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Collaborative network analysis for the interpretation of transcriptomics data in rare diseases, an application to Huntington’s disease

 Ozan Ozisik , Nazli Sila Kara , Tooba Abbassi-Daloii , Morgane Térézol , Núria Queralt-Rosinach , et al.
2023
Pré-publication, Document de travail hal-04255875v1

Refinement of the four-dimensional human heart atlas during the first trimester of gestation with rare and diverse cell states

 Kausar Samina , Herbane Marine , Marechal Elise , Fabienne Lescroart , Lenfant Nicolas , et al.
HCA Developmental and Pediatric Cell Atlas Meeting, Human Cell Atlas, Nov 2022, PARIS, France
Communication dans un congrès hal-04237856v1
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In skeletal muscle and neural crest cells, SMCHD1 regulates biological pathways relevant for Bosma syndrome and facioscapulohumeral dystrophy phenotype

 Camille Laberthonnière , Mégane Delourme , Raphaël Chevalier , Camille Dion , Benjamin Ganne , et al.
Nucleic Acids Research, 2023, ⟨10.1093/nar/gkad523⟩
Article dans une revue hal-04134959v1
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A molecular hypothesis to explain direct and inverse co-morbidities between Alzheimer’s Disease, Glioblastoma and Lung cancer

 Jon Sánchez-Valle , Hector Tejero , Kristina Ibáñez , José Luis Portero , Martin Krallinger , et al.
Scientific Reports, 2017, 7 (1), ⟨10.1038/s41598-017-04400-6⟩
Article dans une revue hal-01610984v1

Network analysis and protein function prediction with the PRODISTIN Web site

 Anaïs Baudot , Ouissem Souiai , C. Brun
Methods in Molecular Biology, 2012, 804, pp.313-26
Article dans une revue hal-01596219v1
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Integrative proteomic and phosphoproteomic profiling of prostate cell lines

 Maria Katsogiannou , Jean-Baptiste Boyer , Alberto Valdeolivas , Elisabeth Remy , Laurence Calzone , et al.
PLoS ONE, 2019, 14 (11), pp.e0224148. ⟨10.1371/journal.pone.0224148⟩
Article dans une revue hal-03614575v1
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Random walk with restart on multiplex and heterogeneous biological networks

 Alberto Valdeolivas , Laurent Tichit , Claire L. Navarro , Sophie Perrin , Gaelle Odelin , et al.
Bioinformatics, 2019, ⟨10.1101/134734⟩
Article dans une revue hal-01946427v1

No paradox, no progress: inverse cancer comorbidity in people with other complex diseases

 Rafael Tabarés-Seisdedos , Nancy Dumont , Anaïs Baudot , Jose M Valderas , Joan Climent , et al.
Lancet Oncology, 2011, 12 (6), ⟨10.1016/S1470-2045(11)70041-9⟩
Article dans une revue hal-01266785v1
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Molecular Evidence for the Inverse Comorbidity between Central Nervous System Disorders and Cancers Detected by Transcriptomic Meta-analyses

 Kristina Ibáñez , César Boullosa , Rafael Tabarés-Seisdedos , Anaïs Baudot , Alfonso Valencia
PLoS Genetics, 2014, 10 (2), pp.e1004173. ⟨10.1371/journal.pgen.1004173⟩
Article dans une revue hal-01266780v1
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AKT Signaling Modifies the Balance between Cell Proliferation and Migration in Neural Crest Cells from Patients Affected with Bosma Arhinia and Microphthalmia Syndrome

 Camille Laberthonnière , Elva-María Novoa-Del-Toro , Raphaël Chevalier , Natacha Broucqsault , Vanitha Venkoba Rao , et al.
Biomedicines, 2021, 9 (7), pp.751. ⟨10.3390/biomedicines9070751⟩
Article dans une revue hal-03280671v1
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miR-376a-3p and miR-376b-3p overexpression in Hutchinson-Gilford progeria fibroblasts inhibits cell proliferation and induces premature senescence

 Diane Frankel , Valerie Delecourt , Elva-María Novoa-Del-Toro , Jérôme Robin-Ducellier , Coraline Airault , et al.
iScience, 2022, 25 (2), pp.103757. ⟨10.1016/j.isci.2022.103757⟩
Article dans une revue hal-03788582v1

The functional landscape of Hsp27 reveals new cellular processes such as DNA repair and alternative splicing and proposes novel anticancer targets.

 Maria Katsogiannou , Claudia Andrieu , Virginie Baylot , Anaïs Baudot , Nelson J Dusetti , et al.
Molecular and Cellular Proteomics, 2014, pp.3585-601. ⟨10.1074/mcp.M114.041228⟩
Article dans une revue hal-01104661v1
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Zoo guide to network embedding

 A Baptista , R J Sánchez-García , A Baudot , G Bianconi
Journal of Physics: Complexity, 2023, 4 (4), pp.042001. ⟨10.1088/2632-072X/ad0e23⟩
Article dans une revue hal-04538874v1
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MultiVERSE: a multiplex and multiplex-heterogeneous network embedding approach

 Léo Pio-Lopez , Alberto Valdeolivas , Laurent Tichit , Élisabeth Remy , Anaïs Baudot
Scientific Reports, 2021, 11 (1), ⟨10.1038/s41598-021-87987-1⟩
Article dans une revue hal-03359094v2
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The gastrin and cholecystokinin receptors mediated signaling network: a scaffold for data analysis and new hypotheses on regulatory mechanisms.

 Sushil Tripathi , Åsmund Flobak , Konika Chawla , Anaïs Baudot , Torunn Bruland , et al.
BMC Systems Biology, 2014, 9, pp.40. ⟨10.1186/s12918-015-0181-z⟩
Article dans une revue hal-01221589v1

Refinement of the four-dimensional human heart atlas during the first trimester of gestation with rare and diverse cell states

 Kausar Samina , Herbane Marine , Marechal Elise , Fabienne Lescroart , Lenfant Nicolas , et al.
Cardiovascular Development and Regeneration, May 2022, Marseille, France
Communication dans un congrès hal-04237843v1
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A multilevel screening pipeline in zebrafish identifies therapeutic drugs for GAN

 Léa Lescouzères , Cédric Hassen-Khodja , Anaïs Baudot , Benoît Bordignon , Pascale Bomont
EMBO Molecular Medicine, 2023, ⟨10.15252/emmm.202216267⟩
Article dans une revue hal-04113353v1

SMCHD1 variants may induce variegated expression in Facio Scapulo Humeral Dystophy and Bosma Arhinia and microphtalmia syndrome

 Camille Laberthonnière , Raphaël Chevalier , Camille Dion , Mégane Delourme , David Hirst , et al.
2022
Pré-publication, Document de travail hal-03634209v1
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Prediction of Disease-associated Genes by advanced Random Walk with Restart on Multiplex and Heterogeneous Biological Networks

 Alberto Valdeolivas , Élisabeth Remy , Laurent Tichit , Gaëlle Odelin , Claire Navarro , et al.
JOBIM 2017, Jul 2017, Lille, France
Communication dans un congrès hal-03582849v1
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Interpreting molecular similarity between patients as a determinant of disease comorbidity relationships

 Jon Sánchez-Valle , Hector Tejero , José María Fernández , David Juan , Beatriz Urda-García , et al.
Nature Communications, 2020, 11 (1), pp.2854. ⟨10.1038/s41467-020-16540-x⟩
Article dans une revue inserm-02878879v1
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Editorial: Direct and Inverse Comorbidities Between Complex Disorders

 Rafael Tabarés-Seisdedos , Anaïs Baudot
Frontiers in Physiology, 2016, 7, ⟨10.3389/fphys.2016.00117⟩
Article dans une revue hal-01352722v1
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Assessment of network module identification across complex diseases

 Sarvenaz Choobdar , Mehmet Ahsen , Jake Crawford , Mattia Tomasoni , Tao Fang , et al.
Nature Methods, 2019, 16 (9), pp.843-852. ⟨10.1038/s41592-019-0509-5⟩
Article dans une revue hal-02333148v1

Facioscapulohumeral dystrophy weakened sarcomeric contractility is mimicked in induced pluripotent stem cells‐derived innervated muscle fibres

 Camille Laberthonnière , Elva-María Novoa-Del-Toro , Mégane Delourme , Raphaël Chevalier , Natacha Broucqsault , et al.
Journal of Cachexia, Sarcopenia and Muscle, 2022, 13 (1), pp.621-635. ⟨10.1002/jcsm.12835⟩
Article dans une revue hal-03586975v1
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Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer

 Forés-Martos Jaume , Catalá-López Ferrán , Sánchez-Valle Jon , Ibáñez Kristina , Tejero Héctor , et al.
Molecular Autism, 2019, 10 (1), ⟨10.1186/s13229-019-0262-8⟩
Article dans une revue hal-02097145v1
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A multi-objective genetic algorithm to find active modules in multiplex biological networks

 Elva-María Novoa-Del-Toro , Efrén Mezura-Montes , Matthieu Vignes , Morgane Térézol , Frédérique Magdinier , et al.
PLoS Computational Biology, 2021, 17 (8), pp.e1009263. ⟨10.1371/journal.pcbi.1009263⟩
Article dans une revue hal-03372492v1
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Universal multilayer network exploration by random walk with restart

 Anthony Baptista , Aitor Gonzalez , Anaïs Baudot
Communications Physics, 2022, 5 (1), pp.170. ⟨10.1038/s42005-022-00937-9⟩
Article dans une revue hal-03800682v1
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A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks

 Elva-María Novoa-Del-Toro , Efrén Mezura-Montes , Matthieu Vignes , Frédérique Magdinier , Laurent Tichit , et al.
2020
Pré-publication, Document de travail hal-02997031v1
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Tracking clusters of patients over time enables extracting information from medico-administrative databases

 Judith Lambert , Anne-Louise Leutenegger , Anne-Sophie Jannot , Anaïs Baudot
Journal of Biomedical Informatics, 2023, 139, pp.104309. ⟨10.1016/j.jbi.2023.104309⟩
Article dans une revue hal-04027783v1

Tracking Temporal Clusters from Patient Networks

 Judith Lambert , Anne-Louise Leutenegger , Anne-Sophie Jannot , Anaïs Baudot
Challenges of Trustable AI and Added-Value on Health, IOS Press, 2022, Studies in Health Technology and Informatics, ⟨10.3233/SHTI220427⟩
Chapitre d'ouvrage hal-03911967v1
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Tracking patient clusters over time enables to extract all the information available in the medico-administrative databases

 Judith Lambert , Anne-Louise Leutenegger , Anne-Sophie Jannot , Anaïs Baudot
2022
Pré-publication, Document de travail hal-03796086v1
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