Archaea thrive in high salt, where, through proteomic adaptation, they cope with the strong osmolarity and extreme ionic conditions…”
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A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea by Aouad, Monique, Flandrois, Jean-Pierre, Jauffrit, Frédéric, Gouy, Manolo, Gribaldo, Simonetta, Brochier-Armanet, Céline

“…The recent rise in cultivation-independent genome sequencing has provided key material to explore uncharted branches of the Tree of Life. This has been…”
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Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria by Boussau, Bastien, Guéguen, Laurent, Gouy, Manolo

“…Despite a large agreement between ribosomal RNA and concatenated protein phylogenies, the phylogenetic tree of the bacterial domain remains uncertain in its…”
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A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history by Daubin, Vincent, Gouy, Manolo, Perrière, Guy

“…It has been claimed that complete genome sequences would clarify phylogenetic relationships between organisms, but up to now, no satisfying approach has been…”
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Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests by Abby, Sophie S, Tannier, Eric, Gouy, Manolo, Daubin, Vincent

“…To understand the evolutionary role of Lateral Gene Transfer (LGT), accurate methods are needed to identify transferred genes and infer their timing of…”
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The molecular signal for the adaptation to cold temperature during early life on Earth by Groussin, Mathieu, Boussau, Bastien, Charles, Sandrine, Blanquart, Samuel, Gouy, Manolo

“…Several lines of evidence such as the basal location of thermophilic lineages in large-scale phylogenetic trees and the ancestral sequence reconstruction of…”
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Phylogenomics of life-or-death switches in multicellular animals: Bcl-2, BH3-Only, and BNip families of apoptotic regulators by Aouacheria, Abdel, Brunet, Frédéric, Gouy, Manolo

“…In this report, we conducted a comprehensive survey of Bcl-2 family members, a divergent group of proteins that regulate programmed cell death by an…”
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Recombination rate and the distribution of transposable elements in the Drosophila melanogaster genome by Rizzon, Carène, Marais, Gabriel, Gouy, Manolo, Biémont, Christian

“…We analyzed the distribution of 54 families of transposable elements (TEs; transposons, LTR retrotransposons, and non-LTR retrotransposons) in the chromosomes…”
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A Nonhyperthermophilic Common Ancestor to Extant Life Forms by Galtier, Nicolas, Tourasse, Nicolas, Gouy, Manolo

“…The G+C nucleotide content of ribosomal RNA (rRNA) sequences is strongly correlated with the optimal growth temperature of prokaryotes. This property allows…”
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Phylogenetic analysis of the complete genome sequence of Encephalitozoon cuniculi supports the fungal origin of microsporidia and reveals a high frequency of fast-evolving genes by Thomarat, Fabienne, Vivarès, Christian P, Gouy, Manolo

“…Microsporidia are unicellular eukaryotes living as obligate intracellular parasites. Lacking mitochondria, they were initially considered as having diverged…”
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Phylogenetic position of the order Lagomorpha (rabbits, hares and allies) by Graur, Dan, Duret, Laurent, Gouy, Manolo

“…Ever since they have been classified as ruminants in the Old Testament (Leviticus 11:6, Deuteronomy 14:7) and equated with hyraxes in the vulgate Latin…”
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Invertebrate Data Predict an Early Emergence of Vertebrate Fibrillar Collagen Clades and an Anti-incest Model by Aouacheria, Abdel, Cluzel, Caroline, Lethias, Claire, Gouy, Manolo, Garrone, Robert, Exposito, Jean-Yves

“…Fibrillar collagens are involved in the formation of striated fibrils and are present from the first multicellular animals, sponges, to humans. Recently, a new…”
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A Mixture Model and a Hidden Markov Model to Simultaneously Detect Recombination Breakpoints and Reconstruct Phylogenies by Boussau, Bastien, Gueguen, Laurent, Gouy, Manolo

“…Bastien Boussau, Laurent Guéguen and Manolo GouyUniversité de Lyon; université Lyon 1; CNRS; UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 43…”
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HOBACGEN: database system for comparative genomics in bacteria by Perrière, G, Duret, L, Gouy, M

“…We present here HOBACGEN, a database system devoted to comparative genomics in bacteria. HOBACGEN contains all available protein genes from bacteria, archaea,…”
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SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building by Gouy, Manolo, Guindon, Stéphane, Gascuel, Olivier

“…We present SeaView version 4, a multiplatform program designed to facilitate multiple alignment and phylogenetic tree building from molecular sequence data…”
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