A5079833473- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- Microbial Metabolic Engineering and Bioproduction
- Protein Structure and Dynamics
- Real-Time Systems Scheduling
- Computational Drug Discovery Methods
- Gene Regulatory Network Analysis
- Scientific Computing and Data Management
- Genetics, Bioinformatics, and Biomedical Research
- Genomics and Phylogenetic Studies
- Embedded Systems Design Techniques
- Machine Learning in Bioinformatics
- Petri Nets in System Modeling
- RNA and protein synthesis mechanisms
- Gene expression and cancer classification
- Cell Image Analysis Techniques
- Acute Kidney Injury Research
- Enzyme Structure and Function
- Formal Methods in Verification
- Parkinson's Disease Mechanisms and Treatments
- Data Visualization and Analytics
- Data Mining Algorithms and Applications
- Research Data Management Practices
- Semantic Web and Ontologies
- Cardiac Arrest and Resuscitation
University of Luxembourg
2016-2025
Luxembourg Institute of Health
2024
Centre Hospitalier de Luxembourg
2024
Laboratoire National de Santé
2024
Abbott Fund
2023
Eurostat
2023
University of Würzburg
2003-2022
Universitätsklinikum Würzburg
1999-2019
Universitätsklinikum Erlangen
2009-2019
Friedrich-Alexander-Universität Erlangen-Nürnberg
1981-2018
Abstract The database of known protein three‐dimensional structures can be significantly increased by the use sequence homology, based on following observations. (1) sequences, currently at more than 12,000 proteins, is two orders magnitude larger structures. (2) most powerful method predicting model building homology. (3) Structural homology inferred from level similarity. (4) threshold similarity sufficient for structural depends strongly length alignment. Here, we first quantify relation...
The Protein Data Bank (PDB) is the world-wide repository of macromolecular structure information. We present a series databases that run parallel to PDB. Each database holds one entry, if possible, for each PDB entry. DSSP secondary proteins. PDBREPORT reports on quality and lists errors. HSSP multiple sequence alignment all PDBFINDER easy parse summaries file content, augmented with essentials from other systems. PDB_REDO re-refined, often improved, copies structures solved by X-ray....
The maintenance of protein function and structure constrains the evolution amino acid sequences. This fact can be exploited to interpret correlated mutations observed in a sequence family as an indication probable physical contact three dimensions. Here we present simple general method analyze correlations mutational behavior between different positions multiple alignment. We then use these predict maps for each 11 families compare result with contacts determined by crystallography. For most...
Understanding complex systems often requires a bottom-up analysis towards biology approach. The need to investigate system, not only as individual components but whole, emerges. This can be done by examining the elementary constituents individually and then how these are connected. myriad of system their interactions best characterized networks they mainly represented graphs where thousands nodes connected with vertices. In this article we demonstrate approaches, models methods from graph...
PredictProtein is a meta-service for sequence analysis that has been predicting structural and functional features of proteins since 1992. Queried with protein it returns: multiple alignments, predicted aspects structure (secondary structure, solvent accessibility, transmembrane helices (TMSEG) strands, coiled-coil regions, disulfide bonds disordered regions) function. The service incorporates methods the identification regions (ConSurf), homology-based inference Gene Ontology terms...
Information on protein subcellular localization is important to understand the cellular functions of proteins. Currently, such information manually curated from literature, obtained high-throughput microscopy-based screens and predicted primary sequence. To get a comprehensive view protein, it thus necessary consult multiple databases prediction tools. address this, we present COMPARTMENTS resource, which integrates all sources listed above as well results automatic text mining. The resource...
By the middle of 1993, >30 000 protein sequences had been listed. For 1000 these, three-dimensional (tertiary) structure has experimentally solved. Another 7000 can be modelled by homology. remaining 21 sequences, secondary prediction provides a rough estimate structural features. Predictions in three states range between 35% (random) and 88% (homology modelling) overall accuracy. Using information about evolutionary conservation as contained multiple sequence alignments, 4700 was predicted...
A multitude of factors contribute to complex diseases and can be measured with 'omics' methods. Databases facilitate data interpretation for underlying mechanisms. Here, we describe the Virtual Metabolic Human (VMH, www.vmh.life) database encapsulating current knowledge human metabolism within five interlinked resources 'Human metabolism', 'Gut microbiome', 'Disease', 'Nutrition', 'ReconMaps'. The VMH captures 5180 unique metabolites, 17 730 reactions, 3695 genes, 255 Mendelian diseases, 818...
Abstract Motivation: Assessing functional associations between an experimentally derived gene or protein set of interest and a database known gene/protein sets is common task in the analysis large-scale genomics data. For this purpose, frequently used approach to apply over-representation-based enrichment analysis. However, has four drawbacks: (i) it can only score overlapping gene/proteins sets; (ii) disregards genes with missing annotations; (iii) does not take into account network...
Medicine and healthcare are undergoing profound changes. Whole-genome sequencing high-resolution imaging technologies key drivers of this rapid crucial transformation. Technological innovation combined with automation miniaturization has triggered an explosion in data production that will soon reach exabyte proportions. How we going to deal exponential increase production? The potential "big data" for improving health is enormous but, at the same time, face a wide range challenges overcome...
Abstract Since 1992 PredictProtein (https://predictprotein.org) is a one-stop online resource for protein sequence analysis with its main site hosted at the Luxembourg Centre Systems Biomedicine (LCSB) and queried monthly by over 3,000 users in 2020. was first Internet server predictions. It pioneered combining evolutionary information machine learning. Given as input, outputs multiple alignments, predictions of structure 1D 2D (secondary structure, solvent accessibility, transmembrane...
The analysis and interpretation of relationships between biological molecules, networks concepts is becoming a major bottleneck in systems biology. Very often the pure amount data their heterogeneity provides challenge for visualization data. There are wide variety graph representations available, which most map on 2D graphs to visualize interactions. These methods applicable range problems, nevertheless many them reach limit terms user friendliness when thousands nodes connections have be...
HSSP is a derived database merging structural (3-D) and sequence (1-D) information. For each protein of known 3-D structure from the Protein Data Bank (PDB), has multiple alignment all available homologues profile characteristic family. The list result search in SwissProt using position-weighted dynamic programming method for (MaxHom). updated frequently. listed are very likely to have same as PDB which they been aligned. As result, not only aligned families, but also implied secondary...
The human neuroblastoma cell line, SH-SY5Y, is a commonly used line in studies related to neurotoxicity, oxidative stress, and neurodegenerative diseases. Although this often as cellular model for Parkinson's disease, the relevance of context disease (PD) other diseases has not yet been systematically evaluated. We have systems genomics approach characterize SH-SY5Y using whole-genome sequencing determine genetic content transcriptomics proteomics data molecular correlations. Further, we...
Researchers around the world join forces to reconstruct molecular processes of virus-host interactions aiming combat cause ongoing pandemic.
The development of computational approaches in systems biology has reached a state maturity that allows their transition to medicine. Despite this progress, intuitive visualisation and context-dependent knowledge representation still present major bottleneck. In paper, we describe the Disease Maps Project, an effort towards community-driven computationally readable comprehensive disease mechanisms. We outline key principles framework required for success initiative, including use best...
Our growing knowledge about various molecular mechanisms is becoming increasingly more structured and accessible. Different repositories of interactions available literature enable construction focused high-quality interaction networks. Novel tools for curation exploration such networks are needed, in order to foster the development a systems biology environment. In particular, solutions visualization, annotation data cross-linking will facilitate usage network-encoded biomedical research....