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Large-scale machine learning for metagenomics sequence classification

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

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

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

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

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

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

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

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

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

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

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

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

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
Nature Communications, 2018, 9 (1)
Journal articles hal-01985432v1

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

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

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

Classification of gene signatures for their information value and functional redundancy

Laura Cantini , Laurence Calzone , Loredana Martignetti , Mattias Rydenfelt , Nils Blüthgen , et al.
npj Systems Biology and Applications, 2018, 4 (1), ⟨10.1038/s41540-017-0038-8⟩
Journal articles hal-02129604v1

A Deep Learning Approach To Identify MRNA Localization Patterns

Rémy Dubois , Arthur Imbert , Aubin Samacoits , Marion Peter , Edouard Bertrand , et al.
2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI), Apr 2019, Venice, France. pp.1386-1390, ⟨10.1109/ISBI.2019.8759235⟩
Conference papers hal-02343547v1

Jointly Embedding Multiple Single-Cell Omics Measurements

Jie Liu , Yuanhao Huang , Ritambhara Singh , Jean-Philippe Vert , William Stafford Noble
19th International Workshop on Algorithms in Bioinformatics (WABI 2019), 2019, ⟨10.4230/LIPIcs.WABI.2019.10⟩
Journal articles hal-02444746v1

Designs for evaluating precision medicine trials

Xavier Paoletti , Bernard Asselain , Christophe Le Tourneau
Pan-cancer Integrative Molecular Portrait Towards a New Paradigm in Precision Medicine, pp.113-131, 2015, 9783319221892. ⟨10.1007/978-3-319-22189-2_8⟩
Book sections hal-02560954v1

Urinary Exosomes of Patients with Cystic Fibrosis Unravel CFTR-Related Renal Disease

Sebastien Gauthier , Iwona Pranke , Vincent Jung , Loredana Martignetti , Véronique Stoven , et al.
International Journal of Molecular Sciences, 2020, 21 (18), pp.6625. ⟨10.3390/ijms21186625⟩
Journal articles hal-03116838v1

martini: an R package for genome-wide association studies using SNP networks

Chloé-Agathe Azencott , Héctor Climente-González
Preprints, Working Papers, ... hal-03122108v1

Pembrolizumab for the treatment of programmed death–ligand 1‒positive advanced carcinoid or pancreatic neuroendocrine tumors: Results from the KEYNOTE-028 study

Janice M. Mehnert , Emily K. Bergsland , Bert H. O’neil , Armando Santoro , Jan H.M. Schellens , et al.
Cancer, 2020, 126 (13), pp.3021-3030. ⟨10.1002/cncr.32883⟩
Journal articles hal-02927423v1

A comparison of phase I dose-finding designs in clinical trials with monotonicity assumption violation

Rachid Abbas , Caroline Rossoni , Thomas F. Jaki , Xavier Paoletti , Pavel Mozgunov
Clinical Trials, 2020, 17 (5), pp.522-534. ⟨10.1177/1740774520932130⟩
Journal articles hal-02984267v1

Origin, Analytical Characterization, and Use of Human Odor in Forensics

Vincent Cuzuel , Guillaume Cognon , Isabelle Rivals , Charles Sauleau , François Heulard , et al.
Journal of Forensic Sciences, 2017, Vol. 62 (n° 2), pp.330-350. ⟨10.1111/1556-4029.13394⟩
Journal articles halshs-02524960v1

The inconvenience of data of convenience: computational research beyond post-mortem analyses

Chloé-Agathe Azencott , Tero Aittokallio , Sushmita Roy , Ankit Agrawal , Emmanuel Barillot , et al.
Nature Methods, 2017, 14 (10), pp.937 - 938. ⟨10.1038/nmeth.4457⟩
Journal articles hal-01679028v1

DNA methylation and hydroxymethylation characterize the identity of D1 and D2 striatal projection neurons

Lucile Marion-Poll , Jean-Pierre Roussarie , Lieng Taing , Cloelia Dard-Dascot , Nicolas Servant , et al.
Communications Biology, 2022, 5 (1), pp.1321. ⟨10.1038/s42003-022-04269-w⟩
Journal articles hal-03939291v1

Exploring isofunctional molecules: design of a benchmark and evaluation of prediction performance

Philippe Pinel , Gwenn Guichaoua , Matthieu Najm , Stéphanie Labouille , Nicolas Drizard , et al.
Molecular Informatics, 2022, ⟨10.1002/minf.202200216⟩
Journal articles hal-03938203v1

Differential CFTR-Interactome Proximity Labeling Procedures Identify Enrichment in Multiple SLC Transporters

Benoît Chevalier , Nesrine Baatallah , Matthieu Najm , Solène Castanier , Vincent Jung , et al.
International Journal of Molecular Sciences, 2022, 23 (16), pp.8937. ⟨10.3390/ijms23168937⟩
Journal articles hal-03940119v1