Medical Systems Biology

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Bioinformatics and Systems Biology (MolMed)

Coordinator: Prof. Dr. H. A. Kestler

Code: MOME.Ma1002

 


Announcement:

- Lectures will start on October 18th


Lectures:

Tuesday (14:00 - 16:00) Room 45.2.101 (Uni West)

Thursday (14:00 - 16:00) Room O23, 2609/10

 

Room changes:

  • Thursday, 20.10.2016 (16:00 - 18:00) Room N23, 2622
  • Thursday, 17.11.2016 (14:00 - 16:00) Room N23, 2622
  • Tuesday, 29.11.2016 (14:00 - 16:00) cancelled
  • Tuesday, 29.11.2016 (16:00 - 18:00) Room 029, 1001

 

Excercises:

Thursday (16:00 - 18:00) Room O29, 3005/3006

 

Exam:

Friday, 10.02.2017 (11:00), Lecture Hall at the University and Rehabilitations Clinics Ulm (RKU) 

 

Slides:

  1. Overview
  2. Signaling
  3. Epigenetics
  4. Omics: High throughput technologies
  5. Introduction to R: Part I
  6. Introduction to R: Part II
  7. Multivariate statistics
  8. Classification
  9. Clustering
  10. Genomics
  11. NGS (supplement: table header for slide 24)
  12. Mass spectrometry and proteomics
  13. Bioinformatics in MS based qualitative and quantitative proteomics
  14. Sequence alignment and phylogenetic inference - Slides (use lectures 6,8 and 9)
  15. Sequence alignment and phylogenetic inference - Script
  16. Simulation and modeling
  17. Boolean networks
  18. Quantitative description of cellular processes

Exercise sheets:

  1. R basics
  2. Multivariate statistics
  3. Data mining
  4. NGS
  5. Proteomics
  6. Sequence alignment and phylogenetic inference
  7. Simulation and modeling
  8. Boolean networks
  9. Quantitative description of cellular processes


Additional material:

  • Exercise 01: Leaves dataset
  • Exercise 02: Dataset
  • Exercise 03: STC dataset
  • Exercise 03: Predicted labels classifier 1
  • Exercise 03: Predicted labels classifier 2
  • Exercise 03: Real labels
  • Exercise 03: Clustering sheet
  • Exercise 04: Genome data
  • Exercise 05: MS/MS-Peaklists
  • Exercise 07: Helping functions (additional information)
  • Exercise 09: Simulation


Job Openings

Wissenschaftlicher Mitarbeiter (m/w/d) 

 

Latest News

 

  1. Integrated, cross-entity information on preventive measures for bowl, breast, and prostate cancer: evaluation study of a web application „Prevent-Take-Upwas published in JMIR Cancer.

Our paper "Identification of ordinal relations and alternative suborders within high-dimensional molecular data" has been published in Frontiers in Bioinformatics.

 

Our paper "Dealing with Class Overlap Through Cluster-BasedSample Weighting" has been published in Computers.

 

Our paper "A novel quantum algorithm for efficient attractor search in gene regulatory networks" has been published in Patterns.

 

Our paper "CLL to Richter syndrome: Integrating network strategies with experiments elucidating disease drivers and personalized therapies" has been published in Science Advances.

 

"Deep Learning Predicts Postoperative Mobility, Activities of Daily Living, and Discharge Destination in Older Adults from Sensor Data" has been published in Sensors.

 

Our paper "Robust signalling entropy estimation for biological process characterization" has been published in Briefings in Bioinformatics.

 

"Proposal for Using AI to Assess Clinical Data Integrity and Generate Metadata: Algorithm Development and Validation" has been published in JMIR Medical Informatics.

 

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 first quantum computing paper "Leveraging quantum computing for dynamic analyses of logical networks in systems biology" has been published in Patterns.