Reconstructing a dated tree of life using phylogenetic incongruence

Publikacje

Resurrection of Ancestral Malate Dehydrogenases Reveals the Evolutionary History of Halobacterial Proteins: Deciphering Gene Trajectories and Changes in Biochemical Properties

Autorzy: Samuel Blanquart, Mathieu Groussin, Aline Le Roy, Gergely J Szöllosi, Eric Girard, Bruno Franzetti, Manolo Gouy, Dominique Madern
Opublikowane w: Molecular Biology and Evolution, Numer Volume 38, Numer 9, Pages 3754–3774, 2021, ISSN 1537-1719
Wydawca: Oxford University Press
DOI: 10.1093/molbev/msab146

Nucleotide Usage Biases Distort Inferences of the Species Tree

Autorzy: Rui Borges, Bastien Boussau, Gergely J Szöllősi, Carolin Kosiol
Opublikowane w: Genome Biology and Evolution, Numer Volume 14, Numer 1, evab290, 2022, ISSN 1759-6653
Wydawca: Oxford University Press
DOI: 10.1093/gbe/evab290

The structure of the hematopoietic system can explain chronic myeloid leukemia progression.

Autorzy: Pérez-Jiménez M, Derényi I, Szöllősi G.J.
Opublikowane w: Scientific Reports, Numer 13, 5411, 2023, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-023-32400-2

Distinguishing excess mutations and increased cell death based on variant allele frequencies

Autorzy: Gergely Tibély, Dominik Schrempf, Imre Derényi , Gergely J. Szöllősi
Opublikowane w: PLoS Computational Biology, Numer 18(4): e1010048, 2022, ISSN 1553-7358
Wydawca: PLOS
DOI: 10.1371/journal.pcbi.1010048

ATP synthase evolution on a cross-braced dated tree of life

Autorzy: Tara A. Mahendrarajah, Edmund R. R. Moody, Dominik Schrempf, Lénárd L. Szánthó, Nina Dombrowski, Adrián A. Davín, Davide Pisani, Philip C. J. Donoghue, Gergely J. Szöllősi, Tom A. Williams, Anja Spang
Opublikowane w: Nature Communications, Numer 14, 2023, Strona(/y) 7456, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-023-42924-w

SpeciesRax: A Tool for Maximum Likelihood Species Tree Inference from Gene Family Trees under Duplication, Transfer, and Loss

Autorzy: Benoit Morel, Paul Schade, Sarah Lutteropp, Tom A Williams, Gergely J Szöllősi, Alexandros Stamatakis
Opublikowane w: Molecular Biology and Evolution, Numer Volume 39, Numer 2, msab365,, 2022, ISSN 1537-1719
Wydawca: Oxford University Press
DOI: 10.1093/molbev/msab365

Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants

Autorzy: Brogan J. Harris, James W. Clark, Dominik Schrempf, Gergely J. Szöllősi, Philip C. J. Donoghue, Alistair M. Hetherington , Tom A. Williams
Opublikowane w: Nature Ecology and Evolution, Numer 6, 1634–1643, 2022, ISSN 2397-334X
Wydawca: Nature Publishing Group
DOI: 10.1038/s41559-022-01885-x

Trade-off between reducing mutational accumulation and increasing commitment to differentiation determines tissue organization

Autorzy: Demeter M., Derényi I., Szöllősi G.J.
Opublikowane w: Nature Communications, Numer 13, 1666, 2022, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-022-29004-1

Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits

Autorzy: Miyauchi Shingo; Kiss Enikő; Kuo Alan; Drula Elodie; Kohler Annegret; SánchezGarcía Marisol; Morin Emmanuelle; Andreopoulos Bill; Barry Kerrie W.; Bonito Gregory; Buée Marc; Carver Akiko; Chen Cindy; Cichocki Nicolas; Clum Alicia; Culley David; Crous Pedro W.; Fauchery Laure; Girlanda Mariangela; Hayes Richard D.; Kéri Zsófia; LaButti Kurt; Lipzen
Opublikowane w: Nature Communications, Numer 11, 5125, 2020, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-020-18795-w

Divergent genomic trajectories predate the origin of animals and fungi

Autorzy: 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
Opublikowane w: Nature, Numer 609, 747–753, 2022, ISSN 1476-4687
Wydawca: Nature Publishing Group
DOI: 10.1038/s41586-022-05110-4

An estimate of the deepest branches of the tree of life from ancient vertically evolving genes

Autorzy: Edmund RR Moody, Tara A Mahendrarajah, Nina Dombrowski, James W Clark, Celine Petit, jean Pierre Offre, Gergely J Szöllősi, Anja Spang, Tom A Williams
Opublikowane w: eLife, Numer 66695, 2022, ISSN 2050-084X
Wydawca: eLife Sciences Publications
DOI: 10.7554/elife.66695

Compositionally Constrained Sites Drive Long-Branch Attraction

Autorzy: Lénárd L Szánthó, Nicolas Lartillot, Gergely J Szöllősi, Dominik Schrempf
Opublikowane w: Systematic Biolog, Numer Volume 72, Numer 4, Pages 767–780,, 2023, ISSN 1076-836X
Wydawca: Oxford University Press
DOI: 10.1093/sysbio/syad013

Parameter Estimation and Species Tree Rooting Using ALE and GeneRax

Autorzy: Tom A Williams, Adrián A Davín, Benoit Morel, Lénárd L Szánthó, Anja Spang, Alexandros Stamatakis, Philip Hugenholtz, Gergely J Szöllősi
Opublikowane w: Genome Biology and Evolution, Numer Volume 15, Numer 7, evad134, 2023, ISSN 1759-6653
Wydawca: Oxford University Press
DOI: 10.1093/gbe/evad134

Recoding amino acids to a reduced alphabet may increase or decrease phylogenetic accuracy

Autorzy: Peter G Foster; Dominik Schrempf; Gergely J Szöllősi; Tom A Williams; Cymon J Cox; T Martin Embley
Opublikowane w: Systematic Biology, Numer Volume 72, Numer 3, Pages 723–737, 2023, ISSN 1076-836X
Wydawca: Oxford University Press
DOI: 10.1093/sysbio/syac042

Integrative modeling of gene and genome evolution roots the archaeal tree of life

Autorzy: Tom A. Williams, Gergely J. Szöllősi, Anja Spang, Peter G. Foster, Sarah E. Heaps, Bastien Boussau, Thijs J. G. Ettema, T. Martin Embley
Opublikowane w: Proceedings of the National Academy of Sciences, Numer 114/23, 2017, Strona(/y) E4602-E4611, ISSN 0027-8424
Wydawca: National Academy of Sciences
DOI: 10.1073/pnas.1618463114

RecPhyloXML: a format for reconciled gene trees

Autorzy: Wandrille Duchemin, Guillaume Gence, Anne-Muriel Arigon Chifolleau, Lars Arvestad, Mukul S Bansal, Vincent Berry, Bastien Boussau, François Chevenet, Nicolas Comte, Adrián A Davín, Christophe Dessimoz, David Dylus, Damir Hasic, Diego Mallo, Rémi Planel, David Posada, Celine Scornavacca, Gergely Szöllősi, Louxin Zhang, Éric Tannier, Vincent Daubin
Opublikowane w: Bioinformatics, Numer 34/21, 2018, Strona(/y) 3646-3652, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/bty389

Genome size evolution in the Archaea

Autorzy: Siri Kellner, Anja Spang, Pierre Offre, Gergely J. Szöllősi, Celine Petitjean, Tom A. Williams
Opublikowane w: Emerging Topics in Life Sciences, Numer 2/4, 2018, Strona(/y) 595-605, ISSN 2397-8554
Wydawca: Siri Kellner, Anja Spang, Pierre Offre, Gergely J. Szöllősi, Celine Petitjean, Tom A. Williams
DOI: 10.1042/etls20180021

Hierarchical tissue organization as a general mechanism to limit the accumulation of somatic mutations

Autorzy: Imre Derényi, Gergely J. Szöllősi
Opublikowane w: Nature Communications, Numer 8, 2017, Strona(/y) 14545, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/ncomms14545

Phylogenomics provides robust support for a two-domains tree of life

Autorzy: Tom A. Williams, Cymon J. Cox, Peter G. Foster, Gergely J. Szöllősi, T. Martin Embley
Opublikowane w: Nature Ecology & Evolution, Numer 4/1, 2020, Strona(/y) 138-147, ISSN 2397-334X
Wydawca: Springer Nature
DOI: 10.1038/s41559-019-1040-x

Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages

Autorzy: Adrián A Davín, Théo Tricou, Eric Tannier, Damien M de Vienne, Gergely J Szöllősi
Opublikowane w: Bioinformatics, Numer 36/4, 2019, Strona(/y) 1286-1288, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btz710

Gene transfers can date the tree of life

Autorzy: Adrián A. Davín, Eric Tannier, Tom A. Williams, Bastien Boussau, Vincent Daubin, Gergely J. Szöllősi
Opublikowane w: Nature Ecology & Evolution, Numer 2/5, 2018, Strona(/y) 904-909, ISSN 2397-334X
Wydawca: Springer Nature
DOI: 10.1038/s41559-018-0525-3

Polymorphism-Aware Species Trees with Advanced Mutation Models, Bootstrap, and Rate Heterogeneity

Autorzy: Dominik Schrempf, Bui Quang Minh, Arndt von Haeseler, Carolin Kosiol
Opublikowane w: Molecular Biology and Evolution, Numer 36/6, 2019, Strona(/y) 1294-1301, ISSN 0737-4038
Wydawca: Oxford University Press
DOI: 10.1093/molbev/msz043

IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era

Autorzy: Bui Quang Minh, Heiko A Schmidt, Olga Chernomor, Dominik Schrempf, Michael D Woodhams, Arndt von Haeseler, Robert Lanfear
Opublikowane w: Molecular Biology and Evolution, Numer ACCEPTED MANUSCRIPT, 2020, Strona(/y) msaa015, ISSN 0737-4038
Wydawca: Oxford University Press
DOI: 10.1093/molbev/msaa015

Scalable empirical mixture models that account for across-site compositional heterogeneity

Autorzy: Dominik Schrempf, Nicolas Lartillot, Gergely Szöllősi
Opublikowane w: Molecular Biology and Evolution, Numer accepted pending revision, 2020, ISSN 0737-4038
Wydawca: Oxford University Press

A compartment size-dependent selective threshold limits mutation accumulation in hierarchical tissues

Autorzy: Dániel Grajzel, Imre Derényi, Gergely J. Szöllősi
Opublikowane w: Proceedings of the National Academy of Sciences, Numer 117/3, 2020, Strona(/y) 1606-1611, ISSN 0027-8424
Wydawca: National Academy of Sciences
DOI: 10.1073/pnas.1913104117

Megaphylogeny resolves global patterns of mushroom evolution

Autorzy: Torda Varga, Krisztina Krizsán, Csenge Földi, Bálint Dima, Marisol Sánchez-García, Santiago Sánchez-Ramírez, Gergely J. Szöllősi, János G. Szarkándi, Viktor Papp, László Albert, William Andreopoulos, Claudio Angelini, Vladimír Antonín, Kerrie W. Barry, Neale L. Bougher, Peter Buchanan, Bart Buyck, Viktória Bense, Pam Catcheside, Mansi Chovatia, Jerry Cooper, Wolfgang Dämon, Dennis
Opublikowane w: Nature Ecology & Evolution, Numer 3/4, 2019, Strona(/y) 668-678, ISSN 2397-334X
Wydawca: Springer Nature
DOI: 10.1038/s41559-019-0834-1

GeneRax: A tool for species tree-aware maximum likelihood based gene tree inference under gene duplication, transfer, and loss

Autorzy: Benoit Morel, Alexey M. Kozlov, Alexandros Stamatakis, Gergely J. Szöllősi
Opublikowane w: Molecular Biology and Evolution, Numer to appear, 2020, ISSN 0737-4038
Wydawca: Oxford University Press

MaxTiC: Fast ranking of a phylogenetic tree by Maximum Time Consistency with lateral gene transfers

Autorzy: Cédric Chauve, Akbar Rafiey, Adrián A. Davín, Celine Scornavacca, Philippe Veber, Bastien Boussau, Gergely J. Szöllősi, Vincent Daubin, Eric Tannier
Opublikowane w: bioRxiv, Numer 10.1101/127548, 2017, Strona(/y) peer-reviewed and recommended by Peer Community In Evolutionary Biology. 10.24072/pci.evolbiol.100037, ISSN 2551-668X
Wydawca: Peer Community In Evolutionary Biology
DOI: 10.1101/127548

Inferring the Deep Past from Molecular Data

Autorzy: Tom A Williams, Dominik Schrempf, Gergely J Szöllősi, Cymon J Cox, Peter G Foster, T Martin Embley
Opublikowane w: Genome Biology and Evolution, Numer Volume 13, Numer 5, evab067, 2021, ISSN 1759-6653
Wydawca: Oxford University Press
DOI: 10.1093/gbe/evab067

Relative Time Constraints Improve Molecular Dating

Autorzy: Gergely J Szöllõsi, Sebastian Höhna, Tom A Williams, Dominik Schrempf, Vincent Daubin, Bastien Boussau
Opublikowane w: Systematic Biology, Numer Volume 71, Numer 4, Pages 797–809, 2022, ISSN 1076-836X
Wydawca: Oxford University Press
DOI: 10.1093/sysbio/syab084

A rooted phylogeny resolves early bacterial evolution

Autorzy: GARETH A. COLEMAN; ADRIÁN A. DAVÍN; TARA A. MAHENDRARAJAH; LÉNÁRD L. SZÁNTHÓ; ANJA SPANG; PHILIP HUGENHOLTZ; GERGELY J. SZÖLLŐSI; TOM A. WILLIAMS;
Opublikowane w: Science, Numer Vol 372, Numer 6542, 2021, ISSN 0036-8075
Wydawca: American Association for the Advancement of Science
DOI: 10.1126/science.abe0511

Fungal Phylogeny in the Age of Genomics: Insights Into Phylogenetic Inference From Genome-Scale Datasets

Autorzy: László G. Nagy, Gergely Szöllősi
Opublikowane w: Fungal Phylogenetics and Phylogenomics, Numer 100, 2017, Strona(/y) 49-72, ISBN 9780-128132616
Wydawca: Elsevier
DOI: 10.1016/bs.adgen.2017.09.008

The Sources of Phylogenetic Conflicts

Autorzy: Schrempf, Dominik; Szöllősi, Gergely
Opublikowane w: Phylogenetics in the Genomic Era, eds. Scornavacca, Celine; Delsuc, Frédéric; Galtier, Nicolas., Numer pp.3.1:1--3.1:23, 2020
Wydawca: No commercial publisher | Authors open access book

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