Divergent genomic trajectories predate the origin of animals and fungi von 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

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

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Integrative modeling of gene and genome evolution roots the archaeal tree of life von Williams, Tom A., Szöllősi, Gergely J., Spang, Anja, Foster, Peter G., Heaps, Sarah E., Boussau, Bastien, Ettema, Thijs J. G., Embley, T. Martin

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Efficient Exploration of the Space of Reconciled Gene Trees von Szöllösi, Gergely J., Rosikiewicz, Wojciech, Boussau, Bastien, Tannier, Eric, Daubin, Vincent

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Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations von Szöllősi, Gergely J, Boussau, Bastien, Abby, Sophie S, Tannier, Eric, Daubin, Vincent

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Damage and fluctuations induce loops in optimal transport networks von Katifori, Eleni, Szöllosi, Gergely J, Magnasco, Marcelo O

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ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony von Jacox, Edwin, Chauve, Cedric, Szöllősi, Gergely J, Ponty, Yann, Scornavacca, Celine

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Quantifying GC-Biased Gene Conversion in Great Ape Genomes Using Polymorphism-Aware Models von Borges, Rui, Szöllősi, Gergely J, Kosiol, Carolin

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Hierarchical tissue organization as a general mechanism to limit the accumulation of somatic mutations von Derényi, Imre, Szöllősi, Gergely J.

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The Inference of Gene Trees with Species Trees von Szöllősi, Gergely J., Tannier, Eric, Daubin, Vincent, Boussau, Bastien

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SpeciesRax: A Tool for Maximum Likelihood Species Tree Inference from Gene Family Trees under Duplication, Transfer, and Loss von Morel, Benoit, Schade, Paul, Lutteropp, Sarah, Williams, Tom A, Szöllősi, Gergely J, Stamatakis, Alexandros

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How Long Does Wolbachia Remain on Board? von Bailly-Bechet, Marc, Martins-Simões, Patricia, Szöllosi, Gergely J, Mialdea, Gladys, Sagot, Marie-France, Charlat, Sylvain

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

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Trade-off between reducing mutational accumulation and increasing commitment to differentiation determines tissue organization von Demeter, Márton, Derényi, Imre, Szöllősi, Gergely J.

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Resurrection of Ancestral Malate Dehydrogenases Reveals the Evolutionary History of Halobacterial Proteins: Deciphering Gene Trajectories and Changes in Biochemical Properties von Blanquart, Samuel, Groussin, Mathieu, Le Roy, Aline, Szöllosi, Gergely J, Girard, Eric, Franzetti, Bruno, Gouy, Manolo, Madern, Dominique

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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 von Morel, Benoit, Williams, Tom A, Stamatakis, Alexandros, Szöllősi, Gergely J

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The structure of the hematopoietic system can explain chronic myeloid leukemia progression von Pérez-Jiménez, Mario, Derényi, Imre, Szöllősi, Gergely J.

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Emergent neutrality in adaptive asexual evolution von Schiffels, Stephan, Szöllosi, Gergely J, Mustonen, Ville, Lässig, Michael

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Distinguishing excess mutations and increased cell death based on variant allele frequencies von Tibély, Gergely, Schrempf, Dominik, Derényi, Imre, Szöllősi, Gergely J

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ATP synthase evolution on a cross-braced dated tree of life von Mahendrarajah, Tara A., Moody, Edmund R. R., Schrempf, Dominik, Szánthó, Lénárd L., Dombrowski, Nina, Davín, Adrián A., Pisani, Davide, Donoghue, Philip C. J., Szöllősi, Gergely J., Williams, Tom A., Spang, Anja

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