Céline Hernandez

Céline Hernandez
Institut Curie · Computational Systems Biology of Cancer

PhD

About

82
Publications
10,592
Reads
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3,350
Citations
Introduction
Epigenomics data and logical modeling at the Biology Institute of Ecole Normale Supérieure (Paris).
Additional affiliations
July 2014 - May 2019
Ecole Normale Supérieure de Paris
Position
  • Bioinformatician
February 2011 - June 2014
Swiss Institute of Bioinformatics
Position
  • Bioinformaticien
November 2008 - June 2014
University of Lausanne
Position
  • Data specialist - Bioinformatics
Education
September 1999 - June 2000
Université de Versailles Saint-Quentin
Field of study
  • Computer science applied to Biology
September 1995 - June 1999
Claude Bernard University Lyon 1
Field of study
  • Population Biology, options: Biomathematics, Bioinformatics, Biostatistics

Publications

Publications (82)
Preprint
Full-text available
Motivation: Core sequencing facilities produce huge amounts of sequencing data that need to be analysed with automated workflows to ensure reproducibility and traceability. Eoulsan is a versatile open-source workflow engine meeting the needs of core facilities, by automating the analysis of a large number of samples. Its core design separates the d...
Article
Full-text available
High-dimensional multi-omics data are now standard in biology. They can greatly enhance our understanding of biological systems when effectively integrated. To achieve proper integration, joint Dimensionality Reduction (jDR) methods are among the most efficient approaches. However, several jDR methods are available, urging the need for a comprehens...
Article
During sea urchin development, secretion of Nodal and BMP2/4 ligands and their antagonists Lefty and Chordin from a ventral organizer region specifies the ventral and dorsal territories. This process relies on a complex interplay between the Nodal and BMP pathways through numerous regulatory circuits. To decipher the interplay between these pathway...
Article
Full-text available
At the crossroad between biology and mathematical modeling, computational systems biology can contribute to a mechanistic understanding of high-level biological phenomenon. But as knowledge accumulates, the size and complexity of mathematical models increase, calling for the development of efficient dynamical analysis methods. Here, we propose the...
Preprint
Full-text available
At the crossroad between biology and mathematical modelling, computational systems biology can contribute to a mechanistic understanding of high-level biological phenomenon. But as knowledge accumulates, the size and complexity of mathematical models increase, calling for the development of efficient dynamical analysis methods. Here, we propose the...
Preprint
Full-text available
During sea urchin development, secretion of Nodal and BMP2/4 ligands and their antagonists Lefty and Chordin from a ventral organizer region specifies the ventral and dorsal territories. This process relies on a complex interplay between the Nodal and BMP pathways through numerous regulatory circuits. To decipher the interplay between these pathway...
Preprint
Full-text available
High-dimensional multi-omics data are now standard in biology. They can greatly enhance our understanding of biological systems when effectively integrated. To achieve this multi-omics data integration, Joint Dimensionality Reduction (jDR) methods are among the most efficient approaches. However, several jDR methods are available, urging the need f...
Article
Full-text available
In neonatal T cells, a low response to infection contributes to a high incidence of morbidity and mortality of neonates. Here we have evaluated the impact of the cytoplasmic and mitochondrial levels of Reactive Oxygen Species of adult and neonatal CD8⁺ T cells on their activation potential. We have also constructed a logical model connecting metabo...
Preprint
Full-text available
A low response of neonatal T cells to infections contributes to a high incidence of morbidity and mortality of neonates. Here we evaluated the impact of the cytoplasmic and mitochondrial levels of Reactive Oxygen Species (ROS) of adult and neonatal CD8+T cells on their activation potential. We further constructed a logical model to decipher the int...
Article
Full-text available
CD4 + T cells recognize antigens through their T cell receptors (TCRs); however, additional signals involving co-stimulatory receptors, for example, CD28, are required for proper T cell activation. Alternative costimulatory receptors have been proposed, including members of the Toll-like receptor (TLR) family, such as TLR5 and TLR2. To understand t...
Article
Full-text available
Throughout the HIV-1 replication cycle, complex host-pathogen interactions take place in the infected cell, leading to the production of new virions. The virus modulates the host cellular machinery in order to support its life cycle, while counteracting intracellular defense mechanisms. We investigated the dynamic host response to HIV-1 infection b...
Article
Full-text available
Boolean and multi-valued logical formalisms are increasingly used to model complex cellular networks. To ease the development and analysis of logical models, a series of software tools have been proposed, often with specific assets. However, combining these tools typically implies a series of cumbersome software installation and model conversion st...
Article
Full-text available
Analysing models of biological networks typically relies on workflows in which different software tools with sensitive parameters are chained together, many times with additional manual steps. The accessibility and reproducibility of such workflows is challenging, as publications often overlook analysis details, and because some of these tools may...
Article
Full-text available
The logical formalism is well adapted to model large cellular networks, in particular when detailed kinetic data are scarce. This tutorial focuses on this well-established qualitative framework. Relying on GINsim (release 3.0), a software implementing this formalism, we guide the reader step by step toward the definition, the analysis and the simul...
Data
The supplemental data “Notebooks” contains several short Jupyter notebooks which demonstrate different usage of the CoLoMoTo interactive notebook, listed in Table 2. The .ipynb files can be imported and executed within the Jupyter interface of the CoLoMoTo notebook, using the Docker image colomoto/colomoto-docker:2018-03-31. For each of these noteb...
Data
The supplemental file “SnakeMake” contains an example of SnakeMake workflow that uses the CoLoMoTo Docker image to execute complementary analyses.
Preprint
Full-text available
Boolean and multi-valued logical formalisms are increasingly used to model complex cellular networks. To ease the development and analysis of logical models, a series of software tools have been proposed, often with specific assets. However, combining these tools typically implies a series of cumbersome software installation and model conversion st...
Preprint
Full-text available
Analysing models of biological networks typically relies on workflows in which different software tools with sensitive parameters are chained together, many times with additional manual steps. The accessibility and reproducibility of such workflows is challenging, as publications often overlook analysis details, and because some of these tools may...
Preprint
Full-text available
The logical formalism is well adapted to model large cellular networks, for which detailed kinetic data are scarce. This tutorial focuses on this well-established qualitative framework. Relying on GINsim (release 3.0), a software implementing this formalism, we guide the reader step by step towards the definition, the analysis and the simulation of...
Article
Full-text available
Developmental genes can harbour multiple transcriptional enhancers that act simultaneously or in succession to achieve robust and precise spatiotemporal expression. However, the mechanisms underlying cooperation between cis-acting elements are poorly documented, notably in vertebrates. The mouse gene Krox20 encodes a transcription factor required f...
Data
Sequences of 4C-seq primers including Illumina adaptors. (PDF)
Data
Chromatin state and accessibility within the Krox20 locus. (A-C) ChIP-seq was performed for the H3K27ac mark on wild type E8.5 embryo heads (light blue) in duplicates and only one replicate is shown. ATAC-seq was performed on dissected regions (r3, r5 and a more posterior region (“post”; see text) from wild type (light blue), Krox20ΔC/ΔC (green) an...
Data
Element C is required for normal development of the r3 territory. (A) Sequence of the deleted element C and associated genomic coordinates (mouse genome assembly mm9). This sequence corresponds to the cloned sequence of the mouse element C described in [13]. (B) In situ hybridization for EphA4 mRNA performed on control (Krox20+/ΔC) and homozygous (...
Data
The Krox20 regulatory neighborhood includes its regulatory elements but not the Nrbf2 gene. (A) The left boundary of the Krox20 TAD, as previously determined from Hi-C in ES cells [11], spreads out over a transition zone with a low Directionality Index of Hi-C interactions in both ES cells and adult cortex ([11]). Hi-C in ES cells and TADs as defin...
Data
Dynamics of enhancer activity of the new mouse element (NE) in zebrafish. A zebrafish transgenic line Tg(NE:gfp), carrying a construct in which NE is linked to the gfp gene driven by a minimal promoter, was analysed by double ISH with krox20 (orange) and gfp (purple) probes at 3s and 10s stages. (TIF)
Article
Cellular differentiation is accompanied by dramatic changes in chromatin structure which direct the activation of lineage-specific transcriptional programs. Structure-specific recognition protein-1 (SSRP1) is a histone chaperone which is important for chromatin-associated processes such as transcription, DNA replication and repair. Since the functi...
Article
Full-text available
RSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding motif analysis (quality assessment, comparisons and clustering), (iii) comparative...
Article
Full-text available
The identification of large regulatory and signalling networks involved in the control of crucial cellular processes calls for proper modelling approaches. Indeed, models can help elucidate properties of these networks, understand their behaviour and provide (testable) predictions by performing in silico experiments. In this context, qualitative, l...
Article
Full-text available
The classical DNA recognition sequence of the glucocorticoid receptor (GR) appears to be present at only a fraction of bound genomic regions. To identify sequences responsible for recruitment of this transcription factor (TF) to individual loci, we turned to the high-resolution ChIP-exo approach. We exploited this signal by determining footprint pr...
Article
Among pollutants released into the environment by human activities, residues of pharmaceuticals are an increasing matter of concern because of their potential impact on ecosystems. The aim of this study was to analyse differences of protein expression resulting from acute (2 days) and middle-term (7 days) exposure of aquatic microcrustacean Daphnia...
Article
Unlabelled: The hepatitis C virus (HCV) NS3-4A protease is not only an essential component of the viral replication complex and a prime target for antiviral intervention but also a key player in the persistence and pathogenesis of HCV. It cleaves and thereby inactivates two crucial adaptor proteins in viral RNA sensing and innate immunity, mitocho...
Article
Since the advent of high-throughput DNA sequencing technologies, the ever-increasing rate at which genomes have been published has generated new challenges notably at the level of genome annotation. Even if gene predictors and annotation softwares are more and more efficient, the ultimate validation is still in the observation of predicted gene pro...
Article
Full-text available
Standard proteomics methods allow the relative quantitation of levels of thousands of proteins in two or more samples. While such methods are invaluable for defining the variations in protein concentrations which follow the perturbation of a biological system, they do not offer information on the mechanisms underlying such changes. Expanding on pre...
Article
Full-text available
The molecular chaperone Hsp90-dependent proteome represents a complex protein network of critical biological and medical relevance. Known to associate with proteins with a broad variety of functions termed clients, Hsp90 maintains key essential and oncogenic signalling pathways. Consequently, Hsp90 inhibitors are being tested as anti-cancer drugs....
Article
Full-text available
ExPASy (http://www.expasy.org) has worldwide reputation as one of the main bioinformatics resources for proteomics. It has now evolved, becoming an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. Scientists can henceforth access seamlessly a wide range of resou...
Article
In the vast majority of bottom-up proteomics studies, protein digestion is performed using only mammalian trypsin. Although it is clearly the best enzyme available, the sole use of trypsin rarely leads to complete sequence coverage, even for abundant proteins. It is commonly assumed that this is because many tryptic peptides are either too short or...
Article
Pancreatic beta-cells are responsible for insulin secretion that regulates blood glucose homeostasis. In the development of type II diabetes, a progressive impairment of insulin secretion by the pancreatic beta-cells occurs called beta-cell dysfunction or beta-cell failure. Chronic hyperglycemia has been shown being involved in beta-cell dysfunctio...
Article
The identification and characterization of peptides from MS/MS data represents a critical aspect of proteomics. It has been the subject of extensive research in bioinformatics resulting in the generation of a fair number of identification software tools. Most often, only one program with a specific and unvarying set of parameters is selected for id...
Article
The use of isoelectric focusing as first dimension of separation is a new trend in shotgun proteomics. In all applications using this approach, peptides are separated into equitable fractions, whereas theoretical distribution of peptides according to p I is heterogeneous. We present the development of a new tool and strategy that generates a fracti...
Article
Full-text available
The identification and characterization of peptides from tandem mass spectrometry (MS/MS) data represents a critical aspect of proteomics. Today, tandem MS analysis is often performed by only using a single identification program achieving identification rates between 10–50% (Elias and Gygi, 2007). Beside the development of new analysis tools, rece...
Article
Full-text available
Stable isotope labeling of amino acids in cell culture was used for Bifidobacterium longum. A comprehensive proteomic strategy was developed and validated by designing an appropriate semidefined medium that allows stable replacement of natural leucine by [13C6]leucine. Using this strategy, proteins having variations of at least 50% in their express...
Article
Full-text available
Biomarker detection is one of the greatest challenges in Clinical Proteomics. Today, great hopes are placed into tandem mass spectrometry (MS/MS) to discover potential biomarkers. MS/MS is a technique that allows large scale data analysis, including the identification, characterization, and quantification of molecules. Especially the identification...
Conference Paper
8. Abstracts & Posters , The following values have no corresponding Zotero field: pub-location: Fortaleza, Brazil