Analyses de Haute Qualité et Approche Collaborative
AltraBio utilise son expertise reconnue en bioinformatique, biostatistique et biologie pour offrir des services d’analyse et d’interprétation de divers types de données omiques (génomique, épigénomique, transcriptomique, protéomique, etc.).
Notre équipe collabore étroitement avec les clients et partenaires pour chaque projet afin de garantir que leurs objectifs sont atteints. Cette approche collaborative assure que nos analyses sont alignées avec vos objectifs de recherche.
Expertise en Biostatistique et Bioinformatique
Avant de réaliser des analyses différentielles, nous mettons en œuvre diverses méthodes pour évaluer la qualité des données et leur cohérence avec la conception expérimentale. Nous traitons les valeurs aberrantes et les effets non liés à la conception, garantissant ainsi la pertinence de l’analyse.
Les conceptions expérimentales impliquent souvent plusieurs facteurs tels que le donneur, le type cellulaire, le traitement, la dose et les points temporels. Pour répondre aux questions biologiques de l’étude, AltraBio identifie le modèle statistique le plus approprié, en tenant compte des conceptions appariées, des corrections d’effets de lot, de l’estimation de facteurs cachés et de la pondération des valeurs aberrantes.
AltraBio excelle dans l’intégration de divers types de données (multi-omiques, cytométrie, données médicales, etc.). Nous utilisons des techniques d’apprentissage automatique supervisé et non supervisé pour des applications telles que l’identification de biomarqueurs, la classification et les modèles prédictifs pour le diagnostic ou la réponse au traitement. Nos clients bénéficient de notre maîtrise des algorithmes d’apprentissage automatique de pointe.
Expertise en Biologie
Nous identifions les processus biologiques et les voies par le biais de méthodes complémentaires d’enrichissement de catégories fonctionnelles. Ces résultats automatisés sont ensuite examinés pour évaluer leur pertinence dans le contexte biologique de l’étude.
Au-delà de la fourniture de listes de molécules et de voies biologiques, AltraBio extrait des informations significatives. Lors de la phase d’interprétation, nous considérons les questions biologiques initiales et évaluons les résultats en intégrant les connaissances biologiques disponibles dans la littérature scientifique et les bases de données. Notre objectif est de comprendre les mécanismes biologiques en jeu et de formuler de nouvelles hypothèses à valider.
Rapports
Tout le travail réalisé est résumé dans un rapport complet, fourni à nos clients et expliqué lors d’une visioconférence. Cet échange permet de clarifier les approches méthodologiques choisies et leurs résultats, assurant une compréhension optimale des données.
Les résultats des analyses statistiques sont également accessibles via l’interface web WikiBioPath. Cette plateforme offre à nos clients un ensemble d’outils de visualisation et d’analyse pour continuer à explorer leurs données. Ils peuvent facilement visualiser des volcano plots, générer de nouvelles heat maps, effectuer des PCA et réaliser des analyses d’enrichissement sur des sélections de gènes.
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. »
Nos Publications
2023
Sanlaville, Amélien; Voissière, Aurélien; Poujol, Dominique; Hubert, Margaux; André, Suzanne; Perret, Clémence; Foy, Jean-Philippe; Goutagny, Nadège; Malfroy, Marine; Durand, Isabelle; Châlons-Cottavoz, Marie; Valladeau-Guilemond, Jenny; Saintigny, Pierre; Puisieux, Alain; Caux, Christophe; Michallet, Marie-Cécile; Puisieux, Isabelle; Bendriss-Vermare, Nathalie
CD4 T cells and neutrophils contribute to epithelial-mesenchymal transition in breast cancer Article de journal
Dans: bioRxiv, 2023.
@article{Sanlaville2023.02.15.528594,
title = {CD4 T cells and neutrophils contribute to epithelial-mesenchymal transition in breast cancer},
author = {Amélien Sanlaville and Aurélien Voissière and Dominique Poujol and Margaux Hubert and Suzanne André and Clémence Perret and Jean-Philippe Foy and Nadège Goutagny and Marine Malfroy and Isabelle Durand and Marie Châlons-Cottavoz and Jenny Valladeau-Guilemond and Pierre Saintigny and Alain Puisieux and Christophe Caux and Marie-Cécile Michallet and Isabelle Puisieux and Nathalie Bendriss-Vermare},
url = {https://www.biorxiv.org/content/early/2023/02/15/2023.02.15.528594},
doi = {10.1101/2023.02.15.528594},
year = {2023},
date = {2023-02-15},
urldate = {2023-01-01},
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
abstract = {Epithelial-mesenchymal transition (EMT) is a central oncogenic mechanism, contributing both to transformation and metastatic dissemination. Inflammation and innate immune cells are known to favor EMT induction, but the role of adaptive immunity still remains unclear. Using an original murine mammary tumor model in immune cell subpopulation depletion experiments, we demonstrated that tumor cells maintain their epithelial phenotype in mice deficient for adaptive immune response, but undergo EMT in the presence of T-cells. This phenotypic conversion involves the major contribution of CD4 T cells, but not CD8 T cells nor B cells, undoubtedly demonstrating the pro-EMT role of CD4 T cells specifically among adaptive immune cells. Moreover, combined intra-tumor immune infiltrate and transcriptomic analyses of murine mammary tumors with various EMT phenotype revealed an inverse correlation between mesenchymal tumor cell and intratumoral neutrophil proportions, due to the reduced ability of mesenchymal cells to recruit neutrophils. Last, selective in vivo depletion of neutrophils and transcriptomic analysis of human breast tumor cohorts demonstrated the pro-EMT role of neutrophils and suggest a cooperation with CD4 T cells in EMT promotion. Collectively, our data highlight a novel mechanism of EMT regulation by both innate and adaptive immune compartments.Competing Interest StatementThe authors have declared no competing interest.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Meier, Johannes P; Möbus, Selina; Heigl, Florian; Asbach-Nitzsche, Alexandra; Niller, Hans Helmut; Plentz, Annelie; Avsar, Korkut; Heiß-Neumann, Marion; Schaaf, Bernhard; Cassens, Uwe; Seese, Bernd; Teschner, Daniel; Handzhiev, Sabin; Graf, Uwe; Lübbert, Christoph; Steinmaurer, Monika; Kontogianni, Konstantina; Berg, Christoph; Maieron, Andreas; Blaas, Stefan H; Wagner, Ralf; Deml, Ludwig; Barabas, Sascha
Performance of T-Track TB, a Novel Dual Marker RT-qPCR-Based Whole-Blood Test for Improved Detection of Active Tuberculosis Article de journal
Dans: Diagnostics (Basel), vol. 13, no. 4, 2023, ISSN: 2075-4418.
@article{pmid36832246,
title = {Performance of T-Track TB, a Novel Dual Marker RT-qPCR-Based Whole-Blood Test for Improved Detection of Active Tuberculosis},
author = {Johannes P Meier and Selina Möbus and Florian Heigl and Alexandra Asbach-Nitzsche and Hans Helmut Niller and Annelie Plentz and Korkut Avsar and Marion Heiß-Neumann and Bernhard Schaaf and Uwe Cassens and Bernd Seese and Daniel Teschner and Sabin Handzhiev and Uwe Graf and Christoph Lübbert and Monika Steinmaurer and Konstantina Kontogianni and Christoph Berg and Andreas Maieron and Stefan H Blaas and Ralf Wagner and Ludwig Deml and Sascha Barabas},
doi = {10.3390/diagnostics13040758},
issn = {2075-4418},
year = {2023},
date = {2023-02-01},
urldate = {2023-02-01},
journal = {Diagnostics (Basel)},
volume = {13},
number = {4},
abstract = {Tuberculosis (TB) is one of the leading causes of death by an infectious disease. It remains a major health burden worldwide, in part due to misdiagnosis. Therefore, improved diagnostic tests allowing the faster and more reliable diagnosis of patients with active TB are urgently needed. This prospective study examined the performance of the new molecular whole-blood test T-Track TB, which relies on the combined evaluation of and mRNA levels, and compared it to that of the QuantiFERON-TB Gold Plus (QFT-Plus) enzyme-linked immunosorbent assay (ELISA). Diagnostic accuracy and agreement analyses were conducted on the whole blood of 181 active TB patients and 163 non-TB controls. T-Track TB presented sensitivity of 94.9% and specificity of 93.8% for the detection of active TB vs. non-TB controls. In comparison, the QFT-Plus ELISA showed sensitivity of 84.3%. The sensitivity of T-Track TB was significantly higher ( < 0.001) than that of QFT-Plus. The overall agreement of T-Track TB with QFT-Plus to diagnose active TB was 87.9%. Out of 21 samples with discordant results, 19 were correctly classified by T-Track TB while misclassified by QFT-Plus (T-Track TB-positive/QFT-Plus-negative), and two samples were misclassified by T-Track TB while correctly classified by QFT-Plus (T-Track TB-negative/QFT-Plus-positive). Our results demonstrate the excellent performance of the T-Track TB molecular assay and its suitability to accurately detect TB infection and discriminate active TB patients from non-infected controls.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Coutier, Julien; Auvré, Frédéric; Lemaître, Gilles; Lataillade, Jean-Jacques; Deleuze, Jean-François; Roméo, Paul-Henri; Martin, Michèle T; Fortunel, Nicolas O
MXD4/MAD4 Regulates Human Keratinocyte Precursor Fate Article de journal
Dans: J Invest Dermatol, vol. 143, no. 1, p. 105–114.e12, 2023, ISSN: 1523-1747.
@article{pmid36007550,
title = {MXD4/MAD4 Regulates Human Keratinocyte Precursor Fate},
author = {Julien Coutier and Frédéric Auvré and Gilles Lemaître and Jean-Jacques Lataillade and Jean-François Deleuze and Paul-Henri Roméo and Michèle T Martin and Nicolas O Fortunel},
doi = {10.1016/j.jid.2022.07.020},
issn = {1523-1747},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {J Invest Dermatol},
volume = {143},
number = {1},
pages = {105--114.e12},
abstract = {Deciphering the pathways that regulate human epidermal precursor cell fate is necessary for future developments in skin repair and graft bioengineering. Among them, characterization of pathways regulating the keratinocyte (KC) precursor immaturity versus differentiation balance is required for improving the efficiency of KC precursor ex vivo expansion. In this study, we show that the transcription factor MXD4/MAD4 is expressed at a higher level in quiescent KC stem/progenitor cells located in the basal layer of human epidermis than in cycling progenitors. In holoclone KCs, stable short hairpin-RNA‒mediated decreased expression of MXD4/MAD4 increases MYC expression, whose modulation increases the proliferation of KC precursors and maintenance of their clonogenic potential and preserves the functionality of these precursors in three-dimensional epidermis organoid generation. Altogether, these results characterize MXD4/MAD4 as a major piece of the stemness puzzle in the human epidermis KC lineage and pinpoint an original avenue for ex vivo expansion of human KC precursors.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}