High Quality Analyses & Collaborative Approach
AltraBio leverages its renowned expertise in bioinformatics, biostatistics, and biology to offer services in the analysis and interpretation of various omics data types, including genomics, epigenomics, transcriptomics, proteomics, and more.
Our team works closely with clients and partners on each project to ensure their goals are met. This collaborative approach guarantees that our analyses align with your research objectives.
Expertise in Biostatistics and Bioinformatics
Before conducting differential analyses, we implement various methods to assess data quality and consistency with the experimental design. We address outliers and effects unrelated to the design, ensuring the relevance of the analysis.
Experimental designs often involve multiple factors such as donor, cell type, treatment, dose, and time points. To address the biological questions of the study, AltraBio identifies the most appropriate statistical model, considering paired designs, batch effect corrections, estimation of hidden factors, and outlier weighting.
AltraBio excels in integrating various data types, including multi-omics, cytometry, and medical data. We employ both supervised and unsupervised machine learning for applications such as biomarker identification, classification, and predictive models for diagnostics or treatment response. Our clients benefit from our proficiency in state-of-the-art machine learning algorithms.
Expertise in Biology
We identify biological processes and pathways through complementary methods of functional category enrichment. These automated results are reviewed to assess their relevance within the biological context of the study.
Beyond providing lists of molecules and pathways, AltraBio extracts meaningful insights. During the interpretation phase, we consider the initial biological questions and evaluate the results while integrating available scientific literature and databases. Our goal is to understand the biological mechanisms and formulate new hypotheses for validation.
Reporting
All work conducted is summarized in a comprehensive report, provided to our clients and explained during a video conference. This exchange clarifies the chosen methodological approaches and their results, ensuring a thorough understanding of the data.
The results of statistical analyses are accessible through the WikiBioPath web interface. This platform provides clients with visualization and analysis tools to continue exploring their data. Users can easily visualize volcano plots, generate heat maps, perform PCA, and conduct enrichment analyses on gene selections.
Testimonials
« 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. »
Our Publications
2017
Bauer, Yasmina; White, Eric S; de Bernard, Simon; Cornelisse, Peter; Leconte, Isabelle; Morganti, Adele; Roux, Sebastien; Nayler, Oliver
MMP-7 is a predictive biomarker of disease progression in patients with idiopathic pulmonary fibrosis Journal Article
In: ERJ Open Res, vol. 3, no. 1, 2017, ISSN: 2312-0541.
@article{pmid28435843,
title = {MMP-7 is a predictive biomarker of disease progression in patients with idiopathic pulmonary fibrosis},
author = {Yasmina Bauer and Eric S White and Simon de Bernard and Peter Cornelisse and Isabelle Leconte and Adele Morganti and Sebastien Roux and Oliver Nayler},
doi = {10.1183/23120541.00074-2016},
issn = {2312-0541},
year = {2017},
date = {2017-01-01},
urldate = {2017-01-01},
journal = {ERJ Open Res},
volume = {3},
number = {1},
abstract = {Idiopathic pulmonary fibrosis (IPF) is a progressive interstitial lung disease with poor prognosis, which is characterised by destruction of normal lung architecture and excessive deposition of lung extracellular matrix. The heterogeneity of disease progression in patients with IPF poses significant obstacles to patient care and prevents efficient development of novel therapeutic interventions. Blood biomarkers, reflecting pathobiological processes in the lung, could provide objective evidence of the underlying disease. Longitudinally collected serum samples from the Bosentan Use in Interstitial Lung Disease (BUILD)-3 trial were used to measure four biomarkers (metalloproteinase-7 (MMP-7), Fas death receptor ligand, osteopontin and procollagen type I C-peptide), to assess their potential prognostic capabilities and to follow changes during disease progression in patients with IPF. In baseline BUILD-3 samples, only MMP-7 showed clearly elevated protein levels compared with samples from healthy controls, and further investigations demonstrated that MMP-7 levels also increased over time. Baseline levels of MMP-7 were able to predict patients who had higher risk of worsening and, notably, baseline levels of MMP-7 could predict changes in FVC as early as month 4. MMP-7 shows potential to be a reliable predictor of lung function decline and disease progression.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2016
Blanc, Pascal; Moro-Sibilot, Ludovic; Barthly, Lucas; Jagot, Ferdinand; This, Sébastien; de Bernard, Simon; Buffat, Laurent; Dussurgey, Sébastien; Colisson, Renaud; Hobeika, Elias; Fest, Thierry; Taillardet, Morgan; Thaunat, Olivier; Sicard, Antoine; Mondière, Paul; Genestier, Laurent; Nutt, Stephen L; Defrance, Thierry
Mature IgM-expressing plasma cells sense antigen and develop competence for cytokine production upon antigenic challenge Journal Article
In: Nat Commun, vol. 7, pp. 13600, 2016, ISSN: 2041-1723.
@article{pmid27924814,
title = {Mature IgM-expressing plasma cells sense antigen and develop competence for cytokine production upon antigenic challenge},
author = {Pascal Blanc and Ludovic Moro-Sibilot and Lucas Barthly and Ferdinand Jagot and Sébastien This and Simon de Bernard and Laurent Buffat and Sébastien Dussurgey and Renaud Colisson and Elias Hobeika and Thierry Fest and Morgan Taillardet and Olivier Thaunat and Antoine Sicard and Paul Mondière and Laurent Genestier and Stephen L Nutt and Thierry Defrance},
doi = {10.1038/ncomms13600},
issn = {2041-1723},
year = {2016},
date = {2016-12-01},
urldate = {2016-12-01},
journal = {Nat Commun},
volume = {7},
pages = {13600},
abstract = {Dogma holds that plasma cells, as opposed to B cells, cannot bind antigen because they have switched from expression of membrane-bound immunoglobulins (Ig) that constitute the B-cell receptor (BCR) to production of the secreted form of immunoglobulins. Here we compare the phenotypical and functional attributes of plasma cells generated by the T-cell-dependent and T-cell-independent forms of the hapten NP. We show that the nature of the secreted Ig isotype, rather than the chemical structure of the immunizing antigen, defines two functionally distinct populations of plasma cells. Fully mature IgM-expressing plasma cells resident in the bone marrow retain expression of a functional BCR, whereas their IgG counterparts do not. Antigen boost modifies the gene expression profile of IgM plasma cells and initiates a cytokine production program, characterized by upregulation of CCL5 and IL-10. Our results demonstrate that IgM-expressing plasma cells can sense antigen and acquire competence for cytokine production upon antigenic challenge.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2015
van Helden, Mary J; Goossens, Steven; Daussy, Cécile; Mathieu, Anne-Laure; Faure, Fabrice; Marçais, Antoine; Vandamme, Niels; Farla, Natalie; Mayol, Katia; Viel, Sébastien; Degouve, Sophie; Debien, Emilie; Seuntjens, Eve; Conidi, Andrea; Chaix, Julie; Mangeot, Philippe; de Bernard, Simon; Buffat, Laurent; Haigh, Jody J; Huylebroeck, Danny; Lambrecht, Bart N; Berx, Geert; Walzer, Thierry
Terminal NK cell maturation is controlled by concerted actions of T-bet and Zeb2 and is essential for melanoma rejection Journal Article
In: J Exp Med, vol. 212, no. 12, pp. 2015–2025, 2015, ISSN: 1540-9538.
@article{pmid26503444,
title = {Terminal NK cell maturation is controlled by concerted actions of T-bet and Zeb2 and is essential for melanoma rejection},
author = {Mary J van Helden and Steven Goossens and Cécile Daussy and Anne-Laure Mathieu and Fabrice Faure and Antoine Marçais and Niels Vandamme and Natalie Farla and Katia Mayol and Sébastien Viel and Sophie Degouve and Emilie Debien and Eve Seuntjens and Andrea Conidi and Julie Chaix and Philippe Mangeot and Simon de Bernard and Laurent Buffat and Jody J Haigh and Danny Huylebroeck and Bart N Lambrecht and Geert Berx and Thierry Walzer},
doi = {10.1084/jem.20150809},
issn = {1540-9538},
year = {2015},
date = {2015-11-01},
urldate = {2015-11-01},
journal = {J Exp Med},
volume = {212},
number = {12},
pages = {2015--2025},
abstract = {Natural killer (NK) cell maturation is a tightly controlled process that endows NK cells with functional competence and the capacity to recognize target cells. Here, we found that the transcription factor (TF) Zeb2 was the most highly induced TF during NK cell maturation. Zeb2 is known to control epithelial to mesenchymal transition, but its role in immune cells is mostly undefined. Targeted deletion of Zeb2 resulted in impaired NK cell maturation, survival, and exit from the bone marrow. NK cell function was preserved, but mice lacking Zeb2 in NK cells were more susceptible to B16 melanoma lung metastases. Reciprocally, ectopic expression of Zeb2 resulted in a higher frequency of mature NK cells in all organs. Moreover, the immature phenotype of Zeb2(-/-) NK cells closely resembled that of Tbx21(-/-) NK cells. This was caused by both a dependence of Zeb2 expression on T-bet and a probable cooperation of these factors in gene regulation. Transgenic expression of Zeb2 in Tbx21(-/-) NK cells partially restored a normal maturation, establishing that timely induction of Zeb2 by T-bet is an essential event during NK cell differentiation. Finally, this novel transcriptional cascade could also operate in human as T-bet and Zeb2 are similarly regulated in mouse and human NK cells.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}