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Études d'association génome entier guidées par des réseaux

Héctor Climente González
Bio-informatique [q-bio.QM]. Université Paris sciences et lettres, 2020. Français. ⟨NNT : 2020UPSLM001⟩
Theses tel-03270879v1
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Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network

Andrei Zinovyev , Urszula Czerwinska , Laura Cantini , Emmanuel Barillot , Klaus M. Frahm , et al.
PLoS Computational Biology, 2020, ⟨10.1371/journal.pcbi.1007652⟩
Journal articles hal-02114063v1
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Synthesis and Simulation of Ensembles of Boolean Networks for Cell Fate Decision

Stéphanie Chevalier , Vincent Noël , Laurence Calzone , Andrei Zinovyev , Loïc Paulevé
18th International Conference on Computational Methods in Systems Biology (CMSB), 2020, Online, Germany. pp.193--209, ⟨10.1007/978-3-030-60327-4_11⟩
Conference papers hal-02898849v2
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BAP1 complex promotes transcription by opposing PRC1-mediated H2A ubiquitylation

Antoine Campagne , Ming-Kang Lee , Dina Zielinski , Audrey A. Michaud , Stéphanie Le Corre , et al.
Nature Communications, 2019, 10, pp.348. ⟨10.1038/s41467-018-08255-x⟩
Journal articles hal-02008379v1
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New insight for pharmacogenomics studies from the transcriptional analysis of two large-scale cancer cell line panels (vol 7, 15126, 2016)

Benjamin Sadacca , Anne-Sophie Hamy , C. Laurent , Pierre Gestraud , Hélène Bonsang-Kitzis , et al.
Scientific Reports, 2018, 8, ⟨10.1038/s41598-018-36812-3⟩
Journal articles hal-02619813v1
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Model learning to identify systemic regulators of the peripheral circadian clock

Julien Martinelli , Sandrine Dulong , Xiao-Mei Li , Michèle Teboul , Sylvain Soliman , et al.
Bioinformatics, 2021, 37 (Supplement_1), pp.9. ⟨10.1093/bioinformatics/btab297⟩
Journal articles hal-03183579v1
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TUMOSPEC: A Nation-Wide Study of Hereditary Breast and Ovarian Cancer Families with a Predicted Pathogenic Variant Identified through Multigene Panel Testing

Fabienne Lesueur , Séverine Eon-Marchais , Sarah Bonnet-Boissinot , Juana Beauvallet , Marie-Gabrielle Dondon , et al.
Cancers, 2021, 13 (15), pp.3659. ⟨10.3390/cancers13153659⟩
Journal articles hal-03345372v1
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Machine learning approaches for drug virtual screening

Benoit Playe
Bioinformatics [q-bio.QM]. Université Paris sciences et lettres, 2019. English. ⟨NNT : 2019PSLEM010⟩
Theses tel-02186833v1
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Mechanical induction of the tumorigenic b-catenin pathway by tumour growth pressure

Maria Elena Fernandez-Sanchez , Sandrine Barbier , Joanne Whitehead , Gaelle Bealle , Aude Michel , et al.
Nature, 2015, 523 (7558), pp.92-95. ⟨10.1038/nature14329⟩
Journal articles inserm-02441063v1
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Identification de facteurs génétiques modifiant le risque de cancer chez les porteuses d'une mutation constitutionnelle d'ATM & profil tumoral des tumeurs du sein associées à une perte de fonction d'ATM.

Anne-Laure Renault
Biochimie, Biologie Moléculaire. Université Paris Saclay (COmUE), 2017. Français. ⟨NNT : 2017SACLS389⟩
Theses tel-01721322v1
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PointFISH -- learning point cloud representations for RNA localization patterns

Arthur Imbert , Florian Mueller , Thomas Walter
Preprints, Working Papers, ... hal-04029994v1
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Giga-SSL: Self-Supervised Learning for Gigapixel Images

Tristan Lazard , Marvin Lerousseau , Etienne Decencière , Thomas Walter
Preprints, Working Papers, ... hal-04030020v1
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Supercritical Fluid Chromatography of Drugs: Parallel Factor Analysis for Column Testing in a Wide Range of Operational Conditions

Ramia Z Al Bakain , Yahya Al-Degs , Bertyl Andri , Didier Thiébaut , Jérôme Vial , et al.
Journal of Analytical Methods in Chemistry, 2017, 2017, pp.1 - 13. ⟨10.1155/2017/5340601⟩
Journal articles hal-04018391v1
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Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes

Yuvia A Pérez-Rico , Valentina Boeva , Allison C Mallory , Angelo Bitetti , Sara Majello , et al.
Genome Research, 2016, 27 (2), pp.259 - 268. ⟨10.1101/gr.203679.115⟩
Journal articles hal-03983132v1
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Machine learning for single-cell genomics data analysis

Félix Raimundo , Laetitia Meng-Papaxanthos , Céline Vallot , Jean-Philippe Vert
Current Opinion in Systems Biology, 2021, 26, pp.64-71. ⟨10.1016/j.coisb.2021.04.006⟩
Journal articles hal-03510346v1
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An interactive murine single-cell atlas of the lung responses to radiation injury

Sandra Curras-Alonso , Juliette Soulier , Thomas Defard , Christian Weber , Sophie Heinrich , et al.
Nature Communications, 2023, 14 (1), pp.2445. ⟨10.1038/s41467-023-38134-z⟩
Journal articles hal-04092147v1
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LOTUS: a single-and multi-task machine-learning algorithm for the prediction of cancer driver genes

Olivier Collier , Véronique Stoven , Jean-Philippe Vert
Preprints, Working Papers, ... hal-01857394v2
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Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C

Ferhat Ay , Thanh H. Vu , Michael J. Zeitz , Nelle Varoquaux , Jan E. Carette , et al.
BMC Genomics, 2015, 16, pp.121. ⟨10.1186/s12864-015-1236-7⟩
Journal articles hal-01152400v1
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Transcriptome analysis of Wnt3a-treated triple-negative breast cancer cells

Sylvie Maubant , Bruno Tesson , Virginie Maire , Mengliang Ye , Guillem Rigaill , et al.
PLoS ONE, 2015, 10 (4), 26 p. ⟨10.1371/journal.pone.0122333⟩
Journal articles hal-02639667v1
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A polygenic risk score for multiple myeloma risk prediction

Federico Canzian , Chiara Piredda , Angelica Macauda , Daria Zawirska , Niels Frost Andersen , et al.
European Journal of Human Genetics, 2021, Online ahead of print. ⟨10.1038/s41431-021-00986-8⟩
Journal articles inserm-03480934v1
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Dosiomics-Based Prediction of Radiation-Induced Valvulopathy after Childhood Cancer

Stefania Chounta , Rodrigue S. Allodji , Maria Vakalopoulou , Mahmoud Bentriou , Duyen Thi Do , et al.
Cancers, 2023, 15 (12), ⟨10.3390/cancers15123107⟩
Journal articles hal-04191649v1
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Role of DNA Repair Variants and Diagnostic Radiology Exams in Differentiated Thyroid Cancer Risk: A Pooled Analysis of Two Case–Control Studies

Monia Zidane , Thérèse Truong , Fabienne Lesueur , Constance Xhaard , Emilie Cordina-Duverger , et al.
Cancer Epidemiology, Biomarkers and Prevention, 2021, 30 (6), pp.1208-1217. ⟨10.1158/1055-9965.EPI-20-1142⟩
Journal articles hal-03378112v1
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GENESIS: a French national resource to study the missing heritability of breast cancer

Olga M Sinilnikova , Marie-Gabrielle Dondon , Séverine Eon-Marchais , Francesca Damiola , Laure Barjhoux , et al.
BMC Cancer, 2016, 16 (1), pp.606 - 606. ⟨10.1186/s12885-015-2028-9⟩
Journal articles hal-01662200v1
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Dynamical Boolean Modeling of Immunogenic Cell Death

Andrea Checcoli , Jonathan Pol , Aurelien Naldi , Vincent Noël , Emmanuel Barillot , et al.
Frontiers in Physiology, 2020, 11, pp.590479. ⟨10.3389/fphys.2020.590479⟩
Journal articles hal-03050475v1
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Prediction of Mutations to Control Pathways Enabling Tumour Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial)

Nicolas Levy , Aurélien Naldi , Céline Hernandez , Gautier Stoll , Denis Thieffry , et al.
Frontiers in Physiology, 2018, 9, pp.787. ⟨10.1101/319780⟩
Journal articles hal-01809081v1
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Setting the basis of best practices and standards for curation and annotation of logical models in biology—highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop

Anna Niarakis , Martin Kuiper , Marek Ostaszewski , Rahuman Malik Sheriff , Cristina Casals-Casas , et al.
Briefings in Bioinformatics, 2021, 22 (2), pp.1848--1859. ⟨10.1093/bib/bbaa046⟩
Journal articles hal-02549796v1
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A high-risk retinoblastoma subtype with stemness features, dedifferentiated cone states and neuronal/ganglion cell gene expression

Jing Liu , Daniela Ottaviani , Meriem Sefta , Céline Desbrousses , Elodie Chapeaublanc , et al.
Nature Communications, 2021, 12 (1), pp.1-20. ⟨10.1038/s41467-021-25792-0⟩
Journal articles hal-03374490v1
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Fibroblast Heterogeneity and Immunosuppressive Environment in Human Breast Cancer

Ana Costa , Yann Kieffer , Alix Scholer-Dahirel , Floriane Pelon , Brigitte Bourachot , et al.
Cancer Cell, 2018, 33 (3), pp.463-479.e10. ⟨10.1016/j.ccell.2018.01.011⟩
Journal articles inserm-02437793v1
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Modeling time-varying exposure using inverse probability of treatment weights

Nathalie Graffeo , Aurélien Latouche , Ronald B Geskus , Sylvie Chevret
Biometrical Journal, 2018, 60 (2), pp.323-332. ⟨10.1002/bimj.201600223⟩
Journal articles inserm-01982183v1
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Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration

David P A Cohen , Loredana Martignetti , Sylvie Robine , Emmanuel Barillot , Andrei Zinovyev , et al.
PLoS Computational Biology, 2015, 11 (11), pp.e1004571. ⟨10.1371/journal.pcbi.1004571⟩
Journal articles inserm-02141625v1