Technical services

Computing services

Penel Simon

Ingénieur d'études

CNRS

Address: 43 bd du 11 novembre 1918
69622 VILLEURBANNE cedex

Tel: 33 04 72 43 29 04

Email

Intérêts :

Phylogénomique, génomique comparative, coévolution multi-échelle, réconciliation phylogénétique, représentation d'arbres, clustering de séquences,  web.

Base de données HOGENOM :  http://hogenom.univ-lyon1.fr/

Logiciel Thirdkind : https://github.com/simonpenel/thirdkind/wiki

 

Développement:

https://github.com/simonpenel

https://gitlab.in2p3.fr/penel

Rust :

https://crates.io/crates/light_phylogeny

https://crates.io/crates/thirdkind

Node.js, D3.js,  Docker :

https://gitlab.in2p3.fr/penel/docker-hogenom-compose

Participation à d'autres projets :

https://gitlab.com/vmiele/silix/

https://project.inria.fr/treerecs/

Formation:

Université Joseph Fourrier, Grenoble

https://www.theses.fr/1997GRE10132

 

 

 

 

Publications

Display of 1 to 30 publications on 36 in total

PhylteR: Efficient Identification of Outlier Sequences in Phylogenomic Datasets

Aurore Comte, Théo Tricou, Eric Tannier, Julien Joseph, Aurélie Siberchicot, Simon Penel...

Molecular Biology and Evolution . 40 ( 11 ) : msad234

DOI: 10.1093/molbev/msad234

Journal article

see the publication

Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation

Simon Penel, Hugo Menet, Théo Tricou, Vincent Daubin, Eric Tannier

Bioinformatics . 38 ( 8 ) : 2350–2352

DOI: 10.1093/bioinformatics/btac062

Journal article

see the publication

Evolutionary stasis of the pseudoautosomal boundary in strepsirrhine primates

Rylan Shearn, Alison E Wright, Sylvain Mousset, Corinne Régis, Simon Penel, Jean-François Lemaître Lemaître...

eLife . 9

DOI: 10.7554/eLife.63650

Journal article

see the publication

Evolutionary plasticity of mating-type determination mechanisms in Paramecium aurelia sibling species

Natalia Sawka-Gądek, Alexey Potekhin, Deepankar Pratap Singh, Inessa Grevtseva, Olivier Arnaiz, Simon Penel...

Genome Biology and Evolution . ( evaa258 )

DOI: 10.1093/gbe/evaa258

Journal article

see the publication

Treerecs: an integrated phylogenetic tool, from sequences to reconciliations.

Nicolas Comte, Benoît Morel, Damir Hasic, Laurent Guéguen, Bastien Boussau, Vincent Daubin...

Bioinformatics . 36 ( 18 ) : 4822-4824

DOI: 10.1093/bioinformatics/btaa615

Journal article

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Studying genetic antagonisms as drivers of genome evolution

Mathieu Joron, Rylan Shearn, Alison E Wright, Sylvain Mousset, Corinne Régis, Simon Penel...

Peer Community In Evolutionary Biology .

DOI: 10.24072/pci.evolbiol.100108

Journal article

see the publication

Gearing up to handle the mosaic nature of life in the quest for orthologs

Kristoffer Forslund, Cécile Pereira, Salvador Capella-Gutiérrez, Alan Sousa da Silva, Adrian M Altenhoff, Jaime Huerta-Cepas...

Bioinformatics . 34 ( 2 ) : 323-329

DOI: 10.1093/bioinformatics/btx542

Journal article

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Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium

Florent Lassalle, Rémi Planel, Simon Penel, David Chapulliot, Valérie Barbe, Audrey Dubost...

Genome Biology and Evolution . 9 ( 12 ) : 3413 - 3431

DOI: 10.1093/gbe/evx255

Journal article

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RiboDB database: a comprehensive resource for prokaryotic systematics

Frédéric Jauffrit, Simon Penel, Stéphane Delmotte, Carine Rey, Damien M de Vienne, Manolo Gouy...

Molecular Biology and Evolution . 33 ( 8 ) : 2170--2172

DOI: 10.1093/molbev/msw088

Journal article

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No Evidence That Nitrogen Limitation Influences the Elemental Composition of Isopod Transcriptomes and Proteomes

Clémentine François, L. Duret, Laurent Simon, Florian Mermillod-Blondin, Florian Malard, Lara Konecny-Dupré...

Molecular Biology and Evolution . 33 ( 10 ) : 2605–2620

DOI: 10.1093/molbev/msw131

Journal article

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L'ADN, mémoire numérique du vivant

Vincent Daubin, Simon Penel, Eric Tannier

Pour la science . : 102-108

Journal article

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High-quality sequence clustering guided by network topology and multiple alignment likelihood.

Vincent Miele, Simon Penel, Vincent Daubin, Franck Picard, Daniel Kahn, L. Duret

Bioinformatics . 28 ( 8 ) : 1078-85

DOI: 10.1093/bioinformatics/bts098

Journal article

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PhEVER: a database for the global exploration of virus-host evolutionary relationships.

Leonor Palmeira, Simon Penel, Vincent Lotteau, Chantal Rabourdin-Combe, Christian Gautier

Nucleic Acids Research . 39 ( Database issue ) : D569-75

DOI: 10.1093/nar/gkq1013

Journal article

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Utilisation de grilles de calcul pour la génomique comparative

Simon Penel, Christophe Blanchet, Pascal Calvat, Yonny Cardenas, Clement Gauthey, Jean Yves Nief...

Rencontres Scientifiques France Grilles 2011 .

Conference paper

see the publication

Databases of Homologous Gene Families for Comparative Genomics

Simon Penel, Anne-Muriel Arigon Chifolleau, Jean-François Dufayard, Anne-Sophie Sertier, Vincent Daubin, L. Duret...

BMC Bioinformatics . 10 (Suppl.6) :S3 : 13

DOI: 10.1186/1471-2105-10-S6-S3

Journal article

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DigiPINS: A database for vertebrate exonic single nucleotide polymorphisms and its application to cancer association studies

Vincent Navratil, Simon Penel, Stephane Delmotte, Dominique Mouchiroud, Christian Gautier, Abdel Aouacheria

Biochimie . 90 ( 4 ) : 563-569

DOI: 10.1016/j.biochi.2007.09.017

Journal article

see the publication

DigiPINS: a database for vertebrate exonic single nucleotide polymorphisms and its application to cancer association studies.

V. Navratil, Simon Penel, Sebastien Delmotte, D. Mouchiroud, Christian Gautier, A. Aouacheria

Biochimie . xxx : 563-569

Journal article

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Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes

A. Studer, Simon Penel, L. Duret, M. Robinson-Rechavi

Genome Research . 18 : 1393-1402

Journal article

see the publication

Integr8 and Genome Reviews: integrated views of complete genomes and proteomes.

P. Kersey, L. Bower, L. Morris, A. Horne, R. Petryszak, C. Kanz...

Nucleic Acids Research . 33 ( Database issue ) : D297-302

DOI: 10.1093/nar/gki039

Journal article

see the publication

Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases.

Jean-François Dufayard, L. Duret, Simon Penel, Manolo Gouy, F. Rechenmann, G. Perrière

Bioinformatics . 21 ( 11 ) : 2596-603

DOI: 10.1093/bioinformatics/bti325

Journal article

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Polymorphix: a sequence polymorphism database

E. Bazin, L. Duret, Simon Penel, N. Galtier

Nucleic Acids Research . 33 : 481-484

Journal article

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YodA from Escherichia coli is a metal-binding lipocalin-like protein

G. David, K. Blondeau, M. Schiltz, Simon Penel, A. Lewit-Bentley

Journal of Biological Chemistry . 278 : 43728-43735

Journal article

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Length preferences and periodicity in beta-strands. Antiparallel edge beta-sheets are more likely to finish in non-hydrogen bonded rings

Simon Penel, R.G. Morrison, P.D. Dobson, R.J. Mortishire-Smith, A.J. Doig

Protein Engineering . 16 : 957-961

Journal article

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Integrated databanks access and sequence/structure analysis services at the PBIL.

G. Perriere, C. Combet, Simon Penel, Christophe Blanchet, J. Thioulouse, C. Geourjon...

Nucleic Acids Research . 31 ( 13 ) : 3393-3399

DOI: 10.1093/nar/gkg530

Journal article

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Rotamer strain energy in protein helices - quantification of a major force opposing protein folding

Simon Penel, A.J. Doig

Journal of Molecular Biology . 305 : 961-968

Journal article

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Effect of the N1 residue on the stability of the alpha-helix for all 20 amino acids

D.A.E. Cochran, Simon Penel, A.J. Doig

Protein Science . 10 : 463-470

Journal article

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Stabilizing nonpolar/polar side-chain interactions in the alpha-helix

C.D. Andrew, Simon Penel, G.R. Jones, A.J. Doig

PROTEINS-STRUCTURE FUNCTION AND GENETICS . 45 : 449-455

Journal article

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Structure stability and folding of the alpha-helix

A.J. Doig, C.D. Andrew, D.A. Cochran, E. Hughes, Simon Penel, J.K. Sun...

Biochemical Society Symposia . 68 : 95-110

Journal article

see the publication