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Genetic markers and phosphoprotein forms of beta-catenin pβ-Cat552 and pβ-Cat675 are prognostic biomarkers of cervical cancer

Suzy M Scholl , Jonas Beal , Leanne de Koning , Elodie Girard , Marina Popovic et al.
EBioMedicine, 2020, 61, pp.103049. ⟨10.1016/j.ebiom.2020.103049⟩
Journal articles hal-03492821v1
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Heterogeneity of neuroblastoma cell identity defined by transcriptional circuitries

Valentina Boeva , Caroline Louis-Brennetot , Agathe Peltier , Simon Durand , Cecile Pierre-Eugene et al.
Nature Genetics, 2017, 49 (9), pp.1408-1413. ⟨10.1038/ng.3921⟩
Journal articles hal-01741718v1
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Variation in breast cancer risk associated with factors related to pregnancies according to truncating mutation location, in the French National BRCA1/2 carrier cohort (GENEPSO).

Julie Lecarpentier , Catherine Noguès , Emmanuelle Mouret-Fourme , Marion Gauthier-Villars , Christine Lasset et al.
Breast Cancer Research, 2012, 14 (4), pp.R99. ⟨10.1186/bcr3218⟩
Journal articles inserm-00724092v1

Nuclei segmentation in histopathology images using deep neural networks

Peter Naylor , Marik Laé , Fabien Reyal , Thomas Walter
2017 IEEE 14th International Symposium on Biomedical Imaging (ISBI 2017), 2017, Melbourne, Australia
Conference papers hal-01683969v1

Segmentation of Nuclei in Histopathology Images by deep regression of the distance map

Peter Naylor , Marick Lae , Fabien Reyal , Thomas Walter
IEEE Transactions on Medical Imaging, 2018, pp.1-12
Journal articles hal-01984033v1
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SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data

Bruno Zeitouni , Valentina Boeva , Isabelle Janoueix-Lerosey , Sophie Loeillet , Patricia Legoix-Né et al.
Bioinformatics Application note, 2010, 26 (15), pp.1895-1896. ⟨10.1093/bioinformatics/btq293⟩
Journal articles inserm-00508372v1

A generic methodological framework for studying single cell motility in high-throughput time-lapse data

Alice Schoenauer Sebag , Sandra Plancade , Céline Raulet-Tomkiewicz , Robert Barouki , Jean-Philippe Vert et al.
Bioinformatics, 2015, 31 (12), pp.i320-i328. ⟨10.1093/bioinformatics/btv225⟩
Journal articles hal-01246689v1

A general and flexible method for signal extraction from single-cell RNA-seq data

Davide Risso , Fanny Perraudeau , Svetlana Gribkova , Sandrine Dudoit , Jean-Philippe Vert et al.
Nature Communications, 2018, 9 (1)
Journal articles hal-01985432v1

Dimeric G-quadruplex motifs determine a large fraction of strong replication origins in vertebrates

Jérémy Poulet-Benedetti , Caroline Tonnerre-Doncarli , Anne-Laure Valton , Marc Laurent , Marie Gérard et al.
Journal articles hal-03932439v1
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A new scoring system in cancer genetics: application to criteria for BRCA1 and BRCA2 mutation screening.

Bernard Bonaïti , Flora Alarcon , Nadine Andrieu , Valérie Bonadona , Marie-Gabrielle Dondon et al.
Journal of Medical Genetics, 2013, 51 (2), epub ahead of print. ⟨10.1136/jmedgenet-2013-101674⟩
Journal articles hal-00923931v1
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An autocrine ActivinB mechanism drives TGF β/Activin signaling in Group 3 medulloblastoma

Morgane Morabito , Magalie Larcher , Florence M G Cavalli , Chloé Foray , Antoine Forget et al.
EMBO Molecular Medicine, 2019, 6, pp.e9830. ⟨10.15252/emmm.201809830⟩
Journal articles hal-02347105v1
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Exome sequencing reveals aberrant signalling pathways as hallmark of treatment-naive anal squamous cell carcinoma

W. Cacheux , V. Dangles-Marie , E. Rouleau , J. Lazartigues , E. Girard et al.
Oncotarget, 2018, 9 (1), pp.464-476. ⟨10.18632/oncotarget.23066⟩
Journal articles hal-01717339v1
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National recommendations of the French Genetics and Cancer Group - Unicancer on the modalities of multi-genes panel analyses in hereditary predispositions to tumors of the digestive tract

Marion Dhooge , Stéphanie Baert-Desurmont , Carole Corsini , Olivier Caron , Nadine Andrieu et al.
European Journal of Medical Genetics, 2020, 63 (12), pp.104080. ⟨10.1016/j.ejmg.2020.104080⟩
Journal articles inserm-03182974v1

Jarid2 Methylation via the PRC2 Complex Regulates H3K27me3 Deposition during Cell Differentiation.

Serena Sanulli , Neil Justin , Aurélie Teissandier , Katia Ancelin , Manuela Portoso et al.
Molecular Cell, 2015, 57 (5), pp.769-783. ⟨10.1016/j.molcel.2014.12.020⟩
Journal articles hal-01110498v1
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Polygenic risk scores and breast and epithelial ovarian cancer risks for carriers of BRCA1 and BRCA2 pathogenic variants

Daniel Barnes , Matti Rookus , Lesley Mcguffog , Goska Leslie , Thea Mooij et al.
Genetics in Medicine, 2020, 22 (10), pp.1653-1666. ⟨10.1038/s41436-020-0862-x⟩
Journal articles inserm-03193473v1
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A new hybrid record linkage process to make epidemiological databases interoperable: application to the GEMO and GENEPSO studies involving BRCA1 and BRCA2 mutation carriers

Yue Jiao , Fabienne Lesueur , Chloé-Agathe Azencott , Maïté Laurent , Noura Mebirouk et al.
BMC Medical Research Methodology, 2021, 21 (1), pp.155. ⟨10.1186/s12874-021-01299-6⟩
Journal articles inserm-03313811v1
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Genomic Instability Signature of Palindromic Non-Coding Somatic Mutations in Bladder Cancer

Sophie Vacher , Voreak Suybeng , Élodie Girard , Julien Masliah Planchon , Grégory Thomson et al.
Cancers, 2020, 12 (10), pp.2882. ⟨10.3390/cancers12102882⟩
Journal articles hal-03011747v1
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The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

Aurélien Naldi , Céline Hernandez , Nicolas Levy , Gautier Stoll , Pedro Monteiro et al.
Frontiers in Physiology, 2018, 9, pp.n°680:1-13. ⟨10.3389/fphys.2018.00680⟩
Journal articles hal-01794294v2
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Impaired PRC2 activity promotes transcriptional instability and favors breast tumorigenesis

Michel Adam Wassef , Verónica Rodilla , Aurélie Teissandier , Bruno Zeitouni , Nadège Gruel et al.
Genes and Development, 2015, 29 (24), pp.2547-2562. ⟨10.1101/gad.269522.115⟩
Journal articles hal-02559123v1

Autoimmunity affecting the biliary tract fuels the immunosurveillance of cholangiocarcinoma

Juliette Paillet , Céleste Plantureux , Sarah Lévesque , Julie Le Naour , Gautier Stoll et al.
Journal of Experimental Medicine, 2021, 218 (10), pp.1-33. ⟨10.1084/jem.20200853⟩
Journal articles hal-03378827v1
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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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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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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

Spatial transcriptomics for respiratory research and medicine

Sandra Curras-Alonso , Juliette Soulier , Thomas Walter , Florian Mueller , Arturo Londoño-Vallejo et al.
European Respiratory Journal, 2021, 58 (1), pp.2004314. ⟨10.1183/13993003.04314-2020⟩
Journal articles hal-03376218v1
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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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Systems biology of Ewing sarcoma: a network model of EWS-FLI1 effect on proliferation and apoptosis

Gautier Stoll , Didier Surdez , Franck Tirode , Karine Laud , Emmanuel Barillot et al.
Nucleic Acids Research, 2013, 41 (19), pp.8853-8871. ⟨10.1093/nar/gkt678⟩
Journal articles inserm-02438745v1
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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