26 documents

Journal articles

  • Lindsay Cooley, Justine Rudewicz, Wilfried Souleyreau, Andrea Emanuelli, Arturo Alvarez-Arenas, et al.. Experimental and computational modeling for signature and biomarker discovery of renal cell carcinoma progression. Molecular Cancer, BioMed Central, 2021, 20 (1), ⟨10.1186/s12943-021-01416-5⟩. ⟨hal-03390517⟩
  • Marie Kostine, Eleonora Mauric, Alice Tison, Thomas Barnetche, Aurélien Barre, et al.. Baseline co-medications may alter the anti-tumoural effect of checkpoint inhibitors as well as the risk of immune-related adverse events. European Journal of Cancer, Elsevier, 2021, 157, pp.474-484. ⟨10.1016/j.ejca.2021.08.036⟩. ⟨hal-03376828⟩
  • Anca Flavia Savulescu, Emmanuel Bouilhol, Nicolas Beaume, Macha Nikolski. Prediction of RNA subcellular localization: learning from heterogeneous data sources. iScience, Elsevier, 2021, pp.103298. ⟨10.1016/j.isci.2021.103298⟩. ⟨hal-03388153⟩
  • Alexis Groppi, Shuo Liu, A. Cornille, David Tricon, Quynh Trang Bui, et al.. Population genomics of apricots unravels domestication history and adaptive events. Nature Communications, Nature Publishing Group, 2021, 12 (1), pp.3956. ⟨10.1038/s41467-021-24283-6⟩. ⟨hal-03282504⟩
  • 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⟩
  • Anca Savulescu, Robyn Brackin, Emmanuel Bouilhol, Benjamin Dartigues, Jonathan Warrell, et al.. Interrogating RNA and protein spatial subcellular distribution in smFISH data with DypFISH. Cell Reports Methods, Cell Press Elsevier, In press, ⟨10.1016/j.crmeth.2021.100068⟩. ⟨hal-03349483⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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⟩