The topics given in the thematic guide are 15-minute lectures.
Theory:
I. blokk: Basics of Bioinformatics
- Introduction to bioinformatics ( Dr. Balázs Győrffy)
- Utilization of a training and test set (Dr. János Tibor Fekete)
- Statistical errors and dichotomania (Dr. János Tibor Fekete)
- Survival analysis: Cox regression and the Kaplan-Meier plot (Prof. Dr. Balázs Győrffy)
- ROC analysis: predicting sensitivity and specificity (Dr. János Tibor Fekete)
- Correlation (Dr. Otília Menyhárt)
- Multiple hypothesis testing (Prof. Dr. Balázs Győrffy)
- Applications of bioinformatics and artificial intelligence (Prof. Dr. Balázs Győrffy)
Block I theoretical hours: 2,7 hours (120 minutes)
II. blokk: Omics
- Introduction to genomics (Prof. Dr. Balázs Győrffy)
- Similar genes and proteins, BLAST (Prof. Dr. Balázs Győrffy)
- Genomics: quality control (Dr. Gyöngyi Munkácsy)
- Genomics: alignment of data to a reference genome (Dr. Gyöngyi Munkácsy)
- Genomics: identifying mutations (SNV, indels) in normal and tumor samples (Dr. Gyöngyi Munkácsy)
- Genomics: determining the consequence of a mutation (Dr. Gyöngyi Munkácsy)
- Genomics: what is the clinical relevance of a mutation, ClinVar, dbSNP (Dr. Gyöngyi Munkácsy)
- Genomics: copy number variations (Dr. Gyöngyi Munkácsy)
- Genomics: identifying processing artefacts and quality issues (Dr. Otília Menyhárt)
- Transcriptomics: processing RNA-seq data (Prof. Dr. Balázs Győrffy)
- Processing single-cell data (Prof. Dr. Balázs Győrffy)
- Genomics: GeneBank and the database of genes (Dr. Attila Marcell Szász)
Block II theoretical hours: 4 hours (180 minutes)
III. blokk: Proteomics
- Proteomics and transcriptomics: pre-processing (Prof. Dr. Balázs Győrffy)
- Proteomics: tools to analyze immunhistochemistry results (Dr. Gyöngyi Munkácsy)
- Proteomics: processing mass spectrometry (Dr. Áron Bartha)
- Proteomics: advantages and limitations of mass spectrometry (Dr. Áron Bartha)
- Protein structure determination: physical/chemical methods (Dr. Gábor Tusnády)
- Modelling protein structure: from simple (homology model) to complex (ab initio) (Dr. Gábor Tusnády)
- Modelling the structure of transmembrane proteins (Dr. Gábor Tusnády)
- Proteomics: understanding molecular functions, Uniprot (Dr. Gyöngyi Munkácsy)
- Signal transduction, KEGG (Dr. Attila Marcell Szász)
- Graphical comparison of two groups: boxplot, violin plot, density plot, heatmap, correlation, matrix (Dr. Áron Bartha)
Block III theoretical hours: 3.3 hours (150 minutes)
IV. blokk: Artificial intelligence
- Machine learning (Dr. János Tibor Fekete)
- The Bayes rule (Dr. János Tibor Fekete)
- Principal component analysis (Dr. Áron Bartha)
- Determining distance (Prof. Dr. Balázs Győrffy)
- Clustering (Prof. Dr. Balázs Győrffy)
- Neural networks (Prof. Dr. Balázs Győrffy)
- Convolutional neural networks (CNN) (Dr. Otília Menyhárt)
- Deep learning (Dr. Otília Menyhárt)
- Clinical application of a decision tree (Dr. Áron Bartha)
- Feature selection (Dr. Otília Menyhárt)
- Support Vector Machines (Dr. János Tibor Fekete)
- Regression (Dr. Otília Menyhárt)
- The general pre-trained transformer (Dr. János Tibor Fekete)
Block IV theoretical hours: 4.3 hours (195 minutes)
V. blokk: Integrative sciences
- Multi-omics (Dr. Otília Menyhárt)
- Gene ontology (Dr. János Tibor Fekete)
- Reproducibility issues in medical research (Dr. Otília Menyhárt)
- Evaluation of Chip-seq and ATAC-seq data (Dr. Bálint Bálint)
- Evaluation of DNA methylation data (Dr. Bálint Bálint)
- Epigenetic databases (Dr. Bálint Bálint)
- Using Excel for database management (Dr. Gyöngyi Munkácsy)
- Data mining: Excel, PubMed, Watson (Dr. Gyöngyi Munkácsy)
- Using REDcap (Dr. Attila Marcell Szász)
- Time distortion and computer addiction (Dr. Otília Menyhárt)
- Blockchain and data security (Dr. Áron Bartha)
Block V theoretical hours: 3.7 hours (165 minutes)
Practical training:
I. blokk: Basics of Bioinformatics
- Survival analysis: Cox regression and the Kaplan-Meier plot, 2 hours ( Dr. Balázs Győrffy)
- ROC analysis, 2 hours (Dr. János Tibor Fekete)
- Multiple hypothesis testing, 2 hours (Prof. Dr. Balázs Győrffy)
- Introduction to Galaxy, 1 hour (Dr. Otília Menyhárt)
Block I Practical hours: 7 hours (315 minutes)
II. blokk: Genomics and transcriptomics
- Quality control, 2 hours (Dr. Gyöngyi Munkácsy)
- Alignment of data to a reference genome, 2 hours (Dr. Gyöngyi Munkácsy)
- Identifying variants, 2 hours (Szonja Anna Kovács)
- Consequences of mutations, 2 hours (Dr. Gyöngyi Munkácsy)
- Transcriptomics: processing RNA-seq data, 2 hours (Prof. Dr. Balázs Győrffy)
Block II Practical hours: 10 hours (450 minutes)
IV. blokk: Artificial intelligence
- Clustering, 1 hour (Dr. Otília Menyhárt)
- Classification, 2 hours (Dr. János Tibor Fekete)
- Regression, 1 hour, (Dr. Otília Menyhárt)
- Deep learning, 2 hours (Dr. János Tibor Fekete)
Block IV Practical hours: 6 hours (270 minutes)
V. blokk: Integrative science
- Epigenetics, 1 hour (Dr. Bálint Bálint)
Block V Practical hours: 1 hour (45 minutes)
A consultation is possible during the last practical session.
Total number of theoretical hours: 18 hours (810 minutes)
Total number of practical hours: 24 hours (1080 minutes)
A tömbösített napi beosztás tematikai elosztással (témaszámok a fenti lista alapján):
Day |
Theory covered |
Practical topics |
Total hours |
1 |
1-8 |
55, 56, 57 |
8.7 |
2 |
9-14, 28-30 |
58, 59, 60 |
8.0 |