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
2022
Roux, Natacha; Miura, Saori; Dussene, Mélanie; Tara, Yuki; Lee, Fiona; 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: bioRxiv, 2022.
@article{Roux2022.03.04.482938,
title = {The multi-level regulation of clownfish metamorphosis by thyroid hormones},
author = {Natacha Roux and Saori Miura and Mélanie Dussene and Yuki Tara and Fiona Lee and Simon 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},
url = {https://www.biorxiv.org/content/early/2022/03/04/2022.03.04.482938},
doi = {10.1101/2022.03.04.482938},
year = {2022},
date = {2022-03-04},
urldate = {2022-01-01},
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
abstract = {Most marine organisms have a biphasic life cycle during which a pelagic larva is transformed into a radically different juvenile. In vertebrates the role of thyroid hormones (TH) 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 integrative analysis of metamorphosis of a marine teleost, the clownfish Amphiprion ocellaris. We reveal how TH coordinate a change in color vision as well as a major metabolic shift in energy production, hence highlighting its central integrative role in regulating this transformation. By manipulating the activity of LXR, a major regulator of metabolism, we also reveal a tight link between metabolic changes and metamorphosis progression. Strikingly, we observed that these regulations are at play in the wild revealing how hormones coordinate energy needs with available resources during life cycle.Competing Interest StatementThe authors have declared no competing interest.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Clément, Flora; Nougarède, Adrien; Combe, Stéphanie; Kermarrec, Frédérique; Dey, Arindam K; Obeid, Patricia; Millet, Arnaud; Navarro, Fabrice P; Marche, Patrice N; Sulpice, Eric; Gidrol, Xavier
Therapeutic siRNAs Targeting the JAK/STAT Signalling Pathway in Inflammatory Bowel Diseases Journal Article
In: J Crohns Colitis, vol. 16, no. 2, pp. 286–300, 2022, ISSN: 1876-4479.
@article{pmid34286840,
title = {Therapeutic siRNAs Targeting the JAK/STAT Signalling Pathway in Inflammatory Bowel Diseases},
author = {Flora Clément and Adrien Nougarède and Stéphanie Combe and Frédérique Kermarrec and Arindam K Dey and Patricia Obeid and Arnaud Millet and Fabrice P Navarro and Patrice N Marche and Eric Sulpice and Xavier Gidrol},
doi = {10.1093/ecco-jcc/jjab129},
issn = {1876-4479},
year = {2022},
date = {2022-02-01},
urldate = {2022-02-01},
journal = {J Crohns Colitis},
volume = {16},
number = {2},
pages = {286--300},
abstract = {BACKGROUND AND AIMS: Inflammatory bowel diseases are highly debilitating conditions that require constant monitoring and life-long medication. Current treatments are focused on systemic administration of immunomodulatory drugs, but they have a broad range of undesirable side-effects. RNA interference is a highly specific endogenous mechanism that regulates the expression of the gene at the transcript level, which can be repurposed using exogenous short interfering RNA [siRNA] to repress expression of the target gene. While siRNA therapeutics can offer an alternative to existing therapies, with a high specificity critical for chronically administrated drugs, evidence of their potency compared to chemical kinase inhibitors used in clinics is still lacking in alleviating an adverse inflammatory response.
METHODS: We provide a framework to select highly specific siRNA, with a focus on two kinases strongly involved in pro-inflammatory diseases, namely JAK1 and JAK3. Using western-blot, real-time quantitative PCR and large-scale analysis, we assessed the specificity profile of these siRNA drugs and compared their efficacy to the most recent and promising kinase inhibitors for Janus kinases [Jakinibs], tofacitinib and filgotinib.
RESULTS: siRNA drugs can reach higher efficiency and selectivity at lower doses [5 pM vs 1 µM] than Jakinibs. Moreover, JAK silencing lasted up to 11 days, even with 6 h pulse transfection.
CONCLUSIONS: The siRNA-based drugs developed hold the potential to develop more potent therapeutics for chronic inflammatory diseases.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
METHODS: We provide a framework to select highly specific siRNA, with a focus on two kinases strongly involved in pro-inflammatory diseases, namely JAK1 and JAK3. Using western-blot, real-time quantitative PCR and large-scale analysis, we assessed the specificity profile of these siRNA drugs and compared their efficacy to the most recent and promising kinase inhibitors for Janus kinases [Jakinibs], tofacitinib and filgotinib.
RESULTS: siRNA drugs can reach higher efficiency and selectivity at lower doses [5 pM vs 1 µM] than Jakinibs. Moreover, JAK silencing lasted up to 11 days, even with 6 h pulse transfection.
CONCLUSIONS: The siRNA-based drugs developed hold the potential to develop more potent therapeutics for chronic inflammatory diseases.
Bonduelle, Olivia; Chaudesaigues, Chloé; Tolazzi, Monica; Suleiman, Ehsan; de Bernard, Simon; Alves, Karine; Nourikyan, Julien; Bohec, Mylene; Baudrin, Laura G; Katinger, Dietmar; Debré, Patrice; Scarlatti, Gabriella; Vieillard, Vincent; Combadière, Behazine
Dichotomy in Neutralizing Antibody Induction to Peptide-Conjugated Vaccine in Squalene Emulsion Contrast With Aluminum Hydroxide Formulation Journal Article
In: Front Immunol, vol. 13, pp. 848571, 2022, ISSN: 1664-3224.
@article{pmid35464449b,
title = {Dichotomy in Neutralizing Antibody Induction to Peptide-Conjugated Vaccine in Squalene Emulsion Contrast With Aluminum Hydroxide Formulation},
author = {Olivia Bonduelle and Chloé Chaudesaigues and Monica Tolazzi and Ehsan Suleiman and Simon de Bernard and Karine Alves and Julien Nourikyan and Mylene Bohec and Laura G Baudrin and Dietmar Katinger and Patrice Debré and Gabriella Scarlatti and Vincent Vieillard and Behazine Combadière},
doi = {10.3389/fimmu.2022.848571},
issn = {1664-3224},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Front Immunol},
volume = {13},
pages = {848571},
abstract = {W614A-3S peptide is a modified 3S motif of the HIV-gp41 (mutation W614A). We previously detected the presence of natural neutralizing antibodies directed against W614A-3S peptide (NAbs) in long-term non-progressor HIV patients. Here, we compared the efficacy of W614A-3S peptide formulated in either squalene emulsion (SQE) or in aluminum hydroxide (Alum) in inducing broadly-NAbs (bNAbs). Rabbit and mouse models were used to screen the induction of bNAbs following 4 immunizations. SQE was more efficient than Alum formulation in inducing W614A-3S-specific bNAbs with up to 67%-93% of HIV strains neutralized. We then analyzed the quality of peptide-specific murine B cells by single-cell gene expression by quantitative reverse transcription-PCR and single-cell V(D)J sequencing. We found more frequent germinal center B cells in SQE than in Alum, albeit with a different gene expression profile. The V(D)J sequencing of W614A-3S-specific BCR showed significant differences in BCR sequences and validates the dichotomy between adjuvant formulations. All sixteen BCR sequences which were cloned were specific of peptide. Adjuvant formulations of W614A-3S-peptide-conjugated immunogen impact the quantity and quality of B cell immune responses at both the gene expression level and BCR sequence.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}