Jessica Andreani's Webpage

Publications

Mahmoudi, Quignot, Martins, Andreani. Structural comparison of protein-RNA homologous interfaces reveals widespread overall conservation contrasted with versatility in polar contacts. bioRxiv. Cold Spring Harbor Laboratory. (2024),[DOI] [bibtex]

@article{Mahmoudi2024.05.24.595654,
  author = {Mahmoudi, Ikram and Quignot, Chlo{\'e} and Martins, Carla and Andreani, Jessica},
  title = {Structural comparison of protein-RNA homologous interfaces reveals widespread overall conservation contrasted with versatility in polar contacts},
  elocation-id = {2024.05.24.595654},
  year = {2024},
  doi = {10.1101/2024.05.24.595654},
  publisher = {Cold Spring Harbor Laboratory},
  abstract = {Protein-RNA interactions play a critical role in many cellular processes and pathologies. However, experimental determination of protein-RNA structures is still challenging, therefore computational tools are needed for the prediction of protein-RNA interfaces. Although evolutionary pressures can be exploited for structural prediction of protein-protein interfaces, and recent deep learning methods using protein multiple sequence alignments have radically improved the performance of protein-protein interface structural prediction, protein-RNA structural prediction is lagging behind, due to the scarcity of structural data and the flexibility involved in these complexes. To study the evolution of protein-RNA interface structures, we first identified a large and diverse dataset of 2,022 pairs of structurally homologous interfaces (termed structural interologs). We leveraged this unique dataset to analyze the conservation of interface contacts among structural interologs based on the properties of involved amino acids and nucleotides. We uncovered that 73\% of distance-based contacts and 68\% of apolar contacts are conserved on average, and the strong conservation of these contacts occurs even in distant homologs with sequence identity below 20\%. Distance-based contacts are also much more conserved compared to what we had found in a previous study of homologous protein-protein interfaces. In contrast, hydrogen bonds, salt bridges, and Ï-stacking interactions are very versatile in pairs of protein-RNA interologs, even for close homologs with high interface sequence identity. We found that almost half of the non-conserved distance-based contacts are due to a small proportion of interface residues that no longer belong to the interface in the interolog, a phenomenon we term {\textquotedblleft}interface switching out{\textquotedblright}. We also examined possible recovery mechanisms for non-conserved hydrogen bonds and salt bridges, uncovering diverse scenarii of switching out, change in amino acid chemical nature, intermolecular and intramolecular compensations. Our findings provide insights for integrating evolutionary signals into predictive protein-RNA structural modeling methods.Competing Interest StatementThe authors have declared no competing interest.},
  url = {https://www.biorxiv.org/content/early/2024/05/25/2024.05.24.595654},
  eprint = {https://www.biorxiv.org/content/early/2024/05/25/2024.05.24.595654.full.pdf},
  journal = {bioRxiv},
}

Bret, Gao, Zea, Andreani, Guerois. From interaction networks to interfaces, scanning intrinsically disordered regions using AlphaFold2. Nat. Commun. 15(1), 597 (2024) [bibtex]

@article{Bret2024-et,
  title = {From interaction networks to interfaces, scanning intrinsically disordered regions using {AlphaFold2}},
  author = {Bret, H{\'e}l{\`e}ne and Gao, Jinmei and Zea, Diego Javier and Andreani, Jessica and Guerois, Rapha{\"e}l},
  abstract = {The revolution brought about by AlphaFold2 opens promising perspectives to unravel the complexity of protein-protein interaction networks. The analysis of interaction networks obtained from proteomics experiments does not systematically provide the delimitations of the interaction regions. This is of particular concern in the case of interactions mediated by intrinsically disordered regions, in which the interaction site is generally small. Using a dataset of protein-peptide complexes involving intrinsically disordered regions that are non-redundant with the structures used in AlphaFold2 training, we show that when using the full sequences of the proteins, AlphaFold2-Multimer only achieves 40\% success rate in identifying the correct site and structure of the interface. By delineating the interaction region into fragments of decreasing size and combining different strategies for integrating evolutionary information, we manage to raise this success rate up to 90\%. We obtain similar success rates using a much larger dataset of protein complexes taken from the ELM database. Beyond the correct identification of the interaction site, our study also explores specificity issues. We show the advantages and limitations of using the AlphaFold2 confidence score to discriminate between alternative binding partners, a task that can be particularly challenging in the case of small interaction motifs.},
  journal = {Nat. Commun.},
  volume = {15},
  number = {1},
  pages = {597},
  month = {},
  year = {2024},
  language = {en},
}

Versini, Sritharan, Aykac Fas, Tubiana, Aimeur, Henri, Erard, Nüsse, Andreani, Baaden, Fuchs, Galochkina, Chatzigoulas, Cournia, Santuz, Sacquin-Mora, Taly. A Perspective on the Prospective Use of AI in Protein Structure Prediction. J Chem Inf Model. 64(1), 26--41 (2024),[DOI] [bibtex]

@article{pmid38124369,
  author = {Versini, R. and Sritharan, S. and Aykac Fas, B. and Tubiana, T. and Aimeur, S. Z. and Henri, J. and Erard, M. and {N\"usse}, O. and Andreani, J. and Baaden, M. and Fuchs, P. and Galochkina, T. and Chatzigoulas, A. and Cournia, Z. and Santuz, H. and Sacquin-Mora, S. and Taly, A.},
  title = {{{A} {P}erspective on the {P}rospective {U}se of {A}{I} in {P}rotein {S}tructure {P}rediction}},
  journal = {J Chem Inf Model},
  year = {2024},
  volume = {64},
  number = {1},
  pages = {26--41},
  month = {Jan},
  doi = {10.1021/acs.jcim.3c01361},
}

Muzyukina, Shkaruta, Guzman, Andreani, Borges, Bondy-Denomy, Maikova, Semenova, Severinov, Soutourina. Identification of an anti-CRISPR protein that inhibits the CRISPR-Cas type I-B system in Clostridioides difficile. mSphere. 8(6), e0040123 (2023),[DOI] [bibtex]

@article{pmid38009936,
  author = {Muzyukina, P. and Shkaruta, A. and Guzman, N. M. and Andreani, J. and Borges, A. L. and Bondy-Denomy, J. and Maikova, A. and Semenova, E. and Severinov, K. and Soutourina, O.},
  title = {{Identification of an anti-CRISPR protein that inhibits the CRISPR-Cas type I-B system in Clostridioides difficile.}},
  journal = {mSphere},
  year = {2023},
  volume = {8},
  number = {6},
  pages = {e0040123},
  month = {Dec},
  doi = {10.1093/molbev/msh194},
}

Kefala Stavridi, Gontier, Morin, Frit, Ropars, Barboule, Racca, Jonchhe, Morten, Andreani, Rak, Legrand, Bourand-Plantefol, Hardwick, Chirgadze, Davey, De Oliveira, Rothenberg, Britton, Calsou, Blundell, Varela, Chaplin, Charbonnier. Structural and functional basis of inositol hexaphosphate stimulation of NHEJ through stabilization of Ku-XLF interaction. Nucleic Acids Res. 51(21), 11732--11747 (2023),[DOI] [bibtex]

@article{pmid37870477,
  author = {Kefala Stavridi, A. and Gontier, A. and Morin, V. and Frit, P. and Ropars, V. and Barboule, N. and Racca, C. and Jonchhe, S. and Morten, M. J. and Andreani, J. and Rak, A. and Legrand, P. and Bourand-Plantefol, A. and Hardwick, S. W. and Chirgadze, D. Y. and Davey, P. and De Oliveira, T. M. and Rothenberg, E. and Britton, S. and Calsou, P. and Blundell, T. L. and Varela, P. F. and Chaplin, A. K. and Charbonnier, J. B.},
  title = {{{S}tructural and functional basis of inositol hexaphosphate stimulation of {N}{H}{E}{J} through stabilization of {K}u-{X}{L}{F} interaction}},
  journal = {Nucleic Acids Res},
  year = {2023},
  volume = {51},
  number = {21},
  pages = {11732--11747},
  month = {Nov},
  doi = {10.1093/nar/gkad863},
}

Bret, Andreani^#, Guerois^#. From interaction networks to interfaces: Scanning intrinsically disordered regions using AlphaFold2. bioRxiv. Cold Spring Harbor Laboratory. (2023),[DOI] [bibtex]

@article{Bret2023.05.25.542287,
  author = {H{\'e}l{\`e}ne Bret and Jessica Andreani\textsuperscript{\#} and Rapha{\"e}l Guerois\textsuperscript{\#}},
  title = {From interaction networks to interfaces: Scanning intrinsically disordered regions using AlphaFold2},
  elocation-id = {2023.05.25.542287},
  year = {2023},
  doi = {10.1101/2023.05.25.542287},
  publisher = {Cold Spring Harbor Laboratory},
  abstract = {The revolution brought about by AlphaFold2 and the performance of AlphaFold2-Multimer open promising perspectives to unravel the complexity of protein-protein interaction networks. Nevertheless, the analysis of interaction networks obtained from proteomics experiments does not systematically provide the delimitations of the interaction regions. This is of particular concern in the case of interactions mediated by intrinsically disordered regions, in which the interaction site is generally small. Using a dataset of protein-peptide complexes involving intrinsically disordered protein regions that are non-redundant with the structures used in AlphaFold2 training, we show that when using the full sequences of the proteins involved in the interaction networks, AlphaFold2-Multimer only achieves 40\% success rate in identifying the correct site and structure of the interface. By delineating the interaction region into fragments of decreasing size and combining different strategies for integrating evolutionary information, we managed to raise this success rate up to 90\%. Beyond the correct identification of the interaction site, our study also explores specificity issues. We show the advantages and limitations of using the AlphaFold2 confidence score to discriminate between alternative binding partners, a task that can be particularly challenging in the case of small interaction motifs.Competing Interest StatementThe authors have declared no competing interest.},
  url = {https://www.biorxiv.org/content/early/2023/05/25/2023.05.25.542287},
  eprint = {https://www.biorxiv.org/content/early/2023/05/25/2023.05.25.542287.full.pdf},
  journal = {bioRxiv},
}

Ouasti, Audin, Freon, Quivy, Tachekort, Cesard, Thureau, Ropars, Varela, Moal, Amadou, Uryga, Legrand, Andreani, Guerois, Almouzni, Lambert, Ochsenbein. Disordered regions and folded modules in CAF-1 promote histone deposition in S. pombe. bioRxiv. Cold Spring Harbor Laboratory. (2023),[DOI] [bibtex]

@article{Ouasti2023.06.02.543505,
  author = {Fouad Ouasti and Maxime Audin and Karine Freon and Jean-Pierre Quivy and Mehdi Tachekort and Elizabeth Cesard and Aur{\'e}lien Thureau and Virginie Ropars and Paloma F. Varela and Gwenaelle Moal and Ibrahim Soumana Amadou and Aleksandra Uryga and Pierre Legrand and Jessica Andreani and Raphael Guerois and Genevi{\`e}ve Almouzni and Sarah Lambert and Francoise Ochsenbein},
  title = {Disordered regions and folded modules in CAF-1 promote histone deposition in S. pombe},
  elocation-id = {2023.06.02.543505},
  year = {2023},
  doi = {10.1101/2023.06.02.543505},
  publisher = {Cold Spring Harbor Laboratory},
  abstract = {Genome and epigenome integrity in eukaryotes depends on the proper coupling of histone deposition with DNA synthesis. This process relies on the evolutionary conserved histone chaperone CAF-1 for which the links between structure and functions are still a puzzle. While studies of the S. cerevisiae CAF-1 complex enabled to propose a model for the histone deposition mechanism, we still lack a framework to demonstrate its generality and in particular, how its interaction with the polymerase accessory factor PCNA is operating. Here, we reconstituted a complete SpCAF-1 from fission yeast. We characterized its dynamic structure using NMR, SAXS and molecular modeling together with in vitro and in vivo functional studies on rationally designed interaction mutants. Importantly, we identify the unfolded nature of the acidic domain which folds up when binding to histones. We also show how the long KER helix mediates DNA binding and stimulates SpCAF-1 association with PCNA. Our study highlights how the organization of CAF-1 comprising both disordered regions and folded modules enables the dynamics of multiple interactions to promote synthesis-coupled histone deposition essential for its DNA replication, heterochromatin maintenance, and genome stability functions.Competing Interest StatementThe authors have declared no competing interest.},
  url = {https://www.biorxiv.org/content/early/2023/08/14/2023.06.02.543505},
  eprint = {https://www.biorxiv.org/content/early/2023/08/14/2023.06.02.543505.full.pdf},
  journal = {bioRxiv},
}

Vilela, Chenon, Velours, Andreani, Llinas, Ménétrey. Insights into the activation of Kinesin1 from the molecular characterisation of JIP3/4 binding to Kif5b. bioRxiv. Cold Spring Harbor Laboratory. (2022),[DOI] [bibtex]

@article{Vilela2022.09.09.507386,
  author = {Fernando Vilela and M{\'e}lanie Chenon and Christophe Velours and Jessica Andreani and Paola Llinas and Julie M{\'e}n{\'e}trey},
  title = {Insights into the activation of Kinesin1 from the molecular characterisation of JIP3/4 binding to Kif5b},
  elocation-id = {2022.09.09.507386},
  year = {2022},
  doi = {10.1101/2022.09.09.507386},
  publisher = {Cold Spring Harbor Laboratory},
  abstract = {Whereas our understanding of kinesin auto-inhibition mechanisms is improving faster, important insights into kinesin activation mechanisms such as those controlled by cargo-motor adaptors are still missing. JIP3 and JIP4 are versatile motor-cargo adaptors for kinesin1 and dynein-dynactin motors enabling bi-directional transport on microtubules. JIP3 activates kinesin1 heavy chains, independently of kinesin1 light chains. In this report, we characterize the molecular details of the binding of the kinesin1 heavy chain, Kif5b to the motor-cargo adaptors, JIP3 and JIP4, using biophysical approaches. The definition of the exact binding site of Kif5b, as well as the specificity of interaction between JIP3 and JIP4 provide new insights into kinesin1 activation.Competing Interest StatementThe authors have declared no competing interest.},
  url = {https://www.biorxiv.org/content/early/2022/09/10/2022.09.09.507386},
  eprint = {https://www.biorxiv.org/content/early/2022/09/10/2022.09.09.507386.full.pdf},
  journal = {bioRxiv},
}

Seif-El-Dahan, Kefala-Stavridi, Frit, Hardwick, Chirgadze, Oliviera, Andreani, Britton, Barboule, Bossaert, Pandurangan, Meek, Blundell, Ropars, Calsou, Charbonnier, Chaplin. PAXX binding to the NHEJ machinery explains functional redundancy with XLF. Science Advances. 9(22), eadg2834 (2023),[DOI] [bibtex]

@article{doi:10.1126/sciadv.adg2834,
  author = {Murielle Seif-El-Dahan and Antonia Kefala-Stavridi and Philippe Frit and Steven W. Hardwick and Dima Y. Chirgadze and Taiana Maia De Oliviera and Jessica Andreani and SÃ©bastien Britton and Nadia Barboule and Madeleine Bossaert and Arun Prasad Pandurangan and Katheryn Meek and Tom L. Blundell and Virginie Ropars and Patrick Calsou and Jean-Baptiste Charbonnier and Amanda K. Chaplin},
  title = {PAXX binding to the NHEJ machinery explains functional redundancy with XLF},
  journal = {Science Advances},
  volume = {9},
  number = {22},
  pages = {eadg2834},
  year = {2023},
  doi = {10.1126/sciadv.adg2834},
  url = {https://www.science.org/doi/abs/10.1126/sciadv.adg2834},
  eprint = {https://www.science.org/doi/pdf/10.1126/sciadv.adg2834},
  abstract = {Nonhomologous end joining is a critical mechanism that repairs DNA double-strand breaks in human cells. In this work, we address the structural and functional role of the accessory protein PAXX [paralog of x-ray repair cross-complementing protein 4 (XRCC4) and XRCC4-like factor (XLF)] in this mechanism. Here, we report high-resolution cryoâelectron microscopy (cryo-EM) and x-ray crystallography structures of the PAXX C-terminal Ku-binding motif bound to Ku70/80 and cryo-EM structures of PAXX bound to two alternate DNA-dependent protein kinase (DNA-PK) end-bridging dimers, mediated by either Ku80 or XLF. We identify residues critical for the Ku70/PAXX interaction in vitro and in cells. We demonstrate that PAXX and XLF can bind simultaneously to the Ku heterodimer and act as structural bridges in alternate forms of DNA-PK dimers. Last, we show that engagement of both proteins provides a complementary advantage for DNA end synapsis and end joining in cells. PAXX and XLF structurally bridge alternate forms of DNA-PK dimers, explaining the redundancy between XLF and PAXX in NHEJ.},
}

Gareil, Gervais, Macaisne, Chevreux, Canman, Andreani, Dumont. An unconventional TOG domain is required for CLASP localization. Curr Biol. 33(16), 3522--3528 (2023),[DOI] [bibtex]

@article{pmid37516114,
  author = {Gareil, N. and Gervais, A. and Macaisne, N. and Chevreux, G. and Canman, J. C. and Andreani, J. and Dumont, J.},
  title = {{{A}n unconventional {T}{O}{G} domain is required for {C}{L}{A}{S}{P} localization}},
  journal = {Curr Biol},
  year = {2023},
  volume = {33},
  number = {16},
  pages = {3522--3528},
  month = {Aug},
  abstract = {although the CLASP domain required for this interaction is not known. Despite its high evolutionary conservation, the CTD remains structurally uncharacterized. Here, we find that the CTD can be structurally modeled as a TOG domain. We identify a surface-exposed and conserved arginine residue essential for CLASP CTD interaction with partner proteins. Together, our results provide a structural mechanism by which the CLASP CTD directs diverse sub-cellular localizations throughout the cell cycle.},
  doi = {10.1021/acs.jproteome.5b00932},
}

Schweke, Xu, Tauriello, Pantolini, Schwede, Cazals, Lhéritier, Fernandez-Recio, Rodríguez-Lumbreras, Schueler-Furman, Varga, Jiménez-García, Réau, Bonvin, Savojardo, Martelli, Casadio, Tubiana, Wolfson, Oliva, Barradas-Bautista, Ricciardelli, Cavallo, Venclovas, Olechnovič, Guerois, Andreani, Martin, Wang, Terashi, Sarkar, Christoffer, Aderinwale, Verburgt, Kihara, Marchand, Correia, Duan, Qiu, Xu, Zhang, Zou, Dey, Dunbrack, Levy, Wodak. Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study. Proteomics. 23(17), e2200323 (2023),[DOI] [bibtex]

@article{pmid37365936,
  author = {Schweke, H. and Xu, Q. and Tauriello, G. and Pantolini, L. and Schwede, T. and Cazals, F. and Lh{\'e}ritier, A. and Fernandez-Recio, J. and Rodr{\'i}guez-Lumbreras, L. A. and Schueler-Furman, O. and Varga, J. K. and Jim{\'e}nez-Garc{\'i}a, B. and R{\'e}au, M. F. and Bonvin, A. M. J. J. and Savojardo, C. and Martelli, P. L. and Casadio, R. and Tubiana, J. and Wolfson, H. J. and Oliva, R. and Barradas-Bautista, D. and Ricciardelli, T. and Cavallo, L. and Venclovas, Ä. and Olechnovi{\v{c}}, K. and Guerois, R. and Andreani, J. and Martin, J. and Wang, X. and Terashi, G. and Sarkar, D. and Christoffer, C. and Aderinwale, T. and Verburgt, J. and Kihara, D. and Marchand, A. and Correia, B. E. and Duan, R. and Qiu, L. and Xu, X. and Zhang, S. and Zou, X. and Dey, S. and Dunbrack, R. L. and Levy, E. D. and Wodak, S. J.},
  title = {{{D}iscriminating physiological from non-physiological interfaces in structures of protein complexes: {A} community-wide study}},
  journal = {Proteomics},
  year = {2023},
  volume = {23},
  number = {17},
  pages = {e2200323},
  month = {Sep},
  abstract = {Reliably scoring and ranking candidate models of protein complexes and assigning their oligomeric state from the structure of the crystal lattice represent outstanding challenges. A community-wide effort was launched to tackle these challenges. The latest resources on protein complexes and interfaces were exploited to derive a benchmark dataset consisting of 1677 homodimer protein crystal structures, including a balanced mix of physiological and non-physiological complexes. The non-physiological complexes in the benchmark were selected to bury a similar or larger interface area than their physiological counterparts, making it more difficult for scoring functions to differentiate between them. Next, 252 functions for scoring protein-protein interfaces previously developed by 13 groups were collected and evaluated for their ability to discriminate between physiological and non-physiological complexes. A simple consensus score generated using the best performing score of each of the 13 groups, and a cross-validated Random Forest (RF) classifier were created. Both approaches showed excellent performance, with an area under the Receiver Operating Characteristic (ROC) curve of 0.93 and 0.94, respectively, outperforming individual scores developed by different groups. Additionally, AlphaFold2 engines recalled the physiological dimers with significantly higher accuracy than the non-physiological set, lending support to the reliability of our benchmark dataset annotations. Optimizing the combined power of interface scoring functions and evaluating it on challenging benchmark datasets appears to be a promising strategy.},
  doi = {10.1002/pmic.202200323},
}

Andreani, Jiménez-García, Ohue. Editorial: Web tools for modeling and analysis of biomolecular interactions Volume II. Front Mol Biosci. 10, 1190855 (2023),[DOI] [bibtex]

@article{pmid37363399,
  author = {Andreani, J. and Jim{\'e}nez-Garc{\'i}a, B. and Ohue, M.},
  title = {{{E}ditorial: {W}eb tools for modeling and analysis of biomolecular interactions {V}olume {I}{I}}},
  journal = {Front Mol Biosci},
  year = {2023},
  volume = {10},
  pages = {1190855},
  doi = {10.3389/fmolb.2023.1190855},
}

Cargemel, Baconnais, Aumont-Nicaise, Noiray, Maurin, Andreani, Walbott, Le Cam, Ochsenbein, Marsin, Quevillon-Cheruel. Structural Insights of the DciA Helicase Loader in Its Relationship with DNA. Int J Mol Sci. 24(2) (2023),[DOI] [bibtex]

@article{pmid36674944,
  author = {Cargemel, C. and Baconnais, S. and Aumont-Nicaise, M. and Noiray, M. and Maurin, L. and Andreani, J. and Walbott, H. and Le Cam, E. and Ochsenbein, F. and Marsin, S. and Quevillon-Cheruel, S.},
  title = {{{S}tructural {I}nsights of the {D}ci{A} {H}elicase {L}oader in {I}ts {R}elationship with {D}{N}{A}}},
  journal = {Int J Mol Sci},
  year = {2023},
  volume = {24},
  number = {2},
  month = {Jan},
  abstract = {-helix 1 demonstrate its importance in the interaction of DciA for various DNA substrates mimicking single-stranded, double-stranded, and forked DNA. Some of these mutations also affect the loading of the helicase by DciA. We come to the hypothesis that DciA could be a DNA chaperone by intercalating itself between the two DNA strands to stabilize it. This work allows us to propose that the direct interaction of DciA with DNA could play a role in the loading mechanism of the helicase.},
  doi = {10.1038/nsb1296-995},
}

Andreani, Ohue, Jiménez-García. Editorial: Web Tools for Modeling and Analysis of Biomolecular Interactions. Front Mol Biosci. 9, 875859 (2022),[DOI] [bibtex]

@article{pmid35480880,
  author = {Andreani, J. and Ohue, M. and Jim{\'e}nez-Garc{\'i}a, B.},
  title = {{{E}ditorial: {W}eb {T}ools for {M}odeling and {A}nalysis of {B}iomolecular {I}nteractions}},
  journal = {Front Mol Biosci},
  year = {2022},
  volume = {9},
  pages = {875859},
  doi = {10.3389/fmolb.2022.875859},
}

Pyatnitskaya, Andreani, Guerois, De Muyt, Borde. The Zip4 protein directly couples meiotic crossover formation to synaptonemal complex assembly. Genes Dev. 36(1-2), 53--69 (2022),[DOI] [bibtex]

@article{pmid34969823,
  author = {Pyatnitskaya, A. and Andreani, J. and Guerois, R. and De Muyt, A. and Borde, V.},
  title = {{{T}he {Z}ip4 protein directly couples meiotic crossover formation to synaptonemal complex assembly}},
  journal = {Genes Dev},
  year = {2022},
  volume = {36},
  number = {1-2},
  pages = {53--69},
  month = {Jan},
  abstract = {Meiotic recombination is triggered by programmed double-strand breaks (DSBs), a subset of these being repaired as crossovers, promoted by eight evolutionarily conserved proteins, named ZMM. Crossover formation is functionally linked to synaptonemal complex (SC) assembly between homologous chromosomes, but the underlying mechanism is unknown. Here we show that Ecm11, a SC central element protein, localizes on both DSB sites and sites that attach chromatin loops to the chromosome axis, which are the starting points of SC formation, in a way that strictly requires the ZMM protein Zip4. Furthermore, Zip4 directly interacts with Ecm11, and point mutants that specifically abolish this interaction lose Ecm11 binding to chromosomes and exhibit defective SC assembly. This can be partially rescued by artificially tethering interaction-defective Ecm11 to Zip4. Mechanistically, this direct connection ensuring SC assembly from CO sites could be a way for the meiotic cell to shut down further DSB formation once enough recombination sites have been selected for crossovers, thereby preventing excess crossovers. Finally, the mammalian ortholog of Zip4, TEX11, also interacts with the SC central element TEX12, suggesting a general mechanism.},
  doi = {10.1101/cshperspect.a016626},
}

Marsin*, Adam*, Cargemel*, Andreani, Baconnais, Legrand, Li de la Sierra-Gallay, Humbert, Aumont-Nicaise, Velours, Ochsenbein, Durand, Le Cam, Walbott, Possoz, Quevillon-Cheruel^#, Ferat^#. Study of the DnaB:DciA interplay reveals insights into the primary mode of loading of the bacterial replicative helicase. Nucleic Acids Research. 49(11), 6569-6586 (2021),[DOI] [bibtex]

@article{Marsin2021,
  author = {Marsin*, StÃ©phanie and Adam*, Yazid and Cargemel*, Claire and Andreani, Jessica and Baconnais, Sonia and Legrand, Pierre and Li de la Sierra-Gallay, Ines and Humbert, Adeline and Aumont-Nicaise, Magali and Velours, Christophe and Ochsenbein, FranÃ§oise and Durand, Dominique and Le Cam, Eric and Walbott, HÃ©lÃ¨ne and Possoz, Christophe and Quevillon-Cheruel\textsuperscript{\#}, Sophie and Ferat\textsuperscript{\#}, Jean-Luc},
  title = {{Study of the DnaB:DciA interplay reveals insights into the primary mode of loading of the bacterial replicative helicase}},
  journal = {Nucleic Acids Research},
  volume = {49},
  number = {11},
  pages = {6569-6586},
  year = {2021},
  month = {06},
  issn = {0305-1048},
  doi = {10.1093/nar/gkab463},
  url = {https://doi.org/10.1093/nar/gkab463},
  eprint = {https://academic.oup.com/nar/article-pdf/49/11/6569/38713230/gkab463.pdf},
}

Dai*, Sanchez*, Adam, Ranjha, Reginato, Chervy, Tellier-Lebegue, Andreani, Guérois, Ropars, Le Du, Maloisel, Martini, Legrand, Thureau, Cejka, Borde^#, Charbonnier^#. Molecular basis of the dual role of the Mlh1-Mlh3 endonuclease in MMR and in meiotic crossover formation. Proceedings of the National Academy of Sciences. National Academy of Sciences. 118(23) (2021),[DOI] [bibtex]

@article{Dai2021,
  author = {Dai*, Jingqi and Sanchez*, Aurore and Adam, C{\'e}line and Ranjha, Lepakshi and Reginato, Giordano and Chervy, Pierre and Tellier-Lebegue, Carine and Andreani, Jessica and Gu{\'e}rois, Rapha{\"e}l and Ropars, Virginie and Le Du, Marie-H{\'e}l{\`e}ne and Maloisel, Laurent and Martini, Emmanuelle and Legrand, Pierre and Thureau, Aur{\'e}lien and Cejka, Petr and Borde\textsuperscript{\#}, Val{\'e}rie and Charbonnier\textsuperscript{\#}, Jean-Baptiste},
  title = {Molecular basis of the dual role of the Mlh1-Mlh3 endonuclease in MMR and in meiotic crossover formation},
  volume = {118},
  number = {23},
  elocation-id = {e2022704118},
  year = {2021},
  doi = {10.1073/pnas.2022704118},
  publisher = {National Academy of Sciences},
  issn = {0027-8424},
  url = {https://www.pnas.org/content/118/23/e2022704118},
  eprint = {https://www.pnas.org/content/118/23/e2022704118.full.pdf},
  journal = {Proceedings of the National Academy of Sciences},
}

Quignot, Postic, Bret, Rey, Granger, Murail, Chacón, Andreani^#, Tufféry^#, Guerois^#. InterEvDock3: a combined template-based and free docking server with increased performance through explicit modeling of complex homologs and integration of covariation-based contact maps. Nucleic Acids Research. 49(W1), W277-W284 (2021),[DOI] [bibtex]

@article{Quignot2021b,
  author = {Quignot, ChloÃ© and Postic, Guillaume and Bret, HÃ©lÃ¨ne and Rey, Julien and Granger, Pierre and Murail, Samuel and Chac{\'o}n, Pablo and Andreani\textsuperscript{\#}, Jessica and Tuff{\'e}ry\textsuperscript{\#}, Pierre and Guerois\textsuperscript{\#}, RaphaÃ«l},
  title = {{InterEvDock3: a combined template-based and free docking server with increased performance through explicit modeling of complex homologs and integration of covariation-based contact maps}},
  journal = {Nucleic Acids Research},
  volume = {49},
  number = {W1},
  pages = {W277-W284},
  year = {2021},
  month = {05},
  issn = {0305-1048},
  doi = {10.1093/nar/gkab358},
  url = {https://doi.org/10.1093/nar/gkab358},
  eprint = {https://academic.oup.com/nar/article-pdf/49/W1/W277/38842198/gkab358\_supplemental\_file.pdf},
}

Postic, Andreani, Marcoux, Reys, Guerois, Rey, Mouton-Barbosa, Vandenbrouck, Cianferani, Burlet-Schiltz, Labesse^#, Tufféry^#. Proteo3Dnet: a web server for the integration of structural information with interactomics data. Nucleic Acids Research. 49(W1), W567-W572 (2021),[DOI] [bibtex]

@article{Postic2021,
  author = {Postic, Guillaume and Andreani, Jessica and Marcoux, Julien and Reys, Victor and Guerois, RaphaÃ«l and Rey, Julien and Mouton-Barbosa, Emmanuelle and Vandenbrouck, Yves and Cianferani, Sarah and Burlet-Schiltz, Odile and Labesse\textsuperscript{\#}, Gilles and Tuff{\'e}ry\textsuperscript{\#}, Pierre},
  title = {{Proteo3Dnet: a web server for the integration of structural information with interactomics data}},
  journal = {Nucleic Acids Research},
  volume = {49},
  number = {W1},
  pages = {W567-W572},
  year = {2021},
  month = {05},
  issn = {0305-1048},
  doi = {10.1093/nar/gkab332},
  url = {https://doi.org/10.1093/nar/gkab332},
  eprint = {https://academic.oup.com/nar/article-pdf/49/W1/W567/38841745/gkab332.pdf},
}

Quignot, Granger, Chacón, Guerois^#, Andreani^#. Atomic-level evolutionary information improves protein-protein interface scoring. Bioinformatics. (2021),[DOI] [Accepted Manuscript PDF] [bibtex]

@article{Quignot2021a,
  title = {Atomic-level evolutionary information improves protein-protein interface scoring},
  author = {Chlo{\'{e}} Quignot and Pierre Granger and Pablo Chac{\'{o}}n and Raphael Guerois\textsuperscript{\#} and Jessica Andreani\textsuperscript{\#}},
  year = {2021},
  journal = {Bioinformatics},
  url = {https://doi.org/10.1093/bioinformatics/btab254},
  doi = {10.1093/bioinformatics/btab254},
  pdf = {http://jessica.andreani.info/papers/202104_Quignot_et_al_AM.pdf},
  text = {Accepted Manuscript},
}

Rahman, Mohiuddin, Keka, Yamada, Tsuda, Sasanuma, Andreani, Guerois, Borde, Charbonnier, Takeda. Genetic evidence for the involvement of mismatch repair proteins, PMS2 and MLH3, in a late step of homologous recombination. Journal of Biological Chemistry. (2020),[DOI] [bibtex]

@article{Rahman2020,
  doi = {10.1074/jbc.RA120.013521},
  url = {https://doi.org/10.1074/jbc.RA120.013521},
  year = {2020},
  author = {Md Maminur Rahman and Mohiuddin Mohiuddin and Islam Shamima Keka and Kousei Yamada and Masataka Tsuda and Hiroyuki Sasanuma and Jessica Andreani and Raphael Guerois and Valerie Borde and Jean-Baptiste Charbonnier and Shunichi Takeda},
  title = {Genetic evidence for the involvement of mismatch repair proteins, PMS2 and MLH3, in a late step of homologous recombination},
  journal = {Journal of Biological Chemistry},
}

Postic, Marcoux, Reys, Andreani, Vandenbrouck, Bousquet, Mouton-Barbosa, Cianférani, Burlet-Schiltz, Guerois, Labesse, Tufféry. Probing Protein Interaction Networks by Combining MS-Based Proteomics and Structural Data Integration. Journal of Proteome Research. American Chemical Society (ACS). (2020),[DOI] [bibtex]

@article{Postic_2020,
  doi = {10.1021/acs.jproteome.0c00066},
  url = {https://doi.org/10.1021%2Facs.jproteome.0c00066},
  year = {2020},
  month = {may},
  publisher = {American Chemical Society ({ACS})},
  author = {Guillaume Postic and Julien Marcoux and Victor Reys and Jessica Andreani and Yves Vandenbrouck and Marie-Pierre Bousquet and Emmanuelle Mouton-Barbosa and Sarah Cianf{\'{e}}rani and Odile Burlet-Schiltz and Raphael Guerois and Gilles Labesse and Pierre Tuff{\'{e}}ry},
  title = {Probing Protein Interaction Networks by Combining {MS}-Based Proteomics and Structural Data Integration},
  journal = {Journal of Proteome Research},
}

Andreani^#, Quignot, Guerois^#. Structural prediction of protein interactions and docking using conservation and coevolution. WIREs Computational Molecular Science. Wiley. (2020),[DOI] [bibtex]

@article{Andreani_2020,
  doi = {10.1002/wcms.1470},
  url = {https://doi.org/10.1002%2Fwcms.1470},
  year = {2020},
  month = {may},
  publisher = {Wiley},
  author = {Jessica Andreani\textsuperscript{\#} and Chlo{\'{e}} Quignot and Raphael Guerois\textsuperscript{\#}},
  title = {Structural prediction of protein interactions and docking using conservation and coevolution},
  journal = {{WIREs} Computational Molecular Science},
}

Nadaradjane, Quignot, Traoré, Andreani^#, Guerois^#. Docking proteins and peptides under evolutionary constraints in Critical Assessment of PRediction of Interactions rounds 38 to 45. Proteins: Structure, Function, and Bioinformatics. 88(8), 986-998 (2020),[DOI] [bibtex]

@article{Nadaradjane2019,
  author = {Nadaradjane, Aravindan Arun and Quignot, ChloÃ© and Traor\'e, Seydou and Andreani\textsuperscript{\#}, Jessica and Guerois\textsuperscript{\#}, RaphaÃ«l},
  title = {Docking proteins and peptides under evolutionary constraints in Critical Assessment of PRediction of Interactions rounds 38 to 45},
  journal = {Proteins: Structure, Function, and Bioinformatics},
  volume = {88},
  number = {8},
  pages = {986-998},
  keywords = {CAPRI, coevolution, evolutionary information, InterEvDock, protein-carbohydrate docking, protein-peptide docking, protein-protein docking, protein-protein interaction},
  doi = {https://doi.org/10.1002/prot.25857},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/prot.25857},
  eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/prot.25857},
  year = {2020},
}

Vilela, Velours, Chenon, Aumont-Nicaise, Campanacci, Thureau, Pylypenko, Andreani, Llinas, Ménétrey. Structural characterization of the RH1-LZI tandem of JIP3/4 highlights RH1 domains as a cytoskeletal motor-binding motif. Scientific Reports. 9(1), 16036 (2019),[DOI] [bibtex]

@article{Vilela2019,
  author = {Vilela, Fernando and Velours, Christophe and Chenon, M{\'e}lanie and Aumont-Nicaise, Magali and Campanacci, Val{\'e}rie and Thureau, Aur{\'e}lien and Pylypenko, Olena and Andreani, Jessica and Llinas, Paola and M{\'e}n{\'e}trey, Julie},
  journal = {Scientific Reports},
  title = {{Structural characterization of the RH1-LZI tandem of JIP3/4 highlights RH1 domains as a cytoskeletal motor-binding motif}},
  year = {2019},
  volume = {9},
  number = {1},
  pages = {16036},
  issn = {2045-2322},
  doi = {10.1038/s41598-019-52537-3},
  url = {https://doi.org/10.1038/s41598-019-52537-3},
}

Bakail, Gaubert, Andreani, Moal, Pinna, Boyarchuk, Gaillard, Courbeyrette, Mann, Thuret, Guichard, Murciano, Richet, Poitou, Frederic, Le Du, Agez, Roelants, Gurard-Levin, Almouzni, Cherradi, Guerois, Ochsenbein. Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1. Cell Chemical Biology. Elsevier. 26(11), 1573-1585.e10 (2019),[DOI] [bibtex]

@article{Bakail2019,
  annote = {doi: 10.1016/j.chembiol.2019.09.002},
  author = {Bakail, May and Gaubert, Albane and Andreani, Jessica and Moal, Gwena{\"{e}}lle and Pinna, Guillaume and Boyarchuk, Ekaterina and Gaillard, Marie-C{\'{e}}cile and Courbeyrette, Regis and Mann, Carl and Thuret, Jean-Yves and Guichard, B{\'{e}}reng{\`{e}}re and Murciano, Brice and Richet, Nicolas and Poitou, Adeline and Frederic, Claire and {Le Du}, Marie-H{\'{e}}l{\`{e}}ne and Agez, Morgane and Roelants, Caroline and Gurard-Levin, Zachary A and Almouzni, Genevi{\`{e}}ve and Cherradi, Nadia and Guerois, Raphael and Ochsenbein, Fran{\c{c}}oise},
  doi = {10.1016/j.chembiol.2019.09.002},
  issn = {2451-9456},
  journal = {Cell Chemical Biology},
  month = {Nov},
  day = {21},
  publisher = {Elsevier},
  volume = {26},
  number = {11},
  pages = {1573-1585.e10},
  title = {{Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1}},
  url = {https://doi.org/10.1016/j.chembiol.2019.09.002},
  year = {2019},
}

Fischböck-Halwachs, Singh, Potocnjak, Hagemann, Solis-Mezarino, Woike, Ghodgaonkar-Steger, Weissmann, Gallego, Rojas, Andreani, Köhler, Herzog. The COMA complex interacts with Cse4 and positions Sli15/Ipl1 at the budding yeast inner kinetochore. eLife. 8, e42879 (2019),[DOI] [bibtex]

@article{fishboeck19,
  article_type = {journal},
  title = {The COMA complex interacts with Cse4 and positions Sli15/Ipl1 at the budding yeast inner kinetochore},
  author = {Fischb\"ock-Halwachs, Josef and Singh, Sylvia and Potocnjak, Mia and Hagemann, G\"otz and Solis-Mezarino, Victor and Woike, Stephan and Ghodgaonkar-Steger, Medini and Weissmann, Florian and Gallego, Laura D and Rojas, Julie and Andreani, Jessica and K\"ohler, Alwin and Herzog, Franz},
  editor = {Akhmanova, Anna and DeLuca, Jennifer G and Biggins, Sue and DeLuca, Jennifer G},
  volume = {8},
  year = {2019},
  month = {may},
  pub_date = {2019-05-21},
  pages = {e42879},
  citation = {eLife 2019;8:e42879},
  doi = {10.7554/eLife.42879},
  url = {https://doi.org/10.7554/eLife.42879},
  keywords = {kinetochore, mass spectrometry, feedback control, chromosome segregation, chemical crosslinking, error correction, chromosomal passenger complex, aurora B},
  journal = {eLife},
  issn = {2050-084X},
}

Lisboa, Celma, Sanchez, Marquis, Andreani, Guerois, Ochsenbein, Durand, Marsin, Cuniasse, Radicella, Quevillon-Cheruel. The C-terminal domain of HpDprA is a DNA-binding Winged Helix domain that does not bind double-stranded DNA. The FEBS Journal. (), (2019),[DOI] [bibtex]

@article{lisboa19,
  author = {Lisboa, Johnny and Celma, Louisa and Sanchez, Dyana and Marquis, Mathilde and Andreani, Jessica and Guerois, Raphael and Ochsenbein, Francoise and Durand, Dominique and Marsin, St\'ephanie and Cuniasse, Philippe and Radicella, J. Pablo and Quevillon-Cheruel, Sophie},
  title = {The C-terminal domain of HpDprA is a DNA-binding Winged Helix domain that does not bind double-stranded DNA},
  journal = {The FEBS Journal},
  volume = {},
  number = {},
  pages = {},
  year = {2019},
  doi = {10.1111/febs.14788},
  url = {https://febs.onlinelibrary.wiley.com/doi/abs/10.1111/febs.14788},
}

Nguyen, Aumont-Nicaise, Andreani, Velours, Chenon, Vilela, Geneste, Varela, Llinas, Ménétrey. Characterization of the binding mode of JNK-interacting protein 1 (JIP1) to kinesin-light chain 1 (KLC1). Journal of Biological Chemistry. 293(36), 13946-13960 (2018),[DOI] [bibtex]

@article{nguyen-18,
  author = {Nguyen, T. Quyen and Aumont-Nicaise, Magali and Andreani, Jessica and Velours, Christophe and Chenon, M\'elanie and Vilela, Fernando and Geneste, Cl\'ementine and Varela, Paloma F. and Llinas, Paola and M\'en\'etrey, Julie},
  title = {Characterization of the binding mode of JNK-interacting protein 1 (JIP1) to kinesin-light chain 1 (KLC1)},
  volume = {293},
  number = {36},
  pages = {13946-13960},
  year = {2018},
  doi = {10.1074/jbc.RA118.003916},
  url = {http://www.jbc.org/content/293/36/13946.abstract},
  eprint = {http://www.jbc.org/content/293/36/13946.full.pdf+html},
  journal = {Journal of Biological Chemistry},
}

Quignot*, Rey*, Yu, Tufféry^#, Guerois^#, Andreani^#. InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs. Nucleic Acids Research. 46(W1), W408-W416 (2018),[DOI] [bibtex]

@article{quignot-18,
  author = {Quignot*, Chlo\'e and Rey*, Julien and Yu, Jinchao and Tuff\'ery\textsuperscript{\#}, Pierre and Guerois\textsuperscript{\#}, Rapha\"{e}l and Andreani\textsuperscript{\#}, Jessica},
  title = {InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs},
  journal = {Nucleic Acids Research},
  volume = {46},
  number = {W1},
  pages = {W408-W416},
  year = {2018},
  doi = {10.1093/nar/gky377},
  url = {http://dx.doi.org/10.1093/nar/gky377},
}

Nadaradjane, Guerois^#, Andreani^#. Protein-Protein Docking Using Evolutionary Information. In "Protein Complex Assembly: Methods and Protocols". Springer New York. 429-447 (2018),[DOI] [bibtex]

@inbook{Nadaradjane2018,
  author = {Nadaradjane, Aravindan Arun and Guerois\textsuperscript{\#}, Raphael and Andreani\textsuperscript{\#}, Jessica},
  editor = {Marsh, Joseph A.},
  title = {Protein-Protein Docking Using Evolutionary Information},
  booktitle = {Protein Complex Assembly: Methods and Protocols},
  year = {2018},
  publisher = {Springer New York},
  address = {New York, NY},
  pages = {429-447},
  isbn = {978-1-4939-7759-8},
  doi = {10.1007/978-1-4939-7759-8_28},
  url = {https://doi.org/10.1007/978-1-4939-7759-8_28},
}

De Muyt, Pyatnitskaya, Andreani, Ranjha, Ramus, Laureau, Fernandez-Vega, Holoch, Girard, Govin, Margueron, Couté, Cejka, Guerois, Borde. A meiotic XPF-ERCC1-like complex recognizes joint molecule recombination intermediates to promote crossover formation. Genes & Development. (2018),[DOI] [bibtex]

@article{demuy-18,
  author = {De Muyt, Arnaud and Pyatnitskaya, Alexandra and Andreani, Jessica and Ranjha, Lepakshi and Ramus, Claire and Laureau, Rapha\"{e}lle and Fernandez-Vega, Ambra and Holoch, Daniel and Girard, Elodie and Govin, J\'{e}rome and Margueron, Rapha\"{e}l and Cout\'{e}, Yohann and Cejka, Petr and Guerois, Rapha\"{e}l and Borde, Val\'{e}rie},
  title = {A meiotic XPF-ERCC1-like complex recognizes joint molecule recombination intermediates to promote crossover formation},
  year = {2018},
  doi = {10.1101/gad.308510.117},
  url = {http://genesdev.cshlp.org/content/early/2018/02/09/gad.308510.117.abstract},
  eprint = {http://genesdev.cshlp.org/content/early/2018/02/09/gad.308510.117.full.pdf+html},
  journal = {Genes \& Development},
}

Nguyen, Chenon, Vilela, Velours, Aumont-Nicaise, Andreani, Varela, Llinas^#, Ménétrey^#. Structural plasticity of the N-terminal capping helix of the TPR domain of kinesin light chain. PLOS One. 12(10) (2017),[DOI] [bibtex]

@article{nguyen-17,
  author = {The Quyen Nguyen AND M\'elanie Chenon AND Fernando Vilela AND Christophe Velours AND Magali Aumont-Nicaise AND Jessica Andreani AND Paloma F. Varela AND Paola Llinas\textsuperscript{\#} AND Julie M\'en\'etrey\textsuperscript{\#}},
  journal = {PLOS One},
  title = {Structural plasticity of the N-terminal capping helix of the TPR domain of kinesin light chain},
  year = {2017},
  month = {10},
  volume = {12},
  number = {10},
  doi = {10.1371/journal.pone.0186354},
  url = {https://doi.org/10.1371/journal.pone.0186354},
}

Méneret, Franz, Trouillard, Oliver, Zagar, Robertson, Welniarz, Gardner, Gallea, Srour, Depienne, Jasoni, Dubacq, Riant, Lamy, Morel, Guérois, Andreani, Fouquet, Doulazmi, Vidailhet, Rouleau, Brice, Chédotal, Dusart, Roze, Markie. Mutations in the netrin-1 gene cause congenital mirror movements. The Journal of Clinical Investigation. 127(11) (2017),[DOI] [bibtex]

@article{meneret-17,
  author = {Aur\'elie M\'eneret AND Elizabeth A. Franz AND Oriane Trouillard AND Thomas C. Oliver AND Yvrick Zagar AND Stephen P. Robertson AND Quentin Welniarz AND R.J. MacKinlay Gardner AND C\'ecile Gallea AND Myriam Srour AND Christel Depienne AND Christine L. Jasoni AND Caroline Dubacq AND Florence Riant AND Jean-Charles Lamy AND Marie-Pierre Morel AND Raphael Gu\'erois AND Jessica Andreani AND Coralie Fouquet AND Mohamed Doulazmi AND Marie Vidailhet AND Guy A. Rouleau AND Alexis Brice AND Alain Ch\'edotal AND Isabelle Dusart AND Emmanuel Roze AND David Markie},
  journal = {The Journal of Clinical Investigation},
  title = {Mutations in the netrin-1 gene cause congenital mirror movements},
  year = {2017},
  month = {9},
  volume = {127},
  url = {https://doi.org/10.1172/JCI95442},
  number = {11},
  doi = {10.1172/JCI95442},
  url = {https://doi.org/10.1172/JCI95442},
}

Baejen*, Andreani*, Torkler, Battaglia, Schwalb, Lidschreiber, Maier, Boltendahl, Rus, Esslinger, Söding^#, Cramer^#. Genome-wide Analysis of RNA Polymerase II Termination at Protein-Coding Genes. Molecular Cell. 66(1), 38-49.e6 (2017),[DOI] [bibtex]

@article{baejen-17,
  title = {Genome-wide Analysis of RNA Polymerase II Termination at Protein-Coding Genes},
  author = {Baejen*, Carlo and Andreani*, Jessica and Torkler, Phillipp and Battaglia, Sofia and Schwalb, Bjoern and Lidschreiber, Michael and Maier, Kerstin C and Boltendahl, Andrea and Rus, Petra and Esslinger, Stephanie and S\"oding\textsuperscript{\#}, Johannes and Cramer\textsuperscript{\#}, Patrick},
  journal = {Molecular Cell},
  year = {2017},
  doi = {10.1016/j.molcel.2017.02.009},
  volume = {66},
  number = {1},
  pages = {38-49.e6},
}

Yu, Andreani, Ochsenbein, Guerois. Lessons from (co-)evolution in the docking of proteins and peptides for CAPRI Rounds 28-35. Proteins. 85(3), 378-390 (2016),[DOI] [bibtex]

@article{yu-16b,
  author = {Yu, Jinchao and Andreani, Jessica and Ochsenbein, Francoise and Guerois, Rapha\"el},
  title = {Lessons from \(co-\)evolution in the docking of proteins and peptides for CAPRI Rounds 28-35},
  volume = {85},
  number = {3},
  pages = {378-390},
  year = {2016},
  doi = {10.1002/prot.25180},
  url = {http://onlinelibrary.wiley.com/doi/10.1002/prot.25180},
  journal = {Proteins},
}

Yu, Vavrusa, Andreani, Rey, Tufféry^#, Guerois^#. InterEvDock: a docking server to predict the structure of protein-protein interactions using evolutionary information. Nucleic Acids Research. 44(W1), W542-W549 (2016),[DOI] [bibtex]

@article{yu-16,
  author = {Yu, Jinchao and Vavrusa, Marek and Andreani, Jessica and Rey, Julien and Tuff\'ery\textsuperscript{\#}, Pierre and Guerois\textsuperscript{\#}, Rapha\"el},
  title = {InterEvDock: a docking server to predict the structure of protein-protein interactions using evolutionary information},
  volume = {44},
  number = {W1},
  pages = {W542-W549},
  year = {2016},
  doi = {10.1093/nar/gkw340},
  url = {http://nar.oxfordjournals.org/content/44/W1/W542.abstract},
  eprint = {http://nar.oxfordjournals.org/content/44/W1/W542.full.pdf+html},
  journal = {Nucleic Acids Research},
}

Andreani^#, Söding^#. bbcontacts: prediction of β-strand pairing from direct coupling patterns. Bioinformatics. 31(11), 1729-1737 (2015),[DOI] [bibtex]

@article{andreani-15,
  author = {Andreani\textsuperscript{\#}, Jessica and S\"oding\textsuperscript{\#}, Johannes},
  title = {bbcontacts: prediction of $\beta$-strand pairing from direct coupling patterns},
  volume = {31},
  number = {11},
  pages = {1729-1737},
  year = {2015},
  doi = {10.1093/bioinformatics/btv041},
  url = {http://bioinformatics.oxfordjournals.org/content/early/2015/01/22/bioinformatics.btv041.abstract},
  journal = {Bioinformatics},
}

Wickles, Singharoy, Andreani, Seemayer, Bischoff, Berninghausen, Soeding, Schulten, van der Sluis, Beckmann. A structural model of the active ribosome-bound membrane protein insertase YidC. eLife. 3, e03035 (2014),[DOI] [bibtex]

@article{wickles-14,
  author = {Wickles, Stephan and Singharoy, Abhishek and Andreani, Jessica and Seemayer, Stefan and Bischoff, Lukas and Berninghausen, Otto and Soeding, Johannes and Schulten, Klaus and van der Sluis, Eli and Beckmann, Roland},
  title = {A structural model of the active ribosome-bound membrane protein insertase YidC},
  volume = {3},
  pages = {e03035},
  year = {2014},
  doi = {10.7554/eLife.03035},
  isbn = {2050-084X},
  url = {http://elifesciences.org/content/early/2014/07/09/eLife.03035},
  journal = {eLife},
}

Andreani^#, Guerois^#. Evolution of Protein Interactions: From Interactomes to Interfaces. Archives of Biochemistry and Biophysics. 554, 65-75 (2014),[DOI] [bibtex]

@article{andreani-14,
  author = {Andreani\textsuperscript{\#}, Jessica and Guerois\textsuperscript{\#}, Raphael},
  title = {Evolution of Protein Interactions: From Interactomes to Interfaces},
  year = {2014},
  volume = {554},
  pages = {65-75},
  doi = {10.1016/j.abb.2014.05.010},
  url = {http://www.sciencedirect.com/science/article/pii/S0003986114001593},
  journal = {Archives of Biochemistry and Biophysics},
}

Lisboa*, Andreani*, Sanchez, Boudes, Collinet, Liger, Tilbeurgh, Guerois^#, Quevillon-Cheruel^#. Molecular determinants of the DprA-RecA interaction for nucleation on ssDNA. Nucleic Acids Research. 42(11), 7395-7408 (2014),[DOI] [bibtex]

@article{lisboa-14,
  author = {Lisboa*, Johnny and Andreani*, Jessica and Sanchez, Dyana and Boudes, Marion and Collinet, Bruno and Liger, Dominique and Tilbeurgh, Herman van and Guerois\textsuperscript{\#}, Raphael and Quevillon-Cheruel\textsuperscript{\#}, Sophie},
  title = {Molecular determinants of the DprA-RecA interaction for nucleation on ssDNA},
  year = {2014},
  volume = {42},
  number = {11},
  pages = {7395-7408},
  doi = {10.1093/nar/gku349},
  url = {http://nar.oxfordjournals.org/content/early/2014/04/29/nar.gku349.abstract},
  eprint = {http://nar.oxfordjournals.org/content/early/2014/04/29/nar.gku349.full.pdf+html},
  journal = {Nucleic Acids Research},
}

Lombardi, Ayach, Beaurepaire, Chenon, Andreani, Guerois, Jupin, Bressanelli. A compact viral processing proteinase / ubiquitin hydrolase from the OTU family. PLoS Pathogens. 9(8), e1003560 (2013),[DOI] [bibtex]

@article{lombardi-13,
  author = {Lombardi, Charlotte and Ayach, Maya and Beaurepaire, Lionel and Chenon, M\'elanie and Andreani, Jessica and Guerois, Rapha\"el and Jupin, Isabelle and Bressanelli, St\'ephane},
  title = {{A compact viral processing proteinase / ubiquitin hydrolase from the OTU family}},
  journal = {PLoS Pathogens},
  volume = {9},
  number = {8},
  pages = {e1003560},
  year = {2013},
  doi = {10.1371/journal.ppat.1003560},
}

Andreani, Faure, Guerois. InterEvScore: a novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution. Bioinformatics. 29(14), 1742-1749 (2013),[DOI] [bibtex]

@article{andreani-13,
  author = {Andreani, Jessica and Faure, Guilhem and Guerois, Rapha\"el},
  title = {{InterEvScore: a novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution}},
  journal = {Bioinformatics},
  year = {2013},
  volume = {29},
  number = {14},
  pages = {1742-1749},
  doi = {10.1093/bioinformatics/btt260},
}

Andreani, Faure, Guerois. Versatility and Invariance in the Evolution of Homologous Heteromeric Interfaces. PLoS Comput Biol. 8(8), e1002677+ (2012),[DOI] [bibtex]

@article{andreani-12,
  author = {Andreani, Jessica and Faure, Guilhem and Guerois, Rapha\"el},
  title = {{Versatility and Invariance in the Evolution of Homologous Heteromeric Interfaces}},
  journal = {PLoS Comput Biol},
  year = {2012},
  month = {aug},
  volume = {8},
  number = {8},
  pages = {e1002677+},
  doi = {10.1371/journal.pcbi.1002677},
}

Faure, Andreani, Guerois. InterEvol database: exploring the structure and evolution of protein complex interfaces. Nucleic Acids Research. 40(D1), 847-856 (2012),[DOI] [bibtex]

@article{faure-12,
  author = {Faure, Guilhem and Andreani, Jessica and Guerois, Rapha\"el},
  title = {{InterEvol database: exploring the structure and evolution of protein complex interfaces}},
  journal = {Nucleic Acids Research},
  volume = {40},
  number = {D1},
  pages = {847-856},
  year = {2012},
  doi = {10.1093/nar/gkr845},
}

* equal contribution
^# co-corresponding authors