index - Computational Biology and Bioinformatics

Publications of the Computational Biology and Bioinformatics team at the IBGC, CNRS (Bordeaux, France)

Fabien Pierron, Débora Heroin, Guillemine Daffe, Flore Daramy, Aurélien Barré, et al.. Genetic and epigenetic interplay allows rapid transgenerational adaption to metal pollution in zebrafish. Environmental Epigenetics, 2022, 8 (1), ⟨10.1093/eep/dvac022⟩. ⟨hal-03832262⟩
Grigorii Sukhorukov, Maryam Khalili, Olivier Gascuel, Thierry Candresse, Armelle Marais, et al.. VirHunter: A Deep Learning-Based Method for Detection of Novel RNA Viruses in Plant Sequencing Data. Frontiers in Bioinformatics, 2022, 2, pp.867111. ⟨10.3389/fbinf.2022.867111⟩. ⟨hal-03671482⟩
Emmanuel Bouilhol, Anca Flavia Savulescu, Edgar Lefevre, Benjamin Dartigues, Robyn Brackin, et al.. DeepSpot: a deep neural network for RNA spot enhancement in smFISH microscopy images. Biological Imaging, 2022, pp.1-18. ⟨10.1017/S2633903X22000034⟩. ⟨hal-03659677⟩
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, 2021, 1 (5), pp.100068. ⟨10.1016/j.crmeth.2021.100068⟩. ⟨hal-03349483⟩
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, 2021, 12 (1), pp.3956. ⟨10.1038/s41467-021-24283-6⟩. ⟨hal-03282504⟩
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⟩
Paôline Laurent, Benoit Allard, Pauline Manicki, Valérie Jolivel, Emeline Levionnois, et al.. TGFβ promotes low IL10-producing ILC2 with profibrotic ability involved in skin fibrosis in systemic sclerosis. Annals of the Rheumatic Diseases, 2021, pp.annrheumdis-2020-219748. ⟨10.1136/annrheumdis-2020-219748⟩. ⟨hal-03386391⟩
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, 2020, 10, ⟨10.1038/s41598-020-75814-y⟩. ⟨hal-03010357⟩
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⟩
Fabienne Soulet, Clément Bodineau, Katarzyna Hooks 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, 2020, 5 (14), ⟨10.1172/jci.insight.129070⟩. ⟨hal-03084443⟩
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, 2020, 38 (1), pp.97-107. ⟨10.1038/s41587-019-0364-z⟩. ⟨hal-02438695⟩
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, 2019, 1 (1), pp.1-12. ⟨10.1093/noajnl/vdz029⟩. ⟨hal-02347439⟩
Thomas Bazin, Katarzyna B 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, 2018, 8 (1), pp.5446. ⟨10.1038/s41598-018-23571-4⟩. ⟨hal-01760163⟩

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