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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

Chromosomal periodicity and positional networks of genes in Escherichia coli

Anthony Mathelier , Alessandra Carbone
Molecular Systems Biology, 2010, 6, ⟨10.1038/msb.2010.21⟩
Journal articles hal-01589160v1
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The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum.

Alessandra Rogato , Hugues Richard , Alexis Sarazin , Björn Voss , Soizic Cheminant Navarro et al.
BMC Genomics, 2014, 15, pp.698. ⟨10.1186/1471-2164-15-698⟩
Journal articles hal-01064372v1
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SPoRE: a mathematical model to predict double strand breaks and axis protein sites in meiosis

Raphaël Champeimont , Alessandra Carbone
BMC Bioinformatics, 2014, 15 (1), pp.391. ⟨10.1186/s12859-014-0391-1⟩
Journal articles hal-01110595v1
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Phylogenetic Reconstruction Based on Synteny Block and Gene Adjacencies

Guénola Drillon , Raphaël Champeimont , Francesco Oteri , Gilles Fischer , Alessandra Carbone et al.
Molecular Biology and Evolution, 2020, 37 (9), pp.2747-2762. ⟨10.1093/molbev/msaa114⟩
Journal articles hal-02968249v1

Crystal structure of chloroplast fructose-1,6-bisphosphate aldolase from the green alga Chlamydomonas reinhardtii

Théo Le Moigne , Edoardo Sarti , Antonin Nourisson , Mirko Zaffagnini , Alessandra Carbone et al.
Journal of Structural Biology, 2022, 214 (3), pp.107873. ⟨10.1016/j.jsb.2022.107873⟩
Journal articles hal-03700038v1
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A global metagenomic map of urban microbiomes and antimicrobial resistance

David Danko , Daniela Bezdan , Evan Afshin , Sofia Ahsanuddin , Chandrima Bhattacharya et al.
Cell, 2021, 184 (13), pp.3376-3393.e17. ⟨10.1016/j.cell.2021.05.002⟩
Journal articles hal-03357730v1
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Protein Fragments: Functional and Structural Roles of Their Coevolution Networks

Linda Dib , Alessandra Carbone
PLoS ONE, 2012, 7 (11), pp.e48124. ⟨10.1371/journal.pone.0048124⟩
Journal articles hal-01527314v1
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SynChro: A Fast and Easy Tool to Reconstruct and Visualize Synteny Blocks along Eukaryotic Chromosomes

Guénola Drillon , Alessandra Carbone , Gilles Fischer
PLoS ONE, 2014, 9 (3), pp.e92621. ⟨10.1371/journal.pone.0092621⟩
Journal articles hal-01358096v1
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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

Combinatorics of chromosomal rearrangements based on synteny blocks and synteny packs

Guénola Drillon , Alessandra Carbone , Gilles Fischer
Journal of Logic and Computation, 2013, 23 (4, SI), pp.815-838. ⟨10.1093/logcom/exr047⟩
Journal articles hal-01528430v1
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CLAG: an unsupervised non hierarchical clustering algorithm handling biological data

Linda Dib , Alessandra Carbone
BMC Bioinformatics, 2012, 13 (1), pp.194. ⟨10.1186/1471-2105-13-194⟩
Journal articles hal-01527271v1

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.e1005992. ⟨10.1371/journal.pcbi.1005992⟩
Journal articles hal-04011118v1

Crystal structure of chloroplast fructose-1,6-bisphosphate aldolase from the green alga Chlamydomonas reinhardtii

Théo Le Moigne , Edoardo Sarti , Antonin Nourisson , Alessandra Carbone , Stéphane Lemaire et al.
2022
Preprints, Working Papers, ... hal-03521911v1
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Histone H1 protects telomeric repeats from H3K27me3 invasion in Arabidopsis

Gianluca Teano , Lorenzo Concia , Léopold Carron , Léa Wolff , Kateřina Adamusová et al.
2021
Preprints, Working Papers, ... hal-03099675v1
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NCIPLOT and the analysis of noncovalent interactions using the reduced density gradient

Rubén Laplaza , Francesca Peccati , Roberto A. Boto , Chaoyu Quan , Alessandra Carbone et al.
WIREs Computational Molecular Science, 2021, 11 (2), pp.e1497. ⟨10.1002/wcms.1497⟩
Journal articles hal-02921299v1

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
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A protein coevolution method uncovers critical features of the Hepatitis C Virus fusion mechanism

Florian Douam , Floriane Fusil , Margot Enguehard , Linda Dib , Francesca Nadalin et al.
PLoS Pathogens, 2018, 14 (3), pp.e1006908. ⟨10.1371/journal.ppat.1006908⟩
Journal articles hal-01917830v1
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A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling

Ari Ugarte , Riccardo Vicedomini , Juliana Bernardes , Alessandra Carbone
Microbiome, 2018, 6, pp.149. ⟨10.1186/s40168-018-0532-2⟩
Journal articles hal-01875977v1
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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
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Coevolution analysis of amino-acids reveals diversified drug-resistance solutions in viral sequences: a case study of hepatitis B virus

Elin Teppa , Francesca Nadalin , Christophe Combet , Diego Javier Zea , Laurent David et al.
Virus Evolution, 2020, 6 (1), pp.veaa006. ⟨10.1093/ve/veaa006⟩
Journal articles hal-02934600v1

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

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

A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling

Ari Ugarte , Riccardo Vicedomini , Juliana Bernardes , Alessandra Carbone
Microbiome, 2018, 6 (1), pp.149. ⟨10.1186/s40168-018-0532-2⟩
Journal articles hal-04028588v1

Annotating unknown species of urban microorganisms on a global scale unveils novel functional diversity and local environment association

Jun Wu , David Danko , Ebrahim Afshinnekoo , Daniela Bezdan , Malay Bhattacharyya et al.
Environmental Research, 2022, 207, pp.112183. ⟨10.1016/j.envres.2021.112183⟩
Journal articles hal-04028621v1
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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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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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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), ⟨10.1186/s12859-020-03867-x⟩
Journal articles hal-03154196v1

NCIPLOT4: fast, robust and quantitative analysis of noncovalent interactions

Roberto A Boto , Francesca Peccati , Rubén Laplaza , Chaoyu Quan , Alessandra Carbone et al.
Journal of Chemical Theory and Computation, 2020, ⟨10.1021/acs.jctc.0c00063⟩
Journal articles hal-02377999v1
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Large scale chromosomal mapping of human microRNA structural clusters

Anthony Mathelier , Alessandra Carbone
Nucleic Acids Research, 2013, 41 (8), pp.4392 - 4408. ⟨10.1093/nar/gkt112⟩
Journal articles hal-01527321v1