This document describes a 3-month genomic data analysis training program offered by OmicsLogic and the Tauber Bioinformatics Research Center. The program consists of 16 online meetings led by experts in genomics, bioinformatics, and data processing. Trainees will learn how to process, analyze, and interpret genomic data through hands-on lessons and independent project work. Topics include processing genomic data from sequencing, understanding DNA variation, analyzing variants, annotation and interpretation using databases and machine learning, and preparing a bioinformatics project.

1. OmicsLogic:
Genomic Data Analysis
TAUBER
Bioinformatics Research
Center

2. OmicsLogic:
Genomic Data Analysis
Processing, Analysis, and Interpretation of Genomic data for
Biologists and Clinicians
TAUBER
Bioinformatics Research
Center
July 23 - September 28, 2019
Length: 3 months, 16 online meetings plus independent project work
with support from our expert staff.

3. Program Speakers and Trainers
OMICSLOGIC: GENOMIC DATA ANALYSIS
Sahil Sethi
Hands-on Training
M.Sc. Biomedical Informatics
Despoina Kalfakakou
Genomics
M.Sc. Bioinformatics
Pratim Chakraborti
Data Processing
Ph.D. Bioinformatics

4. TAUBER
Bioinformatics Research
Center
Introduction to the Program
○ Program Overview: tools and resources for successful learning
○ Expectations, schedule review and important deadlines
○ Introduction to materials, speakers and presenters
July 23, 2019
OMICSLOGIC: GENOMIC DATA ANALYSIS

6. TAUBER
Bioinformatics Research
Center
Processing of Genomic Data (Part I)
○ What is DNA, Variation and Significance
○ Next Generation Sequencing (WES, WGS, Targeted panels)
○ Read length, Mapping NGS data to a reference Genome
July 24, 2019
OMICSLOGIC: GENOMIC DATA ANALYSIS

7. TAUBER
Bioinformatics Research
Center
Processing of Genomic Data (Part II)
○ What is DNA, Variation and Significance
○ Next Generation Sequencing (WES, WGS, Targeted panels)
○ Read length, Mapping NGS data to a reference Genome
July 30, 2019
OMICSLOGIC: GENOMIC DATA ANALYSIS

8. Short Sequence Aligners
for NGS data
§ DNA
§ RNA
§ Methylation
§ miRNA
Source: https://www.ebi.ac.uk/~nf/hts_mappers/

9. OMICSLOGIC: GENOMIC DATA ANALYSIS
TAUBER
Bioinformatics Research
Center
Understanding DNA Variation (Part I)
○ Germline mutations - mapping to reference genome
○ Somatic Mutations - reference and “normal” sample
○ Non-point variations (CNV, chromosomal instability, rearrangements)
July 31, 2019

10. OMICSLOGIC: GENOMIC DATA ANALYSIS
TAUBER
Bioinformatics Research
Center
Understanding DNA Variation (Part II)
○ Germline mutations - mapping to reference genome
○ Somatic Mutations - reference and “normal” sample
○ Non-point variations (CNV, chromosomal instability, rearrangements)
August 6, 2019

13. OMICSLOGIC: GENOMIC DATA ANALYSIS
TAUBER
Bioinformatics Research
Center
Analysis of Genomic Variants (Part I)
○ Filtering - limiting the number of potentially significant variants
○ Accurate detection significance of coverage, distribution
○ Statistical methods for significance, stratification
August 7, 2019

14. OMICSLOGIC: GENOMIC DATA ANALYSIS
TAUBER
Bioinformatics Research
Center
Analysis of Genomic Variants (Part II)
○ Filtering - limiting the number of potentially significant variants
○ Accurate detection significance of coverage, distribution
○ Statistical methods for significance, stratification
August 13, 2019

17. OMICSLOGIC: GENOMIC DATA ANALYSIS
TAUBER
Bioinformatics Research
Center
Annotation and Interpretation (Part I)
○ Types of variants: missense, sense, nonsense
○ Using reference databases, Association studies (GWAS)
August 14, 2019

18. OMICSLOGIC: GENOMIC DATA ANALYSIS
TAUBER
Bioinformatics Research
Center
Annotation and Interpretation (Part II)
○ Prediction of variant effects on protein structure/function or P-P interaction
○ population genetics - phylogeny, hap map
August 20, 2019

20. OMICSLOGIC: GENOMIC DATA ANALYSIS
TAUBER
Bioinformatics Research
Center
Using Machine Learning for Genomic Data (Part I)
○ Regression, factors, and features – Factor Regression Analysis
○ Supervised Machine Learning (Classification, Discriminant Analysis)
○ Mutational Profiling, Signatures and biomarkers
August 21, 2019

21. OMICSLOGIC: GENOMIC DATA ANALYSIS
TAUBER
Bioinformatics Research
Center
Using Machine Learning for Genomic Data (Part II)
○ Regression, factors, and features – Factor Regression Analysis
○ Supervised Machine Learning (Classification, Discriminant Analysis)
○ Mutational Profiling, Signatures and biomarkers
August 27, 2019

22. OMICSLOGIC: GENOMIC DATA ANALYSIS
TAUBER
Bioinformatics Research
Center
Using Machine Learning for Genomic Data (Part III)
○ Regression, factors, and features – Factor Regression Analysis
○ Supervised Machine Learning (Classification, Discriminant Analysis)
○ Mutational Profiling, Signatures and biomarkers
August 28, 2019

23. -0.6
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PCA 12EBV Abundance - PC1 vs PC2
LIGB LI SLK SL -0.6
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EBOV 12 Samples PCA - PC1 and PC2
Liberia Grand Bassa Liberia Pool Sierra Leone: Kailahun Sierra Leone Pool

24. OMICSLOGIC: GENOMIC DATA ANALYSIS
TAUBER
Bioinformatics Research
Center
Preparing a BIOINFORMATICS project
○ Cancer studies (several examples)
○ Development of treatment resistance (Tuberculosis)
○ Case-control studies, GWAS (Breast Cancer Risk)
September 1, 2019 - September 28, 2019
https://www.ncbi.nlm.nih.gov/pubmed/28418444

25. 25
RhizobacteriaCancer Tuberculosis Ebola
Project Examples
Somatic Mutations Drug Resistance Viral Adaptation GWAS example

26. Sahil Sethi
Hands-on Training
M.Sc. Biomedical Informatics
Pratim Chakraborti
Bioinformatics
Ph.D. Bioinformatics
Program Speakers and Trainers
Despoina Kalfakakou
Genomics
M.Sc. Bioinformatics

27. https://edu.t-bio.info/organizations/omicslogic-genomics-training-program/

28. https://edu.t-bio.info/course/
genomics/
https://edu.t-bio.info/course/
introduction-to-genomics/
https://edu.t-bio.info/course/
genomics-2/
Genomics Course Collection
• Basic Concepts and Principles
• Sequencing Techniques
• Data Analysis Approaches
• Processing Genomic Data
• Single Nucleotide Variation
• Visualization of Mapping
• Identifying Significant Variations
• Heterozygosity
• Unsupervised Analysis
https://edu.t-bio.info/collections/genomics/

29. Facilitating Infrastructure
https://server.t-bio.info/

30. Q&A

31. https://edu.t-bio.info/organizations/omicslogic-genomics-training-program/

32. Registration and Cost
Full 3-hour Workshop on NGS Data Analysis:
Mastering RNA-Seq: a critical approach to transcriptomic data analysis. Process-
ing raw RNA-seq data and extracting meaningful insights using machine learning.
CHRISTINE CUTUCACHE
HANDS-ON WORKSHOP
MASTERING RNA-SEQ
Dr. Vladimir Galatenko, Chief Scientist
Tauber Bioinformatics Research Center
DATE
April 17, 2018
O F C O M P L E T I O N
This certificate is presented to
CERTIFICATE OF PARTICIPATION
$135 (2.5 MONTHS)
○ 2.5 MONTHS TRAINING
○ HANDS-ON ANALYSIS PRACTICE
○ ONE-ON-ONE Q&A AND ASSISTANCE
○ 5 TB DATA STORAGE
○ 14 DAY ACCOUNT ON T-BIOINFO
ASK ABOUT EARLY REGISTRATION DISCOUNTS
https://edu.t-bio.info/organizations/omicslogic-genomics-training-program/

33. OmicsLogic:
Genomic Data Analysis
TAUBER
Bioinformatics Research
Center