bioinformatics 2nd degree bologna study programme - Univerza v ...

COURSE SYLLABUS 

Course title: Bioinformatics Algorithms and data structures 

Study programme and level Study field 

Bioinformatics 2 nd degree 

Bologna Study programme 

Academic 

year 

Semester 

Bioinformatics 1 1 

Course type Obligatory subject 

University course code: 

Lectures Seminar Tutorial 

Laboratory 

work 

Field work 

Individ. 

work 

ECTS 

30 30 90 6 

Lecturer: Matjaž Colnarič, PhD, Full professor 

David Podgorelec, PhD, Assistant professor 

Languages: Lectures: Slovene 

Tutorial: Slovene 

Prerequisits: 

- Basic programming skills. 

- Mathematical skills: polynomial, rational, exponential, logarithmical functions, vectors and 

matrices, basic knowledge of graph theory. 

Content (Syllabus outline): 

- Basic concepts: What is an algorithm? Biological and computer algorithms. Time and space 

complexity. Iterative and recursive algorithms. 

- Introduction to data structures: Object orientation of data structures. Elementary data 

types – arrays and connected lists. Abstract data types – stack, queue and list, trees, 

graphs. 

- Algorithm design strategies: Brute force. Greedy method. »Divide-and-conquer« strategy. 

Dynamic programming. Searching strategies. Stochastic algorithms (Monte Carlo 

algorithms, simulated annealing, genetic algorithms). 

- Practical algorithms of bioinformatics: Classification with respect to the algorithm design 

strategy. String algorithms, clustering and trees. Sequence analysis, searching for subsequences 

in longer sequences, sequence alignment, prediction of protein features, 

phylogenetic trees, physical mapping. Graph algorithms. Hidden Markov models. 

- Sorting algorithms: sorting by comparing the key values. Sorting in linear time.

Readings: 

- N. C. Jones, P. A. Pevzner: An Introduction to Bioinformatics Algorithms (Computational 

Molecular Biology), MIT Press, Cambridge, Massachusetts, 2004. 

- C. Gibas, P. Jambeck: Developing Bioinformatics Computer Skills, O'Reilly, Sebastopol, 

California, 2001. 

- T. H. Cormen, S. Clifford, C. E. Leiserson, R. L. Rivest: Introduction to Algorithms, Second 

Edition, MIT Press, Cambridge, Massachusetts, 2001. 

- I. Kononenko, M. Robnik Šikonja: Osnove algoritmov in podatkovnih struktur. Ljubljana, 

FRI, 2004. 

Objectives and competences: 

The objectives of this course are to represent to the students basic data structures and their 

implementation using static and dynamic data types, to introduce the basic algorithm strategies 

and to teach the students how to select among them in concrete problems, to teach the students 

to analyze the algorithms regarding time and space complexity, and to implement some selected 

problems from bioinformatics. 

Intended learning outcomes: 

Knowledge and understanding: 

The students will: 

- be aware of selecting the suitable data structures and their use at algorithms design, 

- understand the fundamental data structures and master their implementations, 

- know the fundamental strategies for algorithms design, 

- be able to determine the time and space complexity of the algorithms, 

- get the computing background for different problems of bioinformatics. 

- The students will be able to harmonize the usage of data structures and algorithm 

strategies at practical problems. 

- The students will skilfully use implemented data structures and algorithms during the 

study and later work. 

- At algorithm design they will reasonable search the compromises among different criteria 

as difficultness of implementation, time and space complexity and quality of the solution. 

- They will be able to use the knowledge and practical experience at different problems of 

bioinformatics. 

Learning and teaching methods: 

Lectures, discussions, demonstration, computer exercises. 

Assessment: 

Type (examination, oral, coursework, 

project): 

Weight (in %) 

coursework (practical 

assignments) 

20 % 

written examination (achievable 30 % 

also with two non obligatory 

colloquia), 

oral examination. 

50 %

Lecturer's references: 

COLNARIČ, Matjaž 

An example of fault detection and reconfiguration-based tolerance in distributed embedded 

control systems / Matjaž Colnarič. - Bibliograija: str. 286. - Abstract.V: Proceedings of COSY 2011 

papers / Special International Conference on Complex systems: synergy of control 

communications and computing, September 16-20, 2011, Ohrid, Republic of Macedonia. - Skopje : 

Society for Electronics, Telecommunications, Automation, and Informatics of the Republic of 

Macedonia, 2011. - Str. 281-286. COBISS.SI-ID 15385366 


Struggle for temporal predictability of processors for real-time environments, revisited 20 years 

after / Matjaž Colnarič. - Abstract. - Bibliografija: str. 11-12.V: Autonomous systems / Herwig 

Unger, Kyandoghere Kyamaky, and Janusz Kacprzyk (Eds.). - Berlin ; Heidelberg : Springer, cop. 

2011. - (Studies in computational intelligence ; Vol. 391, ISSN 1860-949X). - ISBN 978-3-642- 

24805-4. - Str. 3-12. COBISS.SI-ID 15575830 


Distributed embedded control systems : improving dependability with coherent design / Matjaž 

Colnarič, Domen Verber and Wolfgang A. Halang. - Berlin ; London : Springer, 2008. - XVII, 250 str. 

- (Advances in industrial control)ISBN 978-1-84800-051-3 ISBN 978-1-84800-052-0 (e-ISBN) 

COBISS.SI-ID 11970070 

PODGORELEC, David 

Dealing with redundancy and inconsistency in constructive geometric constraint solving / David 

Podgorelec, Borut Žalik, Vid Domiter. - . - Dostopno tudi na: 

http://dx.doi.org/10.1016/j.advengsoft.2007.10.003. - Abstract. - Bibliografija: str. 786.V: 

Advances in engineering software. - ISSN 0965-9978.. - Vol. 39, iss. 9 (Sep. 2008), Str. 770-786. 

. - doi: 10.1016/j.advengsoft.2007.10.003 COBISS.SI-ID 12138006, JCR, WoS, št. citatov do 6. 12. 

2010: 1, brez avtocitatov: 1, normirano št. citatov: 1 

PODGORELEC, David 

Cluster registration in 2D geometric constraint solving / David Podgorelec, Borut Žalik. 

V: 23st European Workshop on Computational Geometry / EWCG'07, march 19-21, 2007, Graz, 

Austria. - Graz : Technische Universität, 2007. - Str. 118-121. COBISS.SI-ID 11615254 

GEOMETRIC data preparation for GIS applications / David Podgorelec ... [et al.]. - Soavtorji: Gregor 

Klajnšek, Sebastian Krivograd, Borut Žalik. - Bibliografija: str. 124-127. - Abstract. 

V: Geoinformation technologies for geocultural landscapes / editors Oliver Bender ... [et al.]. - 

Boca Raton [etc.] : CRC Press/Balkema, cop. 2009. - ISBN 978-0-415-46859-6. - Str. 107-127. 

COBISS.SI-ID 13051670


Course title: Informarion and communication technologies for bioinformatics 




Academic 

year 

Semester 





Laboratory 

work 

Field work 

Individ. 

work 

ECTS 

18 42 90 6 

Lecturer: Milan Zorman, PhD, Full professor 

Domen Verber, PhD, Assistant professor 

Languages: Lectures: slovene 

Tutorial: slovene 

Prerequisits: 

This subject can be selected by all regularly registered students of Master's degree study 

programme Bioinformatics with the background in health or natural sciences 


1. History of computing 

2. Von Neumans Arhitecture, personal computer 

3. Input/output units, central processing unit 

4. Software and hardware 

5. Data bases, 

6. Networks and world wide web 

7. Computers in biology 

8. Computer tools in bioinformatics 

9. Visualisation

Readings: 

E. Turban, R. K. Rainer Jr., R. E. Potter: Introduction to Information Technology. 3rd ed., Wiley, 

2004. 

P. Kokol: Računalništvo v zdravstvu I. Maribor: NICE textbooks from the Phare Tempus program. 

Visoka zdravstvena šola, 1998. 

C. Gibas, P. Jambeck. Developing Bioinformatics Computer Skills: OReily and Associates, 2001 


Student will learn the advanced contents of computer science and methods, used in the field of 




Student: 

Learns the computer architecture and its working principles 

Understands the role of the computer in the health systems related to informatics 

Learns about software and hardware 

Learns the basics of management of databases 

Understands the role of information technology in biology 

Learns the basics of visualisation 


Lectures, seminar work. 

Assessment: 


project): 

Written exam, 

project. 

Weight (in %) 

50 

50 


ZORMAN, Milan 

Classification of follicular lymphoma images : a holistic approach with symbol-based machine 

learning methods / Milan Zorman, José Luis Sánches de la Rosa, Dejan Dinevski. - Graf. prikazi. - 

Abstract ; Zusammenfassung. - Bibliografija: str. 708-709. V: Wiener Klinische Wochenschrift. - 

ISSN 0043-5325.. - Jg. 123, Heft 23/24 (2011), str. 700-709. COBISS.SI-ID 15706134, JCR 

ZORMAN, Milan 

Opening the knowledge tombs - web based text mining as approach for re-evaluation of machine 

learning rules / Milan Zorman, Sandi Pohorec and Boštjan Brumen. - Abstract. - Bibliografija: str. 

542. V: Lecture notes in computer science. - ISSN 0302-9743. - Vol. 6295 (2010), str. 533-542. 


ZORMAN, Milan 

Explanatory approach for evaluation of machine learning-induced knowledge / M. Zorman and M. 

Verlič. - Abstract. - Bibliografija: str. 1550-1551.V: Journal of international medical research. - ISSN

0300-0605.. - Letn. 37, št. 5 (2009), str. 1543-1551. COBISS.SI-ID 13645334, JCR 

VERBER, Domen 

Implementation of non-intrusive fault detection in embedded control systems / Domen Verber, 

Matej Šprogar, Matjaž Colnarič. - Bibliografija: str. 30. V: Informacije MIDEM. - ISSN 0352-9045.. - 

Letn. 37, št. 1(121) (mar. 2007), str. 23-30. COBISS.SI-ID 11552534, JCR 

VERBER, Domen 

Utilization of high performance computing in everyday business applications / Domen Verber. - 

Ilustr. - Bibliografija: str. [5]. - Abstract. V: The proceedings of the 2nd International Conference on 

Information Society and Information Technologies - ISIT 2010, [Dolenjske Toplice, 10-12 

November 2010] / edited by Matej Mertik. - Novo mesto : Faculty of Information Studies, 2010. - 

ISBN 978-961-92509-5-2. - [5] str. COBISS.SI-ID 14700054 

VERBER, Domen 

Decentralized fault and resource management for distributed control systems / Domen Verber. 

V: Applications of systems science / editors Adam Grzech, Paweł Świątek, Krysztof Brzostowski. - 

Warsaw : EXIT, cop. 2010. - ISBN 978-83-60434-78-9. - Str. 237-243. COBISS.SI-ID 14487574


Course title: Selected topics in Biophysics 




Academic 

year 

Semester 


Course type Optional subject 



Laboratory 

work 

Field work 

Individ. 

work 

ECTS 

30 30 90 6 

Lecturer: Aleš Fajmut, PhD, Assistant professor 



Prerequisits: 

No special prerequisites required. 

However, for all students that have not gained the knowledge of fundamental physics in the 1. 

level of university degree this subject is compulsory. 


Mechanics: force, pressure, torque, work, energy, power; deformations; hydrostatics and 

hydrodynamics. Electricity and magnetism; electric and magnetic fields. Thermodynamics: 

thermodynamic laws and potentials, heat and mass flow. Oscillations and waves: sound, light; 

properties of waves, geometric optics. Experiments essential in modern physics. Structure and 

models of atoms, atomic and intermolecular interactions. Structure and stability of atomic 

nucleus, radioactivity. 

Selected illustrative examples from biology: 

1. Biomechanics: forces in bones and muscles; flow of blood in the circulatory system; 

transport of respiratory gases; mechanical properties of biological membranes, cell shape 

and its transformation. 

2. Thermodynamics: the first law of thermodynamics, metabolism, heat, work and power of 

human and animals; the second law of thermodynamics, conditions of minimal free energy 

and maximal entropy in biological systems; regulatory systems and mechanisms, body 

temperature regulation, cell volume regulation. 

3. Electromagnetism: diffusion of ions, the Donnan equilibrium, membrane potential; action

potential and nerve impulses; magnetic fields and orientation of organisms, weak 

magnetic fields in biology 

4. Vibrational and wave motion: biochemical and cellular oscillators; sound and an ear, 

ultrasound; light, an eye. 

5. Molecular biophysics: atomic and molecular interactions and chemical bonds. Biological 

effects of ionizing radiation. 

Students perform 10 laboratory experiments from mechanics, thermodynamics, electricity and 

magnetism, wave nature of light and geometric optics, atomic physics and radioactivity. The 

content of labor work is applied to biological systems. 

Readings: 

R. Kladnik: Visokošolska fizika, 1. del: Mehanika in toplotni pojavi, 2. del: Elektrika, Atomika, 3. del: 

Valovni pojavi, Akustika in optika, Državna založba Slovenije, Ljubljana 1989 

R. Glaser: Biophysics, Springer, Berlin 2001 

G. B: Benedek, F. M. H. Villars: Physics with Illustrative Examples from Medicine and Biology: 

Mechanics, Statistical Physics, Electricity and Magnetism, Springer, New York 2000 

P. R. Bergethon: The Physical Basis of Biochemistry. The Foundations of Molecular Biophysics, 

Springer, New York 1998 

Interna navodila za izvedbo eksperimentalnih vaj/ Guidelines for labor work. 


The main objective is to gain the knowledge of physical concepts and laws which are essential for 

understanding the biological processes. 


Knowledge and Understanding: 

Students get knowledge of structure and function of selected biological systems based on the 

fundamental principles and concepts of physics. 

Transferable/Key Skills and other attributes: 

Students are able to use simple mathematical models for quantitative studies of structure and 

function of biological systems. 


Lectures 

Labor work with concomitant mathematical exercises in problem solving 

Assessment: 

Type (examination, oral, course work, 

project): 

Written test on labor work 

Written exam. 

Oral exam. 

Weight (in %) 

30% 

30% 

40%


FAJMUT, Aleš 

MLC-kinase/phosphatase control of Ca[sup]2+ signal transduction in airway smooth muscles / 

Aleš Fajmut, Milan Brumen. - . - Dostopno tudi na: http://dx.doi.org/10.1016/j.jtbi.2007.10.005. - 

Available online Oct. 11 2007. - Bibliografija: str. 481. V: Journal of theoretical biology. - ISSN 

0022-5193.. - Vol. 252, no. 3 (2008), str. 474-481. 

. - doi: 10.1016/j.jtbi.2007.10.005 COBISS.SI-ID 15856392, JCR, WoS, št. citatov do 6. 5. 2011: 5, 

brez avtocitatov: 4, normirano št. citatov: 2 

CONTRIBUTION of Rho kinase to the early phase of the calcium-contraction coupling in airway 

smooth muscle / Prisca Mbikou ... [et al.]. - Ilustr. - Nasl. z nasl. zaslona. - Opis vira z dne 7. 12. 

2010. - Soavtorji: Ales Fajmut, Milan Brumen, Etienne Roux. - Bibliografija: str. 257-258. - Abstract. 

V: Experimental physiology. - ISSN 0958-0670.. - Vol. 96, issue 2 (2011), str. 240-258. 

. - doi: 10.1113/expphysiol.2010.054635 COBISS.SI-ID 18009864, JCR, WoS, št. citatov do 10. 4. 


DOBOVIŠEK, Andrej 

Role of expression of prostaglandin synthases 1 and 2 and leukotriene C [sub] 4 synthase in 

aspirin-intolerant asthma: a theoretical study / A. Dobovišek, A. Fajmut, M. Brumen. - 

Bibliografija: str. 277-278. - Abstract.V: Journal of pharmacokinetics and pharmacodynamics. - 

ISSN 1567-567X.. - Vol. 38, no. 2 (2011), str. 261-278. . - doi: 10.1007/s10928-011-9192-6 

COBISS.SI-ID 18203144, JCR, WoS, št. citatov do 6. 4. 2012: 1, brez avtocitatov: 0, normirano št. 

citatov: 0


Course title: Selected topics in biochemistry 




Academic 

year 

Semester 





Laboratory 

work 

Field work 

Individ. 

work 

ECTS 

30 30 90 6 

Lecturer: 



Prerequisits: 

Understanding basics of molecular biology and biochemistry. 


Biochemistry: From Atoms to Molecules to Cells, Biomolecules in Water 

Proteins: Amino Acids, Peptides, and Proteins, : Protein Architecture and Biological Function 

Enzymes: Reactions, Kinetics, Inhibition, Coenzymes, Regulation, Abzymes, and Ribozymes. 

Carbohydrates: Structure and Biological Function. 

Lipids: Structure and Biological Function, Biological Membranes and Cellular Transport. 

Nucleid acids; DNA and RNA: Structure and Function. 

Vitamines; Hormones. 

Basic Concepts of Cellular Metabolism and Bioenergetics. 

Metabolism of Carbohydrates. 

Production of NADH and NADPH: The Citric Acid Cycle. 

ATP Formation by Electron-Transport Chains. 

Metabolism of Fatty Acids and Lipids. 

Metabolism of Amino Acids and Other Nitrogenous Compounds. 

Integration, Specialization, and Hormonal Control of Metabolism.

Readings: 

Boyer, Rodney F.: Concepts in biochemistry, 3rd ed., J. Wiley & Sons, Hoboken , 2006 

L. STRAYER et al.: Biochemistry, 4th ed, W.H. Freeman and Company, New York, 1995 

Voet,Donald: Fundamentals of biochemistry : life at the molecular level, 2nd ed., J. Wiley 

& sons, Hoboken (New Jersey), 2006. 

Nelson DL, Cox MM.; Lehninger Principles of Biochemistry, 4th ed, W.H. Freeman and 

Company, New York, 2004 


Students will be provided with structural characteristics of major groups of biomolecules and their 

role in cell metabolism and other important biological processes. 



structural characteristics of biomoleculs 

the role of biomolecules in cell function 


Lectures 

Tutorial 

Assessment: 


project): 

writen and 

oral exemination 


Weight (in %) 

60 

40

Course title: Chemistry 





Academic 

year 

Semester 





Laboratory 

work 

Field work 

Individ. 

work 

ECTS 

30 30 90 6 

Lecturer: Željko Knez, PhD, Full professor 



Prerequisits: 

None. 


Chemical bonds, forces between molecules 

Water: structure, characteristics, H bond, water as dissolvent 

pH, water ionization, Kw, pH, weak and strong electrolyte, acids and bases (titration 

curves, Ka, Kb, pKa, pKb), pufer, pufer systems in organism, biological meaning of pH 

Solutions: gas dissolving in water (Henry law) koligativno characteristics of solutions (Rault 

law, decreasing of freezing point, increasing of boiling point, osmotic pressure), osmotic 

phenomenon in cell (Donnans balance, passive transport – Fickos law) 

Oxidation – reduction : definitions, quantitative characterization redox reactions 

Redox potential and free reaction enthalpy, 

Velocity of chemical reactions: definitions, 

Basics of transportability phenomenon, 

Molecular basics of life: biological important elements, ions and molecules, 

Organics molecules: isomerism, mutual influence of functional groups (inductive and 

resonant effect), 

Short overview of organic compound by functional groups. 

Short review of chemistry: 

- carbon hydrates (monosaccharide, disaccharide, polysaccharide)

- lipid and steroids (steroids, steroli, gall acid, steroids hormones,- structure) 

- aminoacid, 

- nucleotides and nucleic acid. 

Readings: 

- Lazarini F., Brencic J.: Splošna in anorganska kemija, 3. izd. Ljubljana : Državna založba 

Slovenije, 1992 

- Lehninger A.L., Nelson D.L., Cox M.M., Waites J.: Principles of biochemistry : with an 

extended discussion of oxygen-binding proteins, 2nd ed., 9th printing, New York : Worth, 

2000. 

- Ebbing D.D., Gammon S.D.: General chemistry, 6th ed.,Boston, New York : Houghton 

Mifflin, cop. 1999. 

- Hunt, Harold R., Block, Toby F., McKelvy, George M.: Laboratory experiments for general 

chemistry, 4th ed., Australia, United States : Brooks/Cole-Thomson Learning, 2002. 

- Strauss S.H.: Guide to solutions for Inorganic chemistry: 3rd ed. Oxford University Press, 

1999. 


Student will gain knowledge of general chemistry, get familiar with chemical structure of organic 

molecules and reactions between them to better understand the reactions in organism. 



Student will be able to understand selected chemical concepts. 


Lectures, seminar work, workshops. 

Assessment: 


project): 

Seminar 

Oral exam 

Written exam 

Weight (in %) 

40 

30 

30 


KNEZ, Željko, ŠKERGET, Mojca, KNEZ HRNČIČ, Maša. Principles of supercritical fluid extraction and 

applications in the food, beverage and nutraceutical industries. V: RIZVI, Syed S. H. (ur.). 

Separation, extraction and concentration processes in the food, beverage and nutraceutical 

industries. Oxford [etc.]: Woodhead Publishing Limited, 2010. 

KNEZ, Željko, ŠKERGET, Mojca, MANDŽUKA, Zoran. Determination of S-L phase transitions under 

gas pressure. J. supercrit. fluids. [Print ed.], Dec. 2010, vol. 55, iss. 2, str. 648-652. 

KNEZ, Željko, AIONICESEI, Elena, NOVAK, Zoran, KNEZ HRNČIČ, Maša. Processing polymeric 

biomaterials using supercritical CO[sub]2. Chemieingenieurtech., 2011, vol. 83, no. 9, str. 1371- 

1380.


Course title: Molecular biophysics 




Academic 

year 

Semester 





Laboratory 

work 

Field work 

Individ. 

work 

ECTS 

30 30 90 6 

Lecturer: Milan Brumen, PhD, Full professor 



Prerequisits: 

Knowledge of physics on the level of a general university course in physics or biophysics given to 

students of studies others than physics. 


1. Chemical bonds, intra- and intermolecular forces. Structure of biological macromolecules 

(proteins, nucleic acids, polysaccharides). and Cooperative ligand binding to macromolecules. 

Dynamics of conformational changes of macromolecules. Structure of supramolecular complexes 

(lipoproteins, biological membrane). Relation between structure and function of macromolecular 

and supramolecular systems, regulation of biological activity. Water, its structure and meaning for 

biological systems. 

2. Biophysics of cytoskeleton and molecular machines of subcellular scales. Microtubules, 

microfilaments. Motor proteins: myosins, kinesins, dyneins; muscle contraction, mitosis, transport 

of organelles, cilia and flagella movement. protein motors 

3. Cell and cell membrane biophysics. Structure of biological cell. Transport across the cell 

membrane. Intra and intercellular signalisation and communications. 

4. Outline of selected experimental methods in molecular biophysics: X-ray crystallography,

absorption and fluorescence spectroscopy, spectroscopic methods NMR and EPR. 

Readings: 

J.A. Tuszynski, M. Kurzynski: Introduction to Molecular Biophysics, CRC Press 20 

R. Glaser: Biophysics, Springer, New York 2004 

P. R. Bergethon: The Physical Basis of Biochemistry. The Foundations of Molecular 

Biophysics, Springer, New York 1998 

D. Voet, J.G. Voet: Biochemistry, John Wiley & Sons, New York 1995 


Students get knowledge of structure and function of biological systems with respect to different 

levels of organisation and complexity, from molecules, macromolecules and supramolecular 

structures to the cell and tissue. The approach is based on concepts and methods of theoretical 

biophysics. 

Knowledge of biological systems on molecular level that is essential to deal with the data and data 

bases in bioinformatics. 



Students get knowledge and understanding of structure and function of selected biological 

systems based on principles and concepts of physics. 


Lectures 

Coursework from selected field in biophysics 

Tutorials 

Assessment: 


project): 

Written exam 

Oral exam 

Course work 

Weight (in %) 

35% 

35% 

30%


POISSON-Helmholtz-Boltzmann model of the electric double layer : analysis of monovalent ionic 

mixtures / Klemen Bohinc ... [et al.]. - Bibliografija: str. 031130-11-031130-12. V: Physical review. 

E, Statistical, nonlinear, and soft matter physics. - ISSN 1539-3755.. - Vol. 85, no. 3 (2012), str. 

031130-1-031130-12. . - doi: 10.1103/PhysRevE.85.031130 COBISS.SI-ID 4353131, JCR, WoS, št. 

citatov do 6. 5. 2012: 0, brez avtocitatov: 0, normirano št. citatov: 0 

ENZYME kinetics and the maximum entropy production principle / Andrej Dobovišek ... [et al.]. - 

Soavtorji: Paško Županović, Milan Brumen, Željana Bonačić-Lošić, Domagoj Kuić, Davor Juretić. - 

Bibliografija: str. 55. - Abstract.V: Biophysical chemistry. - ISSN 0301-4622.. - Vol. 154, iss. 2/3 

(2011), str. 49-55. . - doi: 10.1016/j.bpc.2010.12.009 COBISS.SI-ID 18206984, JCR, WoS, št. citatov 

do 6. 5. 2011: 0, brez avtocitatov: 0, normirano št. citatov: 0 




V: Experimental physiology. - ISSN 0958-0670.. - Vol. 96, issue 2 (2011), str. 240-258. . - doi: 

10.1113/expphysiol.2010.054635COBISS.SI-ID 18009864, JCR, WoS, št. citatov do 10. 4. 2012: 2, 

brez avtocitatov: 2, normirano št. citatov: 1


Course title: Multivariate statistical methods 




Academic 

year 

Semester 





Laboratory 

work 

Field work 

Individ. 

work 

ECTS 

30 30 90 6 

Lecturer: Petra Povalej Bržan, PhD, Assistant professor 



Prerequisits: 

Basics of statistics, 

basics of databases, 

basics of software package SPSS. 


Basics: 

• Data 

• Identifiers 

• Hypothesis 

• Distribution 

• Data types 

Introduction to statistical data analysis: 

• Data preprocessing 

• Descriptive data analysis 

• Normal distribution 

• Other distributions 

• Generating hypotheses

• Correlations 

• Univariate analysis 

Graphical representation of data for multivariate analysis: 

• Scattered plot 

• Radar plot 

• Polar plot 

• Multidimensional scaling 

Introduction to multivariate analysis: 

• Data preprocessing 

• Multinormal distribution 

• Normalisation 

• Generating hypotheses 

Overview of multivariate analysis methods: 

• MANOVA 

• Covariance 

• Factor analysis 

• Cluster analysis 

• Time series analysis 

• Loglinear models 

Practical examples: 

• Genom analysis example 

• • Molecular biology example 

Readings: 

1. Warren J. Ewens, Gregory R. Grant: Statistical Methods in Bioinformatics: An Introduction, 

Second Edition. Springer Verlag, New York 2005. 

2. Johnson, R.A. & Wichern, D.W.: Applied Multivariate Statistical Analysis. New Jersey: 

PrenticeHall, 2002. 

3. Marija Norusis: SPSS 14.0 Statistical Procedures Companion, Prentice Hall, 2005. ISBN: 0- 

13-199527-8. 

4. Marija Norusis: SPSS 14.0 Advanced Statistical Procedures Companion, Prentice Hall, 2005. 

5. Joseph F. Hair, Bill Black, Barry Babin, Rolph E. Anderson, Ronald L. Tatham: Multivariate 

Data Analysis. Prentice Hall, 2005. 

6. Alexander Isaev: Introduction to Mathematical Methods in Bioinformatics. Springer, 2004. 


Refresh knowledge of basic statistical methods, 

Show different data representations for multivariate analysis, 

Give overview of multivariate methods, 

Teach students which statistical analysis method to choose, 

Demonstrate usage of some methods on microbiology cases. 

Students should know which multivariate statistical method to use in a given case. 

Gained knowledge will be routinely used in their future work. 

Experience gathered here will be aplicable to actual real world cases from the field of 

bioinformatics.



Students: 

Should know how to preprocess and analyse data and how to determine an appropriate 

method according to hypothesis set 

will find out about different graphical data representations 

will find out about different distributions and common normalisation approaches, 

will gain knowledge about most widely used multivariate analysis methods, 

should know how to practically use gained knowledge for solving problems in the field of 



Lectures, discussion, demonstration, theoretical exercises, computer exercises 

Assessment: 


project): 

coursework (practical 

assignments) 

written examination (can be 

achieved also with two non 

obligatory colloquia) 

oral examination. 


Weight (in %) 

20 

30 

50


Course title: Basics of molecular and cell biology 




Academic 

year 

Semester 





Laboratory 

work 

Field work 

Individ. 

work 

ECTS 

30 30 90 6 

Lecturer: Saška Lipovšek Delakorda, PhD, Assistant professor 



Prerequisits: 


DNA structure and characteristics, replication (prokaryotes, eukaryotes), recombination, repair 

and mutations,, structure and function of genes and chromosomes. 

RNA structure characteristics: role of different types of RNA, transcription (prokaryotes, 

eukaryotes), post transcription modification. 

Protein structures, synthesis of proteins, translation, posttranslational modifications, protein 

folding, protein trafficking. 

Regulation of protein synthesis: transcriptional regulation of gene expression,, regulation of 

translation, posttranslational regulation . 

Embryonic development. 

Cell division (meiosis, mitosis). 

Cell cycle: proliferation, differentiation, apoptosis. 

Integration of cells into tissues, communication between cells, signal transduction, receptors, 

hormone signaling. 

Immune system. 

Viruses :HIV, SARS, Avian influence, DNA diagnostics and infection diseases.

Readings: 

1. B. ALBERTS et al.: Molecular biology of the cell., 4th Ed., Gerland Publish, Inc., New York, 2002 

2. LODISH H., Baltimore D., Berk A., Zipursky S.L., Matsudaira P., Darnell J.: Molecular Cell 

Biology, 5th Ed., Scientific American Books, Freeman and Co., New York, 2004 

3. Bruce Alberts, Dennis Bray, Karen Hopkin, Alexander Johnson, Julian Lewis, Martin Raff, Keith 

Roberts, Peter Walter: Essential cell biology, 2nd Ed., Gerland Publish, Inc., New York, 2003 


Students will understand basic molecular mechanisms in the cell, how cells are organized in 

tissues, organs and whole organisms. The focus will be on transfer of genomic information to 

synthesis of proteins. 



basic molecular processes in the cell 


Lectures 

Tutorial 

Assessment: 


project): 

writen and 


Weight (in %) 

60 

40 


The EVIDENCE on the degradation processes in the midgut epithelial cells of the larval antlion 

Euroleon nostras (Geoffroy in Fourcroy, 1785) (Myrmeleontidae, Neuroptera) [Elektronski vir] / 

Saška Lipovšek ... [et al.]. - Ilustr. - Nasl. z nasl. zaslona. - Opis vira z dne 27. 3. 2012. - Soavtorji: 

Ilse Letofsky-Papst, Ferdinand Hofer, Gerd Leitinger, Dušan Devetak. - Bibliografija: str. 664-665. - 

Abstract. V: Micron. - ISSN 0968-4328.. - Vol. 43, iss. 5 (2012), str. 651-665. . - doi: 

10.1016/j.micron.2011.11.012 COBISS.SI-ID 18855176, JCR, WoS, št. citatov do 6. 5. 2012: 0, brez 

avtocitatov: 0, normirano št. citatov: 0 

APPLICATION of analytical electron microscopic methods to investigate the function of spherites 

in the midgut of the larval antlion Euroleon nostras (Neuroptera: Myrmeleontidae) [Elektronski 

vir] / Saška Lipovšek ... [et al.]. - Ilustr. - Nasl. z nasl. zaslona. - Opis vira z dne 27. 3. 2012. - 

Soavtorji: Ilse Letofsky-Papst, Ferdinand Hofer, Maria Anna Pabst, and Dušan Devetak. - 

Bibliografija: str. 406-407. - Abstract. V: Microscopy research and technique. - ISSN 1059-910X.. - 

Vol. 75, iss. 4 (2012), str. 397-407. . - doi: 10.1002/jemt.21069 COBISS.SI-ID 18638856, JCR, WoS, 

št. citatov do 8. 5. 2012: 1, brez avtocitatov: 0, normirano št. citatov: 0 

DUALITY of terrestrial subterranean fauna / Tone Novak ... [et al.]. - Soavtorji: Matjaž Perc, Saška 

Lipovšek and Franc Janžekovič. - Bibliografija: str. 62-64. - Abstract. V: International journal of 

speleology. - ISSN 0392-6672.. - Vol. 41, no. 2 (2012), str. 181-188. . - doi: 10.5038/1827- 

806X.41.2.5 COBISS.SI-ID 19061512, JCR


Course title: Data mining and knowledge discovery 




Academic 

year 

Semester 





Laboratory 

work 

Field work 

Individ. 

work 

ECTS 

30 30 90 6 

Lecturer: Milan Zorman, PhD, Full professor, Vili Podgorelec, PhD, 

Associate professor, Boštjan Brumen, PhD, Assistant professor 



Prerequisits: 

Basic computer user skills: working with mouse, keyboard, MS Windows operating system, 

spreadsheets (MS Excel) 

Computer Science for Bioinformatics 


Introduction to inteligent systems 

Basics of data sets 

Data preprocessing 

Working with missing data 

Methods for supervised machine learning: 

o Decision trees 

o Neural networks 

o Rough sets 

o Hybrid methods 

Evaluation of acquired knowledge

Readings: 

- Zorman Milan, Podgorelec Vili, Lenič Mitja, Povalej Petra, Kokol Peter in Tapajner Alojz: 

Inteligentni sistemi in profesionalni vsakdan, Univerza v Mariboru, Center za 

Interdisciplinarne in multidisciplinarne raziskave in študije UM, Maribor, 2003 

- Toshinori Munakata: Fundamentals of the New Artificial Intelligence: Beyond Traditional 

Paradigms. Springer Verlag New York, 1998. 

- internet sources 


To introduce students to knowledge acquisition from data sets. 

To teach students about intelligent methods for automatic acquisition and evaluation of 

knowledge. 



Data acquisition 

Storing data. 

Data preprocessing for analysis with intelligent methods. 

Basics and usage of intelligent methods. 

Evaluation of results of intelligent methods. 

Usage of acquired knowledge. 

Capability to more efficiently acquire, store and use data. 

Knowledge about data mining and knowledge acquisition in various areas. 

Familiarity with intelligent methods. 


Lectures, discussion, demonstration, computer exercises 

Assessment: 


project): 

- coursework (practical 

assignments) 

- written examination (can be 

achieved also with two non 

obligatory colloquia), 

- oral examination. 

Weight (in %) 

20 

30 

50 


ZORMAN, Milan 




ISSN 0043-5325.. - Jg. 123, Heft 23/24 (2011), str. 700-709. COBISS.SI-ID 15706134, JCR

ZORMAN, Milan 





ZORMAN, Milan 


Verlič. - Abstract. - Bibliografija: str. 1550-1551.V: Journal of international medical research. - ISSN 

0300-0605.. - Letn. 37, št. 5 (2009), str. 1543-1551. COBISS.SI-ID 13645334, JCR 

PODGORELEC, Vili, 1972- 

Taking advantage of education data : advanced data analysis and reporting in virtual learning 

environments / V. Podgorelec, S. Kuhar. - Bibliografija: str. 116. - Abstract. V: Elektronika ir 

elektrotechnika. - ISSN 1392-1215.. - Nr. 8 (2011), str. 111-116. COBISS.SI-ID 15441174, JCR, WoS, 



Supporting the study process using semantic web technologies / V. Podgorelec, M. Gresak. - . - 

Dostopno tudi na: http://www.ee.ktu.lt/journal/2011/10/23__ISSN_1392- 

1215_Supporting%20the%20Study%20Process%20using%20Semantic%20Web%20Technologies.p 

df. - Bibliografija: str. 108. - Abstract.V: Elektronika ir elektrotechnika. - ISSN 1392-1215.. - No. 10 

(2011), str. 105-108. COBISS.SI-ID 15625238, JCR, WoS, št. citatov do 11. 4. 2012: 0, brez 



Expert-assisted classification rules extraction algorithm / Vili Podgorelec. - Abstract. - Bibliografija: 

str. 462.V: Lecture notes in computer science. - ISSN 0302-9743. - Vol. 6295 (2010), str. 450-462. 


ASSESSMENT of classification models with small amounts of data / Boštjan Brumen ... [et al.]. - 

Soavtorji: Matjaž B. Jurič, Tatjana Welzer, Ivan Rozman, Hannu Jaakkola, Apostolos Papadopoulos. 

V: Informatica. - ISSN 0868-4952.. - Vol. 18, no. 3 (2007), str. 343-362. COBISS.SI-ID 11983638, 

JCR, WoS, št. citatov do 10. 2. 2010: 3, brez avtocitatov: 3, normirano št. citatov: 3 

ZORMAN, Milan 



542.V: Lecture notes in computer science. - ISSN 0302-9743. - Vol. 6295 (2010), str. 533-542. 


JEREB, Borut, 1962- 

Upravljanje IT tveganj s pomočjo Risk IT [Elektronski vir] / Borut Jereb, Boštjan Brumen. - ilustr. - 

Sekcija UI: Upravljanje informatike / IT governance. - Nasl. pri prispevku. - Bibliografija: str. 14. 

V: Uravnotežite naložbe, tveganja in razvoj za uspeh [Elektronski vir] / Dnevi slovenske 

informatike 2010 - DSI, Portorož, Slovenija, 14.-16. april 2010. - Ljubljana : Slovensko društvo 

Informatika, 2010. - ISBN 978-961-6165-32-7. - 14 str. COBISS.SI-ID 512183357


Course title: Computational geometry for bioinformatics 




Academic 

year 

Semester 





Laboratory 

work 

Field work 

Individ. 

work 

ECTS 

30 30 90 6 

Lecturer: Borut Žalik, PhD, Full professor 



Prerequisits: 

Basic programming skills are required. 

In addition, the basic understanding of bioinformatics, analytical geometry and linear algebra are 

recommended (distances, surfaces, volume, scalar and vector product).


Introduction (Importance of geometric structures in bioinformatics) 

Convex hulls 

o Algorithms for the convex hull construction (brute force, Jarvish’s approach, 

Graham’s scan, incremental method, sweep-line-based approach, quickhull) 

o Use of convex hull in PSIMAP algorithms 

The closest point problem 

o uniform plane subdivision, 

o spiral algorithm 

o static and dynamical problem 

o Frenet distance (protein backbone construction) 

o closest k-pair search in large sets of imprecise points - proteins 

Triangulation (definition, characteristics, MWT, Hammilton triangulation, Delaunay 

triangulation) 

o Algorithms for Delaunay triangulation construction (random incremental 

algorithms, sweep-line algorithms) 

o Delaunay tetrahedronisation 

o Application of Delaunay tetrahedronisation for shape in position transformations 

of proteins. 

Voronoi diagram (definition, properties) 

o Algorithms for Voronoi diagram construction (brute force, Fortune’s approach) 

o Molecular surface determination from the Voronoi diagrams 

o Determination of proteins’ volume 

Minkowski’s sum 

o Minkowski’ sum construction on points and line segments 

o Application of Minkowski’ sum: van der Waals’ hull 

Collision detection 

o Method with hierarchically organised bounding boxes and spheres; method with 

dimension reduction 

o Collision detection among moving elementary particles 

Readings: 

1. M. de Berg, M. van Kreveld, M.Overmars, O. Schwarzkopf, Computational Geometry - 

Algorithms and Applications, Springer 1997. 

2. F. P. Preparata, M. I. Shamos, Computational Geometry: An Introduction, Springer Verlag, 

1985. 

3. J. O'Rourke, Computational Geometry in C, Cambridge University Press, 1998. 

4. N. C. Jones, P. A. Pevzner, An Introduction to Bioinformatics Algorithms, The MIT Press, 

2004. 


A student gets the knowledge about the importance of computational geometry and its 

applicability in bioinformatics. He/she recognises key problems in processing large amounts of 

geometric data, and acceleration techniques, dealing efficiently with these problems. He/she 

knows to link existing knowledge of computational geometry and apply it to the problems in 

bioinformatics. He knows efficient and stable algorithms of computational geometry, solving tasks 

from the field of bioinformatics.



Students: 

o get knowledge to find the convex hull for a set of points, and to use it in PSIMAP 

algorithms, 

o they recognize the closests point problem and existing solutions. They know how construct 

the protein backbone by using Frenet’s distance 

o they know different kinds of triangulation 

o they know algorithms for Delaunay triangulation construction, 

o they know applications of Delaunay triangulation in bioinformatics 

o they know Voronoi diagrams 

o they are able to determine the surface and the volume of molecules, organised in Voronoi 

structures 

o they know Mikowski’s sum and the algorithms for its construction 

o they know how to generalise the Mikowski’s sum, 

o to Van der Waals’ hulls 

Key skills: 

o they know how to translate problems from the bioinformatics into already solved 

problems of computational geometry, 

o they know to select appropriate algorithm for geometrical problems in bioinformatics, 

o they get skills for implementing geometric algorithms (rounding error, error propagation). 


Explanation, discussion, demonstration, computer exercises 

Assessment: 

Weight (in %) 


project): 

oral examination, 

50 % 

homework, 

20 % 

computer exercises. 

30 % 

Reference nosilca / Lecturer's references: 

1. ŠPELIČ, Denis, ŽALIK, Borut. Lossless compression of threshold-segmented medical images. 

Journal of medical systems, Published online: 15 April 2011, doi: 10.1007/s10916-011-9702-5. 

2. ZADRAVEC, Mirko, BRODNIK, Andrej, MANNILA, Markus, WANNE, Merja, ŽALIK, Borut. A 

practical approach to the 2D incremental nearest-point problem suitable for different point 

distributions. Pattern recognition, Vol. 41, No. 2, 2008, pp. 646-653. 

3. KLAJNŠEK, Gregor, ŽALIK, Borut. Progressive lossless compression of volumetric data using 

small memory load. Computerized medical imaging and graphics, Vol. 29, No. 4, 2005, pp. 305- 

312.


Course title: Applied computer science in bioinformatics 




Academic 

year 

Semester 





Laboratory 

work 

Field work 

Individ. 

work 

ECTS 

30 30 90 6 

Lecturer: Milan Zorman, PhD, Full professor 



Prerequisits: 

Basic computer user skills: working with mouse, keyboard, MS Windows operating system. 


Word processors, advanced – MS Word 

Spreadsheets, advanced – MS Excel 

Working with data bases - MS Access 

o Relational model 

o Entry forms 

o Querying 

o Creating reports 

Internet searchers 

Bibliographic data bases 

Readings: 

Dan Gookin: Word 2003 for Dummies, Wiley publishing, 2003. 

Greg Harvey: Excel 2003 for Dummies, Wiley publishing, 2003. 

John Kaufeld: Access 2003 for Dummies, Wiley publishing, 2003.


- introduce students to applied computer science 

- to teach students how to use word processors 

- to teach students how to use spreadsheets 

- to teach students usage of databases 

- introduce students to internet searchers 

- to teach students how to use bibliographic data bases 



- of basics of applied computer science, 

- of word processors, 

- of spreadsheets, 

- of database basics, 

- of internet searchers, 

- basics of bibliographic data bases 

- using computer for solving problems in everday professional situations 

- improved efficiency 


Lectures, discussion, demonstration, theoretical exercises, computer exercises 

Assessment: 


project): 

- coursework (practical assignments) 

- written examination (can be achieved 

also with two non obligatory colloquia), 


Weight (in %) 

30% 

50% 

20% 


ZORMAN, Milan 




ISSN 0043-5325.. - Jg. 123, Heft 23/24 (2011), str. 700-709. COBISS.SI-ID 15706134, JCR 

ZORMAN, Milan 





ZORMAN, Milan 


Verlič. - Abstract. - Bibliografija: str. 1550-1551.V: Journal of international medical research. - ISSN 

0300-0605.. - Letn. 37, št. 5 (2009), str. 1543-1551. COBISS.SI-ID 13645334, JCR


Course title: Introduction to bioinformatics 




Academic 

year 

Semester 





Laboratory 

work 

Field work 

Individ. 

work 

ECTS 

30 30 90 6 

Lecturer: Uroš Potočnik, PhD, Associate professor 



Prerequisits: 

Understanding basics of molecular biology, biochemistry and molecular genetics. 


Databases in molecular biology and genomics: 

- database indexing and search profiles 

- bibliographic databases (PubMed) 

- text databases (OMIM) 

- surveys of molecular biology databases and servers: nucleotide acid sequence databases 

(GenBank), genome databases, protein sequence databases (Swiss Prot), databases of 

structures, expression databases, databases of metabolic pathways 

- Integrated systems for data retrieving: ENTREZ (NCBI), ExPASy, Ensembl 

Sequence alignments and phylogenetic trees: measures of similarity, computing the alignment of 

two sequences, multiple sequence alignments (profiles, PSI-BLAST, Hidden Markov Models), 

phylogenetic trees (clustering methods, cladistic method, the problem of varying rates of 

evolution) 

Protein structure and drug discovery: protein stability and folding, superposition of structures and 

structural alignments, evolution of protein structures, classification of protein structures, protein 

prediction and modeling, assignment of protein structures to genomes, drug discovery and 

development, computer-assisted drug design

Readings: 

1. Lesk A: (2005) Introduction to Bioinformatics. 2 nd Ed, Oxford University Press, Oxford, UK 

2. Barnes MR, Gray IC: Bioinformatics for geneticist. John Wiley&Sons, R.J.M , West Sussex, 

2003. 

3. Attwood TK, Parry-Smith DJ (1999) Introduction to Bioinformatics. Prentice Hall, Harlow, 

England. 

4. Baxevanis AD, Francis Ouellette BF (1998) Bioinformatics A Practical Guide to the Analysis 

of Genes and Proteins. Wiley-Interscience, A John Wiley & Sons Inc., Publication, New 

York, USA. 

5. Higgins D, Taylor W (2000) Bioinformatics. Sequence, Structure and Databanks. Oxford 

University Press, Oxford, UK. 

6. Kanehisa M (2002) Post-genome Informatics. Oxford University Press, Oxford, United 

Kingdom 


Students will be provided with comprehensive review of the most relevant databases and 

bioinformatic tools in the fields of biochemistry, molecular biology and genomics. 

Students will be able to access and retrieve most relevant data from available databases in the 

field of molecular biology and genomics. 



type and structure of databases 

meaning and interpretation of molecular biology and genomic data 


Lectures 

Tutorial 

Assessment: 


project): 

Weight (in %) 

writen and 

60 


40


POTOČNIK, Uroš, 1969- 

Trenutna komercializacija osebne genetske analize-zanesljiva napoved tveganja za pogoste 

kompleksne bolezni ali zavajanje potrošnikov? [Elektronski vir] = Current commercialization of 

personal genetic analysis-reliable prediction of susceptibility to common complex diseases or 

misleading of the consumers? / Uroš Potočnik. - Povzetek ; Abstract. - Bibliografija: str. 4-5. 

V: Slovenski kemijski dnevi 2011, Portorož, 14-16 september 2011 [Elektronski vir] / [organizirala] 

Fakulteta za kemijo in kemijsko tehnologijo, Univerza v Mariboru [v sodelovanju s Slovenskim 

kemijskim društvom ... et al.]. - Maribor : FKKT, 2011. - ISBN 978-961-248-289-3. - 5 str. 


ŠIMENC, Janez, 1973- 

Rapid differentiation of bacterial species by high resolution melting curve analysis / J. Šimenc and 

U. Potočnik. - Abstract. - Bibliografija: str. 262-263.V: Applied biochemistry and microbiology. - 

ISSN 0003-6838.. - Vol. 47, no. 3 (2011), str. 256-263. . - doi: 10.1134/S0003683811030136 


citatov: 0 

A CYP17A1 gene polymorphism in association with multiple uterine leimyomas; a meta-analysis / 

Maja Pakiz ... [et al.]. - Soavtorji: Uros Potocnik, Igor But, Faris Mujezinovic. - Bibliografija: str. 33- 

34. – Abstract V: Disease markers. Section A, Cancer biomarkers. - ISSN 1574-0153.. - Vol. 8, no. 1 

(2010/2011), str. 29-34. . - doi: 10.3233/DMA-2011-0817 COBISS.SI-ID 4033599, JCR, WoS, št. 

citatov do 6. 10. 2011: 0, brez avtocitatov: 0, normirano št. citatov: 0


Course title: Bioinformatics in genetic research 




Academic 

year 

Semester 





Laboratory 

work 

Field work 

Individ. 

work 

ECTS 

30 30 90 6 




Prerequisits: 

Understanding basics of molecular biology, biochemistry, human genetics and bioinformatics 


Principles and strategies in identifying human disease genes: 

-patients and families enrolled in the study 

-positional cloning and definition of candidate region 

-linkage analysis: selection of microsatellite markers, recombination fraction, LOD score, twopoint 

mapping, multipoint mapping, program tools (GENHUNTER) 

-sib.pair analysis 

-transmission disequilibrium test (TDT) 

-association studies (case:controls), 

-genetic studies from genome sequence: locus definition, identification and extraction of 

sequence between two markers, evaluating genome sequence integrity between two markers, 

definition of known and new genes in the candidate region, candidate gene selection: molecular 

and physiological function, expression; using new markers for fine mapping of candidate region, 

design of panel markers for genotyping 

Identification on Single nucleotide polymorphisms (SNPs) and genotyping protocol, functional and 

biological significant SNPs, PC primer design,validation of genotyping data 

Technology for mutation detection and polymorphism genotyping

Statistical analysis of genotype and allele frequency in patients and controls (Hi2, Fischer exact) 

Haplotype estimation (Expectation maximization algorithm), linkage disequilibrium, 

Mapping quantitative locus traits (QTL) 

Examples of successful identification of disease genes in monogenic (Mendel) and complex traits 

Design, application and interpretation of genetic tests, genetic counseling 

Molecular targets for drug design 

Readings: 

1. Barnes MR, Gray IC: Bioinformatics for geneticist. John Wiley&Sons, R.J.M , West Sussex, 

2003. 

2. STRACHAN T and READ AP: Human Molecular genetics, Gerland Publish, Inc., New York, 

3rd ed., 2004 

3. David J. Balding (Editor), M. Bishop (Editor), C. Cannings (Editor): Handbook of Statistical 

Genetics, Second Edition, John Wiley&Sons, , 2003 

4. Tekoča periodika 


Students will be trained to use available resources, databases and bioinformatics tools for 

research in the field of molecular genetics and genomics. The aim of this course is to keep the 

students up to date with the most important discoveries with highest impact in the field of human 

molecular genetics. The course will address the possibilities of transfer of new discoveries and 

achievements in the field of genomics, molecular genetics and biomedicine into clinical practice 

including improved disease prevention and diagnosis, design and application of molecular drugs 

and personalized medicine. 

The focus will be on identification and mapping of human disease genes and potential molecular 

targets for drug design. 



approaches for identification and mapping of disease gene 

gene function and their role in pathogenesis 


Lectures 

Tutorial 

Assessment: 


project): 

Weight (in %) 

writen and 

60 


40
















citatov: 0 







Course title: DNA micro nets and analyze of expressions of genes 




Academic 

year 

Semester 





Laboratory 

work 

Field work 

Individ. 

work 

ECTS 

15 45 90 6 




Prerequisits: 



Regulation of gene expression: binding of trans-acting proteins to cis elements, modification of 

histones, chromatine remodeling 

Alternative transcription and gene processing 

Allele specific expression: DNA methylation, imprinting, SNPs in regulatory regions 

Transcriptomics 

Chemistry of binding to surface, preparation of microarrays (cDNA and oligo probes) 

Statistical analysis of microarray data: experimental design, normalization issues, Two-sample 

statistics for differential expression (DE) and multiple testing issues, linear models and its 

application in analyzing complex gene expression experiments with two or more treatment 

comparisons, clustering algorithms, cross –validation, functional annotation using Gene Ontology 

and sequence information 

Protein microarrays 

Application of microarray technology in diagnostics and in drug design and development

Readings: 

1. Statistical Analysis of Gene Expression Microarray Data edited by T.P. Speed. 2003. Chapman 

& Hall/CRC. 

2. Mark Schena: Microarray Analysis, John Willey&Sons, 2003 

3. Steen Knudsen: Guide to Analysis of DNA Microarray Data, 2nd Edition, John Willey&Sons 

2004 


This course will introduce, illustrate and evaluate a variety of statistical methods employed in the 

context of microarray data analysis. Techniques covered correspond to commonly encountered 

research questions and study designs and include preprocessing/normalization, linear models, 

multiple hypothesis testing, clustering, discrimination, prediction and annotation with gene 

ontology and sequence information. 



Perform microarray data analyses. 

Identify and use relevant resources (genomic data and tools) for their own research. 

Assess microarray data analyses performed by others. 

Design studies using microarray technology. 


Lectures 

Tutorial 

Assessment: 


project): 

Weight (in %) 

writen and 

60 


40 












Rapid differentiation of bacterial species by high resolution melting curve analysis / J. Šimenc and


ISSN 0003-6838.. - Vol. 47, no. 3 (2011), str. 256-263.. - doi: 

10.1134/S0003683811030136COBISS.SI-ID 14937622, JCR, WoS, št. citatov do 11. 4. 2012: 1, brez 








Course title: Pharmacogenomics 




Academic 

year 

Semester 





Laboratory 

work 

Field work 

Individ. 

work 

ECTS 

15 30 105 6 




Prerequisits: 



The students will be provided with information about the state of art technology and 

bioinformatic tools in pharmacogenomic research including high-throughput genotyping, 

microarrays and mass spectroscopy. The pharmacogenomic markers such as single nucleotide 

polymorphisms (SNPs), alleles, haplotypes, gene expression profiles and proteomes and their role 

in drug discovery and therapy will be discussed. Basics of statistical genetics relevant for 

pharmaogenomics will be explained. Molecular mechanisms and genes involved in drug 

metabolism (Cyp450), drug transport (ABCB1/MDR1) and drug receptors will be described. 

Already known associations between genes and drug response will be comprehensively reviewed. 

Ethic and social economic issues in pharmacogenomic research and application will be discussed.

Readings: 

1. Kalow W. (ed.): Pharmacogenomics, Marcel Dekker; 1st edition 2001 

2. Liciano J. (ed.): Pharmacogenomics, The Search for Individualized Therapies, John 

Wiley&Sons, 2002R.J.M. 

3. Potočnik U, Ferkolj I, Glavač D, Dean M: Polymorphisms in multidrug resistance 1 (MDR1) 

gene are associated with refractory Crohn disease and ulcerative colitis. Genes Immun. 

2004 Nov;5(7):530-9. 


The aim of this course is to provide student with understanding of molecular genetic and 

biochemical mechanisms underlaying different response to drug terapy. Student will be able to 

collaborate with medical doctors doing presonalized medicine and will be able to design and 

conduct research for discovery of molecular markers in pharmacogenomic. 



students will understant molecular genetic and biochemical mechanisms underlying variation in 

drug response among different individuals 


Lectures 

Tutorial 

Assessment: 


project): 

Weight (in %) 

writen and 

60 


40 
















citatov: 0 

A CYP17A1 gene polymorphism in association with multiple uterine leimyomas; a meta-analysis /






Course title: Human moleclar genetics-selcted topics 




Academic 

year 

Semester 





Laboratory 

work 

Field work 

Individ. 

work 

ECTS 

15 15 15 105 6 

Lecturer: Damjan Glavač, PhD, Full professor 



Prerequisits: 

Graduate degree 40 ECTS. 


Advances in functional genomics 

New approaches to treating disease: Gene therapy, embryonic stem cell research and therapeutic 

cloning for tissue repair and regeneration 

Molecular cancer genetics: oncogenes, tumors suppressor genes, hereditary cancer, molecular 

diagnostic and treatment, screening 

Molecular genetics and aging-can we reverse aging? 

Molecular evolution of genomes-what make us human? 

Behavioral genetics and neurobiology 

Readings: 

1. STRACHAN T and READ AP: Human Molecular genetics, Gerland Publish, Inc., New York, 3rd 

ed., 2004 

2. Tekoča periodika


The aim of this course is to inform students about most important and atractive up to date topics 

in the field of human molecular genetics. Students will get deep inside into heredity, structures of 

genes and genomes, comparative genomics, genomic diversity and mutations associated with 

diseases. The possibilities, advantages, risk, limitations and ethical issues of molecular genetic and 

genomic based medicine will be discussed. The interpretation of genetic tests and genetic 

counseling in rare monogenic and common complex multifactorial diseases will be discussed. 



corellations genotype-complex phenotype; heredity of complex phenotypes 

aplication of molecular genetics in medicine 

reading current scientific literature and discussing future developments in the field 


Lectures 

Tutorial 

Assessment: 


project): 

Weight (in %) 

writen and 

60 


40 


ASSESSMENT of the tumourigenic and metastatic properties of SK-MEL28 melanoma cells 

surviving electrochemotherapy with bleomycin = Določitev tumorigenih in metastatskih lastnosti 

melanomskih celic SK-MEL28 po preživetju elektrokemoterapije z bleomicinom / Vesna Todorović 

... [et al.]. - . - Dostopno tudi na: 

http://versita.metapress.com/content/24337t420311w012/fulltext.pdf. - Soavtorji: Gregor Serša, 

Vid Mlakar, Damjan Glavač, Maja Čemažar. - Izvleček v angl. in slov. - Bibliografija str. 44-45. 

V: Radiology and oncology. - ISSN 1318-2099.. - Vol. 46, no. 1 (2012), str. 32-45. 

. - doi: 10.2478/v10019-012-0010-6 COBISS.SI-ID 3203441, JCR, WoS, št. citatov do 11. 4. 2012: 0, 


2.MICRORNAS, innate immunity and ventricular rupture in human myocardial infarction / Nina 

Zidar ... [et al.]. - Soavtorji: Emanuela Boštjančič, Damjan Glavač, Dušan Štajer. - Abstract. - 

Bibliografija na koncu prispevka. V: Disease markers. - ISSN 0278-0240.. - Vol. 31, issue 5 (2011), 

str. 259-265 . - doi: 10.3233/DMA-2011-0827 COBISS.SI-ID 29193689, JCR, WoS, št. citatov do 11. 

4. 2012: 0, brez avtocitatov: 0, normirano št. citatov: 0 

DOWN-regulation of microRNAs of the miR-200 family and miR-205, and an altered expression of 

classic and desmosomal cadherins in spindle cell carcinoma of the head and neck-hallmark of 

epithelial-mesenchymal transition / Nina Zidar ... [et al.]. - Ilustr. - Soavtorji: Emanuela Boštjančič,

Nina Gale, Nika Kojc, Mario Poljak, Damjan Glavač, Antonio Cardesa. - Summary. - Bibliografija na 

koncu prispevka. V: Human pathology. - ISSN 0046-8177.. - Vol. 42, issue 4 (2011), str. 482-488. 

. - doi: 10.1016/j.humpath.2010.07.020 COBISS.SI-ID 28112089, JCR, WoS, št. citatov do 6. 2. 

2012: 1, brez avtocitatov: 1, normirano št. citatov: 0


Course title: Mathematical modeling and simulations in health science 


Academic 

year 

Semester 

Bioinformatics 2nd degree 






Laboratory 

work 

Field work 

Individ. 

work 

ECTS 

15 30 105 6 


Languages: Lectures: Slovenian 

Tutorial: Slovenian 

Prerequisits: 

Formal or informal knowledge of subjects Introduction to Biophysics and Molecular Biophysics is 

required. 


Lectures outline: 

The subject introduces selected examples of mathematical modeling biological processes from 

the health care point of view with emphasis on: 

- blood circulation 

- mechanics of breathing 

- gas exchange in lungs and blood 

- control of cell volume 

- muscle mechanics 

- intracellular and intercellular signaling 

- biological rhythms 

- biomechanics 

- population dynamics 

Laboratory work outline:

- mathematical modeling and computer simulation of selected processes 

- computer simulation and visualization of results with computer tools 

Readings: 

Hoppensteadt F. C., Peskin C. S. Modeling and Simulation in Medicine and the Life Sciences, 

Springer-Verlag, New York 2004. 

Keener J., Sneyd J. Mathematical Physiology, Springer-Verlag, New York 1998 

Goldbeter A. Biochemical Oscillations and Cellular Rhythms, Cambridge University Press, 

Cambridge 1996 

Hobbie R. K. Intermediate Physics for Medicine and Biology, John Wiley & Sons, New York 1988 


The subject is focused on the biological processes on the level of human organism as well as on 

the level of population from the point of view of modeling and simulation. The major aim is to 

study selected processes and its application in health science with methods of mathematical 

modeling and computer simulations. 



Student gets: 

- knowledge and understanding of selected physiological processes on the level of 

mathematical model; 

- knowledge of the selected processes studied in details. This enables her/him further 

research in this field. 


Lectures 

Laboratory work 

Assessment: 


project): 

• Oral 

• Practical work in laboratory 

and Homework 

Weight (in %) 

50 

50 


FAJMUT, Aleš 




0022-5193.. - Vol. 252, no. 3 (2008), str. 474-481. 



CONTRIBUTION of Rho kinase to the early phase of the calcium-contraction coupling in airway












citatov: 0


Course title: Advanced research methodology in bioinformatics 




Academic 

year 

Semester 





Laboratory 

work 

Field work 

Individ. 

work 

ECTS 

15 30 105 6 

Lecturer: Peter Kokol, PhD, Full professor 



Prerequisits: 

None. 


The student gets familiar with methodological issues and process of scientific research expecially 

qualitative and quantitative research. 

This subject aims to prepare students for the practice of undertaking high quality research 

methodology, quantitative and qualitative research in bioinformatics. 

They will upgrade their knowledge about principles of research ethics and became aware of 

specific research questions which appears on the field of bioinformatics. 

Readings: 

1. Trends in Bioinformatics Research. Peter V. Yan. Nova publishers. 2005. 

2. Bioinformatics: New Research. Peter V. Yan. Nova publishers. 2005. 

3. Researching health care consumers : critical approaches / edited by Jennifer Burr and 

Paula Nicolson. - Basingstoke ; New York, N.Y. : Palgrave Macmillan, 2005. 

4. Nursing research : a qualitative perspective / [edited by] Patricia L. Munhall. - 3rd ed. - 

Sudbury, Mass. : Jones and Bartlett Publishers, cop. 2001.

5. The student's guide to research ethics / Paul Oliver. - Maidenhead ;Philadelphia : Open 

University Press, 2003. 


Student: 

- Is acquainted with research paradigms and research approaches which form 

bioinformatics; 

- and recognizes significance and characteristics of research in bioinformatics; 

On successful completion of this subject students should be able to: 

Develop an expertise in qualitative and quantitative advanced research design, with particular 

reference to issues of sampling, access, ethics and rigour. 

Become skilled in the use of a range of techniques for the collection and analysis of qualitative 

and quantitative data. 

Develop the knowledge and skills essential for the effective dissemination and evaluation of 

qualitative and quantitative research. 



Knowledge of advanced research methodology and different research approaches; 

Qualified for independent quantitative and qualitative research; 

Student will be able to independently form and report their observations and results and actively 

comprehend in publishing of research contributions on the field of bioinformatics. 


Lectures, seminars. 

Assessment: 

Weight (in %) 


project): 

Written exam, 

70 

seminary work. 

30 


EVOLUTIONARY design of decision trees for medical application [Elektronski vir] / Peter Kokol ... 

[et al.]. - Soavtorji: Sandi Pohorec, Gregor Štiglic, Vili Podgorelec. - Bibliografija: str. 252-254. 

V: Wiley interdisciplinary reviews. Data mining and knowledge discovery [Elektronski vir]. - ISSN 

1942-4795. - Vol. 2, iss. 3 (May 2012), str. 237-254. . - doi: 10.1002/widm.1056 COBISS.SI-ID 

15997462 

KOKOL, Peter, 1957- 

Intelligent system supported evidence based management [Elektronski vir] / Peter Kokol, Gregor 

Štiglic. - ilustr. - Bibliografija: str. 198. - Abstract. V: CAINE-2011 [Elektronski vir] / 24th 

International Conference on Computers and Their Applications in Industry and Engineering 

November 16-18, 2011, Honolulu, HI USA. - Cary, NC : ISCA, 2011. - ISBN 978-1-880843-83-3. - Str. 

195-198.COBISS.SI-ID 1764516

COMPUTATIONAL complexity : theory, techniques, and applications / editor-in-chief, Robert A. 

Meyers. - New York : Springer, cop. 2012. - 6 zv. (XLIV, 3492 str.) ISBN 1-4614-1799-6 (hbk) 

ISBN 978-1-4614-1799-6 (hbk.) COBISS.SI-ID 1780644


Course title: Basics of molecular and population genetics 




Academic 

year 

Semester 





Laboratory 

work 

Field work 

Individ. 

work 

ECTS 

15 30 90 6 




Prerequisits: 

Understanding basics of molecular biology 


Basic molecular genetics: DNA structure and characteristics, replication (prokaryotes, 

eukaryotes), recombination, repair and mutations, organization, structure and function of 

genes and chromosomes, genome structure (plant, animal, human) transcription 

(prokaryotes, eukaryotes), translation, regulation of gene expression 

Chromosomal basis of heredity, Mendelian inheritance, polygenic inheritance 

Gene mapping, mitochondrial genome 

Mutations, polymorphisms, phenotype, genotype, allele frequency, haplotypes, haplotype 

blocks (HapMap project), the Hardy-Weinberg law, linkage analysis, linkage disequilibrium. 

Size and structure of population 

Natural selection, mutations, genetic drift, gene flow, inbreeding 

Molecular evolution, molecular clocks, how genomes evolve, conservation genetics 

Quantitative traits 

Gene testing in individuals and populations: mutation detection and genotyping methods, 

genetic testing in medicine (genetic diseases with classical Mendelian and complex 

inheritance), DNA analysis in forensics and bone marrow transplantation typing 

Molecular and population genetic and society: ethical, social and economical issues

Readings: 

HEDRICK PW: Genetics of Populations, Jones & Bartlett Publishers, Sudbury, Inc., 3rd ed, 

2004 

STRACHAN T and READ AP: Human Molecular genetics, Gerland Publish, Inc., New York, 3rd 

ed., 2004 

KLUG M and CUMMINGS MR.: Genetics: A Molecular Perspective. Pearson Education, Inc. 

New Jersey, 2003 


Students will be provided with basic population genetics principles. The focus will be on new 

molecular data including genome projects that compare population samples to identify patterns 

of genetic diversity and genes that have been under selection which helps to understand 

molecular evolution. 



principals of heredity and transfer of genetic information between generations 

correlations genotype-phenotype 

factors that influence frequency of DNA polymorphisms and genetic diversity in different 

populations 

the role of mutations and genetic diversity in evolution 


Lectures 

Tutorial 

Assessment: 


project): 

Weight (in %) 

writen and 

60 


40 












Rapid differentiation of bacterial species by high resolution melting curve analysis / J. Šimenc and




citatov: 0 







Course title: Proteine structures and proteomics 




Academic 

year 

Semester 




Lectures Seminar Tutorial Laboratory 

work 

Field work 

Individ. 

work 

ECTS 

15 30 30 6 

Lecturer: Damjan Glavač, PhD, Full professor 



Prerequisits: 

Understanding basics of molecular biology, biochemistry, molecular genetics and bioinformatics 


Proteomics basics: definitions, separation of proteins, chromatographic methods, protein 

identification and characterization, elecrophoresis, image analysis, mass spectrometry, 

protein sequence analysis, proteomics databases 

Basics of protein structure: properties of, amino acids, peptide bond, building blocks of 

protein structures, overview of molecular forces, protein geometry 

Secondary structures, motifs of protein structure, alpha, beta and alpha-beta motifs in 

protein structures 

Basics of protein folding 

Structure- function relationship: DNA binding proteins, examples of enzyme catalysis, 

membrane proteins, signal transduction, fibrous proteins, structures of the immune 

response molecules, virus structures 

Interaction proteomics, protein complexes 

Protein structure determination: X-ray crystallography, protein crystallization, NMR, 

electron microscopy 

Structural genomics: basic principles and methods

Structural based drug design, in silico screening, protein modelling 

Protein data bank (PDB) and its use 

Readings: 

1. Carl-Ivar Branden and John Tooze. Introduction to Protein Structure, 2nd edition, 1999, 

Garland Publishing 

2. Donald Voet & Judith Voet, Biochemistry, J.Wiley&Sons, 2004, 3rd ed. 

3. Gale Rhodes, Crystallography Made Crystal Clear- A Guide for Users of Macromolecular 

Models, Third Edition, February 2006, Elsevier/Academic Press 

4. Twyman, R. M. 2004. Principles of proteomics. BIOS Scientific Publishers, New York. 

5. Liebler, D. C. 2002. Introduction to proteomics: tools for the new biology. Humana Press, 

Totowa, NJ. 

6. Mechanisms of Protein Folding, 2nd edn., (2000) R.H. Pain (ed.), Oxford University Press 

7. A. Skoog, F. J. Holler and T. A. Nieman, Principles of Instrumental Analysis, 5th Edition, 

Saunders College Publishing, Philadelphia, 1998. 


The overall course objective is to provide the student with a broad understanding of the main 

fundamentals of the protein structure, proteomics and methods that are used in that field. 



On successful completion of this course, student should be able to: 

Describe basic principles of protein structure, protein structure motifs, secondary 

structure properties and protein folding. 

Explain structure function relationship. 

Describe methodologies used for protein characterization and structure determination 

and how these techniques can be applied to industry objectives and outcomes 

Use computer sotware to visualise, compare, analyse and interpret protein structures 


Lectures 

Tutorials 

Seminar 

Assessment: 


project): 

Weight (in %) 

writen and oral exemination 70 

seminar 

30 


ASSESSMENT of the tumourigenic and metastatic properties of SK-MEL28 melanoma cells 

surviving electrochemotherapy with bleomycin = Določitev tumorigenih in metastatskih lastnosti 

melanomskih celic SK-MEL28 po preživetju elektrokemoterapije z bleomicinom / Vesna Todorović 

... [et al.]. - . - Dostopno tudi na: 

http://versita.metapress.com/content/24337t420311w012/fulltext.pdf. - Soavtorji: Gregor Serša,

Vid Mlakar, Damjan Glavač, Maja Čemažar. - Izvleček v angl. in slov. - Bibliografija str. 44-45. 

V: Radiology and oncology. - ISSN 1318-2099.. - Vol. 46, no. 1 (2012), str. 32-45. 

. - doi: 10.2478/v10019-012-0010-6 COBISS.SI-ID 3203441, JCR, WoS, št. citatov do 11. 4. 2012: 0, 


2.MICRORNAS, innate immunity and ventricular rupture in human myocardial infarction / Nina 

Zidar ... [et al.]. - Soavtorji: Emanuela Boštjančič, Damjan Glavač, Dušan Štajer. - Abstract. - 

Bibliografija na koncu prispevka. V: Disease markers. - ISSN 0278-0240.. - Vol. 31, issue 5 (2011), 

str. 259-265 . - doi: 10.3233/DMA-2011-0827 COBISS.SI-ID 29193689, JCR, WoS, št. citatov do 11. 

4. 2012: 0, brez avtocitatov: 0, normirano št. citatov: 0 

DOWN-regulation of microRNAs of the miR-200 family and miR-205, and an altered expression of 

classic and desmosomal cadherins in spindle cell carcinoma of the head and neck-hallmark of 

epithelial-mesenchymal transition / Nina Zidar ... [et al.]. - Ilustr. - Soavtorji: Emanuela Boštjančič, 

Nina Gale, Nika Kojc, Mario Poljak, Damjan Glavač, Antonio Cardesa. - Summary. - Bibliografija na 

koncu prispevka. V: Human pathology. - ISSN 0046-8177.. - Vol. 42, issue 4 (2011), str. 482-488. 

. - doi: 10.1016/j.humpath.2010.07.020 COBISS.SI-ID 28112089, JCR, WoS, št. citatov do 6. 2. 

2012: 1, brez avtocitatov: 1, normirano št. citatov: 0


Course title: Recombinant DNA technology 




Academic 

year 

Semester 





Laboratory 

work 

Field work 

Individ. 

work 

ECTS 

15 30 105 6 




Prerequisits: 

Understanding basics of molecular biology and molecular genetics 


Cloning: Host organisms, DNA cloning vectors, cloning strategy in eukaryotes and 

prokaryotes, transformation and transfect ion, expression of recombinant proteins 

preparation of genomic and cDNA libraries 

Hybridization of nucleic acids, DNA micro arrays 

Polymerase DNA reaction (PCR), DNA sequencing 

Yeast two-hybrid system for identification of protein-protein interaction 

Site directed mutagenesis, knock-out technology and animal models-the role in functional 

genomics and animal disease models 

Silencing gene expression: RNAi, antisense RNA technology 

Cloning human genes, reproductive cloning of mammalians, therapeutic cloning 

Transgenic plants and animals 

DNA fingerprinting in forensics 

Gene technology in drug production and diagnostics 

Low regulations and safety precautions for research and applications of genetic modified 

organisms 

Recombinant DNA technology and society: ethic and social economic issues

Readings: 

1. Bernard R. Glick, Jack J. Pasternak: Principles and applications of recombinant DNA, 3rd 

edition, ASM Press, Washington, 2003 

2. Sandy Primrose, Richard Twyman, Bob Old: Principles of Gene Manipulation, 6th edition, 

Blackwell Science, Oxford, 2001 


Students will be provided with basic techniques and applications of recombinant DNA technology 

in research and industry. 



techiques and principals of DNA cloning and other recombinant DNA technology 

applications of recombinant DNA technology in research and industry 


Lectures 

Tutorial 

Assessment: 


project): 

Weight (in %) 

writen and 

60 


40 
















citatov: 0 



34. – Abstract V: Disease markers. Section A, Cancer biomarkers. - ISSN 1574-0153.. - Vol. 8, no. 1




Course title: Theoretical Biophysics 




Academic 

year 

Semester 





Laboratory 

work 

Field work 

Individ. 

work 

ECTS 

30 15 15 90 6 




Prerequisits: 

Formal or informal knowledge of subjects Introduction to Biophysics and Molecular Biophysics is 

required. 


General description of the subject: 

The subject introduces theoretical and computational tools and cutting edge research approaches 

from physics, chemistry, mathematics and computer science in the context of biological problems 

and situations. Functioning of different complex biological systems such as metabolic system, 

signaling networks, organelles, cells, organs, organisms and populations will be discussed from 

the point of view of studying their integral parts. On the basis of understanding the interactions 

and relationships between the systems subunits it will be possible to deduce to the functioning of 

the system as integrity. 

Lectures outline: 

- INTRODUCTION: (principles from physics and mathematics in systems biology, principles of 

working with computer tools for mathematical modeling and working with databases) 

- STANDARD APPROACHES IN MODELING BIOLOGICAL SYSTEMS: (biochemical and enzyme 

kinetics, metabolic networks, control analysis, signal transduction pathways) 

- SELECTED EXAMPLES OF MODELING BIOLOGICAL SYSTEMS: (oscillations in biological

systems, signal transduction, muscle contraction, whole cell modeling, cell cycle, aging, 

gene expression, evolution and self-organization) 

Seminar outline: 

Student chooses one of the themes offered by the lecturer. Project has a form of short scientific 

contribution. After the review of the final version student presents his project for the colleagues. 

Laboratory work outline: 

- work with computer tools like Mathematica, MatLab, Madonna, Gepasi, PLAS, Model 

Maker, Virtual Cell… 

- work with computer databases from the internet like BRENDA, Swiss-Prot, TrEMBL, 

UniProt… 

- modeling of selected problems from systems biology 

- solving of mathematical models and visualization of the results with help of computer 

tools 

Readings: 

1. Klipp E., Herwig R., Kowald A., Wierling C., Lehrach H. Systems Biology in Practice, Wiley- 

VCH, Weinheim 2005 

2. Kitano H. Foundations of Systems Biology, MIT Press, Cambridge 2001 

3. Voit E.O. Computational Analysis of Biochemical Systems: A Practical Guide for 

Biochemists 

and Molecular Biologists, Cambridge University Press, New York 2000 

4. Vodovnik L., Miklavčič D., Kotnik T. Biološki sistemi, Univerza v Ljubljani, Fakulteta za 

elektrotehniko, Ljubljana 1998 


- To develop an understanding of how and why theoretical approaches can drive new 

experiments. 

- To show students how theoretical results can deliver novel insight into the functioning of 

biosystems. 

- To get an insight into the current theoretical research approaches in bio-sciences. 

To get an insight how to test the hypotheses resulting from molecular biology, physiology or 

biochemistry with mathematical modeling. 

Students should leave the subject better able to identify important unsolved problems in biology 

and with an appreciation of how to select and solve problems for which quantitative and 

theoretical approaches will be productive. 



Student gets: 

- knowledge and understanding of physical, chemical, mathematical and computational 

methods in theoretical approach to study biological systems; 

- ability of working with presented computational tools and having acquaintance with 

others; 

- understanding of presented theoretical examples, knowledge of their advantages and 

disadvantages, as well as having acquaintance with other similar examples.


Lectures 

Seminar 

Laboratory work 

Assessment: 


project): 

Oral 

Written 

Project 

Weight (in %) 

40 

30 

30 


FAJMUT, Aleš 




0022-5193.. - Vol. 252, no. 3 (2008), str. 474-481. 















citatov:


Course title: Complexity theory and chaos 




Academic 

year 

Semester 





Laboratory 

work 

Field work 

Individ. 

work 

ECTS 

15 30 105 6 

Lecturer: Peter Kokol, PhD, Full professor 



Prerequisits: 

None. 


History 

The concepts of system theory 

Definition of complexity 

Theory of complexity 

Theory of chaos 

Complex systems and chaos theory in computer science 

Complex systems and chaos theory in biology 

Complex systems and chaos theory in economy 

Application of complex systems and chaos theory in bionformatics 

Soft system theory 

Soft system theory and decision making, problem solving in conflicts situations and 

planning

Readings: 

1. P. Checkland: Systems Thinking Practice, John Wiley & Sons, Chichester, 1981. 

2. P. Checkland, J. Scholes: Soft Systems Methodology in Action, John Wiley & Sons, 

Chichester, 1990. 

3. R. L. Flood, M. C. Jackson: Creative problem Solving: Total System Intervention, John Wiley 

& Sons, 1991. 

4. R. Peitgen: Chaos and Fractals – New Frontiers of Science, Springer Verlag, 1993 

5. K. Frenken: Innovation, Evolution and Complexity Theory, EE Press, 2006) 


The first goal is to teach students to understand the differences between scientific approach and 

system theory and the concepts of system theory, complexity theory and the chaos theory. 

The other more pragmatic goal is to teach the students how to use the above theories in 

bioinformatics. The students should be able to understand the Aristotle’s rule that the whole is 

more then the sum of its parts. 



Student: 

Understands the difference between scientific and system approach 

The student understands the Aristotels rule 

The student has the competencies in system theory, soft system theory, theory of 

complexity and chaos theory 

Students is able to use the above theories in practical applications in bioinformatics 



Assessment: 


project): 

Weight (in %) 

Kolokviji 

30 

Pisni izpit 

20 

Projekt. 

50 






15997462 



Štiglic. - ilustr. - Bibliografija: str. 198. - Abstract. V: CAINE-2011 [Elektronski vir] / 24th



195-198.COBISS.SI-ID 1764516 



ISBN 978-1-4614-1799-6 (hbk.) COBISS.SI-ID 1780644


Course title: Scientific Visualisation 




Academic 

year 

Semester 





Laboratory 

work 

Field work 

Individ. 

work 

ECTS 

15 30 105 6 

Lecturer: Sebastian Krivograd, PhD, Assistant professor 



Prerequisits: 

Basic programming skills and basic knowledge of algorithms and data structures. 


Introduction: why scientific visualisation, historical overview, models for scientific 

visualization, simulation, animation and virtual reality. 

Fundamentals of computer graphics and geometric modelling: different representations of 

geometric objects, geometric transformations, projections, basic principles of rendering. 

Information visualisation: 1D, 2D, 3D and 4D data, plotting trees, grids, and graphs, graphs and 

trees interactions, scalar and vector fields, non-photorealistic rendering. 

Surface visualisation and visualization of volumetric data: surface rendering, direct 

visualisation of voxel data, indirect visualization of sampled objects by surface reconstruction. 

Applications of scientific visualisation: visualisation of chemical structures in biology, 

chemistry and physics, fluid visualisation, geographic, geological and meteorological 

visualization, medical visualisation. 

Bioinformatics visualization: molecular modelling, anatomic visualization, visualization of DNA 

sequences. 

Software for bioinformatics visualization: a survey and use of software packages for structure 

visualization in bioinformatics (Cn3D, Rasmol, Protein Explorer, Chime), analysis and 

comparison of packages.

Readings: 

1. Chaomei Chen: Information Visualization. Springer; 2 edition, 2004. ISBN: 1852337893. 

2. Michael Jünger (Editor), Petra Mutzel (Editor): Graph Drawing Software. Springer, 2003. 

ISBN: 3540008810. 

3. Isaac Bankman: Handbook of Medical Imaging: Processing and Analysis. Academic Press; 

2000. ISBN: 0120777908. 

4. Wen Jei Yang: Handbook of Flow Visualization. Taylor & Francis, 2nd edition, 2001. ISBN: 

1560324171. 


The objective of this course is to enrich student’s experience in using visualisation, to organize, to 

formalize and to widen his knowledge of visualisation by learning the theoretical background, 

data types and algorithms and, consequently, to qualify him for more efficient use, development 

and implementation of scientific visualisation systems. 

Communication skills: oral manner of expression at oral exemination and lab work defense, 

writing report about completed project. 

Use of information technology: use of present software for bioinformatics visualisation, 

present software development tools and special visualisation libraries. 

Problem solving: individual project work. 



On completion of this course the student will be able to: 

- demonstrate broad knowledge of visualisation principles, data types and algorithms, 

- select a proper representation and visualisation technique for soliving real scientific and 

engineering problems, 

- use theoretical knowledge and practical experience for eficient use of visualisation 

software in bioinformatics, 

- evaluate applicability of existing software in a given practical situation and, as necessary, 

design and implement own system, 

- list and illustrate use of scientific visualisation in some other fields (medicine, geography, 

geology, meteorology...). 


Lectures, discussions, demonstration, computer exercises. 

Assessment: 


project): 

Weight (in %) 

- coursework (computer exercises ) 30 

- projects (seminary work) 

20 


50 


KRIVOGRAD, Sebastian 

A hexahedral mesh connectivity compression with vertex degrees / Sebastian Krivograd, Mladen

Trlep, Borut Žalik. - . - Dostopno tudi na: http://dx.doi.org/doi:10.1016/j.cad.2008.10.013. - 

Abstract. - Bibliografija: str. 1112. V: Computer Aided Design. - ISSN 0010-4485.. - Vol. 40, iss. 12 

(Dec. 2008), str. 1105-1112. . - doi: 10.1016/j.cad.2008.10.013 COBISS.SI-ID 12964630, JCR, WoS, 


GEOMETRIC data preparation for GIS applications / David Podgorelec ... [et al.]. - Soavtorji: Gregor 

Klajnšek, Sebastian Krivograd, Borut Žalik. - Bibliografija: str. 124-127. - Abstract. V: 

Geoinformation technologies for geocultural landscapes / editors Oliver Bender ... [et al.]. - Boca 

Raton [etc.] : CRC Press/Balkema, cop. 2009. - ISBN 978-0-415-46859-6. - Str. 107-127. COBISS.SI- 

ID 13051670

Course title: Health informatics 





Academic 

year 

Semester 





Laboratory 

work 

Field work 

Individ. 

work 

ECTS 

15 30 105 6 

Lecturer: Kokol Peter, PhD, Full professor, 

Tatjana Welzer Družovec, PhD, Full professor 



Prerequisits: 

Knowledge in computer science and informatics. 


- Health and nursing informatics 

- Requirements engineering, information system development, implementation. 

- Databases in bioinformatics and health 

- Quality assurance of hospital information systems for health and nursing 

- Intelligent systems 

- Decision trees in health and nursing 

- Telemedicine 

- Informatics in organization and working processes in health systems

Readings: 

1. M.J. Ball et all. Nursing Informatics: Where carring and Technology Meet. 3rd ed./ New 

York: Springer-Verlag, 2000. 

2. L. Burke, B. Weill. Information Technology for the Health Professions. 2nd ed./ Prentice 

Hall, 2004. 

3. E. Turban et all. Introduction to Information Technology. 3rd ed./ Wiley, 2004 

4. Kokol P. Računalništvo v zdravstvo I. Maribor: Visoka zdravstvena šola, 1998 NICE 

textbooks from the Phare Tempus program. 

5. Saba VK, McCormick A. Essentials of Nursing Informatics, IOS Press, 2005. 


Student: 

- will be capable to take an active part in hospital information systems development. 



- understands the importance of information, information systems and information 

technology in health and nursing care; 

- understands the importance of nursing leaders in process of nursing information systems 

development; 

- is able to use theory and practice of information systems development 



Assessment: 

Weight (in %) 


project): 

Written exam, 

40 

project. 

60 






15997462 



Štiglic. - ilustr. - Bibliografija: str. 198. - Abstract. V: CAINE-2011 [Elektronski vir] / 24th 



195-198.COBISS.SI-ID 1764516



ISBN 978-1-4614-1799-6 (hbk.) COBISS.SI-ID 1780644 

VIRTUAL education centre for the development of expert skills and competencies [Elektronski vir] 

/ Tatjana Welzer ... [et al.]. - Nasl. z nasl. zaslona. - Opis vira z dne 21. 11. 2011. - Bibliografija: str. 

54. - Abstract. V: International journal of advanced corporate learning [Elektronski vir]. - ISSN 

Y505-6985. - Vol. 4, no. 4 (2011), str. 51-54. - doi: ijac.v4i4.1747 COBISS.SI-ID 15528726 

HÖLBL, Marko 

Two improved two-party identity-based authenticated key agreement protocols / Marko Hölbl, 

Tatjana Welzer. V: Computer standards & interfaces. - ISSN 0920-5489.. - Vol. 31, iss. 6 (Nov. 

2009), str. 1056-1060. . - doi: 10.1016/j.csi.2008.09.024 COBISS.SI-ID 13379606, JCR, WoS, št. 

citatov do 6. 6. 2012: 3, brez avtocitatov: 3, normirano št. citatov: 2 

WELZER-Družovec, Tatjana 

Culture sensitive aspects in informatics education [Elektronski vir] / Tatjana Welzer, Marjan 

Družovec, Hannu Jaakkola. - Ilustr. - Bibliografija na koncu prispevka. - Abstract. V: EAEEIE2012 

[Elektronski vir] / 23rd EAEEIE annual conference, Cagliary, Italy, February 26-27, 2012. - [S. l. : s. 

n.], cop. 2012. - Str. 1-3. COBISS.SI-ID 15829270

bioinformatics 2nd degree bologna study programme - Univerza v ...

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