bioinformatika · 2020-03-31 · study programme and level Študijska smer study field letnik...

Žitna ulica 15

2000 Maribor, Slovenija

UČNI NAČRTI

ŠTUDIJSKO LETO 2020/2021

ŠTUDIJSKI PROGRAM 2. STOPNJE

BIOINFORMATIKA

2. LETNIK

UČNI NAČRT PREDMETA / COURSE SYLLABUS

Predmet: Bioinformatika in genetske raziskave

Course title: Bioinformatics in genetic research

Študijski program in stopnja Study programme and level

Študijska smer Study field

Letnik Academic year

Semester Semester

Bioinformatika 2. stopnja Bioinformatika 2 3

Bioinformatics 2nd degree Bologna Study programme

Bioinformatics 2 3

Vrsta predmeta / Course type Obvezni predmet / Obligatory subject

Univerzitetna koda predmeta / University course code:

Predavanja Lectures

Seminar Seminar

Sem. vaje Tutorial

Lab. vaje Laboratory work

Teren. vaje Field work

Samost. delo Individ. work

ECTS

30 30 90 6

Nosilec predmeta / Lecturer: Izr. prof. dr. Uroš Potočnik

Jeziki / Languages:

Predavanja/Lectures: slovenski/slovene

Vaje / Tutorial: slovenski/slovene

Pogoji za vključitev v delo oz. za opravljanje študijskih obveznosti:

Prerequisits:

Poznavanje osnov molekularne biologije, biokemije, humane genetike in bioinformatike

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

Vsebina:

Content (Syllabus outline):

Odkrivanje in mapiranje bolezenskih genov: - izbor bolnikov in družin -pozicijsko kloniranje in definicija kandidatnega področja, -Analiza genetske vezave: izbira mikrosatelitnih označevalcev, rekombinacijska frakcija, vrednost LOD, dvotočkovno mapiranje, večtočkovno mapiranje, programska orodja (GENEHUNTER) -test prenosa neravnotežja (ang TDT za transmission disequilibrium test) -analiza -asociacijske študije primeri/kontrole -analiza parov sorodnikov -genetske študije iz genomske sekvence: definicija lokusa; identifikacija in eksrakcija genomske sekvence med dvema markerjema; preverjanje integritete genomske sekvence med dvema markerjema; definicija znanih in novih genov na

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, two-point 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

sekvenci kandidatnega področja genoma; izbira kandidatnih genov za analizo-povezovanje z biološko in fiziološko funkcijo, ekspresijo genov; identifikacija novih markerjev v kandidatnem področju genoma; načrtovanje panela genetskih markerjev za gensko tipizacijo Identifikacija polimorfizmov enega nukleotida (SNP) in načrtovanje protokola genske tipizacije: identifikacija SNPjev; določitev funkcijskih in biološko pomembnih SNPjev, načrtovanje začetnih oligonukleotidov za reakcijo PCR; validacija rezutatov genske tipizacije; Statistična analiza genotipov in alelov pri bolnikih in kontrolah (Hi2, Fischerjev test): določitev strukture haplotipov (algoritem maksimizacije pričakovanega); genetsko neravnotežje (linkage disequilibrium); mapiranje kvantitativnih lokusov (QTL) Pregled metod odkrivanja mutacij in genske tipizacije polimorfizmov Primeri uspešnega mapiranja bolezenskih genov za monogenske in kompleksne bolezni Načrtovanje, izvajanje in interpretacija genetskih testov; genetsko svetovanje Molekularne tarče za načrtovanje bioloških zdravil

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

Temeljni literatura in viri / 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

Cilji in kompetence:

Objectives and competences:

Cilj predmeta je naučiti študente uporabljati razpoložljve podatkovne zbirke in orodja bioinformatike za raziskovanje na področju molekularne genetike in genomike. Študenti bodo seznanjeni z najnovejšimi in najpomembnejšimi dosežki in odkritji na področju humane molekularne genetike ter na možnostih prenosa teh odkritij in znanj v klinično prakso za izboljšanje preprečavenja in diagnosticiranja bolezni, načrtovanje in uporabo molekularnih in bioloških zdravil ter individualiziranemu zdravljenju na osnovi genetskih testov. Poudarek bo na odkrivanju in mapiranju bolezenskih genov ter potencialnih molekularnih tarč za načrtovanje zdravil.

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.

Predvideni študijski rezultati:

Intended learning outcomes:

Znanje in razumevanje:

• metodika mapiranja bolezenskih genov

• funkcija in vloga genov v patogenezi bolezni

Knowledge and understanding:

• approaches for identification and mapping of disease gene

• gene function and their role in pathogenesis

Metode poučevanja in učenja:

Learning and teaching methods:

• Predavanja

• Seminarske vaje

• Lectures

• Tutorial

Načini ocenjevanja:

Delež (v %) / Weight (in %)

Assessment:

Način (pisni izpit, ustno izpraševanje, naloge, projekt)

• pisni in

• ustni izpit

60 40

Type (examination, oral, coursework, project):

• writen and

• oral exemination

Reference nosilca / Lecturer's references:

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. COBISS.SI-ID 15319318 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 COBISS.SI-ID 14937622, JCR, WoS, št. citatov do 11. 4. 2012: 1, brez avtocitatov: 1, normirano št. 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


Predmet: DNA mikromreže in analiza ekspresije genov

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




Semester Semester



Bioinformatics 2 3



Predavanja Lectures

Seminar Seminar

Sem. vaje Tutorial




ECTS

15 45 90 6


Jeziki / Languages:




Prerequisits:



Vsebina:


Regulacija genske ekspresije z vezavo trans delujočih proteinov na cis delujoče regulatorna zaporedja, modifikacija histonov in remodulacija strukture kromatina Alternativna transkripcija in procesiranje posameznih genov Alelno specifična ekspresija: metilacija, DNA vtisnjevanje (imprinting), polimorfizmi v regulatornih zaporedjih Transkriptomika Kemija vezave molekul na površino, priprava biočipov (vezava cDNA in oligo nukleotidnih sond) Statistična analiza ekspresijskih biočipov: načrtovanje eksperimenta, normalizacija, statistika primerjalne analize ekspresije dveh vzorcev, linearni modeli in njihova uporaba pri kompleksnih eksperimentih, kjer primerjamo gensko ekspresijo

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

v dveh ali večih situacijah (npr. različni tretmaji celic), postopki za sestavljanje klastrov, validacija podatkov, funkcijsko vrednoteneje z uporabo podatkovnih zbirk Gene ontology in DNA sekvenc Proteinske mikromreže Uporaba mikromrež v diagnostiki, načrtovanju in razvoju novih zdravil

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


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



Študentom bodo predstavljene in ovrednotene različne statistične metode za analizo podatkov pridobljenih z mikromrežami (biočipi). Osnovni pristopi analize bodo vključevali: procesiranje in normalizacijo rezultatov, linearni modeli, testiranje večih hipotez, sestavljanje klastrov, predikcija in funkcijsko ovrednotenje na osnovi genske ontologije in genomske sekvence.

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.




• izvedba analize podatkov pridobljenih z ekspresijskimi mikromrežami

• odkrivanje in uporaba relevantnih virov (orodij bioinformatike in podatkov o genomu) za lastne analize

• analiza podatkov analiz z biočipi, ki so jih izvedli drugi raziskovalci

• načrtovanje študij z uporabo mikromrež


• 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.



• Predavanja

• Seminarske vaje

• Lectures

• Tutorial



Assessment:


• pisni in

• ustni izpit 60 40


• writen and



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. COBISS.SI-ID 15319318 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/S0003683811030136COBISS.SI-ID 14937622, JCR, WoS, št. citatov do 11. 4. 2012: 1, brez avtocitatov: 1, normirano št. 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


Predmet: Farmakogenomika

Course title: Pharmacogenomics




Semester Semester



Bioinformatics 2 3

Vrsta predmeta / Course type Izbirni predmet/ Optional subject


Predavanja Lectures

Seminar Seminar

Sem. vaje Tutorial




ECTS

15 30 105 6


Jeziki / Languages:




Prerequisits:



Vsebina:


Predstavljene bodo možnosti uporabe najsodobnejših orodij farmakogenomskih raziskav v Sloveniji in svetu, vključno z visoko pretočnimi tehnologijami genske tipizacije, uporabo mikromrež (biočipov) za določanje globalnega profila izražanja genov in uporabo masne spektroskopije v proteomiki. Kandidat bo podrobno seznanjen z različnimi tipi farmakogenomsko molekularnih bioloških označevalcev, kot so polimorfizmi enega nukleotida (SNP), aleli, haplotipi, gensko ekspresijski profili, proteinski profili ter njihovo vlogo v procesu odkrivanja in razvoja novih zdravil kot tudi uporabi že odobrenih zdravil v terapiji. Razložene bodo glavne zakonitosti statistične in populacijske genetike. Prikazani bodo glavni molekularni mehanizmi in geni vključeni v

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.

metabolizem zdravil (Cyp450), transport zdravil (ABCB1/MDR1) in vezavo zdravil na receptrje. Pregledno bodo prikazani konkretni primeri kliničnih študij znanih korelacij genetske raznolikosti z odzivom na zdravila pri različnih boleznih. Diskutirani bodo etični in socialno ekonomski vidiki farmakogenomskih študij in aplikacij.


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.



Cilj predmeta je omogočiti študentu razumevanje molekularno genetskih in biokemijskih osnov, ki pogojujejo raznolik odziv na zdravila glede na posameznikovo genetsko predispozicijo, kar bo omogočilo študentu sodelovanje pri izvajanju individualiziranega zdravljenje v praksi kot tudi vodenje lastne študije iskanja novih povezav med gensko predispozicijo in odzivom na zdravljenje ter preverjanje že znanih povezav na različnih populacijah.

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.



Znanje in razumevanje: Študentje bodo razumeli molekularno genetske in biokemijske mehanizme, ki pogojujejo raznolik odziv na zdravila


students will understant molecular genetic and biochemical mechanisms underlying variation in drug response among different individuals



• Predavanja

• Seminarske vaje

• Lectures

• Tutorial



Assessment:


• pisni in



• writen and



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. COBISS.SI-ID 15319318 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 COBISS.SI-ID 14937622, JCR, WoS, št. citatov do 11. 4. 2012: 1, brez avtocitatov: 1, normirano št. 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


Predmet: Humana molekularna genetika-izbrana poglavja

Course title: Human moleclar genetics-selcted topics




Semester Semester



Bioinformatics 2 3



Predavanja Lectures

Seminar Seminar

Sem. vaje Tutorial




ECTS

15 15 15 105 6

Nosilec predmeta / Lecturer: Prof. dr. Damjan Glavač

Jeziki / Languages:




Prerequisits:


Basic knowledge of molecular biology, biochemistry, human genetics and bioinformatics

Vsebina:


Napredna funkcijska genomika Nove metode zdravljenja: genska terapija, uporaba izvornih matičnih celic in terapevtskega kloniranja za transplantacijsko medicino Molekularna genetika raka: onkogeni, tumorsko zaviralni geni, dedne oblike, molekulska diagnostika in zdravljenje, presejalni testi Molekularna genetika in staranje-ali lahko preprečimo staranje? Molekularna evolucija genomov-kaj nas dela ljudi? Genetika vedenja in nevrobiologija

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


1. STRACHAN T and READ AP: Human Molecular genetics, Gerland Publish, Inc., New York, 3rd ed., 2004 2. Tekoča periodika



Predmet bo seznanil študente z najaktualnejšimi temami na področju humane molekularne genetike. Poseben poudarek bo na poglobljenem razumevanju načinov dedovanja, strukture in primerjave genov in genomov, genetske raznolikosti in genetskih napak povezanih z nastankom bolezni. Študentom bodo predstavljene možnosti, prednosti, omejitve, tveganja in etični vidiki uporabe tehnologij molekularne genetike in genomike v medicinske namene. Poudarek bo tudi na interpretaciji genetskih testov in genetskem svetovanju pri monogenskih in kompleksnih boleznih

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.




• povezave genotipa in kompleksnih fenotipov, zakonitosti dedovanja kompleksnih fenotipov

• uporaba molekularne genetike v medicini

• branje in razumevanje tekoče znanstvene literature in argumentirano razpravljanje o razvoju znanstvenega področja


• 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



• Predavanja

• Seminarske vaje

• Lectures

• Tutorial



Assessment:


• pisni in



• writen and



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, brez

avtocitatov: 0, normirano št. citatov: 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


Predmet: MAGISTRSKA NALOGA

Course title: Master Thesis




Semester Semester



Bioinformatics 2 2

Vrsta predmeta / Course type


Predavanja Lectures

Seminar Seminar

Sem. vaje Tutorial




ECTS

375 15

Nosilec predmeta / Lecturer: Izbrani mentor/ Mentor selected

Jeziki / Languages:




Prerequisits:

Študent lahko prijavi magistrsko nalogo na osnovi predpisanih pogojev v pravilniku.

The student can apply for the degree’s work according to the prescribed conditions in the regulations.

Vsebina:


Prijava teme magistrske naloge v skladu s Statutom UM in pravilniki FZV UM.

The official procedure of the preparation of the Master Thesis accordingly Statute of University of Maribor and regulations of FHS UM.


Relevantna literatura s področja magistrske naloge. / Relevant literature from the topic of the Master Thesis.



Cilji so definirani v prijavi teme magistrske naloge. The objectives are defined in the application for the approval of the topic of the Master Thesis.



Znanje in razumevanje: Znanje širšega strokovnega področja, v katerega sodi magistrska naloga in ožje znanje ter razumevanje pojmovnika, ki ga zajema tema magistrske naloge. Poudarek je na praktičnih znanjih in naprednejših metodologijah zajemanja, obdelovanja in prikazovanja podatkov.

Knowledge and Understanding: Knowledge of the broader professional field to which belongs the Master Thesis and special knowledge of the corresponding glossary. The emphasis is on the practical skills and relatively more advanced methodologies of collecting, processing and presenting data.

Prenesljive/ključne spretnosti in drugi atributi: Strokovno zapisovanje in izražanje vsebine, obvladanje reševanja strokovnih problemov, suverena predstavitev ključnih spoznanj in spretnost argumentiranja.

Transferable/Key Skills and other attributes: Documenting and expressing the subject in a professional way, mastering the solving of the professional problems, independent presentation of the key conclusions and ability in arguing.



Vodeno individualno raziskovalno delo.

Guided individual research work.



Assessment:

Magistrska naloga Zagovor

70% 30%

Master Thesis Presentation


Predmet: Matematično modeliranje in simulacije v zdravstvu

Course title: Mathematical Modeling and Simulations in Health Science




Semester Semester



Bioinformatics 2 3

Vrsta predmeta / Course type Izbirni predmet / Optional subject


Predavanja Lectures

Seminar Seminar

Sem. vaje Tutorial

Lab. vaje Laboratory

work



ECTS

15 30 105 6

Nosilec predmeta / Lecturer: Doc. dr. Aleš Fajmut

Jeziki / Languages:

Predavanja / Lectures: slovenski/Slovenian

Vaje / Tutorial: slovenski/Slovenian


Prerequisits:

Ni pogojev. No prerequisites.

Vsebina:


Vsebina predavanj: Predmet zajema obravnavo izbranih primerov matematičnega modeliranja bioloških procesov s stališča zdravstva s poudarkom na primerih s področja:

- cirkulacije krvi - mehanike dihanja - izmenjave plinov v pljučih in v krvi - kontrole celičnega volumna - mehanike mišic - signalizacije v celici in med celicami - bioloških ritmov - biomehanike - populacijske dinamike

Vsebina laboratorijskih vaj:

- matematično modeliranje in računalniška

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

simulacija izbranih procesov - računalniška simulacija in vizualizacija

rezultatov z računalniškimi orodji

Laboratory work outline:

- mathematical modeling and computer simulation of selected processes

- computer simulation and visualization of results with computer tools


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



Predmet je usmerjen v obravnavo bioloških procesov na ravni človeškega organizma in populacije s stališča modeliranja in simulacij, katerega poglavitni cilj je poglobljen študij izbranih procesov in njihova aplikacija v zdravstvu z metodami matematičnega modeliranja in računalniških simulacij.

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.



Znanje in razumevanje: Študent pridobi:

- poznavanje in razumevanje posameznih fizioloških procesov na ravni matematičnega modela;

- znanje o izbranih procesih v smislu poznavanja aktualne problematike, ki omogoča nadaljnje raziskave.

Knowledge and Understanding: 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.



• Predavanja

• Laboratorijske vaje

• Lectures

• Laboratory work



Assessment:


• Ustni izpit

• Praktično delo v laboratoriju in domače naloge

50 50


• Oral exam • Practical work in laboratory and

Homework


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. 2012: 2, brez avtocitatov: 2, normirano št. citatov: 1 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


Predmet: Napredne raziskovalne metode v bioinformatiki

Course title: Advanced research methodology in bioinformatics




Semester Semester



Bioinformatics 2 4



Predavanja Lectures

Seminar Seminar

Sem. vaje Tutorial




ECTS

15 30 105 6

Nosilec predmeta / Lecturer: Izr. prof. dr. Gregor Štiglic

Jeziki / Languages:




Prerequisits:

Ni pogojev. None.

Vsebina:


Študent pridobi poglobljena znanja s področja metodologije znanstvenega dela, kvantitativnega in kvalitativnega raziskovanja.

Ta predmet je namenjen pripravi študentov za izvajanje visoko kakovostnih raziskav s področja bioinformatike.

Na primerih s področja bioinformatike bodo študentje nadgradili svoje znanje z naprednimi metodami kvalitativne in kvantitativne analize podatkov ter podatkovnega rudarjenja z uporabo programskega jezika R.

The student gets familiar with methodological issues and process of scientific research especially 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. Based on examples from bioinformatics, students will upgrade their knowledge on advanced methods of qualitative and quantitative data analysis using R programing language.


1. Kabacoff, R. (2011). R in Action. Manning Publications Co. (http://www.statmethods.net). 2. Teetor, P. (2011). R cookbook. O'Reilly Media, Inc. (http://www.cookbook-r.com/). 3. Adler, J. (2010). R in a Nutshell, A Desktop Quick Reference, O'Reilly Media, 2010

(http://web.udl.es/Biomath/Bioestadistica/R/Manuals/r_in_a_nutshell.pdf). 4. Garrett, G., Hadley, W. (2016) R for Data Science, O'Reilly (http://garrettgman.github.io/). 5. Hadley W. (2014) Advanced R, Chapman and Hall/CRC (http://adv-r.had.co.nz/).



Študent: - obvlada napredne raziskovalne paradigme

in raziskovalne pristope, ki oblikujejo bioinformatiko in

- spozna pomen in značilnosti raziskovanja in raziskovalnega dela v bioinformatiki;

Ob uspešnem zaključku tega predmeta bodo študenti:

• Poznali postopke za načrtovanje kvalitativnega in kvantitativnega raziskovanja s posebnim poudarkom na temah, ki so zanimive za bioinformatiko;

• Obvladali uporabo različnih tehnik in metod zbiranja in analiziranja kvalitativnih in kvantitativnih podatkov.

• Poznali pristope, ki so nujno potrebni za učinkovito širjenje in vrednotenje kvalitativnega in kvantitativnega raziskovanja.

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 course students will:

• Know the process of qualitative and quantitative research design, with particular emphasis on bioinformatics related topics.

• Become skilled in the use of a range of techniques for the collection and analysis of qualitative and quantitative data.

• Know how to use approaches essential for the effective dissemination and evaluation of qualitative and quantitative research.




− Poznavanje napredne raziskovalne metodologije in raziskovalnih pristopov;

− Usposobljenost za samostojno kvalitativno in kvantitativno raziskovanje;

Študent bo sposoben samostojno oblikovati in sporočati svoja opažanja in svoje rezultate ter se vključevati v aktivno objavljanje raziskovalnih prispevkov na področju bioinformatike.


− 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 in the field of bioinformatics.

http://www.statmethods.net/

http://www.cookbook-r.com/

http://web.udl.es/Biomath/Bioestadistica/R/Manuals/r_in_a_nutshell.pdf

http://garrettgman.github.io/

http://adv-r.had.co.nz/



Predavanja, seminarji.

Lectures, seminars.



Assessment:

Način (pisni izpit, ustno izpraševanje, naloge, projekt) Projekt

100

Type (examination, oral, coursework, project): Project


Callahan, A., Pernek, I., Stiglic, G., Leskovec, J., Strasberg, H. R., & Shah, N. H. (2015). Analyzing Information Seeking and Drug-Safety Alert Response by Health Care Professionals as New Methods for Surveillance. Journal of medical Internet research, 17(8), e204. Stiglic, G., Wang, F., Davey, A., & Obradovic, Z. (2014). Pediatric Readmission Classification Using Stacked Regularized Logistic Regression Models. In AMIA Annual Symposium Proceedings (Vol. 2014, p. 1072). American Medical Informatics Association. Stiglic, G., Kocbek, S., Pernek, I., & Kokol, P. (2012). Comprehensive decision tree models in bioinformatics. PloS one, 7(3), e33812.


Predmet: Osnove molekularne in populacijske genetike

Course title: Basics of molecular and population genetics




Semester Semester



Bioinformatics 2 3



Predavanja Lectures

Seminar Seminar

Sem. vaje Tutorial




ECTS

15 30 90 6


Jeziki / Languages:




Prerequisits:

Poznavanje osnov molekularne biologije. Understanding basics of molecular biology

Vsebina:


• Osnove molekularne genetike: DNA struktura in lastnosti, replikacija (prokarionti, eukarionti), rekombinacija DNA, DNA popravljalni, mehanizmi, mehanizem nastanka DNA mutacij, organizacija, struktura in funkcija genov, struktura genoma (rastlinski, živalski in človeški), transkripcija, translacija, regulacija genske ekspresije

• Osnove dedovanja, kromosomska teorija dednosti, Mendlovo dedovanje, poligensko dedovanje

• Gensko mapiranje, mitohondrijski genom

• Mutacije, polimorfizmi v DNA in v proteinih, fenotip, genotip, alelna frekvenca, haplotipi, haplotiski bloki (projekt HapMap), Hardy-Weinbergov zakon, analiza genetske vezave, vezavno neravnotežje (linkage disequilibrium)

• 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

• Velikost in struktura populacije

• Naravni izbor, mutacije, genetski zdrs, genski pretok, parjenje v sorodstvu

• Molekularna evolucija, molekularna ura, nastanek genomov, genetika ogroženih vrst

• Kvantitativna genetika

• Genetsko testiranje posameznikov in populacije: metode genske tipizacije in določanja mutacij, genski testi v medicini (monogenske genetske bolezni, kompleksne genetske bolezni), preiskava DNA za tipizacijo tkiv in za osebno identifikacijo (forenzika)

• Vloga molekularne in populacijske genetike v sodobni družbi: etični, sociološki in ekonomski vidiki

• 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


• 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



Študenti bodo seznanjeni z osnovnimi koncepti populacijske genetike. Povdarek v razumevanju genetske raznolikosti populacije in evolucijsko pomebnih genov bo na interpretaciji novih informacij pridobljenih z modernimi pristopi molekularne genetike kot so sekvenciranje celotnih genomov in primerjalna genomika.

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.




• zakonitosti prenosa genetske informacije med generacijami

• povezave med genotipom in fenotipom

• dejavniki, ki vplivajo na frekvenco DNA polimorfizmov in genetsko raznolikost v različnih populacijah vloga mutacij in genetske raznolikosti v molekularni evouluciji


• 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



• Predavanja

• Seminarske vaje

• Lectures

• Tutorial



Assessment:


• pisni in



• writen and





Predmet: Proteinske strukture in proteomika

Course title: Proteine structures and proteomics




Semester Semester



Bioinformatics 2 3



Predavanja Lectures

Seminar Seminar

Sem. vaje Tutorial




ECTS

15 30 30 6

Nosilec predmeta / Lecturer: Prof. dr. Damjan Glavač

Jeziki / Languages:




Prerequisits:

Poznavanje osnov molekularne biologije, biokemije, molekularne genetike in bioinformatike

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

Vsebina:


• Osnove proteomike: osnovne definicije, izolacija proteinov, kromatografske metode, identifikacija in karakterizacija proteinov, elektroforeza, analiza gelov, masna spektrometrija, analiza sekvence proteinov, proteomske baze podatkov

• Osnove proteinske strukture: lastnosti aminokislin, peptidna vez, osnovni elementi proteinskih struktur, sile med molekulami, geometrija proteinov

• Sekundarne strukture proteinov in njihovi motivi, primeri alfa, beta in alfa-beta struktur

• Osnove zvijanja proteinov

• Struktura proteinov določa njihovo funkcijo: proteini ki se vežejo na DNK, primeri encimske katalize, membranski

• 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

proteini, prenos signalov, fibrilarni proteini, strukture molekul, ki sodelujejo pri imunskem odzivu, strukture virusov

• Interakcijska proteomika, proteinski kompleksi

• Določanje strukture proteinov: rentgenska kristalografija, NMR, elektronska mikroskopija, kristalizacija proteinov

• Strukturna genomika: osnovni principi in metode

• Načrtovanje zdravil na osnovi struktur proteinov, iskanje primernih tarčnih proteinov in silico, modeliranje proteinov

• Baza podatkov tridimenzionalnih struktur proteinov in uporaba le-te

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


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.



Cilj predmeta je študente sezaniti z osnovnimi principi struktur proteinov, proteomike in metodami, ki se pri tem uporabljajo.

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.



Znanje in razumevanje: Po uspešnem zaključku naj bi bil študent/ka sposoben:

• Opisati osnovne principe strukture proteinov, proteinske motive, lastnosti sekundarne strukture in zvijanja proteinov.

• Pojasniti zvezo med strukturo in funkcijo proteinov

• Opisati metode, ki se uporabljajo pri karakterizaciji proteinov in določanju njihove strukture ter razložiti kako se to lahko uporabi v industriji

Uporabljati računalniške programe za prikaz, primerjavo in analizo proteinskih struktur in te

Knowledge and understanding: 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,

strukture tudi interpretirati. analyse and interpret protein structures



• Predavanja

• Seminarske vaje

• Seminar

• Lectures

• Tutorials

• Seminar



Assessment:


• pisni in ustni izpit

• seminar

70 30


• writen and oral exemination

• seminar


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, brez avtocitatov: 0, normirano št. citatov: 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


Predmet: Rekombinantna DNA tehnologija

Course title: Recombinant DNA technology




Semester Semester



Bioinformatics 2 3



Predavanja Lectures

Seminar Seminar

Sem. vaje Tutorial




ECTS

15 30 105 6


Jeziki / Languages:




Prerequisits:

Poznavanje osnov molekularne biologije in molekularne genetike

Understanding basics of molecular biology and molecular genetics

Vsebina:


• Kloniranje: Gostiteljski organizmi, vektorji, strategije kloniranja v prokariontske in evkariontske orgnizme, transformacija in transfekcija, ekspresija rekombinantnih proteinov

• Priprava genomskih in cDNA knjižnic

• Hibridizacije nukleinskih kislin, mikromreže

• Pomnoževanje molekul DNA v pogojih in vitro (PCR), Sekvenciranje DNA

• Dvohibridni kvasni sistem za določanje interakcij protein-protein

• Spreminjanje genov - in vitro mutageneza, živalski modeli z izbitim genom-pomen v funkcijski genomiki in bolezenskih modelih

• Preprečevanje izražanja genov - protismiselna tehnologija, siRNA

• Kloniranje človeških genov, reproduktivno kloniranje sesalcev, terapeutsko kloniranje

• 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

• Transgene rastline in živali

• Preiskava DNA za tipizacijo tkiv in za osebno identifikacijo

• Genska tehnologija pri proizvodnji zdravil in diagnostičnih sredstev

• Zakonodaja in varnostni predpisi za delo z genetsko spremenjenimi organizmi

• Vloga rekombinantne DNA tehnologije v sodobni družba: etični, sociološki in ekonomski vidiki

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


5. Bernard R. Glick, Jack J. Pasternak: Principles and applications of recombinant DNA, 3rd edition, ASM Press, Washington, 2003

6. Sandy Primrose, Richard Twyman, Bob Old: Principles of Gene Manipulation, 6th edition, Blackwell Science, Oxford, 2001



Študenti bodo spoznali osnovne tehnike in uporabo rekombinantne DNA tehnologije v raziskavah in v praksi.

Students will be provided with basic techniques and applications of recombinant DNA technology in research and industry.




• tehnike in principi kloniranja DNA in ostalih pristopov v rekombinanti DNA tehnologiji

• uporaba rekombinantne DNA tehnologije v raziskavah in praksi


• techiques and principals of DNA cloning and other recombinant DNA technology

• applications of recombinant DNA technology in research and industry



• Predavanja

• Seminarske vaje

• Lectures

• Tutorial



Assessment:


• pisni in



• writen and





Predmet: Seminar

Course title: Seminar




Semester Semester



Bioinformatics 2 2

Vrsta predmeta / Course type


Predavanja Lectures

Seminar Seminar

Sem. vaje Tutorial




ECTS

30 195 9

Nosilec predmeta / Lecturer: Visokošolski učitelji na študijskem programu

Jeziki / Languages:




Prerequisits:

Ni pogojev. No prerequisites.

Vsebina:


Glede na izbrane izbirne predmete ter magistrsko temo bo določena tudi vsebina seminarja, ki bo zajemala predvsem individualno raziskovalno delo. Individualno raziskovalno delo bo študent opisal v poročilu. Poročilo zajema 20-25 strani in bo oblikovano podobno kot magistrska naloga.

Dependent on selected subjects and the theme of master work the content will be defined. The content will consist mainly on the individual research work. Student will present the individual research work in the report, structured in the same manner as master thesis (20-25 pages).


Relevantna literatura s področja seminarske naloge. / Relevant literature from the topic of the coursework.



Pripraviti študenta za individualno raziskovalno delo in uporabo teoretskih konceptov v praksi. V seminarski nalogi študent pokaže sposobnost izbire in uporabe domače ter tuje strokovne literature in dodatnih virov za potrebe rešitve izbranega problema. Strokovno zapisovanje in izražanje vsebine, obvladanje reševanja strokovnih problemov, predstavitev ključnih spoznanj in spretnost argumentiranja.

Prepare student on individual research work and to apply theoretical backgrounds in practical work. In coursework the student presents the ability to choose and use his national and foreign professional literature and additional sources in order to solve the chosen problem. Documenting and expressing the subject in a professional way, mastering the solving of the professional problems, independent presentation of the conclusions and ability in arguing.



Znanje in razumevanje: Znanje širšega strokovnega področja, v katerega sodi seminarska naloga in ožje znanje ter razumevanje pojmovnika, ki ga zajema tema. Poudarek je na praktičnih znanjih in enostavnejših metodologijah zajemanja, obdelovanja in prikazovanja podatkov.

Knowledge and understanding: Knowledge of the broader professional field to which belongs the coursework and special knowledge of the corresponding glossary. The emphasis is on the practical skills and relatively more simple methodologies of collecting, processing and presenting data.



Mentor na konzultacijah preverja vsebinski in strukturni vidik naloge.

The content and the structural aspect of the coursework is monitored by tutor during his consultations.



Assessment:

Način (pisni izpit, ustno izpraševanje, naloge, projekt) Ustna predstavitev seminarske naloge Pisni izdelek seminarske naloge

30 % 70 %

Type (examination, oral, coursework, project): Oral presentation of coursework. Written presentation of coursework.


Predmet: Teoretična biofizika

Course title: Theoretical Biophysics




Semester Semester



Bioinformatics 2 3



Predavanja Lectures

Seminar Seminar

Sem. vaje Tutorial

Lab. vaje Laboratory

work



ECTS

30 15 15 90 6

Nosilec predmeta / Lecturer: Doc. dr. Aleš Fajmut

Jeziki / Languages:




Prerequisits:

Potrebno je formalno ali neformalno znanje pridobljeno pri predmetu Osnove biofizike in Molekularna biofizika.

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

Vsebina:


Splošni opis predmeta: Vsebina predmeta bo temeljila na aplikaciji najnovejših teoretičnih (fizikalnih, kemijskih, matematičnih in računalniških) metod in orodij na biološko orientirane probleme in situacije. Obravnavano bo delovanje različnih kompleksnih bioloških sistemov, kot so metabolični sistemi, signalne mreže, organele, celice, organi, organizmi in populacije z vidika študija in obravnave delovanja njegovih sestavnih delov. Na podlagi razumevanja odnosov in interakcij med pod enotami kompleksnejšega sistema bo na ta način mogoče sklepati tudi na delovanje sistema kot celote. Vsebina predavanj:

- UVOD: (fizikalni in matematični principi,

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

delo z računalniškimi orodji za matematično modeliranje in delo z bazami podatkov)

- STANDARDNI PRISTOPI K MODELIRANJU BIOLOŠKIH SISTEMOV: (biokemijska in encimska kinetika, metabolične mreže, kontrolna analiza, signalne mreže)

- IZBRANI PRIMERI MODELIRANJA BIOLOŠKIH SISTEMOV: (oscilacije v bioloških sistemih, prenos signalov, krčenje mišic, modeliranje delovanja celic, celostno modeliranje celice, celični cikel, staranje, ekspresija genov, evolucija in samoorganizacija)

Vsebina seminarja: Študent izbere eno izmed tem, ki jih razpiše predavatelj. Projektna naloga ima obliko krajšega znanstvenega prispevka. Študent po izdelavi in predavateljevem pregledu naloge pripravi predstavitev pred kolegi. Vsebina laboratorijskih vaj:

- spoznavanje z računalniškimi orodji, kot so npr. Mathematica, MatLab, Madonna, Gepasi, PLAS, Model Maker, Virtual Cell…

- delo z računalniškimi podatkovnimi bazami in orodji na svetovnem spletu kot so npr. BRENDA, Swiss-Prot, TrEMBL, UniProt…

- modeliranje izbranih bioloških sistemov - reševanje matematičnih modelov in

vizualizacija rezultatov s pomočjo računalniških orodij

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


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



- Pri študentih razviti razumevanje kako in zakaj je teoretični pristop k obravnavi bioloških sistemov koristen za razvoj novih eksperimentov

- Študentom prikazati kako lahko dajo teoretični rezultati nov vpogled v delovanje

- 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.

bioloških sistemov - Študente seznaniti z aktualnimi

raziskovalnimi teoretičnimi metodami s področja bio-znanosti

Študent spozna, da se da z matematičnim modeliranjem preizkušati hipoteze, ki izhajajo s področja molekularne biologije, fiziologije ali biokemije. Študentje bodo zapustili predmet z zmožnostjo boljšega identificiranja pomembnih nerešenih problemov v bio-znanostih in z zmožnostjo ocenitve kako izbrati in rešiti probleme pri katerih je teoretični in kvantitativni pristop smiseln in produktiven.

- 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.



Znanje in razumevanje: Študent pridobi:

- poznavanje in razumevanje fizikalnih, kemijskih, matematičnih in računalniških metod, ki se uporabljajo pri teoretičnem študiju bioloških sistemov;

- zmožnost dela s predstavljenimi računalniškimi orodji in poznavanje drugih;

- razumevanje obravnavanih teoretičnih primerov, poznavanje njihovih prednosti in slabosti ter seznanjenost z drugimi podobnimi primeri.


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.



• Predavanja

• Seminar

• Laboratorijske vaje

• Lectures

• Seminar

• Laboratory work



Assessment:


• Ustno in pisno

• Praktično delo v laboratoriju in domače naloge

• Seminarska naloga

40 30 30


• Oral

• Written

• Project


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. 2012: 2, brez avtocitatov: 2, normirano št. citatov: 1 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:


Predmet: Teorija kompleksnosti s kaosom

Course title: Complexity theory and chaos




Semester Semester



Bioinformatics 2 3



Predavanja Lectures

Seminar Seminar

Sem. vaje Tutorial




ECTS

15 30 105 6

Nosilec predmeta / Lecturer: Prof. dr. Peter Kokol

Jeziki / Languages:




Prerequisits:

Ni pogojev.

None.

Vsebina:


− Zgodovina

− Koncepti teorije sistemov

− Definicija kompleksnosti.

− Teorija kompleksnosti.

− Teorija kaosa

− Kompleksni sistemi in teorija kaosa uporabni v računalništvu.

− Kompleksni sistemi in teorija kaosa uporabni v biologiji

− Kompleksni sistemi in teorija kaosa uporabni v ekonomiji

− Aplikacije kompleksnih sistemov in teorije kaosa v bionformatiki

− Mehka teorija sistemov.

− Uporaba mehke teorije sistemov pri odločanju, reševanju konfliktnih položajev in načrtovanju.

− 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


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)



Prvi cilj predmeta je naučiti študente, kakšna je razlika med znanstvenim in sistemskim pristopom in nato metodologije in koncepte sistemskega pristopa, teorija kompleksnosti in teorije kaosa. Drugi, bolj pragmatičen cilj je naučiti študente uporabe zgornjih teorij pri praktičnih primerih iz bioinformatike. Študentje morajo dojeti Aristotelov izrek, ki pravi, da je celota več, kot le vsota njenih posameznih delov.

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.



Znanje in razumevanje: Študent:

− Razume razliko med znanstvenim in sistemskim pristopom

− Študent razume Aristotelov izrek

− Sistem pridobi kompetence iz teorije sistemov, teorije kompleksnosti in teorije kaosa

− Študent ima kompetence da naučene teorije uporabi v praktičnih primerih iz bioinformatike

Knowledge and understanding: 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



Predavanja, seminarji, delavnice.

Lectures, seminar work, workshops.



Assessment:

Način (pisni izpit, ustno izpraševanje, naloge, projekt) Kolokviji Pisni izpit Projekt.

30 20 50

Type (examination, oral, coursework, project): Kolokviji Pisni izpit Projekt.


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-

http://www.amazon.com/gp/product/1843761971/sr=8-15/qid=1147505459/ref=sr_1_15/102-7687267-0241708?%5Fencoding=UTF8

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


Predmet: Vizualizacija znanstvenih podatkov

Course title: Scientific Visualisation




Semester Semester



Bioinformatics 2 3



Predavanja Lectures

Seminar Seminar

Sem. vaje Tutorial




ECTS

15 30 105 6

Nosilec predmeta / Lecturer: doc. dr. Domen Mongus

Jeziki / Languages:




Prerequisits:

Osnovna programerska znanja in poznavanje osnov algoritmov ter podatkovnih struktur.

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

Vsebina:


• Uvod: namen in cilji vizualizacije znanstvenih podatkov, zgodovinski pregled, modeli za znanstveno vizualizacijo, simulacija, animacija in navidezna resničnost.

• Osnove računalniške grafike in geometrijskega modeliranja: tehnike predstavitve geometrijskih objektov, geometrijske transformacije, projekcije, osnove upodabljanja.

• Vizualizacija informacij: 1D, 2D, 3D in 4D podatki, risanje dreves, mrež in grafov, interakcija z drevesi in grafi, skalarna in vektorska polja, “nefotorealistično” upodabljanje.

• Vizualizacija ploskovnih in volumetričnih podatkov: vizualizacija površja, direktno upodabljanje vokselskih podatkov, posredno upodabljanje vzorčenih objektov z

• 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:

rekonstrukcijo površja.

• Aplikacije znanstvene vizualizacije: vizualizacija kemijskih struktur v biologiji, kemiji in fiziki, vizualizacija pretakanja tekočin, geografska, geološka in meteorološka vizualizacija, vizualizacija v medicini.

• Vizualizacija v bioinformatiki: modeliranje in vizualizacija molekul, vizualizacija anatomije, vizualizacija sekvenc DNA .

• Programska oprema za vizualizacijo v bioinformatiki: pregled in uporaba programskih paketov za vizualizacijo struktur v bioinformatiki (Cn3D, Rasmol, Protein Explorer, Chime), analiza in primerjava paketov.

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.


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.



Cilj tega predmeta je obogatiti študentove praktične izkušnje rabe vizualizacije, organizirati, formalizirati in predvsem razširiti njegovo znanje o vizualizaciji s teoretskim ozadjem, s podatkovnimi tipi in algoritmi ter ga tako usposobiti za učinkovitejšo rabo, za razvoj in implementacijo sistemov za vizualizacijo znanstvenih podatkov.

• Spretnosti komuniciranja: ustno izražanje pri ustnem izpitu in zagovoru laboratorijskih vaj, pisanje poročila o opravljenem projektu.

• Uporaba informacijske tehnologije: uporaba sodobnih programov za vizualizacijo v bioinformatiki, sodobnih orodij za razvoj programske opreme in posebnih programskih knjižnic za vizualizacijo.

• Reševanje problemov: samostojno delo na projektu.

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.



Znanje in razumevanje: Po zaključku tega predmeta bo študent sposoben:

- izkazati poglobljeno znanje o principih, podatkovnih strukturah in algoritmih vizualizacije,

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

- demonstrate broad knowledge of visualisation principles, data types and

- izbrati ustrezno tehniko predstavitve in vizualizacije podatkov pri reševanju resničnih znanstvenih in inženirskih problemov,

- uporabiti teoretična znanja in praktične izkušnje pri učinkoviti rabi programske opreme za vizualizacijo v bioinformatiki,

- ovrednotiti uporabljivost obstoječe programske opreme v dani praktični situaciji in po potrebi načrtovati in implementirati lasten sistem.

- navesti in ilustrirati rabo znanstvene vizualizacije tudi na nekaterih drugih področjih (medicina, geografija, geologija, meteorologija...)

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...).



Predavanja, razgovor, demonstracija, računalniške vaje.

Lectures, discussions, demonstration, computer exercises.



Assessment:

Način (pisni izpit, ustno izpraševanje, naloge, projekt) - Naloge (računalniške vaje) - projekt (seminarska naloga), - ustni izpit.

30 20 50

Type (examination, oral, coursework, project): - coursework (computer exercises ) - projects (seminary work) - oral examination.


MONGUS, Domen, REPNIK, Blaž, MERNIK, Marjan, ŽALIK, Borut. A hybrid evolutionary algorithm for tuning a cloth-simulation model. Applied soft computing, Jan. 2012, vol. 12, iss. 1, str. 266-273, doi: 10.1016/j.asoc.2011.08.047. [COBISS.SI-ID 15310102], [JCR, WoS do 6. 10. 2012: št. citatov (TC): 1, čistih citatov (CI): 1, normirano št. čistih citatov (NC): 1, Scopus do 12. 7. 2012: št. citatov (TC): 1, čistih citatov (CI): 1, normirano št. čistih citatov (NC): 1] MONGUS, Domen, ŽALIK, Borut. Parameter-free ground filtering of LiDAR data for automatic DTM generation. ISPRS j. photogramm. remote sens.. [Print ed.], 2012, vol. 67, str. 1-12, ilustr., doi: 10.1016/j.isprsjprs.2011.10.002. [COBISS.SI-ID 15485718], [JCR, WoS do 6. 11. 2012: št. citatov (TC): 1, čistih citatov (CI): 1, normirano št. čistih citatov (NC): 1, Scopus do 2. 1. 2013: št. citatov (TC): 2, čistih citatov (CI): 1, normirano št. čistih citatov (NC): 3] MONGUS, Domen, ŽALIK, Borut. Efficient method for lossless LIDAR data compression. Int. j. remote sens. (Print). [Print ed.], 2011, vol. 32, no. 9, str. 2507-2518, doi: 10.1080/01431161003698385. [COBISS.SI-ID 14953494], [JCR, WoS do 6. 12. 2012: št. citatov (TC): 1, čistih citatov (CI): 0, normirano št. čistih citatov (NC): 0, Scopus do 20. 2. 2013: št. citatov (TC): 5, čistih citatov (CI): 2, normirano št. čistih citatov (NC): 1]


Predmet: Zdravstvena informatika

Course title: Health informatics




Semester Semester



Bioinformatics 2 3



Predavanja Lectures

Seminar Seminar

Sem. vaje Tutorial




ECTS

15 30 105 6

Nosilec predmeta / Lecturer: Prof. dr. Kokol Peter, prof. dr. Tatjana Welzer Družovec

Jeziki / Languages:




Prerequisits:

Znanja s področja računalništva in informatike.

Knowledge in computer science and informatics.

Vsebina:


- Informatika v zdravstvu in zdravstveni negi. - Inžinering zahtev, načrtovanje, modeliranje

in implementacija informacijskih sistemov - Baze podatkov v bionformatiki in

zdravstvu - Zagotavljanje kvalitete informacijskih

sistemov za zdravstvo in zdravstveno nego - Inteligentni sistemi. - Odločitvena drevesa v zdravstvu in

zdravstveni negi - Telemedicina - Pomen informatike pri organizaciji

delovnega procesa v zdravstvenih sistemih

- 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


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.



Študent:

− bo sposoben/a aktivno sodelovati pri razvoju informacijskih sistemov v zdravstvu in zdravstveni negi

Student: - will be capable to take an active part in

hospital information systems development.




− pozna pomembnosti informacije, informacijskih sistemov in informacijske tehnologijev zdravstvu in zdravstveni negi;

− razume pomembnost vloge vodilnih medicinskih sester pri razvoju informacijskih sistemov zdravstvene negi

− zna uporabljati teorijo razvoja informacijskih sistemov zdravstvene nege v praksi

Knowledge and understanding: - 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



Predavanja, seminarji, delavnice.

Lectures, seminar work, workshops.



Assessment:

Način (pisni izpit, ustno izpraševanje, naloge, projekt) Pisni izpit, projekt.

40 60

Type (examination, oral, coursework, project): Written exam, project.


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

http://www.amazon.com/gp/product/0071441972/sr=8-1/qid=1145800908/ref=pd_bbs_1/103-0765209-6154227?%5Fencoding=UTF8

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 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

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