Search Results - "GERGELY, J"

A rooted phylogeny resolves early bacterial evolution by Coleman, Gareth A, Davín, Adrián A, Mahendrarajah, Tara A, Szánthó, Lénárd L, Spang, Anja, Hugenholtz, Philip, Szöllősi, Gergely J, Williams, Tom A

“…A rooted bacterial tree is necessary to understand early evolution, but the position of the root is contested. Here, we model the evolution of 11,272 gene…”
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Efficient Exploration of the Space of Reconciled Gene Trees by Szöllösi, Gergely J., Rosikiewicz, Wojciech, Boussau, Bastien, Tannier, Eric, Daubin, Vincent

“…Gene trees record the combination of gene-level events, such as duplication, transfer and loss (DTL), and specieslevel events, such as speciation and…”
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The Inference of Gene Trees with Species Trees by Szöllősi, Gergely J., Tannier, Eric, Daubin, Vincent, Boussau, Bastien

“…Abstract This article reviews the various models that have been used to describe the relationships between gene trees and species trees. Molecular phylogeny…”
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Integrative modeling of gene and genome evolution roots the archaeal tree of life by Williams, Tom A., Szöllősi, Gergely J., Spang, Anja, Foster, Peter G., Heaps, Sarah E., Boussau, Bastien, Ettema, Thijs J. G., Embley, T. Martin

“…A root for the archaeal tree is essential for reconstructing the metabolism and ecology of early cells and for testing hypotheses that propose that the…”
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ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony by Jacox, Edwin, Chauve, Cedric, Szöllősi, Gergely J, Ponty, Yann, Scornavacca, Celine

“…: A gene tree-species tree reconciliation explains the evolution of a gene tree within the species tree given a model of gene-family evolution. We describe…”
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Hierarchical tissue organization as a general mechanism to limit the accumulation of somatic mutations by Derényi, Imre, Szöllősi, Gergely J.

“…How can tissues generate large numbers of cells, yet keep the divisional load (the number of divisions along cell lineages) low in order to curtail the…”
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Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations by Szöllősi, Gergely J, Boussau, Bastien, Abby, Sophie S, Tannier, Eric, Daubin, Vincent

“…The timing of the evolution of microbial life has largely remained elusive due to the scarcity of prokaryotic fossil record and the confounding effects of the…”
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Damage and fluctuations induce loops in optimal transport networks by Katifori, Eleni, Szöllosi, Gergely J, Magnasco, Marcelo O

“…Leaf venation is a pervasive example of a complex biological network, endowing leaves with a transport system and mechanical resilience. Transport networks…”
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Quantifying GC-Biased Gene Conversion in Great Ape Genomes Using Polymorphism-Aware Models by Borges, Rui, Szöllősi, Gergely J, Kosiol, Carolin

“…As multi-individual population-scale data become available, more complex modeling strategies are needed to quantify genome-wide patterns of nucleotide usage…”
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GeneRax: A Tool for Species-Tree-Aware Maximum Likelihood-Based Gene  Family Tree Inference under Gene Duplication, Transfer, and Loss by Morel, Benoit, Kozlov, Alexey M, Stamatakis, Alexandros, Szöllősi, Gergely J

“…Abstract Inferring phylogenetic trees for individual homologous gene families is difficult because alignments are often too short, and thus contain…”
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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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SpeciesRax: A Tool for Maximum Likelihood Species Tree Inference from Gene Family Trees under Duplication, Transfer, and Loss by Morel, Benoit, Schade, Paul, Lutteropp, Sarah, Williams, Tom A, Szöllősi, Gergely J, Stamatakis, Alexandros

“…Abstract Species tree inference from gene family trees is becoming increasingly popular because it can account for discordance between the species tree and the…”
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Emergent neutrality in adaptive asexual evolution by Schiffels, Stephan, Szöllosi, Gergely J, Mustonen, Ville, Lässig, Michael

“…In nonrecombining genomes, genetic linkage can be an important evolutionary force. Linkage generates interference interactions, by which simultaneously…”
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How Long Does Wolbachia Remain on Board? by Bailly-Bechet, Marc, Martins-Simões, Patricia, Szöllosi, Gergely J, Mialdea, Gladys, Sagot, Marie-France, Charlat, Sylvain

“…Wolbachia bacteria infect about half of all arthropods, with diverse and extreme consequences ranging from sex-ratio distortion and mating incompatibilities to…”
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Divergent genomic trajectories predate the origin of animals and fungi by Ocaña-Pallarès, Eduard, Williams, Tom A., López-Escardó, David, Arroyo, Alicia S., Pathmanathan, Jananan S., Bapteste, Eric, Tikhonenkov, Denis V., Keeling, Patrick J., Szöllősi, Gergely J., Ruiz-Trillo, Iñaki

“…Animals and fungi have radically distinct morphologies, yet both evolved within the same eukaryotic supergroup: Opisthokonta 1 , 2 . Here we reconstructed the…”
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Joint amalgamation of most parsimonious reconciled gene trees by Scornavacca, Celine, Jacox, Edwin, Szöllősi, Gergely J

“…Traditionally, gene phylogenies have been reconstructed solely on the basis of molecular sequences; this, however, often does not provide enough information to…”
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Lateral Gene Transfer from the Dead by Szöllősi, Gergely J., Tannier, Eric, Lartillot, Nicolas, Daubin, Vincent

“…In phylogenetic studies, the evolution of molecular sequences is assumed to have taken place along the phylogeny traced by the ancestors of extant species. In…”
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AleRax: a tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss by Morel, Benoit, Williams, Tom A, Stamatakis, Alexandros, Szöllősi, Gergely J

“…Abstract Motivation Genomes are a rich source of information on the pattern and process of evolution across biological scales. How best to make use of that…”
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Horizontal Gene Transfer and the History of Life by Daubin, Vincent, Szöllősi, Gergely J

“…Microbes acquire DNA from a variety of sources. The last decades, which have seen the development of genome sequencing, have revealed that horizontal gene…”
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Trade-off between reducing mutational accumulation and increasing commitment to differentiation determines tissue organization by Demeter, Márton, Derényi, Imre, Szöllősi, Gergely J.

“…Species-specific differences control cancer risk across orders of magnitude variation in body size and lifespan, e.g., by varying the copy numbers of tumor…”
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