21 documents

Journal articles

  • Cédric Usureau, Edgar Lefèvre, Isabelle Top, Macha Nikolski, Pauline Varlet, et al.. Antibodies against HLA cross-reactivity groups: From single antigen bead assay to immunoinformatics interpretation of epitopes. Molecular Immunology, Elsevier, 2021, 133, pp.154-162. ⟨10.1016/j.molimm.2021.02.020⟩. ⟨hal-03169872⟩
  • Julie Giraud, Domitille Chalopin, Jean-Frédéric Blanc, Maya Saleh. Hepatocellular Carcinoma Immune Landscape and the Potential of Immunotherapies. Frontiers in Immunology, Frontiers, 2021, 12, ⟨10.3389/fimmu.2021.655697⟩. ⟨hal-03257979⟩
  • Matthieu Lagardère, Ingrid Chamma, Emmanuel Bouilhol, Macha Nikolski, Olivier Thoumine. FluoSim: simulator of single molecule dynamics for fluorescence live-cell and super-resolution imaging of membrane proteins. Scientific Reports, Nature Publishing Group, 2020, 10, ⟨10.1038/s41598-020-75814-y⟩. ⟨hal-03010357⟩
  • Fabienne Soulet, Clément Bodineau, Katarzyna B., Jean Descarpentrie, Isabel D. Alves, et al.. ELA/APELA precursor cleaved by furin displays tumor suppressor function in renal cell carcinoma through mTORC1 activation. JCI Insight, American Society for Clinical Investigation, 2020, 5 (14), ⟨10.1172/jci.insight.129070⟩. ⟨hal-03084443⟩
  • Fabienne Soulet, Clément Bodineau, Katarzyna Hooks, Jean Descarpentrie, Isabel Alves, et al.. Furin-cleaved ELA/Apela precursor displays tumor suppressor function in renal cell carcinoma through mTORC1 activation. JCI Insight, American Society for Clinical Investigation, 2020, ⟨10.1172/jci.insight.129070⟩. ⟨hal-02872084⟩
  • Adriana Salcedo, Maxime Tarabichi, Shadrielle Melijah G. Espiritu, Amit Deshwar, Matei David, et al.. A community effort to create standards for evaluating tumor subclonal reconstruction. Nature Biotechnology, Nature Publishing Group, 2020, 38 (1), pp.97-107. ⟨10.1038/s41587-019-0364-z⟩. ⟨hal-02438695⟩
  • Katarzyna Hooks, Maureen O'Malley. Contrasting Strategies: Human Eukaryotic versus Bacterial Microbiome Research. Journal of Eukaryotic Microbiology, Wiley, 2019, ⟨10.1111/jeu.12766⟩. ⟨hal-02306562⟩
  • Thomas Daubon, Joris Guyon, Anne-Aurélie Raymond, Benjamin Dartigues, Justine Rudewicz, et al.. The invasive proteome of glioblastoma revealed by laser-capture microdissection. Neuro-Oncology Advances, Society for NeuroOncology (SNO); the European Association of Neuro-Oncology(EANO); and Oxford University Press, 2019, 1 (1), pp.1-12. ⟨10.1093/noajnl/vdz029⟩. ⟨hal-02347439⟩
  • Anaïs Soula, Mélissa Valere, María-José López-González, Vicky Ury-Thiery, Alexis Groppi, et al.. Small RNA-Seq reveals novel miRNAs shaping the transcriptomic identity of rat brain structures. Life Science Alliance, Life Science Alliance LLC, 2018, 1 (5), pp.e201800018. ⟨hal-01944573⟩
  • Claudine Boiziau, Macha Nikolski, Elodie Mordelet, Justine Aussudre, Karina Vargas-Sanchez, et al.. A Peptide Targeting Inflammatory CNS Lesions in the EAE Rat Model of Multiple Sclerosis. Inflammation, Springer Verlag, 2018, ⟨10.1007/s10753-018-0748-0⟩. ⟨hal-01727277⟩
  • Thomas Bazin, Katarzyna Hooks, Thomas Barnetche, Marie-Elise Truchetet, Raphaël Enaud, et al.. Microbiota Composition May Predict Anti-Tnf Alpha Response in Spondyloarthritis Patients: an Exploratory Study. Scientific Reports, Nature Publishing Group, 2018, 8 (1), pp.5446. ⟨10.1038/s41598-018-23571-4⟩. ⟨hal-01760163⟩
  • Katarzyna Hooks, Jan Pieter Konsman, Maureen O'Malley. Microbiota-gut-brain research: a critical analysis. Behavioral and Brain Sciences, Cambridge University Press (CUP), In press, pp.1 - 40. ⟨10.1017/S0140525X18002133⟩. ⟨hal-01893076⟩
  • E Henriet, Aa Hammoud, Jw Dupuy, B Dartigues, Z Ezzoukry, et al.. Argininosuccinate synthase 1 (ASS1): A marker of unclassified hepatocellular adenoma and high bleeding risk. Hepatology, Wiley-Blackwell, 2017, ⟨10.1002/hep.29336⟩. ⟨hal-01550711⟩
  • Justine Rudewicz, Hayssam Soueidan, Raluca Uricaru, Hervé Bonnefoi, Richard Iggo, et al.. MICADo - Looking for mutations in targeted PacBio cancer data: an alignment-free method. Frontiers in Genetics, Frontiers, 2016, ⟨10.3389/fgene.2016.00214⟩. ⟨hal-01409750⟩
  • Mohammed El-Kebir, Hayssam Soueidan, Thomas Hume, Daniela Beisser, Marcus Dittrich, et al.. xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model. Bioinformatics, Oxford University Press (OUP), 2015, 31 (19), ⟨10.1093/bioinformatics/btv316⟩. ⟨hal-01248545⟩
  • Hayssam Soueidan, Florence Maurier, Alexis Groppi, Pascal Sirand-Pugnet, Florence Tardy, et al.. Finishing bacterial genome assemblies with Mix. BMC Bioinformatics, BioMed Central, 2013, pp.doi:10.1186/1471-2105-14-S15-S16. ⟨hal-00879163⟩

Conference papers

  • R. Enaud, T. Bazin, A. Barré, T. Barnetche, Cédric Hubert, et al.. Impact of intravenous antibiotics on the gut microbiota in children with cystic fibrosis. 40th European Cystic Fibrosis Conference, 2017, Sevilla, Spain. ⟨10.1016/S1569-1993(17)30537-4⟩. ⟨hal-01534674⟩

Poster communications

  • Grigorii Sukhorukov, Macha Nikolski. VirHunter: a deep learning-based method for detection of novel viruses in plant sequencing data. PlantGen 2021, Jun 2021, Novosibirsk, Russia. ⟨hal-03271424⟩
  • Kaoutar Daoud Hiri, Johan Rollin, Sukhorukov Grigorii, Macha Nikolski, Sébastien Massart, et al.. INEXTVIR: High throughput sequencing of the virome of agricultural crops and ecosystems across Europe. ESCS-ECCB 2020, Sep 2020, Barcelona, Spain. ⟨hal-03271520⟩
  • A. Abouhammoud, E. Henriet, J.-W. Dupuy, B. Dartigues, Z. Ezzoukhry, et al.. Proteomic analysis identifies argininosuccinate synthase 1 as a useful biomarker for hepatocellular adenoma classification and patient management. The International Liver Congress, 2017, Amsterdam, Netherlands. 2017, ⟨10.1016/S0168-8278(17)30758-4⟩. ⟨hal-01528470⟩

Book sections

  • Derek Skillings, Katarzyna Hooks. Microbiomes and Holobionts. Reference Module in Earth Systems and Environmental Sciences, 2018. ⟨hal-01893113⟩