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Article
Open AccessA robust clustering strategy for stratification unveils unique patient subgroups in acutely decompensated cirrhosis
Patient heterogeneity poses significant challenges for managing individuals and designing clinical trials, especially in complex diseases. Existing classifications rely on outcome-predicting scores, potentiall...
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Article
Open AccessReusability report: Learning the transcriptional grammar in single-cell RNA-sequencing data using transformers
The rise of single-cell genomics is an attractive opportunity for data-hungry machine learning algorithms. The scBERT method, inspired by the success of BERT (‘bidirectional encoder representations from transf...
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Chapter
Model Discovery and Discrete Inverse Problems with Cellular Automata and Boolean Networks
We introduce and explore some methods based on algorithmic complexity and algorithmic probability that help address the challenge of empirical causal model discovery and inverse problems. These methods, based ...
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Article
Open AccessEvidence-based prediction and prevention of cardiovascular morbidity in adults treated for cancer
Cancer treatment-related morbidity relevantly compromises health status in cancer survivors, and efforts to optimise health-related outcomes in this population are vital to maximising healthy survivorship. A p...
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Article
Open AccessExhaustion of CD4+ T-cells mediated by the Kynurenine Pathway in Melanoma
Kynurenine pathway (KP) activation by the enzymatic activity of indoleamine 2,3-dioxygenase1 (IDO1) and kynurenine (KYN) production represents an attractive target for reducing tumour progression and improving...
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Article
Causal deconvolution by algorithmic generative models
Complex behaviour emerges from interactions between objects produced by different generating mechanisms. Yet to decode their causal origin(s) from observations remains one of the most fundamental challenges in...
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Article
Open AccessTime-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3
Regulatory T cells (Tregs) expressing the transcription factor FOXP3 are crucial mediators of self-tolerance, preventing autoimmune diseases but possibly hampering tumor rejection. Clinical manipulation of Tre...
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Protocol
Predictive Systems Toxicology
In this review we address to what extent computational techniques can augment our ability to predict toxicity. The first section provides a brief history of empirical observations on toxicity dating back to th...
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Article
Open AccessConditional Disease Development extracted from Longitudinal Health Care Cohort Data using Layered Network Construction
Health care data holds great promise to be used in clinical decision support systems. However, frequent near-synonymous diagnoses recorded separately, as well as the sheer magnitude and complexity of the disea...
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Chapter and Conference Paper
Numerical Investigation of Graph Spectra and Information Interpretability of Eigenvalues
We undertake an extensive numerical investigation of the graph spectra of thousands regular graphs, a set of random Erdös-Rényi graphs, the two most popular types of complex networks and an evolving genetic ne...
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Article
Open AccessSystems Medicine: from molecular features and models to the clinic in COPD
Chronic Obstructive Pulmonary Disease (COPD) patients are characterized by heterogeneous clinical manifestations and patterns of disease progression. Two major factors that can be used to identify COPD subtypes a...
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Article
Open AccessDynamic probabilistic threshold networks to infer signaling pathways from time-course perturbation data
Network inference deals with the reconstruction of molecular networks from experimental data. Given N molecular species, the challenge is to find the underlying network. Due to data limitations, this typically is...
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Article
Resource allocation for performance improvement
In this paper the problem of allocating resources among Decision Making Units is considered. This study covers the case in which several homogeneous units are operating under the supervision of a central unit....
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Article
Open AccessNormalizing for individual cell population context in the analysis of high-content cellular screens
High-content, high-throughput RNA interference (RNAi) offers unprecedented possibilities to elucidate gene function and involvement in biological processes. Microscopy based screening allows phenotypic observa...
