A5083106620- Bioinformatics and Genomic Networks
- Microbial Metabolic Engineering and Bioproduction
- Gene Regulatory Network Analysis
- Gene expression and cancer classification
- Genomics and Chromatin Dynamics
- Epigenetics and DNA Methylation
- Computational Drug Discovery Methods
- Biomedical Text Mining and Ontologies
- Molecular Biology Techniques and Applications
- Scientific Computing and Data Management
- Metabolomics and Mass Spectrometry Studies
- Distributed and Parallel Computing Systems
- Machine Learning in Bioinformatics
- Cancer-related Molecular Pathways
- RNA Research and Splicing
- Genetic Syndromes and Imprinting
- Cancer-related gene regulation
- Genetics and Neurodevelopmental Disorders
- Monoclonal and Polyclonal Antibodies Research
- Electrochemical sensors and biosensors
- Cancer-related molecular mechanisms research
- Peer-to-Peer Network Technologies
- Parkinson's Disease Mechanisms and Treatments
- Chronic Lymphocytic Leukemia Research
- Algorithms and Data Compression
Roche Pharma AG (Germany)
2015-2024
Universitätsklinikum Tübingen
2020
University of Tübingen
2006-2016
Bernstein Center for Computational Neuroscience Tübingen
2012
Wellcome Trust
2011-2012
European Bioinformatics Institute
2011-2012
Ludwig-Maximilians-Universität München
2011
Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology
2011
California Institute of Technology
2011
Shanghai Center For Bioinformation Technology
2011
Abstract Background Systems biology projects and omics technologies have led to a growing number of biochemical pathway models reconstructions. However, the majority these are still created de novo , based on literature mining manual processing data. Results To increase efficiency model creation, Path2Models project has automatically generated mathematical from representations using suite freely available software. Data sources include KEGG, BioCarta, MetaCyc SABIO-RK. Depending source data,...
Abstract Summary: The specifications of the Systems Biology Markup Language (SBML) define standards for storing and exchanging computer models biological processes in text files. In order to perform model simulations, graphical visualizations other software manipulations, an in-memory representation SBML is required. We developed JSBML this purpose. contrast prior implementations APIs, has been designed from ground up Java™ programming language, can therefore be used on all platforms...
Abstract Summary: The KEGG PATHWAY database provides a widely used service for metabolic and nonmetabolic pathways. It contains manually drawn pathway maps with information about the genes, reactions relations contained therein. To store these pathways, uses KGML, proprietary XML-format. Parsers translators are needed to process usage in other applications algorithms. We have developed KEGGtranslator, an easy-to-use stand-alone application that can visualize convert KGML formatted XML-files...
The molecular events during nongenotoxic carcinogenesis and their temporal order are poorly understood but thought to include long-lasting perturbations of gene expression. Here, we have investigated the sequence pathological at early stages phenobarbital (PB) mediated liver tumor promotion in vivo. Molecular profiling (mRNA, microRNA [miRNA], DNA methylation, proteins) mouse 13 weeks PB treatment revealed progressive increases hepatic expression long noncoding RNAs miRNAs originating from...
The KEGG PATHWAY database provides a plethora of pathways for diversity organisms. All pathway components are directly linked to other databases, such as COMPOUND or REACTION. Therefore, the can be extended with an enormous amount information and provide foundation initial structural modeling approaches. As drawback, KGML-formatted primarily designed visualization purposes often omit important details sake clear arrangement its entries. Thus, direct conversion into systems biology models...
Abstract Summary: JSBML, the official pure Java programming library for Systems Biology Markup Language (SBML) format, has evolved with advent of different modeling formalisms in systems biology and their ability to be exchanged represented via extensions SBML. JSBML matured into a major, active open-source project contributions from growing, international team developers who not only maintain compatibility SBML, but also drive steady improvements interface promote ease-of-use end users....
Bioinformatics analysis has become an integral part of research in biology. However, installation and use scientific software can be difficult often requires technical expert knowledge. Reasons are dependencies on certain operating systems or required third-party libraries, missing graphical user interfaces documentation, nonstandard input output formats. In order to make bioinformatics easily accessible researchers, we here present a web-based platform. The Center for Tuebingen (ZBIT)...
Abstract Summary: Microarrays are commonly used to detect changes in gene expression between different biological samples. For this purpose, many analysis tools have been developed that offer visualization, statistical and more sophisticated methods. Most of these designed specifically for messenger RNA microarrays. However, today, microarray platforms available. Changes DNA methylation, microRNA or even protein phosphorylation states can be detected with specialized arrays. technologies,...
DNA methylation of CpG islands plays a crucial role in the regulation gene expression. More than half all human promoters contain with tissue-specific pattern differentiated cells. Still today, whole process how methyltransferases determine which region should be methylated is not completely revealed. There are many hypotheses genomic features correlated to epigenome that have yet been evaluated. Furthermore, explorative approaches measuring limited subset genome and thus, cannot employed,...
The process of hepatocarcinogenesis in the diethylnitrosamine (DEN) initiation/phenobarbital (PB) promotion mouse model involves selective clonal outgrowth cells harboring oncogene mutations Ctnnb1, while spontaneous or DEN-only-induced tumors are often Ha-ras- B-raf-mutated. molecular mechanisms and pathways underlying these different tumor sub-types not well characterized. Their identification may help identify markers for xenobiotic promoted versus spontaneously occurring liver tumors....
Abstract Motivation: Statins are the most widely used cholesterol-lowering drugs. The primary target of statins is HMG-CoA reductase, a key enzyme in cholesterol synthesis. However, elicit pleitropic responses including beneficial as well adverse effects liver or other organs. Today, regulatory mechanisms that cause these pleiotropic not sufficiently understood. Results: In this work, genome-wide RNA expression changes human hepatocytes six individuals were measured at up to time points upon...
One of the key mechanisms transcriptional control are specific connections between transcription factors (TF) and cis-regulatory elements in gene promoters. The elucidation these protein-DNA interactions is crucial to gain insights into complex regulatory networks underlying adaptation organisms dynamically changing environmental conditions. As experimental techniques for determining TF binding sites expensive mostly performed selected TFs only, accurate computational approaches needed...
Abstract Motivation: The biological pathway exchange language (BioPAX) and the systems biology markup (SBML) belong to most popular modeling data languages in biology. focus of SBML is quantitative dynamic simulation models, whereas BioPAX specification concentrates mainly on visualization qualitative analysis maps. describes reactions relations. In contrast, core exclusively processes such as reactions. With models extension (qual), it has recently also become possible describe relations...
The current gold-standard method for cancer safety assessment of drugs is a rodent two-year bioassay, which associated with significant costs and requires testing high number animals over lifetime. Due to the absence comprehensive set short-term assays predicting carcinogenicity, new approaches are currently being evaluated. One promising approach toxicogenomics, by virtue genome-wide molecular profiling after compound treatment can lead an increased mechanistic understanding, potentially...
Antibodies are generated with great diversity in nature resulting a set of molecules, each optimized to bind specific target. Taking advantage their and specificity, antibodies make up for large part recently developed biologic drugs. For therapeutic use need fulfill several criteria be safe efficient. Polyspecific can structurally unrelated molecules addition main target, which lead side effects decreased efficacy setting, example via reduction effective drug levels. Therefore, we created...
The current strategy for identifying the carcinogenicity of drugs involves 2-year bioassay in male and female rats mice. As this assay is cost-intensive time-consuming there a high interest developing approaches screening prioritization drug candidates preclinical safety evaluations. Predictive models based on toxicogenomics investigations after short-term exposure have shown their potential assessing carcinogenic risk. In study, we investigated novel method evaluation data ensemble feature...
Parkinson's disease is an age-related whose pathogenesis not completely known. Animal models exist for investigating the but all results can be easily transferred to humans. Therefore, mathematical or probabilistic human are constructed in silico order predict specific processes within a cell, such as dopamine metabolism and transport neuron. We present Systems Biology Markup Language (SBML) model of whole dopaminergic nerve cell consisting 139 reactions 111 metabolites which includes, among...
Traditionally, microarrays were almost exclusively used for the genome-wide analysis of differential gene expression. But nowadays, their scope application has been extended to various genomic features, such as microRNAs (miRNAs), proteins and DNA methylation (DNAm). Most available methods visualization these datasets are focused on individual platforms not capable integratively visualizing multiple microarray from cross-platform studies. Above all, there is a demand that can visualize...
Genome-wide association studies (GWAS) led to the identification of numerous novel loci for a number complex diseases. Pathway-based approaches using genotypic data provide tangible leads which cannot be identified by single marker as implemented in GWAS. The available pathway analysis mainly differ employed databases and applied statistics determining significance associated disease markers. So far, pathway-based GWAS failed consider overlapping genes among different pathways or influence...
Abstract The specifications of the Systems Biology Markup Language (SBML) define standards for storing and exchanging computer models biological processes in text files. In order to perform model simulations, graphical visualizations other software manipulations, an in-memory representation SBML is required. We developed JSBML this purpose. contrast prior implementations APIs, has been designed from ground up Java™ programming language, can therefore be used on all platforms supported by a...
Higher organisms are able to respond continuously changing external conditions by transducing cellular signals into specific regulatory programs, which control gene expression states of thousands different genes. One the central problems in understanding regulation is decipher how combinations transcription factors sets co expressed genes under experimental conditions. Existing methods this field mainly focus on sequence aspects and pattern recognition, e.g., detecting cis-regulatory modules...
Structured peer-to-peer systems are designed for a highly scalable, self organizing, and efficient lookup data. The key space of the so-called distributed hash tables (DHTs) is partitioned each partition with its keys values assigned to node in DHT. For data retrieval however, very nature allows only exact pattern matches. We propose Cerco, simple solution problem range queries by employing hierarchically structured P2P approach based on principles tables. show that dynamic hierarchy DHTs...