A5076617999- Gene Regulatory Network Analysis
- Microbial Metabolic Engineering and Bioproduction
- Bioinformatics and Genomic Networks
- Pancreatic and Hepatic Oncology Research
- Scientific Computing and Data Management
- Cell Adhesion Molecules Research
- CAR-T cell therapy research
- Simulation Techniques and Applications
- Pancreatitis Pathology and Treatment
- Neuroendocrine Tumor Research Advances
- Cancer Genomics and Diagnostics
- Pancreatic function and diabetes
- Psychiatric care and mental health services
- Medical Practices and Rehabilitation
- Biomedical Text Mining and Ontologies
- Medical and Health Sciences Research
- Cancer Cells and Metastasis
- Distributed and Parallel Computing Systems
- Cancer Immunotherapy and Biomarkers
- Galectins and Cancer Biology
- Single-cell and spatial transcriptomics
- Genetics, Bioinformatics, and Biomedical Research
- Protein Structure and Dynamics
- Health and Medical Studies
- Cell Image Analysis Techniques
Heidelberg University
2015-2024
University Hospital Heidelberg
2017-2021
California Institute of Technology
2010-2019
Ludwig-Maximilians-Universität München
1936-2016
German Cancer Research Center
2016
Technical University of Munich
2014
University of Manchester
2012
Leibniz Institute of Plant Genetics and Crop Plant Research
2012
Systems Biology Institute
2012
European Bioinformatics Institute
2012
Abstract Pancreatic cancers with aberrant expression of macrophage migration inhibitory factor (MIF) are particularly aggressive. To identify key signaling pathways that drive disease aggressiveness in tumors high MIF expression, we analyzed the coding and noncoding genes low MIF-expressing multiple cohorts pancreatic ductal adenocarcinoma (PDAC) patients. The identified were linked to patient survival mechanistically, functionally, clinically characterized using cell lines, a genetically...
The increasing use of computational simulation experiments to inform modern biological research creates new challenges annotate, archive, share and reproduce such experiments. recently published Minimum Information About a Simulation Experiment (MIASE) proposes minimal set information that should be provided allow the reproduction among users software tools.In this article, we present Description Markup Language (SED-ML). SED-ML encodes in computer-readable exchange format required by MIASE...
Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational in declarative form that different software systems exchange. SBML oriented towards describing processes of the sort common research on number topics, including metabolic pathways, cell signaling many others. By supporting as an input/output format, tools all operate...
In Brief Objective: The aim of this study was to evaluate existing management guidelines for branch-duct intraductal papillary mucinous neoplasms (IPMNs). Background: According current treatment (Sendai criteria), patients with asymptomatic type IPMNs the pancreas less than 3 cm in diameter without suspicious features preoperative imaging should undergo conservative yearly follow-up examinations. Nevertheless, risk harboring malignancy or invasive cancer remains a significant matter...
Synthetic biology brings together concepts and techniques from engineering biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between computational modeling biological data. Using a CAD application, it would be possible construct models using available "parts" directly generate DNA sequence that represents model, thus increasing efficiency of construction synthetic networks.An application named TinkerCell has been developed serve as tool for visual...
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...
Background: With the ever increasing use of computational models in biosciences, need to share and reproduce results published studies efficiently easily is becoming more important. To this end, various standards have been proposed that can be used describe models, simulations, data or other essential information a consistent fashion. These constitute separate components required given scientific result. Results: We Open Modeling EXchange format (OMEX). Together with standard formats from...
The 2012 international consensus guidelines for the management of intraductal papillary mucinous neoplasms (IPMN) recommend surgical treatment in main-duct IPMN patients with a main pancreatic duct (MPD) diameter ≥10 mm. Aim present study was to analyze cancer risk an MPD less than 10 mm.All consecutive (prospective data protocol) histological proof who underwent surgery between January 2004 and December 2013 were included study. Clinical characteristics, particularly preoperative imaging...
In Brief Objectives: Because neural invasion (NI) is still inconsistently reported and not well characterized within gastrointestinal malignancies (GIMs), our aim was to determine the exact prevalence severity of NI elucidate true impact on patient's prognosis. Background: The union internationale contre le cancer (UICC) recently added as a novel parameter in current TNM classification. However, there are only few existing studies with specific focus NI, so that distinct role GIMs uncertain....
This study aimed to analyze a large single-center population of resected intraductal papillary mucinous neoplasms (IPMN) the pancreas with respect risk factors malignant transformation.There is international consensus that main-duct (MD) as well mixed-type IPMNs should be treated surgically due high malignancy. In contrast, there an ongoing controversy about surgery branch-duct type IPMN (BD-IPMN).All consecutive patients who underwent for between January 2004 and December 2012 were...
The definition of resection margin (R) status in pancreatic cancer is under debate. Although a at least 1 mm an independent predictor survival after for head cancer, its relevance to body and tail cancers remains unclear. This study aimed validate R based on 1-mm tumour-free as prognostic factor resected adenocarcinoma involving the tail.Patients who underwent distal or total pancreatectomy adenocarcinomas between January 2006 December 2014 were identified from prospective database....
Constraint-based modeling is a well established methodology used to analyze and study biological networks on both medium genome scale. Due their large size complexity such steady-state flux models are, typically, analyzed using constraint-based optimization techniques, for example, balance analysis (FBA). The Flux constraints (FBC) Package extends SBML Level 3 provides standardized format the encoding, exchange annotation of models. It includes support concepts as objective functions, bounds...
Reproducibility and reusability of the results data-based modeling studies are essential. Yet, there has been—so far—no broadly supported format for specification parameter estimation problems in systems biology. Here, we introduce PEtab, a which facilitates using Systems Biology Markup Language (SBML) models set tab-separated value files describing observation model experimental data as well parameters to be estimated. We already implemented PEtab support into eight well-established...
Tenascin C (TNC) is a component of the provisional extracellular matrix (ECM) that characterizes solid tumours. Cell surface annexin II high-affinity receptor for large TNC splice variants. The aim this study was to analyse whether and play role in development pancreatic ductal adenocarcinoma (PDAC). PDAC characterized by rich ECM populated stellate cells, which crucial desmoplasia. mRNA protein levels were analysed tissues DNA array, quantitative reverse transcriptase-polymerase chain...
Model exchange in systems and synthetic biology has been standardized for computers with the Systems Biology Markup Language (SBML) CellML, but specialized software is needed generation of models these formats. Text-based model definition languages allow researchers to create simply, then export them a common format. Modular combine complex more easily. We saw use modular text-based language, together translation library other programs read as well.The Antimony language provides way...
ALCAM (activated leucocyte cell adhesion molecule, synonym CD166) is a which belongs to the Ig superfamily. Disruption of ALCAM-mediated adhesiveness by proteolytic sheddases such as ADAM17 has been suggested have relevant impact on tumour invasion. Although expression valuable prognostic and predictive marker in several types epithelial tumours, its role pancreatic cancer not yet reported.In this study, paraffin-embedded samples 97 patients with undergoing potentially curative resection...
Pancreatic ductal adenocarcinoma (PDAC) is thought to originate from structures, exhibiting strong desmoplastic reaction with stromal pancreatic myofibroblasts (PMF), which are supposed drive PDAC tumorigenesis. Previously, we observed high expression of the adhesion molecule L1CAM (CD171) in cells accounting for chemoresistance. Thus, this study aimed investigate whether PMFs involved induction tumoral and contributes malignant transformation Immunohistochemistry tissues chronic...
Abstract Motivation: LibSBGN is a software library for reading, writing and manipulating Systems Biology Graphical Notation (SBGN) maps stored using the recently developed SBGN-ML file format. The (available in C++ Java) makes it easy developers to add SBGN support their tools, whereas format facilitates exchange of between compatible applications. also supports validation maps, which simplifies task ensuring compliance with detailed specifications. With this effort we hope increase adoption...
Pancreatic ductal adenocarcinoma (PDAC) presenting with a micropapillary growth pattern is frequently associated prominent neutrophil infiltration into the tumor. The relevance of infiltrates for tumor progression, however, still debated. To gain insight role polymorphonuclear neutrophils (PMNs) in PDAC, we assessed their effect on pancreatic cells grown vitro as monolayers. Time-lapse video microscopy showed PMN-induced dyshesion cells, and subsequent experiments revealed that this was due...