Céline Hernandez Responsable de la plateforme de séquençage à haut débit de l'I2BC

Identifiants chercheurs

IdHAL :

celine-hernandez

ORCID :

0000-0001-8664-1340

ResearcherID :

F-1164-2016

Présentation

Scientific director at I2BC's High Throughput Sequencing Core Facility

Employment and education

Plateforme de séquençage à heut débit – Institute for Integrative Biology of the Cell (I2BC)

Gif-sur-Yvette (France) from December 2019 to present. IR CNRS.

Bioinformatics and Computational Systems Biology of Cancer – Institut Curie

Paris (France) from May 2019 to November 2019. Supervisors : Emmanuel Barillot, Andrei Zinovyev. Post-doctoral fellow.

Projects: M5 Medulloblastoma (ITMO) and “individualized Pediatric Cure” (iPC, H2020). Analysis, deconvolution and modelling of multi-omics data from pediatric cancers.

Computational Systems Biology Group – Institut de Biologie de l'Ecole Normale Supérieure

Paris (France) from July 2014 to April 2019. Supervisors : Denis Thieffry, Morgane Thomas-Chollier. Senior bioinformatics engineer (Ingénieur d'Etudes, CDD), and also PhD student (ED515 Complexité du vivant) from January 2016 to April 2019. Projects:

From December 2015 to April 2019: ‘Systaim’ project (ITMO Cancer, PhD project). Goal: modelling of T cell co-inhibitory pathways to predict anti-tumour responses to checkpoint inhibitors. Collaboration with B. Malissen (CIML, Marseille).

From July 2015 to December 2015: 'Echinodal' project (ANR). Goal: logical modelling of the regulatory network governing dorsal-ventral axis specification in the sea urchin P. lividus. Collaboration with T. Lepage (IBV, Nice).

From July 2014 to June 2015: 'iBone' project (ANR-BMBF). Goal: understand osteoporosis mechanisms using epigenomics. Development of an automated ChIP-seq data analysis pipeline. Collaboration with E. Hesse (UKE, Hamburg), S. Johnsen (GGNB, Göttingen), V. Geoffroy (INSERM, Nantes).

Thesis defence: “Modélisation des processus inhibiteurs des cellules T dans la réponse anti-tumorale” (June 5th 2019). Teaching: reproducibility of ChIp-seq analyses (NU Singapore), logical modelling (Workshop ECCB16), proteomics (L3 level, ENS). Other: collaborative activities inside the Consortium for Logical Models and Tools (CoLoMoTo).

Protein Analysis Facility – University of Lausanne

Lausanne (Switzerland) from November 2009 to June 2014. Supervisor : Manfredo Quadroni Embedded bioinformatician for the proteomics core facility, including in-house tools development, analysis of proteomics data (R), maintenance of a LIM System as well as dedicated computers and servers (Mascot, MaxQuant, Proteome Discoverer). Teaching: proteomics (course organised by the facility), proteogenomics (ProteomeXchange consortium, University of Bern-Fribourg).

Vital-IT Group – Swiss Institute of Bioinformatics

Lausanne (Switzerland) from December 2010 to June 2014. Supervisor : Ioannis Xenarios Bioinformatician. Participation into miscellaneous server installation/administration (ExPASy, Tranche, World-2DPage). Supervision of other bioinformaticians in collaborative projects between different groups.

Proteome Informatics Group – Swiss Institute of Bioinformatics

Geneva (Switzerland) from November 2002 to November 2010. Supervisors : Ron D. Appel, Frédérique Lisacek. Bioinformatician. Worked on different projects initiated at the Proteome Informatics group (including SwissPIT, Popitam, Aldente) or in collaboration with the GeneBio company (Phenyx), the Biomedical Proteomics Research Group (pICarver, MALDIPepQuant), or the Swiss-Prot group (ExPASy). Supervision of Master students (M2). Teaching assistant for Perl practical classes.

Helix Group – Institut National de Recherche en Informatique et en Automatique

Grenoble (France) from October 2000 to September 2002. Supervisors : Hidde de Jong, François Rechenmann Ingénieur associé. Participation to the development of Genetic Network Analyzer (GNA), a software for genetic regulatory networks description and simulation using a qualitative approach (piecewise-linear differential equations).

DESS “Informatique appliquée à la Biologie” (equivalent to a Masters degree, in Computer science applied to biology) at Université de Versailles Saint-Quentin-en-Yvelines (France).

University year 1999-2000. Mention Très bien.

Expertise

High throughput data analysis

General : quality control (FastQC), mapping (Bowtie2, STAR), visualization (UCSC genome browser, IGV), other software suites (samtools, bedtools, deeptools).

ChIP-seq : peak calling (MACS, danPos), differential peak search (diffBind), analysis of ChIP-exo data (development of ExoProfiler).

Sequence analysis : motif analysis and discovery (RSAT).

Proteomics : identification (Mascot, Scaffold), quantitation for SILAC, iTRAQ, Label free (MaxQuant/Perseus), phosphoproteomics analysis, proteogenomics.

Integration/visualization of systems biology annotations (GO, Reactome) and contextualisation using graphs (PyPath, Cytoscape, iGraph).

Deconvolution : ICA, NMF.

Modelling of regulatory networks

Dynamical modelling using a logical formalism (GINsim), asynchronous/synchronous or stochastic simulation (GINsim, MaBoSS), analysis automation through unit testing, computation of trap spaces (bioLQM), model checking (NuSMV).

Dynamical modelling using the Rule-Based formalism (Kappa language).

Static modelling of biochemical processes (CellDesigner).

Knowledge of standard formats and tools used in Systems Biology (SBML, SBGN, HUPO-PSI).

Other expertise

Programming languages (R, Java, Python).

Reproducibility of analyses using workflow management systems (SnakeMake, Eoulsan, Galaxy) and notebook plaftorms (RMarkdown, Jupyter).

Virtualisation (Docker/DockerHub, VirtualBox).

Project management (Trello, RedMine). Versioning systems (Git, SVN).

Valorisation through presentations (poster/oral presentations during national/international conferences), platform publication (GitHub) and user interface development (Shiny).

Languages

French : mother tongue.

English : full professional working proficiency.

Dutch : elementary proficiency (‘Maatschappelijk Informeel’ INFO certificate 2016).

Japanese : elementary proficiency (Japanese Language Proficiency Test, level 4).

Publications

Article dans une revue (10)

Benchmarking joint multi-omics dimensionality reduction approaches for the study of cancer Laura Cantini,Pooya Zakeri,Céline Hernandez,Aurelien Naldi,Denis Thieffryet al. Nature Communications, 2021, 12, ⟨10.1038/s41467-020-20430-7⟩ Article dans une revue hal-03102088v1
Contribution of ROS and metabolic status to neonatal and adult CD8 + T cell activation José Antonio Sánchez-Villanueva,Otoniel Rodríguez-Jorge,Oscar Ramirez-Pliego,Gabriela Rosas Salgado,Wassim Abou-Jaoudéet al. PLoS ONE, 2019, 14 (12), pp.e0226388. ⟨10.1371/journal.pone.0226388⟩ Article dans une revue inserm-02428783v1
Cooperation between T cell receptor and Toll-like receptor 5 signaling for CD4 + T cell activation Otoniel Rodríguez-Jorge,Linda Kempis-Calanis,Wassim Abou-Jaoudé,Darely Gutiérrez-Reyna,Céline Hernandezet al. Science Signaling, 2019, 12 (577), pp.eaar3641. ⟨10.1126/scisignal.aar3641⟩ Article dans une revue hal-02154906v1
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 Thieffryet al. Frontiers in Physiology, 2018, 9, pp.787. ⟨10.1101/319780⟩ Article dans une revue hal-01809081v1
The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks Aurélien Naldi,Céline Hernandez,Nicolas Levy,Gautier Stoll,Pedro Monteiroet al. Frontiers in Physiology, 2018, 9, pp.n°680:1-13. ⟨10.3389/fphys.2018.00680⟩ Article dans une revue hal-01794294v2
Krox20 hindbrain regulation incorporates multiple modes of cooperation between cis-acting elements Elodie Thierion,Johan Le Men,Samuel Collombet,Céline Hernandez,Fanny Coulpieret al. PLoS Genetics, 2017, 13 (7), pp.e1006903. ⟨10.1371/journal.pgen.1006903⟩ Article dans une revue inserm-02158641v1
RSAT 2015: Regulatory Sequence Analysis Tools Alejandra Medina-Rivera,Matthieu Defrance,Olivier Sand,Carl Herrmann,Jaime A. Castro-Mondragonet al. Nucleic Acids Research, 2015, 43 (W1), pp.W50--W56. ⟨10.1093/nar/gkv362⟩ Article dans une revue hal-01624369v1
Quantitative proteomics identifies the membrane-associated peroxidase GPx8 as a cellular substrate of the hepatitis C virus NS3-4A protease. Kenichi Morikawa,Jérôme Gouttenoire,Céline Hernandez,Viet Loan Dao Thi,Huong T L Tranet al. Hepatology, 2014, 59 (2), pp.423-33. ⟨10.1002/hep.26671⟩ Article dans une revue hal-00972312v1
Qualitative simulation of the initiation of sporulation in Bacillus subtilis. Hidde de Jong,Johannes Geiselmann,Grégory Batt,Céline Hernandez,Michel Page Bulletin of Mathematical Biology, 2004, 66 (2), pp.261-99. ⟨10.1016/j.bulm.2003.08.009⟩ Article dans une revue istex hal-00173847v1
Qualitative simulation of genetic regulatory networks using piecewise-linear models. Hidde de Jong,Jean-Luc Gouzé,Céline Hernandez,Michel Page,Tewfik Sariet al. Bulletin of Mathematical Biology, 2004, 66 (2), pp.301-40. ⟨10.1016/j.bulm.2003.08.010⟩ Article dans une revue istex hal-00173849v1

Pré-publication, Document de travail (4)

The malaria parasite Plasmodium falciparum prepares for life within the host cell by activating a complex gene network Laura Piel,Céline Hernandez,Yan Jaszczyszyn,Delphine Naquin,Joana Santos 2024 Pré-publication, Document de travail hal-04757785v1
The Drosophila Fab-7 boundary element modulates Abd-B gene activity in the genital disc by guiding an inversion of collinear chromatin organization and alternative promoter use Laura Moniot-Perron,Benoit Moindrot,Line Manceau,Joanne Edouard,Yan Jaszczyszynet al. 2022 Pré-publication, Document de travail hal-03818695v1
Eoulsan 2: an efficient workflow manager for reproducible bulk, long-read and single-cell transcriptomics analyses Nathalie Lehmann,Sandrine Perrin,Claire Wallon,Xavier Bauquet,Vivien Deshaieset al. 2021 Pré-publication, Document de travail hal-03784195v1
Benchmarking joint multi-omics dimensionality reduction approaches for cancer study Laura Cantini,Pooya Zakeri,Céline Hernandez,Aurelien Naldi,Denis Thieffryet al. 2020 Pré-publication, Document de travail hal-02998156v1

Poster de conférence (1)

FAIR_bioinfo : a software perspective of reproducibility of bioinformatics analyses Thomas Denecker,Céline Hernandez,Claire Toffano-Nioche Journées Ouvertes de Biologie Informatique et Mathématiques - JOBIM 2020, Jun 2020, Montpellier, France Poster de conférence hal-03071717v1

Rapport (5)

Plans de gestion des données : recommandations pour une gestion responsable et ouverte des données Frédéric de Lamotte,Véronique Stoll,Jean-François Dufayard,Christine Hadrossek,Romain Davidet al. Comité pour la science ouverte. 2025 Rapport hal-05505299v2
Faciliter la documentation des données grâce aux métadonnées dans un projet de recherche Frédéric de Lamotte,Véronique Stoll,Céline Hernandez,Cécile Arènes,Romain Davidet al. Comité pour la science ouverte. 2025 Rapport hal-05455660v1
Qualitative Simulation of the Initiation of Sporulation in B. subtilis Hidde De jong,Johannes Geiselmann,Grégory Batt,Céline Hernandez,Michel Page [Research Report] RR-4527, INRIA. 2002 Rapport (rapport de recherche) inria-00072061v1
Qualitative Simulation of Genetic Regulatory Networks Using Piecewise-Linear Models Hidde De Jong,Jean-Luc Gouzé,Céline Hernandez,Tewfik Sari,Michel Pageet al. [Research Report] RR-4407, INRIA. 2002 Rapport (rapport de recherche) inria-00072181v1
Genetic Network Analyzer: A Tool for the Qualitative Simulation of Genetic Regulatory Networks Hidde de Jong,Johannes Geiselmann,Céline Hernandez,Michel Page [Research Report] RR-4262, INRIA. 2001 Rapport (rapport de recherche) inria-00072325v1