Next Generation Genomics Workshop

Date: June 24-26, 2019  
Place: santralistanbul Campus

This workshop, organized by İstanbul Bilgi University Department of Genetics and Bioengineering,  aims at providing an introduction to genomics applications, focusing on the use of next generation sequencing (NGS) for the analysis of gene expression and genomics variation. Analytical workflows for processing NGS data are presented and students have the opportunity to familiarize themselves with basic statistics, computational skills, bioinformatics resources and analytical approaches needed to process, analyze and interpret NGS data. 

Familiarity with the technology and biological use cases of high throughput sequencing is required, as is some experience with Unix/Linux environment and R/Bioconductor. 

Participants are not required to bring their laptop. Software and Data will be provided.

Lecturers:
Mohamed Hamed, PhD (University Medical School Rostock, Rostock, Germany)   
Yvonne Gladbach, PhD Candidate (Heidelberg University, Heidelberg/ University Medical School Rostock, Rostock, Germany)
Ozlem Ulucan Açan, PhD (İstanbul Bilgi University Department of Genetics and Bioengineering, Istanbul,Turkey)

Who can participate?
This course is aimed at undergraduate students with suitable background. However grad students and researchers who are planning to apply high throughput sequencing technologies and bioinformatics methods in their research are also welcome. The number of participants is limited to 35.

Learning outcomes:

• Discuss the principles applied to quality control of sequencing data, alignment of sequence to the reference genome, calling and annotating sequence variants, and filtering strategies to identify mutations in sequencing data;
  
• Perform basic RNA-seq data analysis and be familiar with open-source software packages for such analysis;
• Gain practical experience of the bioinformatics pipelines for variant calling and RNA-seq.

Workshop Language: English

Application Deadline: June 20, 2019

For registration and payment, please click here.

Fee:
Students: 850 TL (KDV included) 
Other: 1.750 TL (KDV included)

Contact: bioeng@engr.bilgi.edu.tr / ozlem.ulucan@bilgi.edu.tr

PROGRAM
Total 21 hours (6 hours lecture + 15 hours practical)

June 24, 2019

09.00-10.00      Coffee & Registration

10.00-10.15        Welcoming Words

10.15-11.00         Lecture 1: Introduction to NGS 
-History of genome sequencing
-Sequencing technologies/ generations
-Sequencing techniques (synthesis or ligation)

11.00-11.15        Coffee break

11.15-12.00        Lecture 2: NGS Planning and Workflows
-NGS limitations
-Experimental planning (Chip-seq, RNA-seq, WGS, miRNA-seq, Bi-sulfite sequencing,..etc)
-NGS experiment guidelines (10 simple rules)
-General NGS analysis workflows
-NGS file formats(.fasta, .fastq, .vcf, .sam,.bed)

12.00-13.00        Lunch break

13.00-15.00        Tutorial 1: Bash Scripting and Samtools

15.00-17.00        Tutorial 2: Introduction to R 
(basic R syntax, I/O operations, manipulating dataframes, and plotting: barplots, Venn diagrams, and heatmaps)

June 25, 2019

9.30-10.15        Lecture 3: Whole Genome/Exome Sequencing Analysis (WGS, WES) 
-Introduction to WGS and WES
-WGS/WES analysis workflow
-Quality control
-Alignment and Mapping
-PCR duplicates removal 

10.15-10.30        Coffee Break

10.30-12.00        Tutorial 3:  WGS/ WES Pre-processing 

12.00-13.00        Lunch break

13.00-14.00        Lecture 4: Variant Downstream Analysis
-SNP calling
-SNP annotations
-Variant analysis and mutation types
-Data visualization 

14.00-17.00        Tutorial 4: Downstream Analysis of WGS/WES  

June 26, 2019

9.00-10.00        Lecture 5: RNA-Seq 
-Introduction to coding and non-coding RNAs
-RNA-Seq and miRNA-Seq
-RNA-seq analysis workflow
-Quality control
-Alignment and Mapping
-PCR duplicates removal
-Transcript expression quantification

10.00-10.30       Coffee break

10.30-12.00        Tutorial 5: RNA-Seq Pre-processing 

12.00-13.00        Lunch break

13.00- 14.00       Lecture 6: RNA-Seq Downstream Analysis 
-Differential expression analysis
-Functional enrichment analysis
-Data visualization

14.00-17.00        Tutorial 6: Downstream Analysis of RNA-Seq Data

17.00-17.30        Closure and feedback

Mohamed Hamed Fahmy PhD:
Dr. Mohamed Hamed is a research group leader at Rostock University Medical Center, Rostock, Germany. He is enjoying a rich profile of industrial and academic experience in computer science, molecular biology, bioinformatics, and data analysis. His research interests include systems biology, drug combination predictions, cancer genomics, precision medicine, and biological data integration. Dr. Hamed received his BSc degree in systems and biomedical engineering with highest honors from Cairo University before getting a full grant to obtain an IT diploma in the field of software engineering from the Information Technology Institute (ITI) in Egypt.  Dr. Hamed worked for ESRINEA as a senior team leader focusing on developing and integrating enterprise IT solutions. He received his MSc degree from the school of computer science in Nottingham University, UK  and his PhD degree in computer science from Saarland University, Saarbrucken, Germany. Currently he is heading the Integrative OMICs Analysis group in Rostock University and collaborating with multiple research labs worldwide. Dr. Hamed was awarded couple of academic scholarships such as DAAD as well as numerous mobility, research, and travel grants.  He is an active member in the International Society of Computational Biology (ISCB), the German Stem Cell Network (GSCN) and he is the organizer of the bi-annual bioinformatics satellite meeting of stem cell in North Rhine-Westphalia, Germany. He also co-organized the 2nd NGS workshop in Dummerstorf, Germany (2018). Dr. Hamed has published several research and methodological articles in various high-impact peer-reviewed journals. He was invited as a distinguished speaker to give keynote talks in many international conferences and scientific events.

Yvonne Gladbach, PhD Candidate: 
Yvonne Saara Gladbach, is a senior Ph.D. student at the University of Heidelberg in cooperation with the University Medical School Rostock, Germany. Her Ph.D. thesis concerns integrating multi-omics data for predicting new drug targets for Acute Lymphoblastic Leukemia (ALL). Moreover, she is involved in multiple research projects and analyzing heterogeneous NGS data sets of Alzheimer, colon cancer patients. She received her M.Sc. degree in 2016 at Saarland University, Germany where she developed a bioinformatic pipeline for automatic characterization of bacterial isolates based on MultiLocus Sequence Typing (MLST) schemes. Her field of expertise includes next-generation sequencing analyzes of Whole-Transcriptome Sequencing, ChIP-Sequencing, Whole-Genome Sequencing, and RNA-Sequencing including the wet-lab work for RNA-Sequencing.  She got intensive training on the wet-lab RNA-Sequencing techniques at the Weinberg Lab of the Whitehead Institute for Biomedical Research, Cambridge, MA, USA. 

Ozlem Ulucan, PhD: 
Dr. Ulucan is an assistant professor at the department of Genetics and Bioengineering in Istanbul Bilgi University, since 2017. Before moving to Bilgi University, she worked as a research associate at the department of Chemical and Biological Engineering in Koc University, Istanbul. Dr. Ulucan studied Molecular Biology and Genetics in Istanbul University, Istanbul, Turkey. She received her Master of Science degree from Computational Sciences and Engineering in Koc University, Istanbul. She conducted her doctoral studies at Center for Bioinformatics in Saarland University (Germany), in the group of Prof. Dr. Volkhard Helms. Dr. Ulucan uses molecular modeling techniques to study structure, dynamics, energetics and interactions of biomolecules. Recently, she is interested in genomic and transcriptomic data analysis and disease subtyping using statistical learning approaches. In her recent project, she is  aiming at finding the subtypes of gastric cancer and class specific biomarkers, using gene expression data, which is important to better identify effective therapeutic strategies. Besides, she works on targeting the interaction between negative immune check point receptors and their ligands by designing small molecules that bind effectively and specifically to the immune checkpoint ligands.