Discrete Biological Models (2019/2020)

Course code
4S01908
Name of lecturer
Vincenzo Bonnici
Coordinator
Vincenzo Bonnici
Number of ECTS credits allocated
6
Academic sector
INF/01 - INFORMATICS
Language of instruction
Italian
Period
II semestre dal Mar 2, 2020 al Jun 12, 2020.

Lesson timetable

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Learning outcomes

Acquisition of methods of discrete mathematics in the analysis of biological phenomena, with a major emphasis on the computational analysis of genomes. In particular discrete probability and information theory are revisited in the perspective of genome analysis.

Syllabus

Basic notation on sequences and strings. The problems of substring and superstring. Lexicographic ordering and suffix arrays. Advanced combinatorial schemata and discrete probability. Random sequences and fundamental probability laws on them (Bernoulli, Poisson, Exponential, Gauss). Information sources and entropy. Conditional entropy, entropic divergences and mutual information. Genomes, genomic indexes, genomic dictionaries, genomic distributions and entropies. Representations and visualizations of genomes. Types of codes and genetic code. Sequence duplications and double sequences. The sequence paradox and other life paradoxes. Cellular dynamics and recurrent equations. Biological networks and their principal aspects.

Reference books
Author Title Publisher Year ISBN Note
T. M. Cover, J. A. Thomas Elements of Information Theory (Edizione 1) John Wiley & Sons, Inc. 1991 0471062596
Vincenzo Manca Infobiotics Springer 2013
Sebastian Bassi Python for Bioinformatics (Edizione 2) Routledge 2017 1138035262

Assessment methods and criteria

The exam consists of an oral examination plus the development of a project.
The oral exam covers the entire course program and the assessment is expressed with a vote from 0 to 30.
The project is agreed upon with the student starting from a list of projects proposed by the teacher. The evaluation of the project is expressed by a vote from 0 to 30.
The final grade is the average of the two assessments, oral exam and project.