Michael Schubert’s research while affiliated with EMBL-EBI and other places

... PMs have been drawn based on SBGN using the CellDesigner structured diagram editor (Funahashi et al., 2008). CellDesigner is used to graphically represent SBGN-compatible networks, storing the maps in the Systems Biology Markup Language (SBML), a free and open software data format for describing models in systems biology (Keating et al., 2020). CellDesigner does not fully comply with SBGN (e.g. for the shape of the nodes), but we have ensured that the representation of the network is as close as possible to the standard. ...

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Mapping Physiology: A Systems Biology Approach for the Development of Alternative Methods in Toxicology

... Further analysis covered a wide range of cellular phenotypes and focused on calculating the gene signature scores of T cells [15], NK cells [17], B cells [18], macrophages [19], dendritic cells [19], and fibroblasts [20]. These scores were derived via the AddModuleScore function in the seurat framework, which incorporates gene sets (Table S2-7) curated from previous studies [15,[17][18][19][20]. Pathway-responsive genes for activity inference (Progeny) [21] analysis were also utilized to compare and assess the activation levels of specific tumour signaling pathways in epithelial cells between PL and LM. ...

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Comprehensive single-cell atlas of colorectal neuroendocrine tumors with liver metastases: unraveling tumor microenvironment heterogeneity between primary lesions and metastases

... CRC is a highly heterogeneous disease that comprises various phenotypes, a plastic condition greatly discouraging therapy outcomes and patient survival. The extent of intratumor diversity in CRC has been revealed through studies on transcriptomic [34,35], proteomics [36,37], metabolic status [38,39] and functional response [40][41][42]. In particular, the recognition of epigenetic diversity in CRC is well documented and extended to exploring intratumor epigenetic heterogeneity [43][44][45]. ...

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Spatial deconvolution from bulk DNA methylation profiles determines intratumoral epigenetic heterogeneity

... Further analysis covered a wide range of cellular phenotypes and focused on calculating the gene signature scores of T cells [15], NK cells [17], B cells [18], macrophages [19], dendritic cells [19], and fibroblasts [20]. These scores were derived via the AddModuleScore function in the seurat framework, which incorporates gene sets (Table S2-7) curated from previous studies [15,[17][18][19][20]. Pathway-responsive genes for activity inference (Progeny) [21] analysis were also utilized to compare and assess the activation levels of specific tumour signaling pathways in epithelial cells between PL and LM. ...

Reference:

Comprehensive single-cell atlas of colorectal neuroendocrine tumors with liver metastases: unraveling tumor microenvironment heterogeneity between primary lesions and metastases

... At present, there seems to be no marked difference in technical systems of drug development between primary and metastatic tumors. As mentioned above, a vast number of potential drug targets emerge every year [79][80][81][82][83][84][85][86][87]. They are categorized as signal transduction, AMF, HGF/c-Met, TGF-β inhibitors, β-catenin inhibitors, cell movement inhibitors and other drug targets fuel for therapeutic promotion globally. ...

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Antimetastatic Drug, Pharmacologic Challenge and Opportunity

... The combinatorial properties occurring among the alterations are then analyzed and used to define cost functions, for example, based on the tendency of a group of genes to be mutated in a mutually exclusive manner. On the basis of these cost functions, optimal sub-networks are identified and interpreted as novel cancer driver pathways [22][23][24] . However, at the moment there is no consensual method to rigorously define a mathematical metric for mutual exclusivity and compute its statistical significance, and a number of interpretations exist 22,23,[25][26][27] . ...

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Pathway-based dissection of the genomic heterogeneity of cancer hallmarks’ acquisition with SLAPenrich

... Dataset was deposited into a publicly accessible repository (https://data.mendeley.com/preview/2rw5pz75yr). The dynamic 13 C-flux model has been deposited in the Biomodels database (https://www.ebi.ac.uk/biomodels) [45] with the identifier MODEL2310250001. ...

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6‐Phosphogluconolactonase is critical for the efficient functioning of the pentose phosphate pathway

... Additionally, HRP has eight glycosylation sites, contributing to a carbohydrate content of 18% to 20% [5]. In 2014, 28 sequences encoding various HRP isoforms were extracted from a pyrosequenced transcriptome of Armoracia rusticana, revealing divergent characteristics [6]. These characteristics allow for the categorization of HRP isoforms into acidic, neutral, and basic isoenzymes, as determined by their isoelectric points [7]. ...

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A Simple and Cost-Efficient Method for the Production of Recombinant Horseradish Peroxidase in E. coli

... However, in spite of a few attempts [8,9], the model development process is far from being automatic and standardized. Parameter optimization frameworks have been implemented in a diverse manner, with different specification formats for the parameters, the experimental datasets, the parameter bounds, the objective functions and the choice of optimization methods [10][11][12][13][14][15][16][17][18][19][20][21][22][23]. ...

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Mathematical basis and toolchain for hierarchical optimization of biochemical networks