
Céline Hernandez
- Institut de Biologie Intégrative de la Cellule (I2BC)
- France Génomique (UMS CNRS 3628 - INRAE 1396 - Inserm 026)
- Plateforme de séquençage à haut débit (NGS)
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celine-hernandez
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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).
Domaines de recherche
Compétences
Publications
Publications
The malaria parasite Plasmodium falciparum prepares for life within the host cell by activating a complex gene network2024
Pré-publication, Document de travail
hal-04757785
v1
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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 use2022
Pré-publication, Document de travail
hal-03818695
v1
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Eoulsan 2: an efficient workflow manager for reproducible bulk, long-read and single-cell transcriptomics analyses2021
Pré-publication, Document de travail
hal-03784195
v1
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Benchmarking joint multi-omics dimensionality reduction approaches for cancer study2020
Pré-publication, Document de travail
hal-02998156
v1
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FAIR_bioinfo : a software perspective of reproducibility of bioinformatics analysesJournées Ouvertes de Biologie Informatique et Mathématiques - JOBIM 2020, Jun 2020, Montpellier, France
Poster de conférence
hal-03071717
v1
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Qualitative Simulation of Genetic Regulatory Networks Using Piecewise-Linear Models[Research Report] RR-4407, INRIA. 2002
Rapport
(rapport de recherche)
inria-00072181
v1
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Qualitative Simulation of the Initiation of Sporulation in B. subtilis[Research Report] RR-4527, INRIA. 2002
Rapport
(rapport de recherche)
inria-00072061
v1
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Genetic Network Analyzer: A Tool for the Qualitative Simulation of Genetic Regulatory Networks[Research Report] RR-4262, INRIA. 2001
Rapport
(rapport de recherche)
inria-00072325
v1
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