High-quality analyses
AltraBio deploys its recognized expertise in bioinformatics, biostatistic and biology to provide services in the analysis and interpretation of all types of omics data (genomics, epigenomics, transcriptomics, proteomics…).
For each project, AltraBio’s team works in interaction with its clients/partners in order to reach their goals.
Expertise in biostatistics and bioinformatics
Prior to performing differential analyses, various methods are implemented to assess the quality of the data and their agreement with the experimental design. We specifically control for outliers and for effects unrelated to the design in order to correct them with the agreement of our client/partner. Thus the relevance of the performed analysis is guaranteed.
Experimental designs may consist of multiple factors (donor, cell type, treatment, dose, timepoints…) and thus can be analyzed from multiple angles. To answer the biological question(s) of the study, AltraBio determines the most suitable statistical model (paired design, batch effect correction, hidden factor estimation, weighting of outliers…).
AltraBio possesses the know-how to integrate different types of data (multi-omics, cytometry, medical data…). Supervised and unsupervised machine learning can be implemented for various applications: biomarker identification, classification, predictive models for diagnostic or response to treatment. Thus our clients benefit from our strong expertise in using up-to-date machine learning algorithms to extract the maximum value from their data.
Expertise in biology
Biological processes and pathways are identified thanks to the implementation of various and complementary methods of functional categories enrichment. These automatic results are then reviewed to assess their relevance with the biological context of the study.
Beyond providing lists of molecules and biological pathways, AltraBio’s role is also to extract meaning. To this end, the interpretation phase takes into account the biological question(s) at the origin of the study and assesses the results while integrating the biological knowledge available in the scientific literature and databases. The goal is to understand the biological mechanisms at play and to formulate new hypotheses to be validated (examples of synthetic diagrams produced by AltraBio in figures S8A and S9A of this article).
Reporting
All of the work carried out is summarized in a complete report transferred to our client/partner and explained during a video conference. This exchange makes it possible to explain the chosen methodological approaches and their results as well as to ensure that our client/partner has the best understanding of their data.
Statistical analysis results are also available in the WikiBioPath web interface which provides our clients/partners a set of visualisation and analysis tools which enables them to continue the exploration of their data. They can easily generate new volcano plots, heat maps, PCA and enrichment analyses on gene selections.
Our publications in Omics Data Analysis
2022
Salis, Pauline; Peyran, Claire; Morage, Titouan; de Bernard, Simon; Nourikyan, Julien; Coupé, Stéphane; Bunet, Robert; Planes, Serge
RNA-Seq comparative study reveals molecular effectors linked to the resistance of Pinna nobilis to Haplosporidium pinnae parasite Journal Article
In: Sci Rep, vol. 12, no. 1, pp. 21229, 2022, ISSN: 2045-2322.
@article{pmid36482098,
title = {RNA-Seq comparative study reveals molecular effectors linked to the resistance of Pinna nobilis to Haplosporidium pinnae parasite},
author = {Pauline Salis and Claire Peyran and Titouan Morage and Simon de Bernard and Julien Nourikyan and Stéphane Coupé and Robert Bunet and Serge Planes},
doi = {10.1038/s41598-022-25555-x},
issn = {2045-2322},
year = {2022},
date = {2022-12-01},
urldate = {2022-12-01},
journal = {Sci Rep},
volume = {12},
number = {1},
pages = {21229},
abstract = {With the intensification of maritime traffic, recently emerged infectious diseases have become major drivers in the decline and extinction of species. Since 2016, mass mortality events have decimated the endemic Mediterranean Sea bivalve Pinna nobilis, affecting ca. 100% of individuals. These events have largely been driven by Haplosporidium pinnae's infection, an invasive species which was likely introduced by shipping. While monitoring wild populations of P. nobilis, we observed individuals that survived such a mass mortality event during the summer of 2018 (France). We considered these individuals resistant, as they did not show any symptoms of the disease, while the rest of the population in the area was devastated. Furthermore, the parasite was not detected when we conducted a PCR amplification of a species-specific fragment of the small subunit ribosomal DNA. In parallel, the transcriptomic analysis showed evidence of some parasite RNA indicating that the resistant individuals had been exposed to the parasite without proliferating. To understand the underlying mechanisms of resistance in these individuals, we compared their gene expression with that of susceptible individuals. We performed de novo transcriptome assembly and annotated the expressed genes. A comparison of the transcriptomes in resistant and susceptible individuals highlighted a gene expression signature of the resistant phenotype. We found significant differential expressions of genes involved in immunity and cell architecture. This data provides the first insights into how individuals escape the pathogenicity associated with infection.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Todorov, Helena; Prieux, Margaux; Laubreton, Daphne; Bouvier, Matteo; Wang, Shaoying; de Bernard, Simon; Arpin, Christophe; Cannoodt, Robrecht; Saelens, Wouter; Bonnaffoux, Arnaud; Gandrillon, Olivier; Crauste, Fabien; Saeys, Yvan; Marvel, Jacqueline
CD8 memory precursor cell generation is a continuous process Journal Article
In: iScience, vol. 25, no. 9, pp. 104927, 2022, ISSN: 2589-0042.
@article{pmid36065187,
title = {CD8 memory precursor cell generation is a continuous process},
author = {Helena Todorov and Margaux Prieux and Daphne Laubreton and Matteo Bouvier and Shaoying Wang and Simon de Bernard and Christophe Arpin and Robrecht Cannoodt and Wouter Saelens and Arnaud Bonnaffoux and Olivier Gandrillon and Fabien Crauste and Yvan Saeys and Jacqueline Marvel},
doi = {10.1016/j.isci.2022.104927},
issn = {2589-0042},
year = {2022},
date = {2022-09-01},
urldate = {2022-09-01},
journal = {iScience},
volume = {25},
number = {9},
pages = {104927},
abstract = {In this work, we studied the generation of memory precursor cells following an acute infection by analyzing single-cell RNA-seq data that contained CD8 T cells collected during the postinfection expansion phase. We used different tools to reconstruct the developmental trajectory that CD8 T cells followed after activation. Cells that exhibited a memory precursor signature were identified and positioned on this trajectory. We found that these memory precursors are generated continuously with increasing numbers arising over time. Similarly, expression of genes associated with effector functions was also found to be raised in memory precursors at later time points. The ability of cells to enter quiescence and differentiate into memory cells was confirmed by BrdU pulse-chase experiment . Analysis of cell counts indicates that the vast majority of memory cells are generated at later time points from cells that have extensively divided.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Silic, Linda Ljungberg; Lefevre, Marine-Alexia; Bergendorff, Ola; Bernard, Simon De; Nourikyan, Julien; Buffat, Laurent; Nosbaum, Audrey; Bruze, Magnus; Nicolas, Jean-François; Svedman, Cecilia; Vocanson, Marc
Gene profiling reveals a contact allergy signature in most positive Amerchol L-101 patch test reactions Journal Article
In: Contact Dermatitis, vol. 87, no. 1, pp. 40–52, 2022, ISSN: 1600-0536.
@article{pmid35184302,
title = {Gene profiling reveals a contact allergy signature in most positive Amerchol L-101 patch test reactions},
author = {Linda Ljungberg Silic and Marine-Alexia Lefevre and Ola Bergendorff and Simon De Bernard and Julien Nourikyan and Laurent Buffat and Audrey Nosbaum and Magnus Bruze and Jean-François Nicolas and Cecilia Svedman and Marc Vocanson},
doi = {10.1111/cod.14077},
issn = {1600-0536},
year = {2022},
date = {2022-07-01},
urldate = {2022-07-01},
journal = {Contact Dermatitis},
volume = {87},
number = {1},
pages = {40--52},
abstract = {BACKGROUND: Diagnosis of contact allergy (CA) to Amerchol L-101 (AL-101), a marker for lanolin allergy, is problematic. Positive patch test reactions are frequently doubtful or weakly positive and difficult to associate with clinical relevance.
OBJECTIVE: To gain further insight on the allergic or irritant nature of skin reactions induced by AL-101 patch test.
METHODS: We re-tested in a dose-response fashion, 10 subjects with AL-101 CA and performed comprehensive transcriptomic analysis (gene arrays, quantitative real-time polymerase chain reaction [qRT-PCR]) of samples of their skin reactions.
RESULTS: Eight of the 10 CA subjects reacted positively upon re-test, whereas two did not react. Most of AL-101 positive patch tests expressed an allergy signature with strong activation of gene modules associated with adaptive immunity and downregulation of cornification pathway genes. In addition, the breadth of gene modulation correlated with the magnitude of patch test reactions and the concentration of AL-101 applied. However, we observed that some of the positive patch test reactions to AL-101 expressed no/few allergy biomarkers, suggesting the induction of an irritant skin inflammation in these samples.
CONCLUSIONS: This study confirms that AL-101 is an allergen that can cause both contact allergy and contact irritation. Our results also highlight that molecular profiling might help to strengthen clinical diagnosis.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
OBJECTIVE: To gain further insight on the allergic or irritant nature of skin reactions induced by AL-101 patch test.
METHODS: We re-tested in a dose-response fashion, 10 subjects with AL-101 CA and performed comprehensive transcriptomic analysis (gene arrays, quantitative real-time polymerase chain reaction [qRT-PCR]) of samples of their skin reactions.
RESULTS: Eight of the 10 CA subjects reacted positively upon re-test, whereas two did not react. Most of AL-101 positive patch tests expressed an allergy signature with strong activation of gene modules associated with adaptive immunity and downregulation of cornification pathway genes. In addition, the breadth of gene modulation correlated with the magnitude of patch test reactions and the concentration of AL-101 applied. However, we observed that some of the positive patch test reactions to AL-101 expressed no/few allergy biomarkers, suggesting the induction of an irritant skin inflammation in these samples.
CONCLUSIONS: This study confirms that AL-101 is an allergen that can cause both contact allergy and contact irritation. Our results also highlight that molecular profiling might help to strengthen clinical diagnosis.