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COURSE DESCRIPTION

TOPICS AIMS AND OBJECTIVES

The topic of the course is to introduce students to the basic notions of Bioinformatics. Bioinformatics is a combination of Computer Science and Molecular Biology  focusing at the design of data structures and computational methods to facilitate the efficient storage, retrieval and manipulation of biological molecules (DNA, RNA, genes, proteins). Understanding basic computational methods such as string and machine learning algorithms and how they are used to develop software tools to process efficiently biological data is a main objective of this course.

LECTURER: Assoc. prof. Christos Makris, makri@ceid.upatras.gr (https://www.ceid.upatras.gr/webpages/courses/cplusplus/makris/indexen.ht)

CONTENT

• Course introduction to its main notions (Computer Science and Molecular Biology
• Exact string matching algorithms (Boyer - Moore, Knooth-Morris-Pratt, Aho-Corasick Automaton
• Suffix Trees and applications in Bioinformatics
• Inexact matching an sequence alignment
• Multiple sequence alignments
• Bioinformatics Databases and Data Mining
• Phylogeny
• Genome Assembly and Burrows-Wheeler

EXAM REQUIREMENTS

Understanding the basic notions of Bioinformatics, understanding string algorithms and machine learning algorithms and how they apply to problems in Computational Molecular Biology, understanding Biological databases.

ASSESSMENT

Oral examination on the topic of one project  (a research assignments on 2-3 papers with obligations a written report of 20-25 pages on the content and a powerpoint presentation of 20 minutes) (50% of the total degree) and questions about the course (50% of the degree).  Exam duration: 1h. Concerning the topic of the course mainly the understanding of concepts will be tested. The relative importance of the technical and mathematical derivations will be pointed out during the lectures

PREREQUISITES

Understanding of basic notions of computer science and molecular biology is imperative.

BIBLIOGRAPHY 

Algorithms on Strings, Trees and Sequences, D. Gusfield, Cambridge University Press, 10th edition 2007

Bioinformatics Algorithms: An Active Learning Approach by Phillip Compeau, Pavel Pevzner (2018), third edition, Active Learning Publishers

Arthur Lesk, Introduction to Bioinformatics, Oxford University Press, Fifth Edition, 2019

Jonathan Pevsner, Bioinformatics and Functional Genomics, 3rd Edition, Wiley 2015

Gonzalo Navarro, Compact Data Structures: A Practical Approach (2016), https://www.cambridge.org/core/books/compact-data-structures/68A5983E6F1176181291E235D0B7EB44

Wing-Kin Sung, Algorithms in Bioinformatics, A Practical Introduction Routledge, Taylor and Francis, 2010

Jeremy Ramsden, Bioinformatics, An Introduction, 2015, Springer

Handbook of Computational Molecular Biology (Chapman & All/Crc Computer and Information Scieience Series)December 2005,  edited by Srinivas Aluru and Sartaj Sahni

Bioinformatics- From Genomes to Drugs, Edited by Thomas Lengauer, Volumes I & II, WILEY-VCH, 2001

Fundamental Concepts of Bioinformatics, D. Krane and M.L.Raymer, Pearson Education, 2003

Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Edited by A.D.Baxevanis and B.F.F.Ouellette, Wiley-Liss, Inc., 2001