Medical Systems Biology

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Joint research projects

  • BIU-Project (Boehringer Ingelheim Ulm University BioCenter): 
    • Project N7: "Diagnostic role and predictive value of cyclic nucleotides in neuropsychiatric co-morbidities of Alzheimer’s disease"
  • Symbol-HF (BMBF, eMed): "Systems Medicine to dissect the Biology of Heart Failure"
  • SFB 1074(DFG): "Experimental Models and Clinical Translation in Leukemia"
    • Project Z1: "Parallel Algorithms for Robust Clustering, Classification, and Visualization"
  • CAM-PaC(European Comission, FP7): "Integrative Analysis of Gene Functions in Cellular and Animal Models of Pancreatic Cancer"
    • WP10: "Data Integration and Modeling"
  • SyStaR(BMBF, GerontoSys 2): "Molecular Systems Biology of Impaired Stem Cell Function and Regeneration during Aging"
    • Research Group Kestler
    • Research Group Senior PI (provisional)
    • Research Group Junior PI (provisional)
  • Genomics Core Facility, Ulm University
    • HAK is coordinator of bioinformatics
  • International Graduate School in Molecular Medicine, Ulm University
    • HAK is member of the PhD Committee
 

Research Training Projects

  

  • Research Training Group 2254: "Heterogeneity and Evolution in Solid Tumours" (HEIST):
    • Project A2: "Systems biology of tumour evolution: Estimating partial orders from omics data"
    • HAK is co-director of HEIST

 

Finished joint research projects


  • NGFN-Plus (BMBF): "Translational Genome Research Network in Pancreatic Cancer"
    • Project TP11B: "Molecular Diagnosis of Pancreatic Cancer"
  • SFB 518 (DFG): "Inflammation, Regeneration and Transformation in the Pancreas"
    • Project C05: "Robust Algorithms for Clustering and Classification of Pancreatic Cells and Tissues"

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.


  1. "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.

  1.  

    "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.

     

  2. "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.