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Convergence towards equilibrium for a model with partial diffusion

Delphine Salort , Didier Smets
Preprints, Working Papers, ... hal-03845918v1
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Deep Local Analysis evaluates protein docking conformations with locally oriented cubes

Yasser Mohseni Behbahani , Simon Crouzet , Elodie Laine , Alessandra Carbone
Bioinformatics, 2022, 38 (19), pp.4505-4512. ⟨10.1093/bioinformatics/btac551⟩
Journal articles hal-03906697v1

iBIS2Analyzer: a web server for a phylogeny-driven coevolution analysis of protein families

Francesco Oteri , Edoardo Sarti , Francesca Nadalin , Alessandra Carbone
Nucleic Acids Research, 2022, 50 (W1), pp.W412-W419. ⟨10.1093/nar/gkac481⟩
Journal articles hal-03700047v1

Predicting substitutions to modulate disorder and stability in coiled-coils

Yasaman Karami , Paul Saighi , Rémy Vanderhaegen , Denis Gerlier , Sonia Longhi et al.
BMC Bioinformatics, 2020, 21 (S19), pp.573. ⟨10.1186/s12859-020-03867-x⟩
Journal articles hal-03911459v1
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Local Interaction Signal Analysis Predicts Protein-Protein Binding Affinity

Raffaele Raucci , Elodie Laine , Alessandra Carbone
Structure, 2018, 26 (6), pp.905 - 915.e4. ⟨10.1016/j.str.2018.04.006⟩
Journal articles hal-01844368v1
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Meet-U: educating through research immersion

Nika Abdollahi , Alexandre Albani , Eric Anthony , Agnes Baud , Mélissa Cardon et al.
PLoS Computational Biology, 2018, 14 (3), pp.1-10. ⟨10.1371/journal.pcbi.1005992⟩
Journal articles hal-01722019v1
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Jointly aligning a group of DNA reads improves accuracy of identifying large deletions

Anish M S Shrestha , Martin C. Frith , Kiyoshi Asai , Hugues Richard
Nucleic Acids Research, 2018, 46 (3), pp.e18. ⟨10.1093/nar/gkx1175⟩
Journal articles hal-01727521v1

The evolution of the temporal program of genome replication

Nicolas Agier , Stéphane Delmas , Qing Zhang , Aubin Fleiss , Yan Jaszczyszyn et al.
Nature Communications, 2018, 9 (1), pp.2199. ⟨10.1038/s41467-018-04628-4⟩
Journal articles hal-02175123v1
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INTerface Builder: a fast protein-protein interface reconstruction tool

Chloé Dequeker , Elodie Laine , Alessandra Carbone
Journal of Chemical Information and Modeling, 2017, ⟨10.1021/acs.jcim.7b00360⟩
Journal articles hal-01617113v1

Protein-protein interaction specificity is captured by contact preferences and interface composition

Francesca Nadalin , Alessandra Carbone
Journal articles hal-01596388v1
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DiNAMO: Exact method for degenerate IUPAC motifs discovery, characterization of sequence-specific errors

Chadi Saad , Laurent Noé , Hugues Richard , Julie Leclerc , Marie-Pierre Buisine et al.
JOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2017, Lille, France
Conference papers hal-01574630v1
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BIS2Analyzer: a server for co-evolution analysis of conserved protein families

Francesco Oteri , Francesca Nadalin , Raphaël Champeimont , Alessandra Carbone
Nucleic Acids Research, 2017, pp.W307-W314. ⟨10.1093/nar/gkx336⟩
Journal articles hal-01520493v1
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Plasmobase: a comparative database of predicted domain architectures for Plasmodium genomes

Juliana Bernardes , Catherine Vaquero , Alessandra Carbone
Malaria Journal, 2017, 16, pp.241. ⟨10.1186/s12936-017-1887-8⟩
Journal articles hal-01556734v1

Decrypting how protein move and change their shape

Elodie Laine
Proceeding of 16th International Symposium on Mathematical and Computational Biology, 2017
Book sections hal-01587939v1

Conservation, co-évolution et dynamique : de la séquence à la fonction

Alessandra Carbone
ISTE Éditions Ltd. Colloque de Cerisy “Sciences de la vie, sciences de l’information”, , 2017, Colloque de Cerisy “Sciences de la vie, sciences de l’information”, 978-1-78405-287-4
Book sections hal-01592629v1

Resonances and $CP$ violation in $B_s^0$ and $\overline{B}_s^0 \to J/\psi K^+K^-$ decays in the mass region above the $\phi(1020)$

Roel Aaij , Bernardo Adeva , Marco Adinolfi , Ziad Ajaltouni , Simon Akar et al.
JHEP, 2017, 08, pp.037. ⟨10.1007/JHEP08(2017)037⟩
Journal articles hal-01582785v1
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Combining machine learning and evolution for the annotation of metagenomics data

Ari Ugarte
Biotechnology. Université Pierre et Marie Curie - Paris VI, 2016. English. ⟨NNT : 2016PA066732⟩
Theses tel-01666046v1
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Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence

Juliana Bernardes , Gerson Zaverucha , Catherine Vaquero , Alessandra Carbone
PLoS Computational Biology, 2016, 12 (7), pp.e1005038. ⟨10.1371/journal.pcbi.1005038⟩
Journal articles hal-01390566v1

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report

Ariel Chernomoretz , Gustavo Stolovitzky , Pawel P. Labaj , Alexandra B. Graf , Aaron Darling et al.
Microbiome, 2016, 4, pp.24. ⟨10.1186/s40168-016-0168-z⟩
Journal articles hal-01528508v1
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Great interactions: How binding incorrect partners can teach us about protein recognition and function

Lydie Vamparys , Benoist Laurent , Alessandra Carbone , Sophie Sacquin-Mora
Proteins - Structure, Function and Bioinformatics, 2016, 84 (10), pp.1408-1421 ⟨10.1002/prot.25086⟩
Journal articles hal-01347160v1
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Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus

Nikolaos Vakirlis , Véronique Sarilar , Guénola Drillon , Aubin Fleiss , Nicolas Agier et al.
Genome Research, 2016, 26 (7), pp.918-932. ⟨10.1101/gr.204420.116⟩
Journal articles hal-01331620v1
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Marine diatoms change their gene expression profile when exposed to microscale turbulence under nutrient replete conditions

Alberto Amato , Gianluca Dell’aquila , Francesco Musacchia , Rossella Annunziata , Ari Ugarte et al.
Scientific Reports, 2016, 7 (1), pp.347A-348A. ⟨10.1038/s41598-017-03741-6⟩
Journal articles hal-01528507v1

Diatom Phytochromes Reveal the Existence of Far-Red-Light-Based Sensing in the Ocean

Antonio Emidio Fortunato , Marianne Jaubert , Gen Enomoto , Jean-Pierre Bouly , Raffaella Raniello et al.
The Plant cell, 2016, 28 (3), pp.616-628. ⟨10.1105/tpc.15.00928⟩
Journal articles hal-01528502v1
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Dissecting protein architecture with communication blocks and communicating segment pairs

Yasaman Karami , Elodie Laine , Alessandra Carbone
BMC Bioinformatics, 2016, 17 (S2), pp.133-148. ⟨10.1186/s12859-015-0855-y⟩
Journal articles hal-01260475v1
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JET2 Viewer: a database of predicted multiple, possibly overlapping, protein–protein interaction sites for PDB structures

Hughes Ripoche , Elodie Laine , Nicoletta Ceres , Alessandra Carbone
Nucleic Acids Research, 2016, 45 (D1), pp.D236-D242. ⟨10.1093/nar/gkw1053⟩
Journal articles hal-01417190v1
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Coevolution analysis of Hepatitis C virus genome to identify the structural and functional dependency network of viral proteins

Raphaël Champeimont , Elodie Laine , Shuang-Wei Hu , Francois Penin , Alessandra Carbone et al.
Scientific Reports, 2016, 6, pp.26401. ⟨10.1038/srep26401⟩
Journal articles hal-01320023v1
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Tma108, a putative M1 aminopeptidase, is a specific nascent chain-associated protein in Saccharomyces cerevisiae

Thierry Delaveau , Dimitri Davoine , Ariane Jolly , Antoine Vallot , Jérôme O. Rouvière et al.
Nucleic Acids Research, 2016, 44 (18), pp.8826-8841. ⟨10.1093/nar/gkw732⟩
Journal articles hal-01361729v1
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Protein social behavior makes a stronger signal for partner identification than surface geometry

Elodie Laine , Alessandra Carbone
Proteins - Structure, Function and Bioinformatics, 2016, 85 (1), pp.137-154 ⟨10.1002/prot.25206⟩
Journal articles hal-01400887v1

How binding incorrect partners can lead to the prediction of correct interfaces: Results from a massive cross-docking study on proteins

Sophie Sacquin-Mora , Lydie Vamparys , Alessandra Carbone
Protein Science, 2015, 24 (1, SI), pp.243-244
Journal articles hal-01528524v1
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E-Biothon: an experimental platform for BioInformatics

Michel Daydé , Benjamin Depardon , Alain Franc , Jean-François Gibrat , Romaric Guillier et al.
International Conference on Computer Science and Information Technologies, Sep 2015, Yerevan, Armenia. ⟨10.1109/CSITechnol.2015.7358239⟩
Conference papers hal-01207320v1