A5022724143- Bioinformatics and Genomic Networks
- Gene Regulatory Network Analysis
- Microbial Metabolic Engineering and Bioproduction
- MicroRNA in disease regulation
- Genetics, Bioinformatics, and Biomedical Research
- Gene expression and cancer classification
- Computational Drug Discovery Methods
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- RNA Research and Splicing
- Scientific Computing and Data Management
- Biomedical Text Mining and Ontologies
- Cancer-related molecular mechanisms research
- Fuzzy Logic and Control Systems
- Semantic Web and Ontologies
- vaccines and immunoinformatics approaches
- Neural Networks and Applications
- Molecular Biology Techniques and Applications
- Melanoma and MAPK Pathways
- Mathematical Biology Tumor Growth
- Microtubule and mitosis dynamics
- Genomics and Chromatin Dynamics
- Metabolomics and Mass Spectrometry Studies
- Cytokine Signaling Pathways and Interactions
- Cell Image Analysis Techniques
University of Rostock
2016-2025
Stellenbosch University
2016-2025
Leibniz-Institute for Food Systems Biology at the Technical University of Munich
2021-2025
Albert Einstein College of Medicine
2024
Universitätsklinikum Erlangen
2015-2024
Chhattisgarh Swami Vivekanand Technical University
2017-2024
Technical University of Munich
2024
Laboratoire d'Informatique de Paris-Nord
2012-2023
Czech Academy of Sciences, Institute of Computer Science
2011-2023
Institute for Advanced Study
2013-2015
We propose an innovative, integrated, cost-effective health system to combat major non-communicable diseases (NCDs), including cardiovascular, chronic respiratory, metabolic, rheumatologic and neurologic disorders cancers, which together are the predominant problem of 21st century. This proposed holistic strategy involves comprehensive patient-centered integrated care multi-scale, multi-modal multi-level systems approaches tackle NCDs as a common group diseases. Rather than studying each...
Numerous centrality measures have been introduced to identify "central" nodes in large networks. The availability of a wide range for ranking influential leaves the user decide which measure may best suit analysis given network. choice suitable is furthermore complicated by impact network topology on measures. To approach this problem systematically, we examined profile yeast protein-protein interaction networks (PPINs) order detect succeeding predicting proteins. We studied how different...
Researchers around the world join forces to reconstruct molecular processes of virus-host interactions aiming combat cause ongoing pandemic.
Reproducibility of experiments is a basic requirement for science. Minimum Information (MI) guidelines have proved helpful means enabling reuse existing work in modern biology. The Required the Annotation Models (MIRIAM) promote exchange and biochemical computational models. However, information about model alone not sufficient to enable its efficient setting. Advanced numerical algorithms complex modeling workflows used biology make reproduction simulations difficult. It therefore essential...
The discovery of microRNAs (miRNAs) has added a new player to the regulation gene expression. With increasing number molecular species involved in regulatory networks, it is hard obtain an intuitive understanding network dynamics. Mathematical modelling can help dissecting role miRNAs and we shall here review most recent developments that utilise different mathematical approaches provide quantitative insights into function Key miRNA features have been elucidated via include: (i)...
Imaging flow cytometry (IFC) captures multichannel images of hundreds thousands single cells within minutes. IFC is seeing a paradigm shift from low- to high-information-content analysis, driven partly by deep learning algorithms. We predict wealth applications with potential translation into clinical practice. combines the high-throughput, multiparameter capabilities conventional morphological and spatial information, all at single-cell resolution. Multichannel digital individual can be...
Abstract The Synthetic Minority Oversampling TEchnique (SMOTE) is widely-used for the analysis of imbalanced datasets. It known that SMOTE frequently over-generalizes minority class, leading to misclassifications majority and effecting overall balance model. In this article, we present an approach overcomes limitation SMOTE, employing Localized Random Affine Shadowsampling (LoRAS) oversample from approximated data manifold class. We benchmarked our algorithm with 14 publicly available...
Cancer is a disease of subverted regulatory pathways. In this paper, we reconstruct the network around E2F, family transcription factors whose deregulation has been associated to cancer progression, chemoresistance, invasiveness, and metastasis. We integrate gene expression profiles cell lines from two E2F1-driven highly aggressive bladder breast tumors, use analysis methods identify tumor type-specific core network. By combining logic-based modeling, in vitro experimentation, patient...
Abstract White blood cell (WBC) differential counting is an established clinical routine to assess patient immune system status. Fluorescent markers and a flow cytometer are required for the current state‐of‐the‐art method determining WBC counts. However, this process requires several sample preparation steps may adversely disturb cells. We present novel label‐free approach using imaging machine learning algorithms, where live, unstained WBCs were classified. It achieved average F1‐score of...
Long non-coding RNAs (lncRNAs) have emerged as integral components of E2F1-regulated gene regulatory networks (GRNs), but their implication in advanced or treatment-refractory malignancy is unknown. Methods: We combined high-throughput transcriptomic approaches with bioinformatics and structure modeling to search for lncRNAs that participate E2F1-activated prometastatic GRNs phenotypic targets the highly-relevant case E2F1-driven aggressive bladder cancer (BC). RNA immunoprecipitation was...
Stored red blood cells (RBCs) are needed for life-saving transfusions, but they undergo continuous degradation. RBC storage lesions often assessed by microscopic examination or biochemical and biophysical assays, which complex, time-consuming, destructive to fragile cells. Here we demonstrate the use of label-free imaging flow cytometry deep learning characterize lesions. Using brightfield images, a trained neural network achieved 76.7% agreement with experts in classifying seven clinically...
With the availability of quantitative data on transcriptome and proteome level, there is an increasing interest in formal mathematical models gene expression regulation. International conferences, research institutes groups concerned with systems biology have appeared recent years theory, study organisation behaviour per se, indeed a natural conceptual framework for such task. This is, however, not first time that theory has been applied modelling cellular processes. Notably 1960s enjoyed...
Mathematical modeling and dynamic simulation of signal transduction pathways is a central theme in systems biology increasingly attracting attention the postgenomic era. The estimation model parameters from experimental data remains bottleneck for major breakthrough this area. This study’s aim to introduce new strategy design based on parameter sensitivity analysis. approach identifies key parameters/variables pathway can thereby provide biologists with guidance which proteins consider...
Systems biology is a reemerging paradigm which, among other things, focuses on mathematical modeling and simulation of biochemical reaction networks in intracellular processes. For most tools publications, they are usually characterized by either preferring stochastic or rate equation models. The use occasionally accompanied with arguments against equations. Motivated these arguments, we discuss this paper the relationship between two forms representation. Toward end, provide novel compact...
MicroRNA (miRNA) target hubs are genes that can be simultaneously targeted by a comparatively large number of miRNAs, class non-coding RNAs mediate post-transcriptional gene repression. Although the details hub regulation remain poorly understood, recent experiments suggest pairs miRNAs cooperate if their binding sites reside in close proximity. To test this and other hypotheses, we established novel approach to investigate mechanisms collective miRNA The presented here combines prediction...