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.
2024
Wang, Shaoying; Prieux, Margaux; de Bernard, Simon; Dubois, Maxence; Laubreton, Daphne; Djebali, Sophia; Zala, Manon; Arpin, Christophe; Genestier, Laurent; Leverrier, Yann; Gandrillon, Olivier; Crauste, Fabien; Jiang, Wenzheng; Marvel, Jacqueline
Exogenous IL-2 delays memory precursors generation and is essential for enhancing memory cells effector functions Journal Article
In: iScience, vol. 27, no. 4, pp. 109411, 2024, ISSN: 2589-0042.
@article{pmid38510150,
title = {Exogenous IL-2 delays memory precursors generation and is essential for enhancing memory cells effector functions},
author = {Shaoying Wang and Margaux Prieux and Simon de Bernard and Maxence Dubois and Daphne Laubreton and Sophia Djebali and Manon Zala and Christophe Arpin and Laurent Genestier and Yann Leverrier and Olivier Gandrillon and Fabien Crauste and Wenzheng Jiang and Jacqueline Marvel},
doi = {10.1016/j.isci.2024.109411},
issn = {2589-0042},
year = {2024},
date = {2024-04-01},
urldate = {2024-04-01},
journal = {iScience},
volume = {27},
number = {4},
pages = {109411},
abstract = {To investigate the impact of paracrine IL-2 signals on memory precursor (MP) cell differentiation, we activated CD8 T cell in the presence or absence of exogenous IL-2 (ex-IL-2). We assessed memory differentiation by transferring these cells into virus-infected mice. Both conditions generated CD8 T cells that participate in the ongoing response and gave rise to similar memory cells. Nevertheless, when transferred into a naive host, T cells activated with ex-IL-2 generated a higher frequency of memory cells displaying increased functional memory traits. Single-cell RNA-seq analysis indicated that without ex-IL-2, cells rapidly acquire an MP signature, while in its presence they adopted an effector signature. This was confirmed at the protein level and in a functional assay. Overall, ex-IL-2 delays the transition into MP cells, allowing the acquisition of effector functions that become imprinted in their progeny. These findings may help to optimize the generation of therapeutic T cells.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2023
Nedachi, Taku; Bonod, Christelle; Rorteau, Julie; Chinoune, Wafae; Ishiuchi, Yuri; Hughes, Sandrine; Gillet, Benjamin; Bechetoille, Nicolas; Sigaudo-Roussel, Dominique; Lamartine, Jérôme
Chronological aging impacts abundance, function and microRNA content of extracellular vesicles produced by human epidermal keratinocytes Journal Article
In: Aging (Albany NY), vol. 15, no. 22, pp. 12702–12722, 2023, ISSN: 1945-4589.
@article{pmid38015712,
title = {Chronological aging impacts abundance, function and microRNA content of extracellular vesicles produced by human epidermal keratinocytes},
author = {Taku Nedachi and Christelle Bonod and Julie Rorteau and Wafae Chinoune and Yuri Ishiuchi and Sandrine Hughes and Benjamin Gillet and Nicolas Bechetoille and Dominique Sigaudo-Roussel and Jérôme Lamartine},
doi = {10.18632/aging.205245},
issn = {1945-4589},
year = {2023},
date = {2023-11-01},
urldate = {2023-11-01},
journal = {Aging (Albany NY)},
volume = {15},
number = {22},
pages = {12702--12722},
abstract = {The disturbance of intercellular communication is one of the hallmarks of aging. The goal of this study is to clarify the impact of chronological aging on extracellular vesicles (EVs), a key mode of communication in mammalian tissues. We focused on epidermal keratinocytes, the main cells of the outer protective layer of the skin which is strongly impaired in the skin of elderly. EVs were purified from conditioned medium of primary keratinocytes isolated from infant or aged adult skin. A significant increase of the relative number of EVs released from aged keratinocytes was observed whereas their size distribution was not modified. By small RNA sequencing, we described a specific microRNA (miRNA) signature of aged EVs with an increase abundance of miR-30a, a key regulator of barrier function in human epidermis. EVs from aged keratinocytes were found to be able to reduce the proliferation of young keratinocytes, to impact their organogenesis properties in a reconstructed epidermis model and to slow down the early steps of skin wound healing in mice, three features observed in aged epidermis. This work reveals that intercellular communication mediated by EVs is modulated during aging process in keratinocytes and might be involved in the functional defects observed in aged skin.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Roux, Natacha; Miura, Saori; Dussenne, Mélanie; Tara, Yuki; Lee, Shu-Hua; de Bernard, Simon; Reynaud, Mathieu; Salis, Pauline; Barua, Agneesh; Boulahtouf, Abdelhay; Balaguer, Patrick; Gauthier, Karine; Lecchini, David; Gibert, Yann; Besseau, Laurence; Laudet, Vincent
The multi-level regulation of clownfish metamorphosis by thyroid hormones Journal Article
In: Cell Rep, vol. 42, no. 7, pp. 112661, 2023, ISSN: 2211-1247.
@article{pmid37347665,
title = {The multi-level regulation of clownfish metamorphosis by thyroid hormones},
author = {Natacha Roux and Saori Miura and Mélanie Dussenne and Yuki Tara and Shu-Hua Lee and Simon de Bernard and Mathieu Reynaud and Pauline Salis and Agneesh Barua and Abdelhay Boulahtouf and Patrick Balaguer and Karine Gauthier and David Lecchini and Yann Gibert and Laurence Besseau and Vincent Laudet},
doi = {10.1016/j.celrep.2023.112661},
issn = {2211-1247},
year = {2023},
date = {2023-06-01},
urldate = {2023-06-01},
journal = {Cell Rep},
volume = {42},
number = {7},
pages = {112661},
abstract = {Most marine organisms have a biphasic life cycle during which pelagic larvae transform into radically different juveniles. In vertebrates, the role of thyroid hormones (THs) in triggering this transition is well known, but how the morphological and physiological changes are integrated in a coherent way with the ecological transition remains poorly explored. To gain insight into this question, we performed an integrated analysis of metamorphosis of a marine teleost, the false clownfish (Amphiprion ocellaris). We show how THs coordinate a change in color vision as well as a major metabolic shift in energy production, highlighting how it orchestrates this transformation. By manipulating the activity of liver X regulator (LXR), a major regulator of metabolism, we also identify a tight link between metabolic changes and metamorphosis progression. Strikingly, we observed that these regulations are at play in the wild, explaining how hormones coordinate energy needs with available resources during the life cycle.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}