` ISB 2020 Schedule - Spring 2017

ISB 2020 - Genomics for Systems Biology

Course Schedule (Spring Term 2017)
  Course instructors and directors: Takis Benos and Dennis Kostka

Date / Instructor


Material covered

4-Jan-2017 No class  
9-Jan-2017 /
Takis & Dennis
Statistical aspects for Genomics / Discussion of paper Lecture 1: Information about the course - Statistics intro
Paper: High-throughput sequencing for biology and medicine (Review)
11-Jan-2017 / Dennis Inroduction to genomics, data wrangling Lecture 2: Databases and formats
16-Jan-2017 NO CLASS (Dr. Martin Luther King Jr. Day)  
18-Jan-2017 / Dennis Lecture (Probabilities) and Discussion of a paper Lecture 3: Probabilities
Paper: From profiles to function in epigenomics (Review)
Homework: hwrk-1
23-Jan-2017 / Dennis Multiple testing Lecture 4: Multiple testing
Homework: hwrk-2
25-Jan-2017/ Dennis Data visualization, clustering Lecture 5: Data visualization, clustering
30-Jan-2017 / Dennis Enrichment analysis Lecture 6: Enrichment analysis
1-Feb-2017 / Dennis Discussion of paper Paper: A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome
Homework: hwrk-3
6-Feb-2017 / Takis Genome sequencing and assembly Lecture 7: Genome sequencing and assembly
Lecture 7b: Tumor heterogeneity
8-Feb-2017 / Takis Tumor heterogeneity / Discussion of paper Paper: Clonal evolution in breast cancer revealed by single nucleus genome sequencing
13-Feb-2017 / Takis Introduction to genome variation Lecture 8: "Genome variations and their effects"
15-Feb-2017 / Takis Discussion of paper Paper: Universality of human microbial dynamics
Homework: hwrk-4
20-Feb-2017 / Takis Introduction to graphical models Lecture 9: GWAS, QTL, eQTL
22-Feb-2017 / Takis Discussion of paper Paper: An integrated map of structural variation in 2,504 human genomes
Homework: hwrk-5
27-Feb-2017 / Takis An introduction to Big Data and methods for analyzing them Lecture 10: "Analyzing big biomedical data"
1-Mar-2017 / Takis & Dennis MIDTERMS  
6-Mar-2017 NO CLASS (Spring break)  
8-Mar-2017 NO CLASS (Spring break)  
13-Mar-2017 / Dennis RNA sequencing: technologies, data processing and analysis Lecture 11: "High-throughput technologies: RNA sequencing
15-Mar-2017 / Dennis GTEx transcriptome / Discussion of paper Paper: "The human transcriptome across tissues and individuals"
20-Mar-2017 / Dennis Models for RNA-seq Lecture 12: "Analyzing RNA sequencing data"
22-Mar-2017 / Dennis Presenting and interpreting RNA-seq data Lecture 13: "Analyzing RNA sequencing data II"
Homework: hwrk-6
27-Mar-2017 / Dennis Discussion of paper Paper: "A survey of best practices for RNA-seq data analysis"
29-Mar-2017 / Dennis Discussion of paper Paper: "Understanding development and stem cells using single cell-based analyses of gene expression"
Homework: hwrk-7
3-Apr-2017 / Takis Transcription factor binding, chromatin states, DNA-seq data collection and analysis Lecture 14: "TF binding motifs and epigenetic marks"
5-Apr-2017 / Takis Discussion of paper Paper: "Transcriptional regulators form diverse groups with context-dependent regulatory functions"
Homework: hwrk-8
10-Apr-2017 / Takis Transcriptional and post-transcriptional regulation Lecture 15: ""Non-coding RNAs""
12-Apr-2017 / Takis Discussion of paper Paper: "Impact of Dietary Interventions on Noncoding RNA Networks and mRNAs Encoding Chromatin-Related Factors"
17-Apr-2017 / Takis Biological networks Lecture 16: "Gene networks"
19-Apr-2017 FINAL EXAM  
24-Apr-2017 FINAL PROJECTS  

Last Updated: January 4, 2016.