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Multi-omics Analysis Classifies Colorectal Cancer into Distinct Methylated Immunogenic and Angiogenic Subtypes Based on Anatomical Laterality Hasselt University
Weemployed supervised machine learning algorithms to a cohort of colorectal cancer patients from the NCI to differentiate and classify the heterogenous disease based on anatomical laterality and multi-omics stratification, in a first of its kind. Multi-omics integrative analysis shows distinct clustering of left and right colorectal cancer with disentangled representation of methylome and delineation of transcriptome and genome. We present novel ...
SUBATOMIC : a SUbgraph BAsed mulTi-OMIcs clustering framework to analyze integrated multi-edge networks Ghent University
Background: Representing the complex interplay between different types of biomolecules across different omics layers in multi-omics networks bears great potential to gain a deep mechanistic understanding of gene regulation and disease. However, multi-omics networks easily grow into giant hairball structures that hamper biological interpretation. Module detection methods can decompose these networks into smaller interpretable modules. However, ...
Omics and multi-omics analysis for the early identification and improved outcome of patients with psoriatic arthritis Ghent University KU Leuven Flanders Institute for Biotechnology
The definitive diagnosis and early treatment of many immune-mediated inflammatory diseases (IMIDs) is hindered by variable and overlapping clinical manifestations. Psoriatic arthritis (PsA), which develops in similar to 30% of people with psoriasis, is a key example. This mixed-pattern IMID is apparent in entheseal and synovial musculoskeletal structures, but a definitive diagnosis often can only be made by clinical experts or when an extensive ...
Charting plant gene functions in the multi-omics and single-cell era Ghent University Flanders Institute for Biotechnology
BioMOBS: A multi-omics visual analytics workflow for biomolecular insight generation Hasselt University KU Leuven
One of the challenges in multi-omics data analysis for precision medicine is the efficient exploration of undiscovered molecular interactions in disease processes. We present BioMOBS, a workflow consisting of two data visualization tools integrated with an open-source molecular information database to perform clinically relevant analyses (https://github.com/driesheylen123/BioMOBS). We performed exploratory pathway analysis with BioMOBS and ...
Improved production of novel (bola) glycolipid biosurfactants with the yeast Starmerella bombicola through an integrative approach combining genetic engineering and multiomics analyses Ghent University
Starmerella bombicola is well known for its natural efficient capacity to produce glycolipids sophorolipids (SLs) at high titers (> 200 g/L) and high-volumetric productivities (> 2 g/L h). These traits make this nonpathogenic yeast industrially relevant, resulting in valorization of SLs as microbial biosurfactants by several companies. The efficient glycolipid machinery of S. bombicola has, on the other hand, been employed toward the ...
Integrative multi-omics analyses of date palm (Phoenix dactylifera) roots and leaves reveal how the halophyte land plant copes with sea water KU Leuven
Date palm (Phoenix dactylifera L.) is able to grow and complete its life cycle while being rooted in highly saline soils. Which of the many well-known salt-tolerance strategies are combined to fine-tune this remarkable resilience is unknown. The precise location, whether in the shoot or the root, where these strategies are employed remains uncertain, leaving us unaware of how the various known salt-tolerance mechanisms are integrated to ...
Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation KU Leuven Flanders Institute for Biotechnology
In the mammalian liver, hepatocytes exhibit diverse metabolic and functional profiles based on their location within the liver lobule. However, it is unclear whether this spatial variation, called zonation, is governed by a well-defined gene regulatory code. Here, using a combination of single-cell multiomics, spatial omics, massively parallel reporter assays and deep learning, we mapped enhancer-gene regulatory networks across mouse liver cell ...