Advanced Bioinformatics for Biotechnology
A.Y. 2018/2019
Learning objectives
The course will present some of the most widely used experimental techniques based on next-generation sequencing (NGS). Different state of the art approaches to the bioinformatic analysis of NGS data will be outlined both in theory and in practice. During lab classes, students will apply different bioinformatic tools to selected case studies
Expected learning outcomes
Undefined
Lesson period: Second semester
Assessment methods: Esame
Assessment result: voto verbalizzato in trentesimi
Single course
This course cannot be attended as a single course. Please check our list of single courses to find the ones available for enrolment.
Course syllabus and organization
Single session
Responsible
Lesson period
Second semester
Course syllabus
- Next generation sequencing in modern biology
- Genetic and epigenetic regulation of transcription
- Chromatin Immunoprecipitation followed by sequencing (ChIP-Seq): genome wide mapping of transcription factor binding and histone modifications.
- ChIP-Seq data analysis: read mapping
- ChIP-Seq data analysis: peak calling for the identification of transcription factor binding sites
- ChIP-Seq data analysis: genome segmentation for the mapping of histone modifications
- ChIP-Seq data post processing: identification of transcription factor binding sites; identification and characterization of target genes.
- Gene expression and transcriptome analysis
- Oligonucleotide microarrays and next generation sequencing of RNAs (RNA-Seq)
- Microarray data analysis: identification of differential expression
- RNA-Seq data analysis: read mapping and assembly, identification of alternative splicing
- RNA-Seq data analysis: computing transcript levels
- RNA-Seq data analysis: identification of differential expression
- Integrated analysis of ChIP- and RNA-Seq data
REFERENCE MATERIAL
Slides, notes and selected articles will be provided
PREREQUISITES AND EXAMINATION PROCEDURES
Written test
TEACHING METHODS
Lectures and lab exercises, where each student will have a personal computer at his/her disposal
LANGUAGE
English
WEB PAGES
http://www.beaconlab.it/advancedbioinfo
- Genetic and epigenetic regulation of transcription
- Chromatin Immunoprecipitation followed by sequencing (ChIP-Seq): genome wide mapping of transcription factor binding and histone modifications.
- ChIP-Seq data analysis: read mapping
- ChIP-Seq data analysis: peak calling for the identification of transcription factor binding sites
- ChIP-Seq data analysis: genome segmentation for the mapping of histone modifications
- ChIP-Seq data post processing: identification of transcription factor binding sites; identification and characterization of target genes.
- Gene expression and transcriptome analysis
- Oligonucleotide microarrays and next generation sequencing of RNAs (RNA-Seq)
- Microarray data analysis: identification of differential expression
- RNA-Seq data analysis: read mapping and assembly, identification of alternative splicing
- RNA-Seq data analysis: computing transcript levels
- RNA-Seq data analysis: identification of differential expression
- Integrated analysis of ChIP- and RNA-Seq data
REFERENCE MATERIAL
Slides, notes and selected articles will be provided
PREREQUISITES AND EXAMINATION PROCEDURES
Written test
TEACHING METHODS
Lectures and lab exercises, where each student will have a personal computer at his/her disposal
LANGUAGE
English
WEB PAGES
http://www.beaconlab.it/advancedbioinfo
Professor(s)
Reception:
Tuesday or Friday, h. 15.00- 17.00
Via Celoria 26 (Department of Biosciences)/Online