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


Latest News

 

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.

 

Our paper "Unsupervised domain adaptation for the detection of cardiomegaly in cross-domain chest X-ray images" has been published in Frontiers in Artificial Intelligence.

 

  1. "The HLA ligandome of oropharyngeal squamous cell carcinomas reveals shared tumour-exclusive peptides for semi-personalised vaccination" has been published online first in the British Journal of Cancer.

 

"Vaccine Side Effects in Health Care Workers after Vaccination against SARS-CoV-2: Data from TüSeRe:exact Study" has been published in Viruses-Basel.

 

"PREDICT-juvenile-stroke: PRospective evaluation of a prediction score determining individual clinical outcome three months after ischemic stroke in young adults – a study protocol" has been published in BMC Neurology.

 

Our paper "Federated Electronic Data Capture (fEDC): Architecture and Prototype" has been accepted for publiaction in the Journal of Biomedical Informatics.

 

Our paper "Efficient cross-valdation traversals in feature subset selection" has been published in Scientific Reports.

 

Our paper "CANTATA - prediction of missing links in Boolean networks using genetic programming" has been published in Bioinformatics.

 

Our paper "Interaction Empowerment in Mobile Health: Concepts, Challenges, and Perspectives" has been published in the Journal of Medical Internet Research mhealth and uhealth.

 

Our paper "Identification of dynamic driver sets controlling phenotypical landscapes" has been published in the Computational and Structural Biotechnology Journal.