Topic outline

  • General

    General info for 2022

    Lectures: 

    • On Tuesdays 12:15-14:00 in TU1
    • On Fridays 12:15-14:00 in TU2
    • First lecture: October 25, 2022


    Exercises: 

    • On Fridays 14:15-16:00 at A046
    • First exercise: November 4, 2022

    Lecturer:

    • Harri Lähdesmäki, email: harri.lahdesmaki@aalto.fi

    Teaching assistants:

    • Yunseon Lee, email: sunnie.lee@aalto.fi
    • Dani Korpela, email: XX@aalto.fi

    Learning outcome:

    The course provides you with basic understanding of high-throughput data and computational methods that are commonly used for analysing biological and biomedical problems. After the course you have skills to apply various computational methods in real biological problems and study the field further.

    Notes:

    The course is also accepted as a postgraduate course

    Preliminary syllabus:

    • Introduction, recap on hypothesis testing and multiple testing
    • High-throughput sequencing technology
    • Short sequencing read alignment
    • Genotype calling and de novo assembly 
    • Gene expression analysis using RNA-sequencing
    • Chromatin immunoprecipitation sequencing: protein-DNA interactions
    • Epigenetic data analysis: DNA methylation
    • Single-cell genomics
    • Receptor and antibody protein analysis
    • Metagenomics
    • Pathway and enrichment analysis
    • Visiting lecturers

    Prerequisites: 

    • Good knowledge of basics of: probability, statistics, linear algebra, applied math 
    • Basic programming skills

    Requirements:

    • Exercises: Participation in the exercise sessions is recommended (but not mandatory) but you will need to submit written reports
    • Final examination

    Grading (tentative):

    • Exercises: 3 * 5 points, 15 points in total
    • Exam: 30 points
    • Total: max. 45 points
    • Approx. 20 points required to pass the course
    • Approx. 37 points will give you the maximum grade 5/5

    List of materials:

    • Lecture notes
    • Material will be supplemented by scientific (review) articles

    Supplementary reading (available at our library), but not official course material:

    • Wing-Kin Sung, Algorithms for Next-Generation Sequencing, Chapman and Hall/CRC, 1st edition, 2017.

    Exam

    • Check the date and place of the exam from Sisu. 
    • If you cannot attend the first exam, there will be at least one (perhaps) two exams in the spring term (check again Sisu). 
    • You are NOT allowed to use any materials or devices (such lecture notes or calculator) in the exam.