index - Computational Biology and Bioinformatics

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

Valentina Pacella, Victor Nozais, Lia Talozzi, Majd Abdallah, Demian Wassermann, et al.. The morphospace of the brain-cognition organisation. Nature Communications, 2024, 15 (1), pp.8452. ⟨10.1038/s41467-024-52186-9⟩. ⟨hal-04714643⟩
Johanna Galvis, Joris Guyon, Benjamin Dartigues, Helge Hecht, Björn Grüning, et al.. DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data. Bioinformatics, 2024, 40 (5), pp.btae282. ⟨10.1093/bioinformatics/btae282⟩. ⟨hal-04591269⟩
Stéphane Leon, Vincent Simon, Thomas Lee, Lukas Steuernagel, Samantha Clark, et al.. Single cell tracing of Pomc neurons reveals recruitment of ‘Ghost’ subtypes with atypical identity in a mouse model of obesity. Nature Communications, 2024, 15 (1), pp.3443. ⟨10.1038/s41467-024-47877-2⟩. ⟨hal-04591277⟩
Julie Giraud, Domitille Chalopin, Eloïse Ramel, Thomas Boyer, Atika Zouine, et al.. THBS1+ myeloid cells expand in SLD hepatocellular carcinoma and contribute to immunosuppression and unfavorable prognosis through TREM1. Cell Reports, 2024, 43 (2), pp.113773. ⟨10.1016/j.celrep.2024.113773⟩. ⟨hal-04473035⟩
Slim Karkar, Ashwini Sharma, Carl Herrmann, Yuna Blum, Magali Richard. DECOMICS, a shiny application for unsupervised cell type deconvolution and biological interpretation of bulk omic data. Bioinformatics Advances, 2024, 4 (1), pp.vbae136. ⟨10.1093/bioadv/vbae136⟩. ⟨hal-04660629v2⟩
Valentine Chirokoff, Sylvie Berthoz, Melina Fatseas, David Misdrahi, Maud Dupuy, et al.. Identifying the role of (dis)inhibition in the vicious cycle of substance use through ecological momentary assessment and resting-state fMRI. Translational Psychiatry, 2024, 14 (1), pp.260. ⟨10.1038/s41398-024-02949-1⟩. ⟨hal-04804003⟩
Macha Nikolski, Eivind Hovig, Fatima Al-Shahrour, Niklas Blomberg, Serena Scollen, et al.. Roadmap for a European cancer data management and precision medicine infrastructure. Nature Cancer, In press, ⟨10.1038/s43018-023-00717-6⟩. ⟨hal-04473020⟩
Emmanuel Bouilhol, Thierno Barry, Florian Levet, Anne Beghin, Virgile Viasnoff, et al.. SalienceNet: An Unsupervised Image-to-Image Translation Method for Nuclei Saliency Enhancement in Microscopy Images. 10th International Conference on Bioimaging, Feb 2023, Lisbon, Portugal. pp.41-51, ⟨10.5220/0011623500003414⟩. ⟨hal-04040453⟩
Fabien Pierron, Guillemine Daffe, Flore Daramy, Débora Heroin, Aurélien Barré, et al.. Transgenerational endocrine disruptor effects of cadmium in zebrafish and contribution of standing epigenetic variation to adaptation. Journal of Hazardous Materials, 2023, 455, pp.131579. ⟨10.1016/j.jhazmat.2023.131579⟩. ⟨hal-04093643⟩
Joris Guyon, Ignacio Fernandez-Moncada, Claire Larrieu, Cyrielle Bouchez, Antonio Pagano Zottola, et al.. Lactate dehydrogenases promote glioblastoma growth and invasion via a metabolic symbiosis. EMBO Molecular Medicine, 2022, 14 (12), pp.4316. ⟨10.15252/emmm.202115343⟩. ⟨hal-04288691⟩
Edgar Lefevre, Emmanuel Bouilhol, Antoine Chauvière, Wilfried Souleyreau, Marie-Alix Derieppe, et al.. Deep learning model for automatic segmentation of lungs and pulmonary metastasis in small animal MR images. Frontiers in Bioinformatics, 2022, 2, pp.999700. ⟨10.3389/fbinf.2022.999700⟩. ⟨hal-03821458⟩
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⟩
Fabien Pierron, Débora Heroin, Guillemine Daffe, Flore Daramy, Aurélien Barré, et al.. Genetic and epigenetic interplay allows rapid transgenerational adaptation to metal pollution in zebrafish. Environmental Epigenetics, 2022, 8 (1), ⟨10.1093/eep/dvac022⟩. ⟨hal-04065814⟩
Faten Merhi, Karla Alvarez-Valadez, Jenifer Trepiana, Claire Lescoat, Alexis Groppi, et al.. Targeting CAMKK2 and SOC Channels as a Novel Therapeutic Approach for Sensitizing Acute Promyelocytic Leukemia Cells to All-Trans Retinoic Acid. Cells, 2021, 10 (12), pp.3364. ⟨10.3390/cells10123364⟩. ⟨hal-03457279⟩
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, 2021, 20, pp.136. ⟨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, 2021, 157, pp.474-484. ⟨10.1016/j.ejca.2021.08.036⟩. ⟨hal-03671495⟩
Anca Flavia Savulescu, Emmanuel Bouilhol, Nicolas Beaume, Macha Nikolski. Prediction of RNA subcellular localization: learning from heterogeneous data sources. iScience, 2021, pp.103298. ⟨10.1016/j.isci.2021.103298⟩. ⟨hal-03388153⟩
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⟩
Julie Giraud, Domitille Chalopin, Jean-Frédéric Blanc, Maya Saleh. Hepatocellular Carcinoma Immune Landscape and the Potential of Immunotherapies. Frontiers in Immunology, 2021, 12, ⟨10.3389/fimmu.2021.655697⟩. ⟨hal-03257979⟩
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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