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HB-10 Workshops


Tuesday, September 5th, 2017

Theme:           Workshops

Chair:              Michalis Aivaliotis

Lecture Hall:  Alkiviades Payatakis

Morning workshop  

09:00-13:00 Proteomics Workshop – Hands-on

Proteomics Bioinformatics: From raw MS-data to knowledge

Chair: Michalis Aivaliotis

09:00-09:15 Michalis Aivaliotis

  • Introduction to proteomics
    • Brief history of MS-based proteomics
    • State-of-the-art proteomics

09:15-10:30 M. Aivaliotis, N. Kountourakis, K. Psatha, C. Seitanidou

  • Bioinformatics I – MS-Raw data processing
    • Proteome Identification and quantitation using commercial available and free bioinformatic platforms
    • Quality control and filtering of proteomics data

10:30-13:00 M. Aivaliotis, N. Kountourakis, K. Psatha, C. Seitanidou

  • Bioinformatics II – Meta-data analysis and visualization
    • Comparative proteomics analysis
    • Functional proteome annotation
    • GO terms and pathways enrichment analysis
    • Protein-protein interaction networks
    • Visualization of proteomics data
  • 13:00-14:00 Lunch Break

Evening workshop

14:00-18:00 Advanced RNA-Seq and ChIP-Seq data analysis – Hands-on
Chair: Pantelis Topalis

14:00-14:15 Pantelis Topalis

  • Introduction to RNA-Seq and ChIP-Seq
    • Experimental Design and Data analysis
    • Quality Control

14:15-16:00 P. Topalis, E. Dialynas, G. Papagiannakis

  • RNA-Seq Data Analysis
    • De novo transcriptome assembly
    • Differential Gene Expression
    • Everything you always wanted to know about batch effects but you were afraid to ask

16:00-18:00 P. Topalis, E. Dialynas

  • ChIP-Seq Data Analysis
    • Peak finding (Transcription Factors, Histone modifications, Super Enhancers)
    • Irreproducible Discovery Rate (IDR) pipeline
    • Peak annotation

Important Notes:

  1. Number of maximum participants 35.
  2. A digital textbook and references will be provided to all participants in advance.
  3. All the participants need to have their own laptops. No computers will be provided by the organizers.
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