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Deposit type : Notice

Learning with minimal effort: leveraging in silico labeling for cell and nucleus segmentation

Thomas Bonte , Maxence Philbert , Emeline Coleno , Edouard Bertrand , Arthur Imbert et al.
ECCV 2022 proceedings (Bio-image computing workshop), 2023
Proceedings hal-03935104v1

Where Do We Stand in Regularization for Life Science Studies?

Veronica Tozzo , Chloé-Agathe Azencott , Samuele Fiorini , Emanuele Fava , Andrea Trucco et al.
Journal of Computational Biology, 2021, ⟨10.1089/cmb.2019.0371⟩
Journal articles hal-03367708v1

A systematic analysis of gene-gene interaction in multiple sclerosis

Lotfi Slim , Clément Chatelain , Hélène de Foucauld , Chloé-Agathe Azencott
BMC Medical Genomics, 2022, 15 (1), pp.100. ⟨10.1186/s12920-022-01247-3⟩
Journal articles hal-03122122v1

Nonlinear post-selection inference for genome-wide association studies

Lotfi Slim , Clément Chatelain , Chloé-Agathe Azencott
Pacific Symposium on Biocomputing, Jan 2022, Kohala Coast, Hawaii, United States. ⟨10.1101/2020.09.30.320515⟩
Conference papers hal-03122125v1

NetNorM: Capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis

Marine Le Morvan , Andrei Zinovyev , Jean-Philippe Vert
PLoS Computational Biology, 2017, 13 (6), ⟨10.1371/journal.pcbi.1005573⟩
Journal articles hal-01679005v1

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

Measuring significant changes in chromatin conformation with ACCOST

Kate Cook , Borislav Hristov , Karine Le roch , Jean Philippe Vert , William Stafford Noble et al.
Nucleic Acids Research, 2020, 48 (5), pp.2303-2311. ⟨10.1093/nar/gkaa069⟩
Journal articles hal-03114387v1

Molecular Underpinnings and Environmental Drivers of Spontaneous Loss of Heterozygosity in Drosophila Intestinal Stem Cells

Lara Al Zouabi , Marine Stefanutti , Nick Riddiford , Natalia Rubanova , Mylène Bohec et al.
Preprints, Working Papers, ... hal-03842697v1

On evaluating how well a biomarker can predict treatment response with survival data

Bassirou Mboup , Paul Blanche , Aurélien Latouche
Pharmaceutical Statistics, 2020, 19 (4), pp.410-423. ⟨10.1002/pst.2002⟩
Journal articles hal-03724634v1

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

The Weighted Kendall and High-order Kernels for Permutations

Yunlong Jiao , Jean-Philippe Vert
35th International Conference on Machine Learning, Jul 2018, Stockholm, Sweden. pp.2314--2322
Conference papers hal-01717385v1

Robust Seriation and Applications to Cancer Genomics

Antoine Recanati , Nicolas Servant , Jean-Philippe Vert , Alexandre d'Aspremont
Preprints, Working Papers, ... hal-01851960v1

Efficient multi-task chemogenomics for drug specificity prediction

Benoit Playe , Chloé-Agathe Azencott , Véronique Stoven
PLoS ONE, 2018, 13 (10), pp.e0204999. ⟨10.1371/journal.pone.0204999⟩
Journal articles hal-01984828v1

Contribution of epigenetic landscapes and transcription factors to X-chromosome reactivation in the inner cell mass

Maud Borensztein , Ikuhiro Okamoto , Laurène Syx , Guillaume Guilbaud , Christel Picard et al.
Nature Communications, 2017, 8 (1), ⟨10.1038/s41467-017-01415-5⟩
Journal articles hal-03437406v1

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

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

Learning with Minimal Effort: Leveraging in Silico Labeling for Cell and Nucleus Segmentation

Thomas Bonte , Maxence Philbert , Emeline Coleno , Edouard Bertrand , Arthur Imbert et al.
ECCV 2022 Workshops. Lecture Notes in Computer Science, 13804, Springer Nature Switzerland, pp.423-436, 2023, Lecture Notes in Computer Science, 978-3-031-25068-2. ⟨10.1007/978-3-031-25069-9_28⟩
Proceedings hal-04029154v1

Prognosis and chemosensitivity of non-V600E BRAF mutations in metastatic colorectal carcinoma (mCRC): An AGEO French multicenter retrospective cohort.

Aline Derosiere , Vincent Nicolai , David Malka , Astrid Pozet , Julien Lazartigues et al.
Journal of Clinical Oncology, 2019, 37 (15, S), ⟨10.1200/JCO.2019.37.15\_suppl.3575⟩
Journal articles hal-03606012v1

Large-scale machine learning for metagenomics sequence classification

Kevin Vervier , Pierre Mahé , Maud Tourmoud , Jean-Baptiste Veyrieras , Jean-Philippe Vert et al.
Bioinformatics, 2016, 32 (7), pp.1023-32
Journal articles hal-01420829v1

Telomere length, ATM mutation status and cancer risk in Ataxia-Telangiectasia families

Anne Laure Renault , Noura Mebirouk , Eve Cavaciuti , Dorothée Le Gal , J. Lecarpentier et al.
Carcinogenesis, 2017, 38 (10), pp.994-1003. ⟨10.1093/carcin/bgx074⟩
Journal articles hal-01658591v1

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

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

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

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

Endoscopic management of 345 small rectal neuroendocrine tumours: A national study from the French group of endocrine tumours (GTE)

Caroline Fine , Guillaume Roquin , Eric Terrebonne , Thierry Lecomte , Romain Coriat et al.
United European Gastroenterology Journal, 2019, 7 (8), pp.1102-1112. ⟨10.1177/2050640619861883⟩
Journal articles hal-02549178v1

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

The French Early Breast Cancer Cohort (FRESH): A Resource for Breast Cancer Research and Evaluations of Oncology Practices Based on the French National Healthcare System Database (SNDS)

Elise Dumas , Lucie Laot , Florence Coussy , Beatriz Grandal Rejo , Eric Daoud et al.
Cancers, 2022, 14 (11), pp.2671. ⟨10.3390/cancers14112671⟩
Journal articles hal-03901737v1

Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology

Anna Niarakis , Dagmar Waltemath , James Glazier , Falk Schreiber , Sarah Keating et al.
Briefings in Bioinformatics, 2022, 23 (4), pp.1-11. ⟨10.1093/bib/bbac212⟩
Journal articles hal-03690604v1

Molecular profiling of non-small-cell lung cancer patients with or without brain metastases included in the randomized SAFIR02-LUNG trial and association with intracranial outcome

Alice Mogenet , Fabrice Barlesi , Benjamin Besse , Stefan Michiels , Maryam Karimi et al.
Lung Cancer, 2022, 169, pp.31-39. ⟨10.1016/j.lungcan.2022.05.004⟩
Journal articles hal-03925563v1

The Kendall and Mallows Kernels for Permutations

Yunlong Jiao , Jean-Philippe Vert
IEEE Transactions on Pattern Analysis and Machine Intelligence, 2018, 40 (7), pp.1755-1769. ⟨10.1109/TPAMI.2017.2719680⟩
Journal articles hal-01679012v1