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Semester B

Computational Analysis of Biomolecular Sequences

Semester: B’

Course Type: Compulsory

Course Curriculum

  • Introduction – DNA and Protein sequences
  • Detecting sequence similarity: Sequence homology  and similarity and their importance; Dynamic programming algorithms; Global alignment and the Needleman-Wunsch algorithm; Local Alignment and the Smith-Waterman algorithm; Statistical significance in sequence alignments;  Substitution matrices and their importance;  Alignment gaps and gap penalties; Heuristic methods and databases searches (BLAST, FASTA etc).
  • Multiple Sequence Alignments: Multidimensional dynamic programming algorithms;  Heuristic methods for multiple sequence alignments (CLUSTAL, DIALIGN, MULTIALIN etc); Phylogenetic trees and sequence alignments.
  • Sequence-based prediction methods for DNA and proteins: Empirical statistical methods; clustering algorithms; Artificial Neural Networks; Hidden Markov Models; Genetic algorithms; applications: protein secondary structure prediction; prediction of transmembrane protein topology; gene identification in whole genomes; Refinement of sequence alignments with profile Hidden Markov Models (HMMER, SAM, HMM-Pro etc); sequence classification.
  • Pattern and periodicity recognition and classification in protein and DNA sequences
  • Plasmid and bacterial genome annotation
  • Introduction to theoretical and computational genomics: genomes, organisms and evolution; language features in genomic sequences; the origins of life; pre and pro-biotic evolution as mirrored in genome sequences.
  • Analysis of bacterial genomes: application to oxygalactic bacteria
  • Analysis of small genomes: the mitochondral DNA in fungi

Administrator

  • Assist. Prof. V. Iconomidou

 Instructors

  • Assoc. Prof. P. Bagos
  • Assist. Prof. V. Iconomidou
  • Dr. I. Almyrantis
  • Assist. Prof. V. Kouvelis
  • Dr. C. Papadimitriou
  • Dr. M. Theodoropoulou

 

Computational Analysis of Biomolecular Structures

Semester: B’

Course Type: Compulsory

Course Curriculum

  • Introduction – Biomolecular Structures – Structure determination methods
  • Fold Recognition
  • Structure superposition and alignment. Comparative modeling (homology modeling – threading)
  • Modeling protein structure with Molecular Mechanics and Molecular Dynamics.
  • Protein-ligand docking – Drug design.
  • Protein-protein recognition –  protein-protein docking.
  • Structure quality assessment and evaluation.  Geometrical analysis of biomolecular structures.

Administrator

  • Prof. C. Vorgias

 Instructors

  • Emer. Prof. S. Hamodrakas
  • Assist. Prof. V. Iconomidou
  • Prof. C. Vorgias
  • Prof. E. Iliopoulos
  • Dr. G. Nounesis
  • Dr. G. Chryssikos
  • Dr. V. Gionis
  • Dr. N. C. Papandreou
  • Dr. N. A. Papandreou

 

Programming Languages and Software Tools in Bioinformatics II

Semester: B’

Course Type: Compulsory

Course Curriculum

Part I JAVA

  • Object-oriented programming: classes and objects
  • Fundamental Java classes, applets and applications
  • Graphical User Interfaces, JavaBeans
  • Java and Bioinformatics applications

Part II PERL

  • Variable types: scalars, lists, arrays, strings.
  • Data structures.  Subroutines and argument passing.  Hash tables, input/output manipulation, conditional clauses, loops.
  • Regular expressions, pattern matching.
  • Perl and Bioinformatics applications

Administrator

  • Prof. C. Vorgias

 Instructors

  • Prof. C. Vorgias
  • Dr. Z. I. Litou
  • Dr. J. Hamodrakas
  • Dr. M. Theodoropoulou
  • Dr. G. Tsaousis

 

Molecular Recognition – Molecular Diseases – Structural Drug Design

Semester: B;

Course Type: Compulsory

Course Curriculum

  • Biomolecular Structures: Molecule dimensions and the surrounding environment.
  • Biomolecular Interactions: Protein-protein, protein-ligand and protein-DNA interactions.
  • Molecular Recognition: Association and dissociation constants, binding energy, examples in molecular recognition, ion charges and stabilization. Entropic contributions in protein-protein complexes.  Recognition levels – affinity, specificity and selectivity.  Molecular recognition and its evolution.
  • Energetic analysis of biomolecular interactions: Molecular Mechanics, introduction to ab-initio protein folding, Empirical energy functions and Force Fields, Energy Minimization algorithms, Free Energy Surfaces, Molecular Dynamics, Enthalpic and Entropic terms.
  • Subcellular Location and protein translocation: endoplasmic reticulum and its functions, ligand binding, target recognition and signal transduction
  • Protein folding – molecular chaperones: new viewpoints and theories for protein folding and organization.  The importance of topology. Chaperone proteins.
  • Biological membranes and membrane proteins: expression, purification and structure determination. Membrane protein structure and function, Membrane protein classifications, Ion channels and receptors, α-helical transmembrane proteins and transmembrane β-barrels
  • Drug design: methods for drug design, target based screening and challenges; drug resistant diseases and cancer
  • Signal transduction: mechanisms for signal transduction, hormones, neurotransmitters, second molecule messengers.  Signal transduction in the membrane and cell interior. Steroids and their receptors, pheromones, G-protein coupled receptors etc.

Administrator

  • Prof. E. Iliopoulos

 Instructors

  • Prof. E. Iliopoulos
  • Dr. N. A. Papandreou
  • Dr. N. C. Papandreou
  • Dr. Z. I. Litou
  • Dr. M. Zervou
  • Dr. T. Calogeropoulou
  • Dr. I. Michalopoulos

Methodology of Research

Semester: B’

Course Type: Compulsory

Course Curriculum

  • Science, scientists and research.
  • Biological sciences, research and the role of Bioinformaticians. Bioinformatics as a novel science field.
  • Codes of conduct and ethics in scientific research, emphasizing in biological sciences. Bioethics.
  • Searching the scientific literature. Pubmed, Scopus etc
  • How to publish: writing, evaluating and publishing research results in peer review (journals, conferences etc).
  • How to publish: choosing the right journal (sources, information, instructions for authors, peer reviewing, impact factors and quality).
  • How to publish: article types (research articles, reviews, notes, letters to the editor etc).  Basic structure of a scientific publication (abstract, introduction, materials and methods, results, discussion, conclusions)
  • How to publish: The peer review process: response to reviewers and revisions
  • Evaluation of scientific publications

Administrator

  • Prof. C. Vorgias

 Instructors

  • Prof. C. Vorgias
  • Emer. Prof. S. Hamodrakas
  • Assoc. Prof. P. Bagos
  • Dr. Z. I. Litou