A5000170757- Gene Regulatory Network Analysis
- Radiomics and Machine Learning in Medical Imaging
- Bioinformatics and Genomic Networks
- Medical Imaging Techniques and Applications
- Microbial Metabolic Engineering and Bioproduction
- Advanced MRI Techniques and Applications
- MRI in cancer diagnosis
- Mobile Health and mHealth Applications
- Computational Drug Discovery Methods
- Neuroscience and Neuropharmacology Research
- Glioma Diagnosis and Treatment
- Digital Mental Health Interventions
- SARS-CoV-2 detection and testing
- Biomedical Text Mining and Ontologies
- Gene expression and cancer classification
- COVID-19 diagnosis using AI
- Cancer survivorship and care
- Pancreatic function and diabetes
- Artificial Intelligence in Healthcare
- Single-cell and spatial transcriptomics
- Cancer Genomics and Diagnostics
- COVID-19 Digital Contact Tracing
- Electronic Health Records Systems
- Cell Image Analysis Techniques
- Cancer Cells and Metastasis
Universität Ulm
2016-2024
Siemens (Germany)
1981-2022
Werner Siemens-Stiftung
2013
Hertie Institute for Clinical Brain Research
2013
Institute for Atomic and Molecular Physics
2013
University of Tübingen
2013
University Hospital of Zurich
2013
Cells and tissues are exposed to stress from numerous sources. Senescence is a protective mechanism that prevents malignant tissue changes constitutes fundamental of aging. It can be accompanied by senescence associated secretory phenotype (SASP) causes chronic inflammation. We present Boolean network model-based gene regulatory the SASP, incorporating published interaction data. The simulation results describe current biological knowledge. model predicts different in-silico knockouts...
In its most trending interpretation, empowerment in health care is implemented as a patient-centered approach. the same sense, many mobile (mHealth) apps are being developed with primary focus on individual user. The integration of mHealth into system has potential to counteract existing challenges, including incomplete or nonstandardized medical data and lack communication, especially intersectional context (eg, patients, forces). However, concerns about security privacy, regional...
Regulatory dependencies in molecular networks are the basis of dynamic behaviors affecting phenotypical landscape. With advance high throughput technologies, detail omics data has arrived at single-cell level. Nevertheless, new strategies required to reconstruct regulatory based on populations data. Here, we present a approach generate gene from RNA-sequencing (scRNA-seq) Our exploits heterogeneity pseudo-timepoints. This allows for first time uncouple network reconstruction direct...
Abstract Differential diagnosis and therapy of heterogeneous breast tumors poses a major clinical challenge. To address the need for comprehensive, noninvasive strategy to define molecular functional profiles in vivo, we investigated novel combination metabolic PET diffusion-weighted (DW)-MRI polyoma virus middle T antigen transgenic mouse model cancer. The implementation voxelwise analysis clustering intra- intertumoral heterogeneity this resulted multiparametric profile based on...
Aging is a complex biological process, which determines the life span of an organism. Insulin-like growth factor (IGF) and Wnt signaling pathways govern process aging. Both share common downstream targets that allow competitive crosstalk between these branches. Of note, shift from IGF to has been observed during aging satellite cells. Biological regulatory networks necessary recreate have not yet discovered. Here, we established mathematical in silico model robustly recapitulates signaling....
The metabolites, transporters, and enzymes involved in choline metabolism are regarded as biomarkers for disease progression a variety of cancers, but their vivo detection is not ideal. Both magnetic resonance spectroscopy [MRS using chemical shift imaging (CSI) total (tCho)] C-choline positron emission tomography (PET) can probe this pathway, they have been compared side by side. In study, we used the spontaneous murine astrocytoma model SMA560 injected intracranially into syngeneic VM/Dk...
A common approach to address biological questions in systems biology is simulate regulatory mechanisms using dynamic models. Among others, Boolean networks can be used model the dynamics of processes biology. network models allow simulating qualitative behaviour modelled processes. central objective simulation computation their long-term - so-called attractors. These attractors are special interest as they often linked biologically relevant behaviours. Changing internal and external...
Hematopoietic stem cells (HSCs) provide all types of blood during the entire life organism. HSCs are mainly quiescent and can eventually enter cell cycle to differentiate. maintained tightly regulated in a particular environment. The niche regulates dormancy awakening. Deregulations this interplay lead hematopoietic failure diseases. In paper, we present Boolean network model that recapitulates HSC regulation virtue external signals coming from niche. This integrates summarizes current...
Mathematical models and their simulation are increasingly used to gain insights into cellular pathways regulatory networks. Dynamics of factors can be modeled using Boolean networks (BNs), among others. Text-based representations precise descriptions, but hard understand interpret. ViSiBooL aims at providing a graphical way modeling simulating By visualizations static dynamic network properties simultaneously, it is possible directly observe the effects changes in structure on behavior. In...
Cofilin-1 (CFL1) overexpression in pancreatic cancer correlates with high invasiveness and shorter survival. Besides a well-documented role actin remodeling, additional cellular functions of CFL1 remain poorly understood. Here, we unraveled molecular tumor-promoting cancer. For this purpose, first show that knockdown results reduced growth proliferation rates vitro vivo, while apoptosis is not induced. By mechanistic modeling were able to predict the underlying regulation. Model simulations...
The dynamics of cellular mechanisms can be investigated through the analysis networks. One simplest but most popular modeling strategies involves logic-based models. However, these models still face exponential growth in simulation complexity compared with a linear increase nodes. We transfer this approach to quantum computing and use upcoming technique field simulate resulting Leveraging logic has many benefits, including reduction algorithms for systems biology tasks. To showcase...
Abstract Motivation Boolean networks can serve as straightforward models for understanding processes such gene regulation, and employing logical rules. These rules either be derived from existing literature or by data-driven approaches. However, in the context of large networks, exhaustive search intervention targets becomes challenging due to exponential expansion a network’s state space multitude potential target candidates, along with their various combinations. Instead, we employ...
Motivation: Personalized decision-making for cancer therapy relies on molecular profiling from sequencing data in combination with database evidence and expert knowledge. Molecular tumor boards (MTBs) bring together clinicians scientists diverse expertise are increasingly established the clinical routine therapeutic interventions. However, analysis documentation of patients still time-consuming difficult to manage MTBs, especially as few tools available amount information required. Results:...
Biological pathways are thought to be robust against a variety of internal and external perturbations. Fail-safe mechanisms allow for compensation perturbations maintain the characteristic function pathway. Pathways can undergo changes during aging, which may lead in their stability. Less stable or less consequential increase susceptibility development diseases. Among others, NF- κ B signaling is crucial pathway process aging. The system involved immune response dealing with various...
Cancer is a very distressing disease, not only for the patients themselves, but also their family members and relatives. Therefore, are regularly monitored to decide whether psychological treatment necessary applicable. However, such monitoring processes costly in terms of required staff time. Mobile data collection an emerging trend various domains. The medical field benefits from approach, which enables experts quickly collect large amount individual health data. applications enable more...
Mobile applications have increasingly entered the healthcare sector. Besides being daily companions, so-called mHealth potential to enable individuals collect data, document issues, and share them with professionals better adjust medical treatment, side effects, or quality of life. While patient empowerment should be a paramount goal, setup these in reliable communication-effective way is under discussion. In particular, including clinical practice routine crucial boost their development....
Abstract Pancreatic neuroendocrine tumors (PanNETs) are a rare tumor entity with largely unpredictable progression and increasing incidence in developed countries. Molecular pathways involved PanNETs development still not elucidated, specific biomarkers missing. Moreover, the heterogeneity of makes their treatment challenging most approved targeted therapeutic options for lack objective responses. Here, we applied systems biology approach integrating dynamic modeling strategies, foreign...
The occurrence of adverse events frequently accompanies tumor treatments. Side effects should be detected and treated as soon possible to maintain the best treatment outcome. Besides standard reporting system Common Terminology Criteria for Adverse Events (CTCAE), physicians have recognized potential patient-reporting systems. These are based on a more subjective description current patient symptoms. Patient-reported symptoms essential define impact given quality life patient's wellbeing....
Background Overcoming the COVID-19 crisis requires new ideas and strategies for online communication of personal medical information patient empowerment. Rapid testing a large number subjects is essential monitoring delaying spread SARS-CoV-2 in order to mitigate pandemic’s consequences. People who do not know that they are infected may stay quarantine and, thus, risk infecting others. Unfortunately, massive tests performed challenging both laboratories units conduct throat swabs communicate...
Interaction graphs are able to describe regulatory dependencies between compounds without capturing dynamics. In contrast, mathematical models that based on interaction allow investigate the dynamics of biological systems. However, since dynamic complexity these grows exponentially with their size, exhaustive analyses and consequently screening all possible interventions eventually becomes infeasible. Thus, we designed an approach identify dynamically relevant static network topology.Here,...
The staging and local management of breast cancer involves the evaluation extent completeness excision both invasive carcinoma component also intraductal or ductal in situ. When coincident situ are present, assessment localization components is required for optimal therapeutic planning. We have used a mouse model to evaluate feasibility applying molecular imaging assess status cancers vivo. Multi-tracer positron emission tomography (PET) magnetic resonance (MRI) characterize transition from...
As the Corona Disease 2019 (COVID-19) caused by SARS-CoV-2 persists, vaccination is one of key measures to contain spread. Side effects (SE) from are reasons for reluctance vaccinate. We systematically investigated self-reported SE after first, second, and booster vaccinations. The data were collected during TüSeRe: exact study (Tübinger Monitoring Studie zur exakten Analyse der Immunantwort nach Vakzinierung). Employees health research institutions invited participate. Study participants...
Controlling phenotypical landscapes is of vital interest to modern biology. This task becomes highly demanding because cellular decisions involve complex networks engaging in crosstalk interactions. Previous work on control theory indicates that small sets compounds can single phenotypes. However, a dynamic approach missing determine the drivers whole network dynamics. By analyzing 35 biologically motivated Boolean networks, we developed method identify sufficient decide entire landscape....