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Studying genetic antagonisms as drivers of genome evolution

 Mathieu Joron , Rylan Shearn , Alison E Wright , Sylvain Mousset , Corinne Régis , et al.
Peer Community In Evolutionary Biology, 2020, ⟨10.24072/pci.evolbiol.100108⟩
Article dans une revue hal-03424539v1

Polymorphix: a sequence polymorphism database

 E. Bazin , L. Duret , Simon Penel , N. Galtier
Nucleic Acids Research, 2005, 33, pp.481-484
Article dans une revue hal-00427707v1

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes

 A. Studer , Simon Penel , L. Duret , M. Robinson-Rechavi
Genome Research, 2008, 18, pp.1393-1402
Article dans une revue hal-00428199v1
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Databases of Homologous Gene Families for Comparative Genomics

 Simon Penel , Anne-Muriel Arigon Chifolleau , Jean-François Dufayard , Anne-Sophie Sertier , Vincent Daubin , et al.
BMC Bioinformatics, 2009, 10 (Suppl.6) :S3, pp.13. ⟨10.1186/1471-2105-10-S6-S3⟩
Article dans une revue lirmm-00400099v1

Determination of alpha-helix N1 energies after addition of N1 N2 and N3 preferences to helix/coil theory

 J.K. Sun , Simon Penel , A.J. Doig
Protein Science, 2000, 9, pp.750-754
Article dans une revue hal-00427107v1

Side-chain structures in the first turn of the alpha-helix

 Simon Penel , E. Hughes , A.J. Doig
Journal of Molecular Biology, 1999, 287, pp.127-143
Article dans une revue hal-00428454v1

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

 P. Kersey , L. Bower , L. Morris , A. Horne , R. Petryszak , et al.
Nucleic Acids Research, 2005, 33 (Database issue), pp.D297-302. ⟨10.1093/nar/gki039⟩
Article dans une revue hal-00427773v1

Neutron crystallographic evidence of lipase-colipase complex activation by a micelle

 J. Hermoso , D. Pignol , Simon Penel , M. Roth , C. Chapus , et al.
EMBO Journal, 1997, 16, pp.5531-5536
Article dans une revue hal-00434986v1
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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 , et al.
Bioinformatics, 2018, 34 (2), pp.323-329. ⟨10.1093/bioinformatics/btx542⟩
Article dans une revue hal-01758841v1

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 , et al.
Molecular Biology and Evolution, 2016, 33 (10), pp.2605-2620. ⟨10.1093/molbev/msw131⟩
Article dans une revue hal-01370129v1
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Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation

 Simon Penel , Hugo Menet , Théo Tricou , Vincent Daubin , Eric Tannier
Bioinformatics, 2022, 38 (8), pp.2350-2352. ⟨10.1093/bioinformatics/btac062⟩
Article dans une revue hal-03563666v1

Ultra-fast sequence clustering from similarity networks with SiLiX

 V. Miele , Simon Penel , L. Duret
BMC Bioinformatics, 2011, 12(116), pp.1-9. ⟨10.1186/1471-2105-12-116⟩
Article dans une revue hal-00698365v1

Structure stability and folding of the alpha-helix

 A.J. Doig , C.D. Andrew , D.A. Cochran , E. Hughes , Simon Penel , et al.
Biochemical Society Symposia, 2001, 68, pp.95-110
Article dans une revue hal-00427130v1

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

 G. Perriere , C. Combet , Simon Penel , Christophe Blanchet , J. Thioulouse , et al.
Nucleic Acids Research, 2003, 31 (13), pp.3393-3399. ⟨10.1093/nar/gkg530⟩
Article dans une revue hal-00313743v1
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tidy tree : A New Layout for Phylogenetic Trees

 Simon Penel , Damien de Vienne
Molecular Biology and Evolution, 2022, 39 (10), pp.msac204. ⟨10.1093/molbev/msac204⟩
Article dans une revue hal-03844239v1

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 , et al.
Bioinformatics, 2005, 21 (11), pp.2596-603. ⟨10.1093/bioinformatics/bti325⟩
Article dans une revue hal-00427861v1

L'ADN, mémoire numérique du vivant

 Vincent Daubin , Simon Penel , Eric Tannier
Pour la science, 2013, pp.102-108
Article dans une revue hal-00878875v1

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

 Simon Penel , A.J. Doig
Journal of Molecular Biology, 2001, 305, pp.961-968
Article dans une revue hal-00427185v1

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, 2003, 278, pp.43728-43735
Article dans une revue hal-00427400v1

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, 2011, 39 (Database issue), pp.D569-75. ⟨10.1093/nar/gkq1013⟩
Article dans une revue hal-00562509v1
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Evolutionary plasticity of mating-type determination mechanisms in Paramecium aurelia sibling species

 Natalia Sawka-Gądek , Alexey Potekhin , Deepankar Pratap Singh , Inessa Grevtseva , Olivier Arnaiz , et al.
Genome Biology and Evolution, 2020, evaa258, ⟨10.1093/gbe/evaa258⟩
Article dans une revue hal-03102341v1

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 , et al.
Biochimie, 2008, xxx, pp.563-569
Article dans une revue hal-00315152v1

Detergent binding in trigonal crystals of OmpF porin from Escherichia coli

 Simon Penel , E. Pebay-Peyroula , J. Rosenbusch , G. Rummel , T. Schirmer , et al.
Biochimie, 1998, 80, pp.543-551
Article dans une revue hal-00428497v1

RiboDB database: a comprehensive resource for prokaryotic systematics

 Frédéric Jauffrit , Simon Penel , Stéphane Delmotte , Carine Rey , Damien M de Vienne , et al.
Molecular Biology and Evolution, 2016, 33 (8), pp.2170--2172. ⟨10.1093/molbev/msw088⟩
Article dans une revue hal-01800061v1

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, 2003, 16, pp.957-961
Article dans une revue hal-00427475v1

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

 Vincent Miele , Simon Penel , Vincent Daubin , Franck Picard , Daniel Kahn , et al.
Bioinformatics, 2012, 28 (8), pp.1078-85. ⟨10.1093/bioinformatics/bts098⟩
Article dans une revue hal-00965711v1

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, 2001, 45, pp.449-455
Article dans une revue hal-00427126v1

MAINDEX - manual indexation for area-detector crystallographic data

 Simon Penel , P. Legrand
Journal of Applied Crystallography, 1997, 30, pp.206-206
Article dans une revue hal-00434970v1
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Utilisation de grilles de calcul pour la génomique comparative

 Simon Penel , Christophe Blanchet , Pascal Calvat , Yonny Cardenas , Clement Gauthey , et al.
Rencontres Scientifiques France Grilles 2011, Sep 2011, Lyon, France
Communication dans un congrès hal-00653022v1
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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 , et al.
Genome Biology and Evolution, 2017, 9 (12), pp.3413 - 3431. ⟨10.1093/gbe/evx255⟩
Article dans une revue hal-01913841v1
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