High-quality analyses
AltraBio harnesses its renowned expertise in bioinformatics, biostatistics, and biology to offer services in the analysis and interpretation of various omics data types (genomics, epigenomics, transcriptomics, proteomics, etc.).
Our team collaborates closely with clients and partners for each project to ensure their goals are met.
Expertise in biostatistics and bioinformatics
Before conducting differential analyses, we implement various methods to assess the data quality and its consistency with the experimental design. We specifically address outliers and effects unrelated to the design to correct them in agreement with of our client/partner. This ensures the relevance of the analysis performed.
Experimental designs may involve multiple factors such as donor, cell type, treatment, dose, and timepoints, allowing for analysis from various perspectives. To address the biological question(s) of the study, AltraBio identifies the most appropriate statistical model (paired design, batch effect correction, estimation of hidden factors, outlier weighting, etc.).
AltraBio has the expertise to integrate various types of data (multi-omics, cytometry, medical data, etc.). We employ supervised and unsupervised machine learning for various applications including biomarker identification, classification, predictive models for diagnostics or treatment response. Our clients benefit from our strong proficiency in utilizing state-of-the-art machine learning algorithms to extract maximum value from their data.
Expertise in biology
Biological processes and pathways are identified through the implementation of various complementary methods of functional category enrichment. These automated 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 to extract meaning. In the interpretation phase, we consider the biological question(s) that initiated the study and evaluate the results while integrating biological knowledge available in scientific literature and databases. Our goal is to understand the biological mechanisms at play and formulate new hypotheses for validation. Examples of synthetic diagrams produced by AltraBio can be found in figures S8A and S9A of this article).
Reporting
All the work conducted is summarized in a comprehensive report provided to our client/partner and explained during a video conference. This exchange allows us to clarify the chosen methodological approaches and their results, ensuring that our client/partner has the best understanding of their data.
The results of statistical analysis are also accessible through the WikiBioPath web interface, providing our clients/partners with a set of visualisation and analysis tools to continue exploring their data. They can easily visualize volcano plots, generate new heat maps, perform PCA, and conduct enrichment analyses on gene selections.
Our publications in Omics Data Analysis
2019
Girardeau-Hubert, Sarah; Deneuville, Céline; Pageon, Hervé; Abed, Kahina; Tacheau, Charlotte; Cavusoglu, Nükhet; Donovan, Mark; Bernard, Dominique; Asselineau, Daniel
Reconstructed Skin Models Revealed Unexpected Differences in Epidermal African and Caucasian Skin Journal Article
In: Sci Rep, vol. 9, no. 1, pp. 7456, 2019, ISSN: 2045-2322.
@article{pmid31092846,
title = {Reconstructed Skin Models Revealed Unexpected Differences in Epidermal African and Caucasian Skin},
author = {Sarah Girardeau-Hubert and Céline Deneuville and Hervé Pageon and Kahina Abed and Charlotte Tacheau and Nükhet Cavusoglu and Mark Donovan and Dominique Bernard and Daniel Asselineau},
doi = {10.1038/s41598-019-43128-3},
issn = {2045-2322},
year = {2019},
date = {2019-05-01},
urldate = {2019-05-01},
journal = {Sci Rep},
volume = {9},
number = {1},
pages = {7456},
abstract = {Clinical observations of both normal and pathological skin have shown that there is a heterogeneity based on the skin origin type. Beside external factors, intrinsic differences in skin cells could be a central element to determine skin types. This study aimed to understand the in vitro behaviour of epidermal cells of African and Caucasian skin types in the context of 3D reconstructed skin. Full-thickness skin models were constructed with site matched human keratinocytes and papillary fibroblasts to investigate potential skin type related differences. We report that reconstructed skin epidermis exhibited remarkable differences regarding stratification and differentiation according to skin types, as demonstrated by histological appearance, gene expression analysed by DNA microarray and quantitative proteomic analysis. Signalling pathways and processes related to terminal differentiation and lipid/ceramide metabolism were up-regulated in epidermis constructed with keratinocytes from Caucasian skin type when compared to that of keratinocytes from African skin type. Specifically, the expression of proteins involved in the processing of filaggrins was found different between skin models. Overall, we show unexpected differences in epidermal morphogenesis and differentiation between keratinocytes of Caucasian and African skin types in in vitro reconstructed skin containing papillary fibroblasts that could explain the differences in ethnic related skin behaviour.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Nauroy, Pauline; Guiraud, Alexandre; Chlasta, Julien; Malbouyres, Marilyne; Gillet, Benjamin; Hughes, Sandrine; Lambert, Elise; Ruggiero, Florence
Gene profile of zebrafish fin regeneration offers clues to kinetics, organization and biomechanics of basement membrane Journal Article
In: Matrix Biol, vol. 75-76, pp. 82–101, 2019, ISSN: 1569-1802.
@article{pmid30031067,
title = {Gene profile of zebrafish fin regeneration offers clues to kinetics, organization and biomechanics of basement membrane},
author = {Pauline Nauroy and Alexandre Guiraud and Julien Chlasta and Marilyne Malbouyres and Benjamin Gillet and Sandrine Hughes and Elise Lambert and Florence Ruggiero},
doi = {10.1016/j.matbio.2018.07.005},
issn = {1569-1802},
year = {2019},
date = {2019-01-01},
urldate = {2019-01-01},
journal = {Matrix Biol},
volume = {75-76},
pages = {82--101},
abstract = {How some animals regenerate missing body parts is not well understood. Taking advantage of the zebrafish caudal fin model, we performed a global unbiased time-course transcriptomic analysis of fin regeneration. Biostatistics analyses identified extracellular matrix (ECM) as the most enriched gene sets. Basement membranes (BMs) are specialized ECM structures that provide tissues with structural cohesion and serve as a major extracellular signaling platform. While the embryonic formation of BM has been extensively investigated, its regeneration in adults remains poorly studied. We therefore focused on BM gene expression kinetics and showed that it recapitulates many aspects of development. As such, the re-expression of the embryonic col14a1a gene indicated that col14a1a is part of the regeneration-specific program. We showed that laminins and col14a1a genes display similar kinetics and that the corresponding proteins are spatially and temporally controlled during regeneration. Analysis of our CRISPR/Cas9-mediated col14a1a knockout fish showed that collagen XIV-A contributes to timely deposition of laminins. As changes in ECM organization can affect tissue mechanical properties, we analyzed the biomechanics of col14a1a regenerative BM using atomic force microscopy (AFM). Our data revealed a thinner BM accompanied by a substantial increase of the stiffness when compared to controls. Further AFM 3D-reconstructions showed that BM is organized as a checkerboard made of alternation of soft and rigid regions that is compromised in mutants leading to a more compact structure. We conclude that collagen XIV-A transiently acts as a molecular spacer responsible for BM structure and biomechanics possibly by helping laminins integration within regenerative BM.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2017
Nauroy, Pauline; Barruche, Vincent; Marchand, Laetitia; Nindorera-Badara, Steven; Bordes, Sylvie; Closs, Brigitte; Ruggiero, Florence
vol. 137, no. 8, 2017, ISSN: 1523-1747.
@proceedings{pmid28428131,
title = {Human Dermal Fibroblast Subpopulations Display Distinct Gene Signatures Related to Cell Behaviors and Matrisome},
author = {Pauline Nauroy and Vincent Barruche and Laetitia Marchand and Steven Nindorera-Badara and Sylvie Bordes and Brigitte Closs and Florence Ruggiero},
doi = {10.1016/j.jid.2017.03.028},
issn = {1523-1747},
year = {2017},
date = {2017-08-01},
urldate = {2017-08-01},
journal = {J Invest Dermatol},
volume = {137},
number = {8},
pages = {1787--1789},
keywords = {},
pubstate = {published},
tppubtype = {proceedings}
}