Kaisa_2012_3_photo by Veikko Somerpuro

Seminar is given by Visiting Professor Brendan Mumey.

Note: remaining lectures will be conducted online only.

Seminar is suitable for students of
Master's Programme in Life Science Informatics,
Master's Programme in Data Science,
Master's Programme in Computer Science

Teaching language is English.

In this MSc level seminar we will cover some recent algorithms-related papers in computational biology over several different topic areas.

The main idea is to choose a scientific article presenting such a computational method, understand it, and explain it in detail, through an oral presentation and a 8-10 page seminar report (*reduced as students will present two papers each rather than one). This will also entail that you do an in-depth presentation of the basic definitions and methods used in the article. Thus, you may need to read some related papers and/or look up some background computational methods.

A tentative list of the proposed topics and papers is given below. You may also propose your own topic/paper.

PAN-GENOMICS AND GRAPHS:

[PG1] Alignment- and Reference-Free Phylogenomics with Colored de Bruijn Graphs
https://drops.dagstuhl.de/opus/volltexte/2019/11032/pdf/LIPIcs-WABI-2019...

[PG2] Validating Paired-End Read Alignments in Sequence Graphs
https://drops.dagstuhl.de/opus/volltexte/2019/11047/pdf/LIPIcs-WABI-2019...

[PG3] On the Complexity of Sequence to Graph Alignment
https://link.springer.com/chapter/10.1007%2F978-3-030-17083-7_6

[PG4] An Efficient, Scalable and Exact Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search
https://link.springer.com/chapter/10.1007%2F978-3-030-17083-7_1

[PG5] Sparse Dynamic Programming on DAGs with Small Width
https://dl.acm.org/doi/10.1145/3301312

COMPUTATIONAL GENOMICS:

[CG1] Practical Universal k-mer Sets for Minimizer Schemes
https://dl.acm.org/citation.cfm?doid=3307339.3342144

[CG2] A practical fpt algorithm for Flow Decomposition and transcript assembly
https://epubs.siam.org/doi/abs/10.1137/1.9781611975055.7

[CG3] Context-Aware Seeds for Read Mapping
https://drops.dagstuhl.de/opus/volltexte/2019/11045/pdf/LIPIcs-WABI-2019...

SINGLE CELL DATA

[SC1] Dynamic Pseudo-time Warping of Complex Single-Cell Trajectories
https://www.biorxiv.org/content/10.1101/522672v1

[SC2] Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data
https://link.springer.com/content/pdf/10.1007%2F978-3-030-17083-7_11.pdf

[SC3] A Combinatorial Approach for Single-cell Variant Detection via Phylogenetic Inference
https://drops.dagstuhl.de/opus/volltexte/2019/11052/pdf/LIPIcs-WABI-2019...

MISCELANEOUS

[M1] Succinct Text Indexing with Wildcards
https://link.springer.com/content/pdf/10.1007%2F978-3-642-03784-9_5.pdf

[M2] Bounded-Length Smith Waterman Alignment
https://drops.dagstuhl.de/opus/volltexte/2019/11046/pdf/LIPIcs-WABI-2019...

[M3] Few Matches or Almost Periodicity: Faster Pattern Matching with Mismatches in Compressed Texts
https://epubs.siam.org/doi/abs/10.1137/1.9781611975482.69

[M4] A Duality-Based Method for Identifying Elemental Balance Violations in Metabolic Network Models
https://drops.dagstuhl.de/opus/volltexte/2018/9303/pdf/LIPIcs-WABI-2018-...

TIMETABLE:
- 13.1.2020 - 17.1.2020: You choose a paper and are nominated as opponent of a colleague. Send me 3 choices by e-mail (brendan.mumey@montana.edu), ranked in order of preference. Deadline 17.1.2019.

- 27.1.2020: You hold a 5-10 minute presentation briefly outlining your first paper topic. Determine opponents.
Oral presentations of first papers (35 minutes + 10 minutes of questions), two presentation per meeting. One week before your presentation you send a draft version of the report and of the slides to your opponent. Your opponent starts the 10-minute question session.

- 10.2.2020: Paper 1: [CG1] presenter: JM, opponent: CG. Paper 2: [PG3] presenter: MC, opponent: PP

- 24.2.2020: Paper 3: [M3] presenter: PP, opponent: MC. Paper 4: [M4] presenter: CG, opponent: JM

- 2.3.2020: Introductions to second papers.

- 23.3.2020: Paper 5: [M2] presenter: JM, opponent: PP Paper 6: [M1] presenter: PP, opponent: CG (via Webex)

- 30.3.2020: Paper 7: [SC1] presenter: CG, opponent: MC Paper 8: [PG5] presenter: MC, opponent: JM (Also, we will decide peer review assignments.) (via Webex)

- 13.4.2020: Submit report to me and peer-reviewer.

- 20.4.2020: Submit peer reviews to me and the person you reviewed.

- 27.4.2020: Submit your revised report based on the peer review. Briefly explain how you addressed the peer review comments.

PRESENTATION SCHEDULE:

Here are the planned meeting dates and times.
Location: Exactum, B119, Pietari Kalmin katu 5

Mon 13.1.2020 10:15 - 12:00
Mon 27.1.2020 10:15 - 12:00
Mon 10.2.2020 10:15 - 12:00
Mon 24.2.2020 10:15 - 12:00
Mon 2.3.2020 10:15 - 12:00
Mon 23.3.2020 10:15 - 12:00 Webex
Mon 30.3.2020 10:15 - 12:00 Webex

Enrol

Timetable

Here is the course’s teaching schedule. Check the description for possible other schedules.

DateTimeLocation
Mon 13.1.2020
10:15 - 12:00
Mon 20.1.2020
10:15 - 12:00
Mon 27.1.2020
10:15 - 12:00
Mon 3.2.2020
10:15 - 12:00
Mon 10.2.2020
10:15 - 12:00
Mon 17.2.2020
10:15 - 12:00
Mon 24.2.2020
10:15 - 12:00
Mon 9.3.2020
10:15 - 12:00
Mon 16.3.2020
10:15 - 12:00
Mon 23.3.2020
10:15 - 12:00
Mon 30.3.2020
10:15 - 12:00
Mon 6.4.2020
10:15 - 12:00
Mon 20.4.2020
10:15 - 12:00
Mon 27.4.2020
10:15 - 12:00

Other teaching

Description

Master's Programme in Computer Science is responsible for the course.

The course belongs to Discrete Algorithms module.

The course is available to students from other degree programmes, especially from the Life Science informatics / Algorithmic Bioinformatics study track.

Knowledge of algorithms and some computational biology will be assumed.

Courses/seminars in either algorithms or biology-related topics

An ability to give scientific and technical presentations. An ability to peer-review and provide feedback on written work and on oral presentations. Improved scientific writing skills on computational biology. In-depth theoretical understanding of an advanced topic in algorithms for computational biology.

After the course CSM12101 Design and Analysis of Algorithms.

Spring 2020

This seminar course will survey recent algorithmic topics from computational biology/bioinformatics.

Recent papers from computational biology literature including conferences and journals.

Wing-Kin Sung, Algorithms in Bioinformatics: A Practical Introduction, CRC Press

Textbook website: www.comp.nus.edu.sg/~ksung/algo_in_bioinfo/

Grading (at scale 1-5) is based on an overall assessment of both oral and written work, as well as participation.

The course is primarily available as a 5-ECTS seminar consisting of a seminar presentation, written work, and peer review. Active participation in the seminar meetings is expected.

Brendan Murney