Pareto-optimal balancing conflicting objectives in genome subgroup analysis
A Microsoft Excel add-in that visualizes gene expression ratios. The software is freely available upon request.
A new tool linking human cytomegalovirus drug resistance mutations to resistance phenotypes: HCMV drug resistance mutations
An open-source Java program for visualizing genomic abnormalities: IdeogramBrowser Software
JANet (Javascript AgeFactDB Network-viewer) is a specialized 3D Network Exploration and Visualization for Lifespan Data Exploration from AgeFactDB.
Software to analyze array CGH data with direct GPR import (Microsoft Excel add-in, Windows): MCGH Analyzer Software.
McKmeans: A highly efficient multi-core k-means algorithm for clustering extremely large datasets.
Structural RNA alignment by multi-objective optimization: RNA-Pareto
Differential expression analysis for sequence count data: RNASeq Count Analyzer
Perl program to create receiver operator charateristic (ROC) curves: http://www.CPAN.org.
Visualization of Ant Colony Optimization (contributed by Michael Grönert): Swarm
Swat is a java commandline software based on dynamic programming to calculate optimal local alignments of DNA/ RNA sequences and protein sequences.
TraqBio is a intuitively useable and a readily implementable open-source web application for progress tracking in core units. Its main intention is the communication of projects status between a core unit and its users: Source and Documentation
An open-source Java program for drawing area proportional Venn/Euler diagrams:VennMaster Software
ViSiBooL-visualization and simulation of Boolean networks with temporal constraints
An R package for the generation, reconstruction, simulation and analysis of Boolean networks: BoolNet R package
An R package toolbox for various enrichment analysis methods and quantification of uncertainty of gene sets: GiANT R package
An R package that analyzes cluster alternatives based on multi-objective optimization of cluster validation indices: MOCCA R package
An R package that provides fast screening procedures for reflections of ordinal phenotype relations in highdimensional feature representations. It allows the detection of evidence for hypothesised orderings and explorative screenings for unknown relationships.
An R package for multi-objective parameter selection for classifiers: TunePareto R package
Wissenschaftlicher Mitarbeiter (m/w/d)
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.
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.
"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.
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.