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Céline Hernandez

Senior bioinformatician
Dynamical Modelling, High Throughput Data Analysis

 

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, Head of bioinformatics at I2BC's Sequencing Core Facility.


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).

Journal articles10 documents

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

Poster communications1 document

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

Preprints, Working Papers, ...1 document

  • Laura Cantini, Pooya Zakeri, Céline Hernandez, Aurelien Naldi, Denis Thieffry, et al.. Benchmarking joint multi-omics dimensionality reduction approaches for cancer study. 2020. ⟨hal-02998156⟩

Reports3 documents

  • Hidde De Jong, Jean-Luc Gouzé, Céline Hernandez, Tewfik Sari, Michel Page, et al.. Qualitative Simulation of Genetic Regulatory Networks Using Piecewise-Linear Models. [Research Report] RR-4407, INRIA. 2002. ⟨inria-00072181⟩
  • Hidde De jong, Johannes Geiselmann, Grégory Batt, Céline Hernandez, Michel Page. Qualitative Simulation of the Initiation of Sporulation in B. subtilis. [Research Report] RR-4527, INRIA. 2002. ⟨inria-00072061⟩
  • Hidde de Jong, Johannes Geiselmann, Céline Hernandez, Michel Page. Genetic Network Analyzer: A Tool for the Qualitative Simulation of Genetic Regulatory Networks. [Research Report] RR-4262, INRIA. 2001. ⟨inria-00072325⟩