Tailored Omics Data Analysis Solutions for Your Research Projects
Based in Lyon, AltraBio specializes in omics data analysis, combining 20 years of expertise in bioinformatics, biostatistics, and biology to analyze your omics data (transcriptomics, proteomics, epigenomics, etc.). Our collaborative approach ensures results aligned with your research goals, whether for biomarker discovery, biological mechanism deciphering, or multi-omics data integration.
Expertise in Bioinformatics for Omics Data Analysis
Our team evaluates data quality (RNA-Seq, proteomics, etc.) and ensures consistency with experimental design. We address outliers and non-design-related effects to guarantee meaningful omics data analysis.
Experimental designs often involve multiple factors (donor, cell type, treatment, dose, time points). We identify the optimal statistical model for your omics data (e.g., batch effect corrections, multi-factor analysis).
Specializing in data integration (transcriptomics, cytometry, medical data), we leverage AI to uncover biomarkers and molecular signatures.
Omics Data Analysis Services by Type
Transcriptomics studies all RNA in a cell to reveal active genes and expression levels. In Lyon, AltraBio uses this approach to identify biomarkers and gene regulation mechanisms, including RNA-Seq, single-cell, and spatial transcriptomics.
Extended services: Partnerships with european NGS platforms for data generation.
Proteomics quantifies proteins and their modifications, complementing transcriptomic insights. Our team identifies therapeutic targets and validates protein biomarkers.
Genomics explores genetic variations (SNPs, mutations) and their phenotypic associations.
Extended services: Partnerships with european NGS platforms for data generation.
Epigenomics examines DNA modifications (methylation, chromatin) that regulate gene expression without altering sequences. We analyze these to understand mechanisms like aging or treatment responses.
Extended services: Partnerships with european NGS platforms for data generation.
Multi-omics integration combines datasets (transcriptomics + proteomics) for systemic biological insights. We cross-reference data to identify unique molecular signatures.
Biological Expertise
We analyze your omics data (transcriptomics, proteomics, epigenomics) in biological context to extract actionable insights.
Beyond gene lists, we integrate literature and database knowledge to understand biological mechanisms and formulate testable hypotheses.
Reports and Tools
Our reports for researchers and industries include visualizations (volcano plots, heatmaps) and clear recommendations.
Each project concludes with a meeting to clarify methodologies and results.
Explore statistical results via our WikiBioPath web interface for dynamic omics data visualization (PCA, enrichment analysis, etc.).
Discover WikiBioPath
Why Choose AltraBio?
With two decades of expertise in maths, stats, biology, and medical science, AltraBio delivers actionable insights without hype. A trusted partner in Lyon for omics data analysis.
« Even in the age of generative AI, Altrabio’s two decades of expertise in maths, stats, biology, and medical science remain invaluable. They don’t just talk, they do. No flashy marketing, no inflated costs, just solid, thoughtful work from study design to actionable insights. A trusted partner, for twenty years, in a world full of noise. Highly recommend working with them to make real sense of your complex biomedical and omics data. »
Discover how our tailored solutions in omics data analysis can accelerate your R&D projects.
Publications
Discover our peer-reviewed publications on omics data analysis, recognized by the scientific community.
2026
Elliott, Tamara; Wang, Ziyin; Bonduelle, Olivia; Evans, Abbey; Day, Suzanne; McFarlane, Leon R.; de Bernard, Simon; Alves, Karine; Nourikyan, Julien; Wokam, Michele; Pollock, Katrina; Cheeseman, Hannah M.; Combadiere, Behazine; Shattock, Robin J.; Tregoning, John S.
Systems vaccinology analysis of saRNA immunization identifies an acute innate immune signature correlated with adaptive immunity Journal Article
In: Molecular Therapy Advances, vol. 34, no. 1, 2026, ISSN: 3117-387X.
@article{Elliott2026,
title = {Systems vaccinology analysis of saRNA immunization identifies an acute innate immune signature correlated with adaptive immunity},
author = {Tamara Elliott and Ziyin Wang and Olivia Bonduelle and Abbey Evans and Suzanne Day and Leon R. McFarlane and Simon de Bernard and Karine Alves and Julien Nourikyan and Michele Wokam and Katrina Pollock and Hannah M. Cheeseman and Behazine Combadiere and Robin J. Shattock and John S. Tregoning},
doi = {10.1016/j.omta.2026.201706},
issn = {3117-387X},
year = {2026},
date = {2026-03-12},
urldate = {2026-03-12},
journal = {Molecular Therapy Advances},
volume = {34},
number = {1},
publisher = {Elsevier BV},
abstract = {Self-amplifying ribonucleic acid (saRNA) vaccines are a next-generation RNA vaccine platform with great potential. Systems vaccinology provides a potent tool to interrogate vaccine-induced responses in volunteers and to dissect the mechanisms by which vaccines elicit a protective immune response or cause reactogenicity. In the current study, we performed transcriptomic analysis on blood samples collected from volunteers vaccinated as part of a phase I study of an saRNA vaccine expressing the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike antigen. We observed significant gene over-expression following both the prime and boost vaccinations. Over-expressed genes were predominantly associated with type I interferon signaling pathways and innate immune cell recruitment. This transcriptomic signature was reflected by an increase in cytokines in the plasma at the same time points and a significant increase in monocytes in the blood, both of which correlated with the antibody response to the vaccine. When individuals were segregated by the degree of reactogenicity, we also detected differences in gene expression related to immune responses. Overall, results show that saRNA induces a potent, acute inflammatory response with similarities to other RNA vaccines, and it will be important to further dissect the role of the over-expressed genes in immunogenicity and reactogenicity.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2025
Ribeiro, Sara; Alves, Karine; Nourikyan, Julien; Lavergne, Jean-Pierre; de Bernard, Simon; Buffat, Laurent
Identifying potential novel widespread determinants of bacterial pathogenicity using phylogenetic-based orthology analysis Journal Article
In: Front. Microbiol., vol. 16, 2025, ISSN: 1664-302X.
@article{Ribeiro2025,
title = {Identifying potential novel widespread determinants of bacterial pathogenicity using phylogenetic-based orthology analysis},
author = {Sara Ribeiro and Karine Alves and Julien Nourikyan and Jean-Pierre Lavergne and Simon de Bernard and Laurent Buffat},
doi = {10.3389/fmicb.2025.1494490},
issn = {1664-302X},
year = {2025},
date = {2025-05-01},
urldate = {2025-05-01},
journal = {Front. Microbiol.},
volume = {16},
publisher = {Frontiers Media SA},
abstract = {<jats:sec><jats:title>Introduction</jats:title><jats:p>The global rise in antibiotic resistance and emergence of new bacterial pathogens pose a significant threat to public health. Novel approaches to uncover potential novel diagnostic and therapeutic targets for these pathogens are needed.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>In this study, we conducted a large-scale, phylogenetic-based orthology analysis (OA) to compare the proteomes of pathogenic to humans (HP) and non-pathogenic to humans (NHP) bacterial strains across 734 strains from 514 species and 91 families.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>Using a dedicated workflow, we identified 4,383 hierarchical orthologous groups (HOGs) significantly associated with the HP label, many of which are linked to critical factors such as stress tolerance, metabolic versatility, and antibiotic resistance. Both known virulence factors (VFs) and potential novel widespread pathogenicity determinants were uncovered, supported by both statistical testing and complementary protein domain analysis.</jats:p></jats:sec><jats:sec><jats:title>Discussion</jats:title><jats:p>By integrating curated strain-level pathogenicity annotations from BacSPaD with phylogeny-based OA, we introduce a novel approach and provide a novel resource for bacterial pathogenicity research.</jats:p></jats:sec>},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Bonduelle, Olivia; Delory, Tristan; Moscardini, Isabelle Franco; Ghidi, Marion; Bennacer, Selma; Wokam, Michele; Lenormand, Mathieu; Petrier, Melissa; Rogeaux, Olivier; de Bernard, Simon; Alves, Karine; Nourikyan, Julien; Lina, Bruno; Combadiere, Behazine; Janssen, Cécile
Boosting effect of high-dose influenza vaccination on innate immunity among elderly: a randomized-control trial Journal Article
In: JCI Insight, 2025, ISSN: 2379-3708.
@article{pmid40036077,
title = {Boosting effect of high-dose influenza vaccination on innate immunity among elderly: a randomized-control trial},
author = {Olivia Bonduelle and Tristan Delory and Isabelle Franco Moscardini and Marion Ghidi and Selma Bennacer and Michele Wokam and Mathieu Lenormand and Melissa Petrier and Olivier Rogeaux and Simon de Bernard and Karine Alves and Julien Nourikyan and Bruno Lina and Behazine Combadiere and Cécile Janssen},
doi = {10.1172/jci.insight.184128},
issn = {2379-3708},
year = {2025},
date = {2025-03-01},
urldate = {2025-03-01},
journal = {JCI Insight},
abstract = {BACKGROUND: The high-dose quadrivalent influenza vaccine (QIV-HD) showed superior efficacy against laboratory-confirmed illness than the standard-dose quadrivalent influenza vaccine (QIV-SD) in randomized-controlled trials with elderly. However, specific underlying mechanism remains unclear.nnMETHODS: This Phase-IV randomized control trial compared early innate responses induced by QIV-HD and QIV-SD in 59 subjects aged >65 years. Systemic innate cells and gene signatures at Day (D) 0 and D1, hemagglutinin inhibition antibody (HIA) titers at D0 and D21 post-vaccination were assessed.nnRESULTS: QIV-HD elicited robust humoral response with significantly higher antibody titers and seroconversion rates than QIV-SD. At D1 post-vaccination, QIV-HD recipients showed significant reduction in innate cells, including conventional dendritic cells and natural killer cells than QIV-SD, correlating with significantly increased HIA titers at D21. Blood transcriptomic analysis revealed greater amplitude of gene expression in QIV-HD arm, encompassing genes related to innate immune response, interferons, and antigen processing and presentation and correlated with humoral responses. Interestingly, comparative analysis with a literature dataset from young adults vaccinated with influenza standard-dose vaccine highlighted strong similarities in gene expression patterns and biological pathways with the elderly vaccinated with QIV-HD.nnCONCLUSION: QIV-HD induces higher HIA titers than QIV-SD, a youthful boost of the innate gene expression significantly associated with high HIA titers.nnTRIAL REGISTRATION: EudraCT Number: 2021-004573-32.},
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pubstate = {published},
tppubtype = {article}
}