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Modular logical modelling of the budding yeast cell cycle

Adrien Fauré , Aurélien Naldi , Fabrice LOPEZ , Claudine Chaouiya , Andrea Ciliberto , et al.
Molecular BioSystems, 2009, 5 (12), pp.1787. ⟨10.1039/B910101m⟩
Article dans une revue hal-04541114v1

Logical modelling of regulatory networks with GINsim 2.3

A. Naldi , D. Berenguier , A. Fauré , F. LOPEZ , D. Thieffry , et al.
BioSystems, 2009, 97 (2), pp.134-139. ⟨10.1016/j.biosystems.2009.04.008⟩
Article dans une revue hal-04541149v1

AGScan: a pluggable microarray image quantification software based on the ImageJ library

R. Cathelin , Fabrice LOPEZ , Ch. Klopp
Bioinformatics, 2007, 23 (2), pp.247-248. ⟨10.1093/bioinformatics/btl564⟩
Article dans une revue hal-04541193v1
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ChagasDB: 80 years of publicly available data on the molecular host response to Trypanosoma cruzi infection in a single database

Pauline Brochet , Jean-Christophe Mouren , Laurent Hannouche , Fabrice Lopez , Benoit Ballester , et al.
Database - The journal of Biological Databases and Curation, 2023, 2023, pp.baad037. ⟨10.1093/database/baad037⟩
Article dans une revue hal-04284853v1
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Feature extraction and signal processing for nylon DNA microarrays.

Fabrice Lopez , Jacques Rougemont , Béatrice Loriod , Aude Bourgeois , Laurence Loï , et al.
BMC Genomics, 2004, 5 (1), pp.38. ⟨10.1186/1471-2164-5-38⟩
Article dans une revue inserm-00112016v1

SAmBA: An interactive software for optimizing the design of biological macromolecules crystallization experiments

Stéphane Audic , Fabrice LOPEZ , Jean-Michel Claverie , Olivier Poirot , Chantal Abergel
Proteins: Structure, Function, and Genetics, 1997, 29 (2), pp.252-257. ⟨10.1002/(sici)1097-0134(199710)29:2<252::aid-prot12>3.0.co;2-n⟩
Article dans une revue hal-04541227v1
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TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database

F. Lopez , J. Textoris , A. Bergon , G. Didier , E. Rémy , et al.
PLoS ONE, 2008, 3 (12), pp.e4001. ⟨10.1371/journal.pone.0004001⟩
Article dans une revue hal-01595819v1

The disparate nature of “intergenic” polyadenylation sites

Fabrice Lopez , Samuel Granjeaud , Takeshi Ara , Badih Ghattas , Daniel Gautheret
RNA, 2006, 12 (10), pp.1794-1801. ⟨10.1261/rna.136206⟩
Article dans une revue hal-03582610v1

Genomic trajectories to fluoroquinolone resistance in Francisella tularensis subsp. holarctica live vaccine strain

Vivien Sutera , Aurélie Hennebique , Fabrice Lopez , Nicolas Fernandez , Dominique Schneider , et al.
International Journal of Antimicrobial Agents, 2020, 56, ⟨10.1016/j.ijantimicag.2020.106153⟩
Article dans une revue hal-03139160v1
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AltTrans: transcript pattern variants annotated for both alternative splicing and alternative polyadenylation.

Vincent Le Texier , Jean-Jack Riethoven , Vasudev Kumanduri , Chellappa Gopalakrishnan , Fabrice Lopez , et al.
BMC Bioinformatics, 2006, 7, pp.169. ⟨10.1186/1471-2105-7-169⟩
Article dans une revue inserm-00080444v1

Differential repression of alternative transcripts : a screen for miRNA targets

M. Legendre , W. Ritchie , F. Lopez , D. Gautheret
PLoS Computational Biology, 2006, 2, pp.n° e43
Article dans une revue hal-00109544v1
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Explore, edit and leverage genomic annotations using Python GTF toolkit

Fabrice Lopez , Guillaume Charbonnier , Yasmina Kermezli , Mohamed Belhocine , Quentin Ferré , et al.
Article dans une revue hal-02078147v1

Large-Scale Statistical Analyses of Rice ESTs Reveal Correlated Patterns of Gene Expression

Rob Ewing , Alia Ben Kahla , Olivier Poirot , Fabrice LOPEZ , Stéphane Audic , et al.
Genome Research, 1999, 9 (10), pp.950-959. ⟨10.1101/gr.9.10.950⟩
Article dans une revue hal-04541211v1

Reverse Transcriptase-Polymerase Chain Reaction Validation of 25 “Orphan” Genes from Escherichia coli K-12 MG1655

Jean-Philippe Alimi , Olivier Poirot , Fabrice LOPEZ , Jean-Michel Claverie
Genome Research, 2000, 10 (7), pp.959-966. ⟨10.1101/gr.10.7.959⟩
Article dans une revue hal-04541206v1
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ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments

Fayrouz Hammal , Pierre De langen , Aurélie Bergon , Fabrice Lopez , Benoit Ballester
Nucleic Acids Research, 2022, ⟨10.1093/nar/gkab996⟩
Article dans une revue hal-03433360v1
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Defect in the nuclear pore membrane glycoprotein 210-like gene is associated with extreme uncondensed sperm nuclear chromatin and male infertility: a case report

Karim Arafah , Fabrice Lopez , Caroline Cazin , Zine‐eddine Kherraf , Virginie Tassistro , et al.
Human Reproduction, 2021, 36 (3), pp.693-701. ⟨10.1093/humrep/deaa329⟩
Article dans une revue hal-02985525v1

ASTD: The Alternative Splicing and Transcript Diversity database.

Gautier Koscielny , Vincent Le Texier , Chellappa Gopalakrishnan , Vasudev Kumanduri , Jean-Jack Riethoven , et al.
Genomics / Physiol Genomics, 2009, 93 (3), pp.213-20. ⟨10.1016/j.ygeno.2008.11.003⟩
Article dans une revue hal-00529496v1

The disparate nature of "intergenic" polyadenylation sites

F. Lopez , S. Granjeaud , D. Gautheret
RNA (New York, N.Y.), 2006, 12, p 1794-1801
Article dans une revue hal-00105073v1
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Conservation of Alternative Polyadenylation Patterns in Mammalian genes.

Takeshi Ara , Fabrice Lopez , William Ritchie , Philippe Benech , Daniel Gautheret
BMC Genomics, 2006, 7, pp.189. ⟨10.1186/1471-2164-7-189⟩
Article dans une revue inserm-00089585v1

The difficulty of identifying genes in anonymous vertebrate sequences

Jean-Michel Claverie , Olivier Poirot , Fabrice LOPEZ
Computers and Chemistry, 1997, 21 (4), pp.203-214. ⟨10.1016/s0097-8485(96)00039-3⟩
Article dans une revue istex hal-04541231v1

Alternate Polyadenylation in Human mRNAs: A Large-Scale Analysis by EST Clustering

Daniel Gautheret , Olivier Poirot , Fabrice LOPEZ , Stéphane Audic , Jean-Michel Claverie
Genome Research, 1998, 8 (5), pp.524-530. ⟨10.1101/gr.8.5.524⟩
Article dans une revue hal-04541221v1

Chromatin-to-nucleoprotamine transition is controlled by the histone H2B variant TH2B.

Emilie Montellier , Fayçal Boussouar , Sophie Rousseaux , Kai Zhang , Thierry Buchou , et al.
Genes and Development, 2013, 27 (15), pp.1680-92
Article dans une revue hal-01322388v1
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Introducing the novel Cytoscape app TimeNexus to analyze time-series data using temporal MultiLayer Networks (tMLNs)

Michaël Pierrelée , Ana Reynders , Fabrice Lopez , Aziz Moqrich , Laurent Tichit , et al.
Scientific Reports, 2021, 11 (1), ⟨10.1038/s41598-021-93128-5⟩
Article dans une revue hal-03358832v1
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ReMap 2020: a database of regulatory regions from an integrative analysis of Human and Arabidopsis DNA-binding sequencing experiments

Jeanne Chèneby , Zacharie Ménétrier , Martin Mestdagh , Thomas Rosnet , Allyssa Douida , et al.
Nucleic Acids Research, 2020, ⟨10.1093/nar/gkz945⟩
Article dans une revue hal-02351736v1
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TranscriptomeBrowser 3.0 : introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks.

Cyrille Lepoivre , Aurélie Bergon , Fabrice Lopez , Narayanan Perumal , Catherine Nguyen , et al.
BMC Bioinformatics, 2012, 13 (1), pp.19. ⟨10.1186/1471-2105-13-19⟩
Article dans une revue inserm-00676438v1
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Differential repression of alternative transcripts: a screen for miRNA targets.

Matthieu Legendre , William Ritchie , Fabrice Lopez , Daniel Gautheret
PLoS Computational Biology, 2006, 2, pp.e43. ⟨10.1371/journal.pcbi.0020043⟩
Article dans une revue inserm-00080130v1

Bromodomain-dependent stage-specific male genome programming by Brdt: Brdt: a master regulator of spermatogenesis

Jonathan Gaucher , Fayçal Boussouar , Emilie Montellier , Sandrine Curtet , Thierry Buchou , et al.
EMBO Journal, 2012, 31 (19), pp.3809 - 3820. ⟨10.1038/emboj.2012.233⟩
Article dans une revue hal-03388049v1

A Positive Feed-forward Loop Associating EGR1 and PDGFA Promotes Proliferation and Self-renewal in Glioblastoma Stem Cells

Fabrice Lopez , Philipe Paquis , Fabien Almairac , Denys Fontaine , Nathalie Baeza-Kallee , et al.
Journal of Biological Chemistry, 2016, 291 (20), pp.10684-10699. ⟨10.1074/jbc.M116.720698⟩
Article dans une revue hal-01460121v1