BioinformaticsAndMe

DAY 1: Public Bio Big Data and Cancer Immunotherapy

          2월 10일(월)

시간

  주  제

강 사

8:30 ~ 9:30

9:30 ~ 9:50

Translational Bioinformatics: Thousands of Public Data Analysis

 김주한 교수

9:50 ~ 10:40

The Cancer Genome Atlas (TCGA) Project and Cancer Genome Research
- TCGA Introduction
- TCGA Data and Scientific Findings
- Impact of TCGA and Future

 김태민 교수
(카톨릭의대)

10:50 ~ 12:10

실 습 I: TCGA Somatic Mutation Landscape
          Find Significantly Mutated Genes
          Identify Driver Groups of Mutations

유승원, 김기태

12:10 ~ 13:10

  중  식

13:10 ~ 14:00

Informatics for Cancer immunotherapy
- Genomics in cancer immunotherapy
- Tumor mutation burden(TMD) and neoantigen
- Gene expression and immune cells

김상우 교수
(연세의대)

14:10 ~ 15:30

실 습 II: Tumor mutation burden(TMB) calculation
          Neoantigen Prediction
          Identification of marker for immune cells

임영균, 부은경

15:40 ~ 16:30

Public Genome and Exome Data and Human Genome Diversity
- Applications of The 1000 Genomes Project data
- The genome Aggregation Database (gnomAD)
- Mutation Frequencies in Diverse Populations

이계화 교수
(서울대병원)

16:40 ~ 18:00

실 습 III: The 1000 Genomes Project Browser
         Allele and Genotypic Frequency Calculation
         Understanding interethnic variability
         Identification of Rare Deleterious Mutations  

박유미, 유경훈

DAY 2: Methodology and Application for Next Generation Sequencing

           2월 11일(화)

시간

  주  제

강 사

8:30 ~ 9:30

9:30 ~ 9:50

김주한 교수

9:50 ~ 10:40

NGS Platforms and Applications
- Current NGS Platforms
- NGS Data Formats
- NGS Data Analysis Technologies
- NGS Applications

김지훈 박사
(녹십자지놈)

10:50 ~ 12:10

실 습 I: NGS Data Processing
          NGS Data Format Converting
          NGS Visualization Tools

김주연, 윤선민

12:10 ~ 13:10

  중  식

13:10 ~ 14:00

NGS Data Analysis
- Sequence Alignment Algorithms
- Whole Genome and Exome Data Analysis
- Variation Detection and Reference Genome

최무림 교수
(서울의대)

14:10 ~ 15:30

실 습 II: Exome Sequencing Alignment
           SNP and Indel Identification
           Variation Filtering

채정환, 임영균

15:40 ~ 16:30

Exome Sequencing Analysis
- Exome Sequencing Data
- Study Design and Workflow
- Exome Sequencing of Familial Disease

 한미령 교수
(고려의대)

16:40 ~ 18:00

실 습 III: Trio-Exome-Sequencing Data Analysis
           Known Variant Filtering
           Detection of Disease-causing Variations            Disease Gene Prioritization

한봄, 부은경

DAY 3: Cancer Genome Bioinformatics

          2월 12일(수)

시간

  주  제

강 사

8:30 ~ 9:30

9:30 ~ 9:50

Cancer Genome Bioinformatics

 김주한 교수

9:50 ~ 10:40

Cancer Genome Bioinformatics
- Cancer Genome Analysis
- Genomic Rearrangement and Copy Number
- Somatic Variant detection/ Gene Fusion Analysis
- Survival analysis

송영수
(한양의대)

10:50 ~ 12:10

실 습 I: Somatic Variant Detection
          Survival Analysis
          Gene Fusion Analysis

이우승, 유승원

12:10 ~ 13:10

  중  식

13:10 ~ 14:00

Advanced Cancer Genome Data Analysis
- Different types of variation in cancer
- Matched normal and tumor pair data analysis
- Cancer clonality and sequencing depth
- Visualizing cancer genomics data

정제균 박사
(삼성유전체연구소)

14:10 ~ 15:30

실 습 II: Somatic mutation/CNV detection and genome data processing
           Mutual exclusivity and coverage
           Visualization of cancer study

안세환, 김기태

15:40 ~ 16:30

Multiomics and Precision Medicine
- Genome, Transcriptome, and Proteom Integration
- miRNA and Exosome Analysis
- Application for Precision Medicine

류성호 교수
(순천향대학교)

16:40 ~ 18:00

실 습 III: Cell line Data at GDSC & CCLE
           Gene expression in human cancer cell line
           Comparing Drug sensitivity by cell lines
           Epigenetic Regulation of Gene Expression

한봄, 권호식

DAY 4: RNA-Seq and Transcriptome Data Analysis

          2월 13일(목)

시간

  주  제

강 사

8:30 ~ 9:30

9:30 ~ 9:50

RNA-Seq Data Analysis

 김주한 교수

9:50 ~ 10:40

Non-coding RNA Analysis
- miRNA-seq Expression Profile Analysis
- Novel Transcript Discovery
- Non-coding RNA Characterization

백대현 교수
(서울대)

10:50 ~ 12:10

실 습 I: RNA-Seq Gene Expression Analysis
         miRNA Sequencing Data Process
         miRNA Expression Profiling

안세환, 임영균

12:10 ~ 13:10

  중  식

13:10 ~ 14:00

Sequence-level Transcriptome Analysis
- Alternative Splicing Events
- Alternative Polyadenylation Analysis
- RNA Editing Analysis

박지연 박사
(카톨릭의대)

14:10 ~ 15:30

실 습 II: Alternative Splicing Identification
          RNA-DNA Difference (RDD) Analysis
          RNA Editing Site Annotation

유경훈, 박유미

15:40 ~ 16:30

RNA-Seq Data Analysis
- Read Alignment Methods
- Expression Quantification Strategy
- Differentially Expressed Genes Identification

정인경 교수
(KAIST)

16:40 ~ 18:00

실 습 III: RNA-seq Data Preprocessing
           Old Tuxedo Pipeline(tophat, cufflinks)
           New Tuxedo Pipeline(hisat2, stringtie)
           DEG analysis

권호식, 최선

DAY 5: Advanced NGS Data Analysis

          2월 17일(월)

시간

  주  제

강 사

8:30 ~ 9:30

9:30 ~ 9:50

Advanced NGS Data Analysis

 김주한 교수

9:50 ~ 10:40

Epigenome Data Analysis
- Epigenetic Mechanisms
- DNA Methylation Analysis
- Histone Modification Analysis
- Discovery of Epigenetic Biomarkers

류성호 교수
(순천향대학교)

10:50 ~ 12:10

실 습 I: Epigenome Tools & Databases
           Visualization of DNA Methylation Data
           Identification of Methylated Genes

유승원, 부은경

12:10 ~ 13:10

  중  식

13:10 ~ 14:00

Advanced methods and algorithms for genetic association analysis
- Statistical methods for genomic association tests
- HLA imputation and fine-mapping
- Analysis of clinical heterogeneity and pleiotropy

한범 교수
(서울의대)

14:10 ~ 15:30

실 습 II: : Statistical tests for association (Chi-square, Fisher's exact test and Odds ratio)
           Rare variant association tests (Burden tests, SKAT, SKAT-O)

최선, 김주연

15:40 ~ 16:30

Pathway and Network Analysis
- Characteristics of Biological Network
- Cancer Gene Network Construction and Clustering
- Identification of Aberrant Pathway in Cancers

한현욱 교수
(차의대)

16:40 ~ 18:00

실 습 III: Pathway analysis of TCGA using PARADIGM methods
          Network Visualization in Cancers

유경훈, 채정환