Medical Systems Biology
Visualization
Visual inspection is often a first step in identifying key features of data. The high dimensionality of biological data sets prohibits an intuitive understanding and requires advanced visualization techniques. Our group develops visualization tools to support researchers in inspecting different types of biological data, e.g. for automatic tracking of cells in live cell imaging, displaying locations of SNPs on a caryogram, linking human cytomegalovirus drug resistance mutations to phenotypes, or visualizing the stability of selected gene subsets. Our heavily used VennMaster software provides algorithms to display area-proportional Venn diagrams of set intersections.
Selected publications
L. Lausser, C. Müssel, M. Maucher, and H. A. Kestler. Measuring and visualizing the stability of biomarker selection techniques. Computational Statistics, 28(1):51–65, 2013.
J. Huth, M. Buchholz, J. M. Kraus, K. Molhave, C. Gradinaru, G. von Wichert, T. M. Gress, H. Neumann, and H. A. Kestler. TimeLapseAnalyzer: multi-target analysis for live-cell imaging and time-lapse microscopy. Comput Methods Programs Biomed, 104(2):227–34, 2011.
M. Chevillotte, J. von Einem, B. M. Meier, F. M. Lin, H. A. Kestler, and T. Mertens. A new tool linking human cytomegalovirus drug resistance mutations to resistance phenotypes. Antiviral Res., 85:318–327, 2010.
H. A. Kestler, A. Müller, J. M. Kraus, M. Buchholz, T. M. Gress, H. Liu, D. W. Kane, B. R. Zeeberg, and J. N. Weinstein. VennMaster: Area-proportional Euler diagrams for functional GO analysis of microarrays. BMC Bioinformatics, 9(1):67, 2008.
A. Müller, K.-H. Holzmann, and H. A. Kestler. Visualization of genomic aberrations using Affymetrix SNP arrays. Bioinformatics, 23(4):496–7, 2007.
H. A. Kestler, A. Müller, M. Buchholz, T. Gress, and G. Palm. A perceptually optimized scheme for vsiualizing gene expression ratios with confidence values. In E. André, L. Dybkjær, W. Minker, H. Neumann, and M. Weber, editors, Perception and Interactive Technologies (PIT 06), volume LNAI 4021, pages 73–84. Springer-Verlag, Heidelberg, 2006.
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.