IN BRIEF

The course covers selected algorithm design areas that have grown around molecular biology problems.

Topics include fragment assembly, transcriptomics and metagenomics data analysis, haplotyping, and evolution-related algorithmics such as genome rearrangements, motif discovery, and phylogeny.

The course consists of lectures, study groups, and exercises, as follows:

First week
Mon 12-14 - First lecture
Thu 10-12 - Study group

Weeks 2-6
Mon 10-12 - Exercise session on the previous week's topics
Mon 12-14 - Lecture
Thu 10-12 - Study group (or another lecture)

Last week
Mon 10-12 - Exercise session on the previous week's topics
Mon 12-14 - Lecture
Thu 10-12 - Exercise session on all topics covered

Lecture introduces each week's topic. Study groups delve into proofs / example simulations / applications. Exercises assess the gathered knowledge and work as miniexams: Course evaluation is based on the exercises; there is no course exam!

Ilmoittaudu

Aikataulu

Tästä osiosta löydät kurssin opetusaikataulun. Tarkista mahdolliset muut aikataulut kuvauksesta.

PäivämääräAikaOpetuspaikka
Ma 16.1.2017
12:15 - 14:00
To 19.1.2017
10:15 - 12:00
Ma 23.1.2017
12:15 - 14:00
To 26.1.2017
10:15 - 12:00
Ma 30.1.2017
12:15 - 14:00
To 2.2.2017
10:15 - 12:00
Ma 6.2.2017
12:15 - 14:00
To 9.2.2017
10:15 - 12:00
Ma 13.2.2017
12:15 - 14:00
To 16.2.2017
10:15 - 12:00
Ma 20.2.2017
12:15 - 14:00
To 23.2.2017
10:15 - 12:00
Ma 27.2.2017
12:15 - 14:00
To 2.3.2017
10:15 - 12:00

Muu opetus

23.01. - 27.02.2017 Ma 10.15-12.00
Tuukka Norri
Opetuskieli: englanti

Materiaalit

Content
Mon 16.1 12-14. Introduction to course content + Fragment assembly I (lecture on de Bruijn graphs, contig assembly). MBCT Sections 13-13.2.2.
Thu 19.1 10-12. Fragment assembly II (study group on scaffolding and gap filling). MBCT Sections 13.3-13.4.
Mon 23.1 10-12. Exercise 1
Mon 23.1 12-14. Transcriptomics I (lecture on splicing graphs, annotated transcript expression prediction, differential expression analysis). MBCT Sections 15-15.1.
Thu 26.1 10 -12. Transcriptomics II (study group on gene alignment, co-linear chaining). MBCT Sections 6.5 and 15.4.
Mon 30.1 10-12. Exercise 2
Mon 30.1 12-14. Transcriptomics III (lecture on path covers in splicing graphs). MBCT Sections 5.4.2, 15.2-15.2.2.
Thu 2.2 10-12. Transcriptomics IV (study group on simultaneous transcript assembly and expression estimation). Section 15.3.
Mon 6.2 10-12. Exercise 3.
Mon 6.2 12-14. Haplotype assembly I (lecture on coverage-exponential algorithm and NP-hardness). MBCT Section 14.3.
Thu 9.2 10-12. Haplotype assembly II (study group on extensions and proofs continued). MBCT Section 14.3.
Mon 13.2 10-12. Exercise 4.
Mon 13.2 12-14 Genome rearrangements I (lecture on sorting by reversals in pol. time: RDD, reversals<->#cycles). Ohlebusch Chapter 9
Thu 16.2 10-12 Genome rearrangements II (lecture on sorting by reversals in pol. time continued: finishing good components case, defining hurdles). Ohlebusch Chapter 9.
Mon 20.2 10-12. Exercise 5.
Mon 20.2 12-14. Genome rearrangements III (overview of bad components case), Phylogenies I (Introduction, ultrametric and additive matrices). Ohlebusch Chapter 10.
Thu 23.2 10-12 Phylogenies II (study group on reduction from additive case to ultrametric). Ohlebusch Chapter 10.
Mon 30.2 10-12. Exercise 6
Mon 30.2 12-14. Phylogenies III (lecture on optimal construction of ultrametric trees). Ohlebusch Chapter 10. Permutation patterns (lecture on Parikh mapping and naming technique). Parida 10.4.
Thu 2.3 10-12. Exercise 7

Check separate exam dates here: http://www.cs.helsinki.fi/exams

There is a project course following in the next period with hands-on training on fragment assembly algorithms.

Literature and material

The first half follows the book
Veli Mäkinen, Djamal Belazzougui, Fabio Cunial, and Alexandru I. Tomescu. Genome-Scale Algorithms Design: Biological sequence analysis in the era of high-throughput sequencing. Cambridge University Press. 2015.

The latter half uses material from the book
Enno Ohlebusch. Bioinformatics Algorithms: Sequence Analysis, Genome Rearrangements, and Phylogenetic Reconstruction. 2013.

The last 45 minutes lecture is based on
Laxmi Parida. Pattern Discovery in Bioinformatics: Theory & Algorithms. Chapman & Hall/CRC, 2008.

Kurssin suorittaminen

There will be 7 exercises, each with 5 assignments. Course grading is based on exercise points; there is no course exam.

18 p -> 1
21 p -> 2
24 p -> 3
27 p -> 4
30 p -> 5