Explore the words cloud of the GENECLOCKS project. It provides you a very rough idea of what is the project "GENECLOCKS" about.
The following table provides information about the project.
EOTVOS LORAND TUDOMANYEGYETEM
|Coordinator Country||Hungary [HU]|
|Total cost||1˙453˙542 €|
|EC max contribution||1˙453˙542 € (100%)|
1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
|Duration (year-month-day)||from 2017-07-01 to 2022-06-30|
Take a look of project's partnership.
|1||EOTVOS LORAND TUDOMANYEGYETEM||HU (BUDAPEST)||coordinator||1˙453˙542.00|
With the advent of genome-scale sequencing, molecular phylogeny, which reconstructs gene trees from homologous sequences, has reached an impasse. Instead of answering open questions, new genomes have reignited old debates. The problem is clear, gene trees are not species trees, each is the unique result of series of evolutionary events. If, however, we model these differences in the context of a common species tree, we can access a wealth of information on genome evolution and the diversification of species that is not available to traditional methods. For example, as horizontal gene transfer (HGT) can only occur between coexisting species, HGTs provide information on the order of speciations. When HGT is rare, lineage sorting can generate incongruence between gene trees and the dating problem can be formulated in terms of biologically meaningful parameters (such as population size), that are informative on the rate of evolution and hence invaluable to molecular dating. My first goal is to develop methods that systematically extract information on the pattern and timing of genomic evolution by explaining differences between gene trees. This will allow us to, for the first time, reconstruct a dated tree of life from genome-scale data. We will use parallel programming to maximise the number of genomes analysed. My second goal is to apply these methods to open problems, e.g.: i) to resolve the timing of microbial evolution and its relationship to Earth history, where the extreme paucity of fossils limits the use of molecular dating methods, by using HGT events as “molecular fossils”; ii) to reconstruct rooted phylogenies from complete genomes and harness phylogenetic incongruence to answer long standing questions, such as the of diversification of animals or the position of eukaryotes among archaea; and iii) for eukaryotic groups such as Fungi, where evidence of significant amounts of HGT is emerging our methods will also allow the quantification of the extent of HGT.
|year||authors and title||journal||last update|
DÃ¡niel Grajzel, Imre DerÃ©nyi, Gergely J. SzÃ¶llÅ‘si
A compartment size-dependent selective threshold limits mutation accumulation in hierarchical tissues
published pages: 1606-1611, ISSN: 0027-8424, DOI: 10.1073/pnas.1913104117
|Proceedings of the National Academy of Sciences 117/3||2020-03-05|
Bui Quang Minh, Heiko A Schmidt, Olga Chernomor, Dominik Schrempf, Michael D Woodhams, Arndt von Haeseler, Robert Lanfear
IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era
published pages: msaa015, ISSN: 0737-4038, DOI: 10.1093/molbev/msaa015
|Molecular Biology and Evolution ACCEPTED MANUSCRIPT||2020-03-05|
CÃ©dric Chauve, Akbar Rafiey, AdriÃ¡n A. DavÃn, Celine Scornavacca, Philippe Veber, Bastien Boussau, Gergely J. SzÃ¶llÅ‘si, Vincent Daubin, Eric Tannier
MaxTiC: Fast ranking of a phylogenetic tree by Maximum Time Consistency with lateral gene transfers
published pages: peer-reviewed an, ISSN: 2551-668X, DOI: 10.1101/127548
Dominik Schrempf, Nicolas Lartillot, Gergely SzÃ¶llÅ‘si
Scalable empirical mixture models that account for across-site compositional heterogeneity
published pages: , ISSN: 0737-4038, DOI:
|Molecular Biology and Evolution accepted pending revision||2020-03-05|
Benoit Morel, Alexey M. Kozlov, Alexandros Stamatakis, Gergely J. SzÃ¶llÅ‘si
GeneRax: A tool for species tree-aware maximum likelihood based gene tree inference under gene duplication, transfer, and loss
published pages: , ISSN: 0737-4038, DOI:
|Molecular Biology and Evolution to appear||2020-03-05|
Dominik Schrempf, Bui Quang Minh, Arndt von Haeseler, Carolin Kosiol
Polymorphism-Aware Species Trees with Advanced Mutation Models, Bootstrap, and Rate Heterogeneity
published pages: 1294-1301, ISSN: 0737-4038, DOI: 10.1093/molbev/msz043
|Molecular Biology and Evolution 36/6||2020-03-05|
Torda Varga, Krisztina KrizsÃ¡n, Csenge FÃ¶ldi, BÃ¡lint Dima, Marisol SÃ¡nchez-GarcÃa, Santiago SÃ¡nchez-RamÃrez, Gergely J. SzÃ¶llÅ‘si, JÃ¡nos G. SzarkÃ¡ndi, Viktor Papp, LÃ¡szlÃ³ Albert, William Andreopoulos, Claudio Angelini, VladimÃr AntonÃn, Kerrie W. Barry, Neale L. Bougher, Peter Buchanan, Bart Buyck, ViktÃ³ria Bense, Pam Catcheside, Mansi Chovatia, Jerry Cooper, Wolfgang DÃ¤mon, Dennis
Megaphylogeny resolves global patterns of mushroom evolution
published pages: 668-678, ISSN: 2397-334X, DOI: 10.1038/s41559-019-0834-1
|Nature Ecology & Evolution 3/4||2020-03-05|
Tom A. Williams, Cymon J. Cox, Peter G. Foster, Gergely J. SzÃ¶llÅ‘si, T. Martin Embley
Phylogenomics provides robust support for a two-domains tree of life
published pages: 138-147, ISSN: 2397-334X, DOI: 10.1038/s41559-019-1040-x
|Nature Ecology & Evolution 4/1||2020-02-28|
AdriÃ¡n A. DavÃn, Eric Tannier, Tom A. Williams, Bastien Boussau, Vincent Daubin, Gergely J. SzÃ¶llÅ‘si
Gene transfers can date the tree of life
published pages: 904-909, ISSN: 2397-334X, DOI: 10.1038/s41559-018-0525-3
|Nature Ecology & Evolution 2/5||2020-02-28|
AdriÃ¡n A DavÃn, ThÃ©o Tricou, Eric Tannier, Damien M de Vienne, Gergely J SzÃ¶llÅ‘si
Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages
published pages: 1286-1288, ISSN: 1367-4803, DOI: 10.1093/bioinformatics/btz710
Imre DerÃ©nyi, Gergely J. SzÃ¶llÅ‘si
Hierarchical tissue organization as a general mechanism to limit the accumulation of somatic mutations
published pages: 14545, ISSN: 2041-1723, DOI: 10.1038/ncomms14545
|Nature Communications 8||2019-09-17|
Siri Kellner, Anja Spang, Pierre Offre, Gergely J. SzÃ¶llÅ‘si, Celine Petitjean, Tom A. Williams
Genome size evolution in the Archaea
published pages: 595-605, ISSN: 2397-8554, DOI: 10.1042/etls20180021
|Emerging Topics in Life Sciences 2/4||2019-09-17|
Tom A. Williams, Gergely J. SzÃ¶llÅ‘si, Anja Spang, Peter G. Foster, Sarah E. Heaps, Bastien Boussau, Thijs J. G. Ettema, T. Martin Embley
Integrative modeling of gene and genome evolution roots the archaeal tree of life
published pages: E4602-E4611, ISSN: 0027-8424, DOI: 10.1073/pnas.1618463114
|Proceedings of the National Academy of Sciences 114/23||2019-09-17|
Wandrille Duchemin, Guillaume Gence, Anne-Muriel Arigon Chifolleau, Lars Arvestad, Mukul S Bansal, Vincent Berry, Bastien Boussau, FranÃ§ois Chevenet, Nicolas Comte, AdriÃ¡n A DavÃn, Christophe Dessimoz, David Dylus, Damir Hasic, Diego Mallo, RÃ©mi Planel, David Posada, Celine Scornavacca, Gergely SzÃ¶llÅ‘si, Louxin Zhang, Ã‰ric Tannier, Vincent Daubin
RecPhyloXML: a format for reconciled gene trees
published pages: 3646-3652, ISSN: 1367-4803, DOI: 10.1093/bioinformatics/bty389
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