Medical Systems Biology
Boolean networks
Boolean networks are qualitative models of regulatory processes that represent the state of a node by a simple bistable switch, e.g. genes can be transcribed or not transcribed. Although being highly abstract, Boolean networks have proven to approximate the real nature of gene-regulatory processes well.
Illustration: © 2012 Springer, Paper: M. Hopfensitz, C. Müssel, M. Maucher, and H. A. Kestler. Attractors in Boolean networks – a tutorial. Computational Statistics, 28(1):19–36, 2013.
The research of our group covers the complete process of construction, analysis and simulation of the networks. This includes approaches for the binarization of time series measurements, inference of networks from such time series, literature-based network assembly, simulation and attractor search.
Selected publications
M. Grieb, A. Burkovski, J. E. Sträng, J. M. Kraus, A. Groß, G. Palm, M. Kühl, H. A. Kestler. Predicting Variabilities in Cardiac Gene Expression with a Boolean Network Incorporating Uncertainty. PloS one, 10 (7), e0131832, 2015.
A. Naldi, P. T. Monteiro, C. Müssel, the Consortium for Logical Models and Tools, H. A. Kestler, D. Thieffry, I. Xenarios, J. Saez-Rodriguez, T. Helikar, and C. Chaouiya. Cooperative development of logical modelling standards and tools with CoLoMoTo. Bioinformatics, 31(7):1154-1159, 2015.
M. Hopfensitz, C. Müssel, M. Maucher, and H. A. Kestler. Attractors in Boolean networks – a tutorial. Computational Statistics, 28(1):19–36, 2013.
M. Hopfensitz, C. Müssel, C. Wawra, M. Maucher, M. Kühl, H. Neumann, and H. A. Kestler. Multiscale binarization of gene expression data for reconstructing Boolean networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(2):487–498, 2012.
M. Maucher, B. Kracher, M. Kühl, and H. A. Kestler. Inferring Boolean network structure via correlation. Bioinformatics, 27(11):1529–36, 2011.
C. Müssel, M. Hopfensitz, and H. A. Kestler. BoolNet - an R package for generation, reconstruction, and analysis of Boolean networks. Bioinformatics, 26(10):1378–1380, 2010.
Job Openings
Wissenschaftlicher Mitarbeiter (m/w/d)
Latest News
Our paper "Sparse keypoint segmentation of lung fissures: efficient geometric deep learning for abstracting volumetric images" has been published in the International Journal of Computer Assisted Radiology and Surgery. Please find electronical supplementary material here.
- "Hydra has mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype" has been published in Genome Research.
Our paper "Boolean network modeling and its integration with experimental read-outs: An interdiscipliary presentation using a leukemia model" has been published online first in Pathologie.
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"Combined analysis of a serum mRNA/miRNA marker signature and CA 19-9 for timely and accurate diagnosis of recurrence after resection of pancreatic ductal adenocarcinoma: A prospective multicenter cohort study" has been published online first in the United European Gastroenterology Journal.
"Identifications of Similarity Metrics for Patients With Cancer: Protocol for a Scoping Review" has been published in JMIR Research Protocols.
"Recent Trends and Future Challenges in Learning from Data" has been published with Springer.
Our paper "Permutation-invariant linear classifiers" has been published in Machine Learning.
Our paper "Prediction of resistance to bevacizumab plus FOLFOX in metastatic colorectal cancer-Results of the prospective multicenter PERMAD trial" has been published in PLoS One.
- "Introducing a machine learning algorithm for delirium prediction—the Supporting SURgery with GEriatric Co-Management and AI project (SURGE-Ahead)" has been published in Age and Ageing.
Our paper "Segmentation-based cardiomegaly detection based on semi-supervised estimation of cardiothoracic ratio" has been published in Scientific Reports.
"Prospective study validating a multidimensional treatment decision score predicting the 24-month outcome in untreated patients with clinically isolated syndrome and early relapsing–remitting multiple sclerosis, the ProVal-MS study" has been published in Neurological Research and Practice.
Our paper "GatekeepR: an R shiny application for the identification of nodes with high dynamic impact in boolean networks" has been published online first in Bioinformatics.
Our paper "The Necessity of Interoperability to Uncover the Full Potential of Digital Health Devices" has been published in JMIR Medical Informatics.
"Multicentric pilot study to standardize clinical whole exome sequencing (WES) for cancer patients" has been published in npj Precision Oncology.
Our paper "AMBAR-interactive alteration annotations for molecular tumor boards" has been published in Computer Methods and Programs in Biomedicine.
"A protocol for the use of cloud-based quantum computers for logical network analysis of biological systems" has been published in STAR Protocols.
Our paper "A systems biology approach to define mechanisms, phenotypes, and drivers in PanNETs with a personalized perspective" has been published in npj systems biology and applications.
"Supporting SURgery with GEriatric Co-Management and AI (SURGE-Ahead): A study protocol for the development of a digital geriatrician" has been published in PLoS One.
"Self-Assessment of Having COVID-19 With the Corona Check Mhealth App" has been published in IEEE Journal of Biomedical and Health Informatics.
Our first quantum computing paper "Leveraging quantum computing for dynamic analyses of logical networks in systems biology" has been published in Patterns.