Publications
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Publications référencées sur HAL COMBI en 2025 
Nombre de publications référencées : 30
Ventilation par types
Revues internationales avec comité de lecture
- [1] C. Ghassemi Nedjad, M. Bolteau, L. Bourneuf, L. Paulevé, C. Frioux. Seed2LP: seed inference in metabolic networks for reverse ecology applications, in Bioinformatics, vol. 41, no. 4, pp. btaf140, 2025 DOI
- [2] G. Siqueira, A. Alexandrino, A. Oliveira, G. Jean, G. Fertin, Z. Dias. Partition Based Algorithms for Rearrangement Distances with Flexible Intergenic Regions, in IEEE/ACM Transactions on Computational Biology and Bioinformatics, pp. 1-14, 2025 DOI
- [3] M. Bolteau, C. Messaoudi, L. David, J. Bourdon, C. Guziolowski. Deep exploration of logical models of cell differentiation in human preimplantation embryos, in npj Systems Biology and Applications, vol. 11, no. 1, pp. 57, 2025 DOI
- [4] U. Chandola, M. Gaudin, C. Trottier, L. Lavier-Aydat, E. Manirakiza, S. Menicot, E. Fischer, I. Louvet, T. Lacour, T. Chaumier, A. Tanaka, G. Pohnert, S. Chaffron, L. Tirichine. Non-cyanobacterial diazotrophs support the survival of marine microalgae in nitrogen-depleted environment, in Genome Biology, vol. 26, no. 1, pp. 146, 2025 DOI
- [5] E. Benoist, G. Fertin, G. Jean. The Exact Subset MultiCover problem, in Theoretical Computer Science, vol. 1024, pp. 114936, 2025 DOI
- [6] S. Ramondenc, D. Eveillard, K. Metfies, M. Iversen, E. Nöthig, D. Piepenburg, C. Hasemann, T. Soltwedel. Unveiling pelagic-benthic coupling associated with the biological carbon pump in the Fram Strait (Arctic Ocean), in Nature Communications, vol. 16, no. 1, pp. 840, 2025 DOI
- [7] S. Sow, W. van de Poll, R. Eveleth, J. Rich, H. Ducklow, P. Rozema, C. Luria, H. Bolhuis, M. Meredith, L. Amaral-Zettler, J. Engelmann. Spatial and temporal variation of Antarctic microbial interactions: a study around the west Antarctic Peninsula, in Environmental Microbiome, vol. 20, no. 1, pp. 21, 2025 DOI
- [8] É. Benoist, G. Jean, H. Rogniaux, G. Fertin, D. Tessier. SpecPeptidOMS Directly and Rapidly Aligns Mass Spectra on Whole Proteomes and Identifies Peptides That Are Not Necessarily Tryptic : Implications for Peptidomics, in Journal of Proteome Research, vol. 24, no. 4, pp. 2159-2172, 2025 DOI
- [9] J. Pierella Karlusich, K. Cosnier, L. Zinger, N. Henry, C. Nef, G. Bernard, E. Scalco, E. Dvorak, S. Acinas, M. Babin, P. Bork, E. Boss, C. Bowler, G. Cochrane, C. de Vargas, G. Gorsky, N. Grimsley, L. Guidi, D. Iudicone, O. Jaillon, S. Kandels, L. Karp-Boss, E. Karsenti, F. Not, H. Ogata, S. Pesant, N. Poulton, C. Sardet, S. Speich, L. Stemmann, M. Sullivan, S. Sunagawa, P. Wincker, F. Rocha Jimenez Vieira, E. Delage, S. Chaffron, S. Ovchinnikov, A. Zingone, C. Bowler. Patterns and drivers of diatom diversity and abundance in the global ocean, in Nature Communications, vol. 16, no. 1, pp. 3452, 2025 DOI
- [10] M. Boosten, C. Sant, O. da Silva, S. Chaffron, L. Guidi, L. Leclère. Independent transitions to fully planktonic life cycles shaped the global distribution of medusozoans in the epipelagic zone, in Proceedings of the National Academy of Sciences of the United States of America, vol. 122, no. 22, pp. e2415979122, 2025 DOI
- [11] A. Régimbeau, O. Aumont, C. Bowler, L. Guidi, G. Jackson, E. Karsenti, L. Mémery, A. Tagliabue, D. Eveillard. Unveiling the link between phytoplankton molecular physiology and biogeochemical cycling via genome-scale modeling, in Science Advances, vol. 11, no. 23, 2025 DOI
- [12] J. Houriet, P. Manwill, A. Magaña, V. Anderson, M. Beniddir, S. Bertrand, J. Choi, T. Clark, L. Foster, M. Halabalaki, A. Jarmusch, N. de Jonge, A. Khadilkar, J. Macmillan, C. Maier, L. Marney, G. Marti, E. Mikropoulou, D. Olivier-Jimenez, A. Perez, J. van der Hooft, M. Zdouc, R. Linington, N. Cech. Multilaboratory Untargeted Mass Spectrometry Metabolomics Collaboration to Identify Bottlenecks and Comprehensively Annotate A Single Dataset, in Analytical Chemistry, vol. 97, no. 30, pp. 16110-16122, 2025 DOI
- [13] L. Paré, P. Bordron, L. David, M. Mahé, A. Bihouée, D. Eveillard. HUMESS: integrating quantitative transcriptomic analysis and metabolic modeling to unveil condition-specific gene signatures, in Bioinformatics, vol. 41, no. 8, pp. btaf448, 2025 DOI
- [14] O. Esteban-Cantillo, A. Abreu, S. Bourgeois-Gironde, E. Wanek, U. Gurchani, D. Eveillard, R. Casati. Six key policy recommendations to advocate for marine conservation that matches the ocean’s dynamism, in npj Ocean Sustainability, vol. 4, 2025 DOI
- [15] H. Sarmento, P. Huber, C. Santos-Júnior, A. Abreu, T. Makhalanyane, N. Karenyi, E. Rocke, S. Acinas, L. Amaral-Zettler, M. Araujo, C. Arboleda-Baena, G. Bachi, D. Bănaru, É. Becker, M. Bellacicco, F. Benedetti, C. Bowler, B. Buongiorno Nardelli, L. Campese, D. Canu, U. Cardini, R. Casotti, S. Chaffron, D. Couet, H. Cruz de Carvalho, D. D’alelio, G. Dall’olmo, N. Dames, C. de Vargas, C. Delgado, C. Dimier, D. Eveillard, S. Faye, M. Flores, P. Galand, L. Gammage, J. Gasol, M. Gehlen, A. Green Koettker, V. Guinder, T. Heggeset, L. Heimbürger-Boavida, A. Hidas, C. Hörstmann, F. Ibarbalz, O. Jaillon, D. Johns, F. Jordán, P. Junger, K. Labadie, R. Laxenaire, S. Libralato, C. Longo, R. Lopes, M. Loschi, S. Mafwila, L. Maiorano, M. Meredith, E. Muxagata, G. Nguyen, S. Nicolau, P. Oliveira, L. Olivier, R. Palmela de Oliveira, N. Patin, P. Pita, G. Pohnert, A. Ruggiero, A. S. Freire, M. Saraceno, R. Schwamborn, A. Soccodato, C. Solidoro, D. Sousa, S. Speich, S. Sunagawa, A. Tagliabue, L. Thompson, R. Troublé, L. Veado, F. Vincent, M. Vogt, S. Zunino, S. Pesant, D. Iudicone. The southern gap in ocean microbiome science, in Ocean Microbiology, vol. 1, no. 1, pp. 6, 2025 DOI
- [16] D. Talmy, C. Howard-Varona, D. Eveillard, M. Covert, M. Sullivan. Viruses in multi-scale ocean models: challenges and opportunities, in Frontiers in Marine Science, vol. 12, 2025 DOI
Conférences internationales avec comité de lecture et actes
- [17] B. Quemeneur, A. Bihouée, S. Chaffron, C. Médigue, H. Ménager, A. Gaignard. A multi-modal and temporal antibiotic resistance knowledge graph, in SWAT4HCLS 2025 – 16th International SWAT4HCLS conference : Semantic Web Applications and Tools for Health Care and Life Sciences, Barcelone, Espagne, 2025
- [18] M. Kieffer, H. Chabane, P. Serrano Alvarado, K. Belhajjame. LP-4P : Link Prediction over Annotated Knowledge Graphs with Four Patterns, in K-CAP '25: Knowledge Capture Conference 2025, Dayton OH USA, états-Unis, 2025 DOI
Conférences nationales avec comité de lecture et actes
- [19] O. El Khettari, S. Quiniou, S. Chaffron. Summarization for Generative Relation Extraction in the Microbiome Domain, in 20e Conférence en Recherche d’Information et Applications (CORIA) 32ème Conférence sur le Traitement Automatique des Langues Naturelles (TALN) 27ème Rencontre des Étudiants Chercheurs en Informatique pour le Traitement Automatique des Langues (RECITAL) Les 18e Rencontres Jeunes Chercheurs en RI (RJCRI), Marseille, France, 2025
Theses et HDR
- [20] G. Fakih. Relâchement de requêtes SPARQL en présence de réification RDF, 2025 DOI
Autres publications
- [21] G. Jean, C. Lemaitre, M. Salson. SeqBIM 2025 Abstracts and Proceedings, in SeqBIM 2025, Nantes, France, 2025
- [22] N. Appel, J. Bourdon, N. Bousquet, J. Cohen, A. Genitrini, P. Georgeon, Y. Grandvalet, K. Jaffrès-Runser, A. Legrand, D. Markham, A. Muscholl, A. Paparrizou, L. Paulevé, M. Poss, M. Gradinariu Potop-Butucaru, J. Raymond, R. Rouvoy, Y. Sallent, P. Senellart, T. Seiller, Y. Song, A. Tchana, H. Waeselynck. Section 06 Sciences de l’information : fondements de l’informatique, calculs, algorithmes, représentations, exploitations, 2025
- [23] G. Castel, D. Meistermann, B. Bretin, J. Firmin, J. Blin, S. Loubersac, A. Bruneau, S. Chevolleau, S. Kilens, C. Chariau, A. Gaignerie, Q. Francheteau, H. Kagawa, E. Charpentier, L. Flippe, V. François-Campion, S. Haider, B. Dietrich, M. Knöfler, T. Arima, J. Bourdon, N. Rivron, D. Masson, T. Fournier, H. Okae, T. Freour, L. David. Generation of human induced trophoblast stem cells, 2025 DOI
- [24] G. Douglas, N. Tromas, M. Gaudin, P. Lypaczewksi, L. Bobay, B. Shapiro, S. Chaffron. Co-occurrence drives horizontal gene transfer among marine prokaryotes, 2025 DOI
- [25] A. Régimbeau, F. Tian, G. Smith, V. Riddell, C. Andreani, P. Bordron, M. Budinich, C. Howard-Varona, A. Larhlimi, E. Ser-Giacomi, C. Trottier, L. Guidi, S. Hallam, D. Iudicone, E. Karsenti, A. Maass, M. Sullivan, D. Eveillard. Planetary-scale heterotrophic microbial community modeling assesses metabolic synergy and viral impacts, 2025 DOI
- [26] L. Paré, P. Bordron, L. David, M. Mahé, A. Bihouée, D. Eveillard. HUMESS: Integrating Quantitative Transcriptomic Analysis and Metabolic Modeling to Unveil Condition-Specific Gene Signatures, 2025 DOI
- [27] A. Berthier, E. Benoist, G. Fertin, G. Jean, H. Rogniaux. Global Spectrum Interpretation (GSI): A global, integrative approach for the protein inference problem, in EuPA 2025, Saint-Malo, France, 2025
- [28] E. Benoist, G. Jean, H. Rogniaux, G. Fertin, D. Tessier. SpecPeptidOMS allows fast and without a priori peptide identification in a peptidomics context., in EuPA conference, Saint-Malo, France, 2025
- [29] B. Quemeneur, A. Bihouée, S. Chaffron, C. Médigue, H. Ménager, A. Gaignard. A multi-modal and temporal antibiotic resistance knowledge graph, in JOBIM 2025, Bordeaux, France, 2025
- [30] H. Lefeuvre, A. Bihouée, B. Batut, S. Chaffron, C. Médigue, P. Glaser. ABRomics-analysis : developing Metagenomic Workflows for National Antibiotic Resistance Surveillance Platform, in JOBIM, Bordeaux, France, 2025