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. 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.