Céline Hernandez

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).