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Kernel methods in genomics and computational biology

Jean-Philippe Vert
Preprints, Working Papers, ... hal-00012124v1
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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

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

CCL2/CCR2-Dependent Recruitment of Functional Antigen-Presenting Cells into Tumors upon Chemotherapy

Yuting Ma , Stephen R Mattarollo , Sandy Adjemian , Heng Yang , Laetitia Aymeric , et al.
Cancer Research, 2014, 74 (2), pp.436-445. ⟨10.1158/0008-5472.can-13-1265⟩
Journal articles hal-02047410v1

ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays

Guillem Rigaill , Philippe Hupé , Anna Almeida , Philippe La Rosa , Jean-Philippe Meyniel , et al.
Bioinformatics, 2008, 24 (6), pp.768-774. ⟨10.1093/bioinformatics/btn048⟩
Journal articles hal-02655786v1

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
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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

Glutathione Levels and BAX Activation during Apoptosis Due to Oxidative Stress in Cells Expressing Wild-type and Mutant Cystic Fibrosis Transmembrane Conductance Regulator

Thomas Jungas , Iris Motta , Francis Duffieux , Pascale Fanen , Véronique Stoven , et al.
Journal of Biological Chemistry, 2002, 277 (31), pp.27912-27918. ⟨10.1074/jbc.M110288200⟩
Journal articles hal-03116896v1
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Zebrafish as a model to determine conserved gene regulatory mechanisms in vertebrates

Yuvia Alhelí Pérez Rico
Biochemistry, Molecular Biology. Sorbonne Université, 2018. English. ⟨NNT : 2018SORUS535⟩
Theses tel-02892255v1
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COVID-19 in breast cancer patients: a cohort at the Institut Curie hospitals in the Paris area

Perrine Vuagnat , Maxime Frelaut , Toulsie Ramtohul , Clémence Basse , Sarah Diakité , et al.
Preprints, Working Papers, ... hal-02559160v2

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

Insight into cystic fibrosis by structural modelling of CFTR first nucleotide binding fold (NBF1)

Jean-Philippe Annereau , Véronique Stoven , François Bontems , Joël Barthe , Gérard Lenoir , et al.
Comptes Rendus de l'Académie des Sciences - Series III - Sciences de la Vie, 1997, 320 (2), pp.113-121. ⟨10.1016/s0764-4469(97)85002-0⟩
Journal articles istex hal-03116843v1

Identification of chemogenomic features from drug-target interaction networks using interpretable classifiers

Y. Tabei , E. Pauwels , Véronique Stoven , K. Takemoto , Y. Yamanishi
Bioinformatics, 2012, 28 (18), pp.i487-i494. ⟨10.1093/bioinformatics/bts412⟩
Journal articles hal-03116929v1

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

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
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Parental-to-embryo switch of chromosome organization in early embryogenesis

Samuel Collombet , Noemie Ranisavljevic , Takashi Nagano , Csilla Varnai , Tarak Shisode , et al.
Nature, 2020, 580 (7801), pp.142 - 146. ⟨10.1038/s41586-020-2125-z⟩
Journal articles hal-03027197v1

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
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Robust and Scalable Learning of Complex Intrinsic Dataset Geometry via ElPiGraph

Luca Albergante , Evgeny Mirkes , Jonathan Bac , Huidong Chen , Alexis Martin , et al.
Entropy, 2020, 22 (3), pp.296. ⟨10.3390/e22030296⟩
Journal articles hal-02971955v1
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Deconvolution of transcriptomes and miRNomes by independent component analysis provides insights into biological processes and clinical outcomes of melanoma patients

Petr V Nazarov , Anke K Wienecke-Baldacchino , Andrei Zinovyev , Urszula Czerwińska , Arnaud Muller , et al.
BMC Medical Genomics, 2019, 12 (1), pp.132. ⟨10.1186/s12920-019-0578-4⟩
Journal articles inserm-02305420v1
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A review of the use of time‐varying covariates in the Fine‐Gray subdistribution hazard competing risk regression model

Peter Austin , Aurélien Latouche , Jason Fine
Statistics in Medicine, 2019, ⟨10.1002/sim.8399⟩
Journal articles hal-02349043v1
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FDG PET/CT for assessing tumour response to immunotherapy : Report on the EANM symposium on immune modulation and recent review of the literature

Nicolas Aide , Rodney J Hicks , Christophe Le Tourneau , Stéphanie Lheureux , Stefano Fanti , et al.
European Journal of Nuclear Medicine and Molecular Imaging, 2019, 46 (1), pp.238-250. ⟨10.1007/s00259-018-4171-4⟩
Journal articles inserm-02101049v1

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
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Total metabolic tumor volume and spleen metabolism on baseline [18F]-FDG PET/CT as independent prognostic biomarkers of recurrence in resected breast cancer

Romain-David Seban , Roman Rouzier , Aurelien Latouche , Nicolas Deleval , Jean-Marc Guinebretiere , et al.
European Journal of Nuclear Medicine and Molecular Imaging, 2021, 48 (11), pp.3560-3570. ⟨10.1007/s00259-021-05322-2⟩
Journal articles hal-03441739v1
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The Phosphatase PRL-3 Is Involved in Key Steps of Cancer Metastasis

Laura Duciel , Luis Cristobal Monraz Gomez , Maria Kondratova , Inna Kuperstein , Simon Saule
Journal of Molecular Biology, 2019, 431, pp.3056 - 3067. ⟨10.1016/j.jmb.2019.06.008⟩
Journal articles hal-03487705v1

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

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
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Prediction of Treatment Response in Triple Negative Breast Cancer From Whole Slide Images

Peter Naylor , Tristan Lazard , Guillaume Bataillon , Marick Laé , Anne Vincent-Salomon , et al.
Frontiers in Signal Processing, 2022, 2, ⟨10.3389/frsip.2022.851809⟩
Journal articles hal-03942865v1
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Meta-Analysis of Esophageal Cancer Transcriptomes Using Independent Component Analysis

Ainur Seisenova , Asset Daniyarov , Askhat Molkenov , Aigul Sharip , Andrei Zinovyev , et al.
Frontiers in Genetics, 2021, 12, ⟨10.3389/fgene.2021.683632⟩
Journal articles hal-03447487v1
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Demarcation of Topologically Associating Domains Is Uncoupled from Enriched CTCF Binding in Developing Zebrafish

Yuvia Pérez-Rico , Emmanuel Barillot , Alena Shkumatava
iScience, 2020, 23 (5), pp.101046. ⟨10.1016/j.isci.2020.101046⟩
Journal articles hal-03983028v1