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Mathematical and Computational Evolutionary Biology (2013)

Olivier Gascuel, Tanja Stadler
2014 Systematic Biology  
We started in 2003 (under a slightly different name: "Mathematics of Evolution and Phylogeny") at the Mathematics Research Center Henri Poincaré, Paris, with well-known speakers like Walter Fitch and Joe  ...  This special issue of Systematic Biology contains review articles, contributed by keynote speakers after the fifth edition of the "Mathematical and Computational Evolutionary Biology" conference (MCEB;  ... 
doi:10.1093/sysbio/syu086 pmid:25504791 fatcat:4etizmqpcbappoayy57w6vyode

Page 5399 of Mathematical Reviews Vol. , Issue 98H [page]

1998 Mathematical Reviews  
: some new results (111-131); Kevin Atteson, The performance of the neighbor-joining method of phylogeny reconstruction (133-147); Olivier Gascuel, Concern- ing the NJ algorithm and its unweighted version  ...  Edited by Boris Mirkin, F. R. McMorris, Fred S. Roberts and Andrey Rzhetsky. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 37.  ... 

Reconstructing the Duplication History of Tandemly Repeated Genes

Olivier Elemento, Olivier Gascuel, Marie-Paule Lefranc
2002 Molecular biology and evolution  
We first describe the mathematical model of evolution by tandem duplication and introduce duplication histories and duplication trees.  ...  Address for correspondence and reprints: Olivier Gascuel, Département d'Informatique Fondamentale et Applications, LIRMM,  ...  Acknowledgments We thank David Bryant, Andy McKenzie, Eric Rivals, two anonymous referees, and Mike Hendy for their helpful comments on the preliminary versions of the manuscript. LITERATURE CITED  ... 
doi:10.1093/oxfordjournals.molbev.a004081 pmid:11861887 fatcat:556xitrf2jb2hgltiav54s52hu

Calebasses anthropophages et dévoreurs africains

Jean-Loïc Le Quellec
2019 Afriques  
., Gascuel, O., 2002, « Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle », Journal of Computational Biology , 9 (5), p. 687-705.  ...  ., Olivier, G., 2015, « FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program », Molecular biology and evolution , 32 (10), p. 2798-2800.  ... 
doi:10.4000/afriques.2288 fatcat:isap34ciazda5c23tw4wecssua

Shifts in diversification rates and host jump frequencies shaped the diversity of host range among Sclerotiniaceae fungal plant pathogens

Olivier Navaud, Adelin Barbacci, Andrew Taylor, John P. Clarkson, Sylvain Raffaele
2018 Molecular Ecology  
Mathematical analyses and studies of the host range of insect herbivores suggest that host range expansion could involve the emergence of a "pre-adaptation" followed by the colonization of new hosts (  ...  First, we used a neighbour-joining approach in FastME 2.0 (Lefort, Desper, & Gascuel, 2015) with the LogDet substitution model and tree refinement by subtree pruning and regrafting (File S5).  ... 
doi:10.1111/mec.14523 pmid:29421852 pmcid:PMC5900718 fatcat:bsymqsnbn5e6nofbrfu336sbya

Shifts in diversification rates and host jump frequencies shaped the diversity of host range amongSclerotiniaceaefungal plant pathogens [article]

Olivier Navaud, Adelin Barbacci, Andrew Taylor, John P Clarkson, Sylvain Raffaele
2017 bioRxiv   pre-print
The range of hosts that a parasite can infect in nature is a trait determined by its own evolutionary history and that of its potential hosts.  ...  These results have important implications for our understanding of fungal parasites evolution and are of particular relevance for the durable management of disease epidemics.  ...  Molecular phylogeny and evolution of Monilinia (Sclerotiniaceae) 570 based on coding and noncoding rDNA sequences.  ... 
doi:10.1101/229930 fatcat:k7naatcluvgt5n7gyjc3fy3t2y

Do plants have a segregated germline?

Robert Lanfear
2018 PLoS Biology  
Answering these questions is vital to understanding one of the most fundamental aspects of plant development and evolution.  ...  How can we reconcile the new evidence with existing knowledge of plant development? And is there a way to reliably establish the timing of germline segregation in both model and nonmodel plants?  ...  Acknowledgments I would like to thank Eleanor Beavan, Lindell Bromham, Olivier Gascuel, and Alejandro Morales-Suarez for extensive and lively discussions on this topic.  ... 
doi:10.1371/journal.pbio.2005439 pmid:29768400 pmcid:PMC5973621 fatcat:abqexjskanggpmd4eqmsvmv7qq

Comparing Timeline Rhythms in Pygmy and Bushmen Music

Adrian Poole
2018 Empirical Musicology Review  
The findings suggest that Pygmy and Bushmen timelines are interrelated and that most are organised according to the principles of 'rhythmic oddity' and maximal evenness.  ...  Combining theories of African rhythm from ethno/musicology and findings from anthropological research and population genetics with musical analyses based on transcriptions and computational phylogenetic  ...  node (Gascuel, 1997) .  ... 
doi:10.18061/emr.v12i3-4.5823 fatcat:tq4vtup2ungwpbt4tueiojsdzi

Barking Up The Wrong Treelength: The Impact of Gap Penalty on Alignment and Tree Accuracy

K. Liu, S. Nelesen, S. Raghavan, C.R. Linder, T. Warnow
2009 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
Since this optimization depends upon the specific edit distance criterion used to score a tree, our study considers the impact of the gap penalty (in particular, affine versus simple) on the accuracy of  ...  The current technique for estimating phylogenies from sequence data uses two phases: first, the sequences are aligned, and then the tree is estimated using the obtained alignment.  ...  This work was supported by the Sir Isaac Newton Institute for Mathematical Sciences, and by the US National Science Foundation under Grants DEB-07330209, ITR-0331453, ITR-0121680, ITR-0114387, and EIA-  ... 
doi:10.1109/tcbb.2008.63 pmid:19179695 fatcat:q7kgyyjw7zbpfebrgowc4dsjla

Review Paper: The Shape of Phylogenetic Treespace

St. John Katherine
2016 Systematic Biology  
The underlying structure of the spaces of trees yields rich insights that can improve the search for optimal trees, both in accuracy and in running time, and the analysis and visualization of results.  ...  We review the past work on analyzing and comparing trees by their shape as well as recent work that incorporates trees with weighted branch lengths.  ...  ACKNOWLEDGMENTS The author would like to thank the organizing committee of the Mathematical and Computational Evolutionary Biology 2015 conference, to Olivier Gascuel and David Bryant for inviting this  ... 
doi:10.1093/sysbio/syw025 pmid:28173538 pmcid:PMC5837343 fatcat:mh3uhoqssfanjmjrcuaxzdoecu

A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios [article]

Sota Ishikawa, Anna Zhukova, Wataru Iwasaki, Olivier Gascuel
2018 bioRxiv   pre-print
The reconstruction of ancestral scenarios is widely used to study the evolution of characters along a phylogenetic tree.  ...  The results on simulated data consistently show the accuracy and robustness of the approach.  ...  Simulations performed by Gascuel and Steel (2014) showed that the predictions and accuracy of both are extremely close.  ... 
doi:10.1101/379529 fatcat:iehcpdwxcrhshjcpgn77d2rz3e

Divisions asymétriques ovocytaires / Asymmetric divisions in oocytes

Marie-Hélène Verlhac
2020 Annuaire du Collège de France : Résumé Des Cours et Travaux  
Indeed, innervation of peripheral resistance arteries by autonomic sympathetic nerves controls response to stress and blood supply to organs by regulating vascular tone (Storkebaum E. et al., 2011).  ...  Netrin-1 is produced by SMCs at the onset of innervation and signals via its receptor deleted in colorectal cancer (DCC) to attract sympathetic growth cones.  ...  Dynamics is limited in this case first by the slow regulation of surface tensions, and morphogenesis is well captured by a quasi-static mechanical description, as we recently proposed for compaction and  ... 
doi:10.4000/annuaire-cdf.16183 fatcat:3tl5qpboe5ftnjm3pa35hjfejq

EMBnet.journal 17 Suppl. A

EMBnet Journal
2011 EMBnet journal  
The ReNaBi-SO regional centre brings together 30 people from teams, platforms and a biotechnology company (BIOGEMMA) located in Toulouse and Bordeaux. ReNaBi-GS 7 -Coordinator Olivier Gascuel.  ...  ReNaBi-GO 4 -Coordinator Olivier Collin.  ...  several families of proteins 14 ; b. drug design; c. development of algorithms for next generation sequencing data; d. comparative analysis of performance of phylogeny reconstruction methods.  ... 
doi:10.14806/ej.17.a.261 fatcat:yofrffbhlrhfhdhqzxghsxyhn4

Report from Dagstuhl Seminar 12291

Alberto Apostolico, Andreas Dress, Laxmi Parida
unpublished
Abstracts of the presentations given during the seminar, as well as abstracts of seminar results and ideas, are put together in this report.  ...  Both veterans and new participants took part in this edition. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed.  ...  Mike Steel (University of Canterbury, Christchurch, NZ) License Creative Commons BY-NC-ND 3.0 Unported license © Mike Steel Joint work of Steel, Mike; Gascuel, Olivier; Mooers, Arne; Li, Thomas; Stadler  ... 
fatcat:a4v54vduk5bhlfyceq5m6c4jfe

Markovian codon models of evolution for phylogeny inference

Marcelo Serrano Zanetti
2013
Maria Anisimova, who was abundantly helpful and offered invaluable assistance, support and guidance, specially in the moments of great panic. Deepest gratitude are also due to Prof.  ...  This master thesis project would not have been possible without the support of many people. The author wishes to express his gratitude to his supervisor, Dr.  ...  Acknowledgement Acknowledgments The authors are grateful to Ste ´phane Guindon for support with PhyML code and Ziheng Yang, Olivier Gascuel, and Gaston Gonnet for discussions on code optimization strategies  ... 
doi:10.3929/ethz-a-009772928 fatcat:l6omajccwfaxnpull3i6ekxfpm
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