Topic outline

  • General

    General info for October 2020

    Course will be arranged entirely online.

    Lectures: 

    • On Tuesdays 12:15-14:00
    • On Fridays 12:15-14:00
    • First lecture: October 27, 2020
    • Some lectures will be arrange as live/online lectures, whereas some lectures will be available as pre-recorded video lectures (for course participants only). In case of video lectures, we will have time for questions and discussion during the lecture time slot.
    • For online lectures, we will use zoom program. Link will be provided on the course web page a little before the beginning of the lecture. 

    Exercises: 

    • On Fridays 14:15-16:00
    • Extra exercise sessions (for additional questions etc.) on Tuesdays 15:00-16:00
    • First exercise: October 30, 2020

    Teachers:

    • Harri Lähdesmäki, email: harri.lahdesmaki@aalto.fi
    • Viivi Halla-aho, email: viivi.halla-aho@aalto.fi
    • Juhi Somani, email: juhi.somani@aalto.fi
    • Maria Osmala, email: maria.osmala@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: histone modifications, chromatin accessibility, DNA methylation
    • Single-cell genomics
    • Receptor and antibody protein analysis
    • Metagenomics
    • Flow cytometry and mass cytometry analysis
    • Microarray technology and analysis
    • Enrichment analysis

    Prerequisites: 

    • Basic knowledge 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 (minimum of 5 points)
    • One assignment project
    • Final examination

    Grading (tentative):

    • Exercises: 3 * 5 points, 15 points in total
    • Assignment project: 15 points
    • Exam: 30 points
    • Total: max. 60 points
    • Approx. 30 points required to pass the course
    • Approx. 50 points will give you the maximum grade 5/5

    List of materials:

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

    Exam

    • Exam on Monday 14.12.2020 between 13-16.
    • The second exam on Friday, February 26, 2021 between 13-16.
    • Exams will be done remotely / online.
    • Exam questions will be made available via mycourses webpage in pdf format.
    • Exam questions will be available starting at about 13:00.
    • You can use whatever material you may want during the exam, including lecture notes (and even lecture video recordings if you wish).
    • Answers must be written by yourself (i.e., direct copy-pasting of any material is not allowed).
    • You are not allowed to communicate with anyone during the exam.
    • You can prepare your answers either with pen and paper or with computer (or a combination of these two).
    • Use of diagrams/drawings/equations are especially encouraged.
    • Submission should be in pdf-format (in case pdf-format is problematic, jpg is also accepted).
    • Answers can be returned via the mycourses webpage by uploading your pdf document.
    • Additional instruction will be on the exam question sheet.
    • You are not allowed to distribute the exam questions to anyone/anywhere.
    • A few students have requested a special exam time due to another overlapping exam. I have contacted those students separately via email. In case I have missed some students, please contact me via email.