UČNI NAČRTI ŠTUDIJSKO LETO

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 Bioinformatika 2. stopnja Bioinformatika 2 3 Bioinformatics 2 nd degree Bologna Bioinformatics Study programme 2 3 Vrsta predmeta / Course type Obvezni predmet / Obligatory subject Univerzitetna koda predmeta / University course code: Predavanja Lectures Sem. vaje Tutorial Lab. vaje Laboratory work Teren. vaje Field work Samost. delo Individ. work 30 30 90 6 ECTS Nosilec predmeta / Lecturer: Izr. prof. dr. Uroš Potočnik Jeziki / Languages: Predavanja/Lectures: Vaje / Tutorial: Pogoji za vključitev v delo oz. za opravljanje študijskih obveznosti: Poznavanje osnov molekularne biologije, biokemije, humane genetike in bioinformatike Prerequisits: Understanding basics of molecular biology, biochemistry, human genetics and bioinformatics Vsebina: 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 Content (Syllabus outline): 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: 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. Objectives and competences: 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: Znanje in razumevanje: metodika mapiranja bolezenskih genov funkcija in vloga genov v patogenezi bolezni Intended learning outcomes: Knowledge and understanding: approaches for identification and mapping of disease gene gene function and their role in pathogenesis Metode poučevanja in učenja: Predavanja ske vaje Learning and teaching methods: Lectures Tutorial Načini ocenjevanja: Način (pisni izpit, ustno izpraševanje, naloge, projekt) pisni in ustni izpit Delež (v %) / Weight (in %) 60 40 Assessment: 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

UČNI NAČRT PREDMETA / COURSE SYLLABUS Predmet: DNA mikromreže in analiza ekspresije genov Course title: DNA micro nets and analyze of expressions of genes Študijski program in stopnja Study programme and level Študijska smer Study field Letnik Academic year Bioinformatika 2. stopnja Bioinformatika 2 3 Bioinformatics 2 nd degree Bologna Bioinformatics Study programme 2 3 Vrsta predmeta / Course type Obvezni predmet / Obligatory subject Univerzitetna koda predmeta / University course code: Predavanja Lectures Sem. vaje Tutorial Lab. vaje Laboratory work Teren. vaje Field work Samost. delo Individ. work ECTS 15 45 90 6 Nosilec predmeta / Lecturer: Izr. prof. dr. Uroš Potočnik Jeziki / Languages: Predavanja/Lectures: Vaje / Tutorial: Pogoji za vključitev v delo oz. za opravljanje študijskih obveznosti: Poznavanje osnov molekularne biologije, biokemije, humane genetike in bioinformatike Prerequisits: Understanding basics of molecular biology, biochemistry, human genetics and bioinformatics 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 Content (Syllabus outline): Regulation of gene expression: binding of transacting 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 Temeljni literatura in viri / 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 Cilji in kompetence: 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. Predvideni študijski rezultati: Znanje in razumevanje: 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 Objectives and competences: 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. Intended learning outcomes: Knowledge and understanding: 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. Metode poučevanja in učenja: Predavanja ske vaje Learning and teaching methods: 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/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

UČNI NAČRT PREDMETA / COURSE SYLLABUS Predmet: Farmakogenomika Course title: Pharmacogenomics Študijski program in stopnja Study programme and level Študijska smer Study field Letnik Academic year Bioinformatika 2. stopnja Bioinformatika 2 3 Bioinformatics 2 nd degree Bologna Study programme Bioinformatics 2 3 Vrsta predmeta / Course type Izbirni predmet/ Optional subject Univerzitetna koda predmeta / University course code: Predavanja Lectures Sem. vaje Tutorial Lab. vaje Laboratory work Teren. vaje Field work Samost. delo Individ. work ECTS 15 30 105 6 Nosilec predmeta / Lecturer: Izr. prof. dr. Uroš Potočnik Jeziki / Languages: Predavanja/Lectures: Vaje / Tutorial: Pogoji za vključitev v delo oz. za opravljanje študijskih obveznosti: Poznavanje osnov molekularne biologije, biokemije, humane genetike in bioinformatike Prerequisits: Understanding basics of molecular biology, biochemistry, human genetics and bioinformatics 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 Content (Syllabus outline): The students will be provided with information about the state of art technology and bioinformatic tools in pharmacogenomic research including highthroughput 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. Temeljni literatura in viri / 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. Cilji in kompetence: 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. Predvideni študijski rezultati: Znanje in razumevanje: Študentje bodo razumeli molekularno genetske in biokemijske mehanizme, ki pogojujejo raznolik odziv na zdravila Objectives and competences: 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. Intended learning outcomes: Knowledge and understanding: students will understant molecular genetic and biochemical mechanisms underlying variation in drug response among different individuals Metode poučevanja in učenja: Predavanja ske vaje Learning and teaching methods: Lectures Tutorial

Načini ocenjevanja: Način (pisni izpit, ustno izpraševanje, naloge, projekt) pisni in ustni izpit Delež (v %) / Weight (in %) 60 40 Assessment: 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

UČNI NAČRT PREDMETA / COURSE SYLLABUS Predmet: Humana molekularna genetika-izbrana poglavja Course title: Human moleclar genetics-selcted topics Študijski program in stopnja Study programme and level Študijska smer Study field Letnik Academic year Bioinformatika 2. stopnja Bioinformatika 2 3 Bioinformatics 2 nd degree Bologna Study programme Bioinformatics 2 3 Vrsta predmeta / Course type Izbirni predmet/ Optional subject Univerzitetna koda predmeta / University course code: Predavanja Lectures Sem. vaje Tutorial Lab. vaje Laboratory work Teren. vaje Field work Samost. delo Individ. work ECTS 15 15 15 105 6 Nosilec predmeta / Lecturer: Prof. dr. Damjan Glavač Jeziki / Languages: Predavanja/Lectures: Vaje / Tutorial: Pogoji za vključitev v delo oz. za opravljanje študijskih obveznosti: Poznavanje osnov molekularne biologije, biokemije, humane genetike in bioinformatike 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 Content (Syllabus outline): 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

Temeljni literatura in viri / Readings: 1. STRACHAN T and READ AP: Human Molecular genetics, Gerland Publish, Inc., New York, 3rd ed., 2004 2. Tekoča periodika Cilji in kompetence: 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 Predvideni študijski rezultati: Znanje in razumevanje: 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 Objectives and competences: 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. Intended learning outcomes: Knowledge and understanding: 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 Metode poučevanja in učenja: Predavanja ske vaje Learning and teaching methods: Lectures Tutorial Načini ocenjevanja: Način (pisni izpit, ustno izpraševanje, naloge, projekt) pisni in ustni izpit Delež (v %) / Weight (in %) 60 40 Assessment: Type (examination, oral, coursework, project): writen and oral exemination Reference nosilca / Lecturer's references: 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 epithelialmesenchymal 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

UČNI NAČRT PREDMETA / COURSE SYLLABUS Predmet: MAGISTRSKA NALOGA Course title: Master Thesis Študijski program in stopnja Study programme and level Študijska smer Study field Letnik Academic year Bioinformatika 2. stopnja Bioinformatika 2 2 Bioinformatics 2 nd degree Bologna Study programme Bioinformatics 2 2 Vrsta predmeta / Course type Univerzitetna koda predmeta / University course code: Predavanja Lectures Sem. vaje Tutorial Lab. vaje Laboratory work Teren. vaje Field work Samost. delo Individ. work ECTS 375 15 Nosilec predmeta / Lecturer: Izbrani mentor/ Mentor selected Jeziki / Languages: Predavanja/Lectures: Vaje / Tutorial: Pogoji za vključitev v delo oz. za opravljanje študijskih obveznosti: Študent lahko prijavi magistrsko nalogo na osnovi predpisanih pogojev v pravilniku. Prerequisits: 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. Content (Syllabus outline): The official procedure of the preparation of the Master Thesis accordingly Statute of University of Maribor and regulations of FHS UM. Temeljni literatura in viri / Readings: Relevantna literatura s področja magistrske naloge. / Relevant literature from the topic of the Master Thesis. Cilji in kompetence: Cilji so definirani v prijavi teme magistrske naloge. Objectives and competences: The objectives are defined in the application for the approval of the topic of the Master Thesis.

Predvideni študijski rezultati: 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. Prenesljive/ključne spretnosti in drugi atributi: Strokovno zapisovanje in izražanje vsebine, obvladanje reševanja strokovnih problemov, suverena predstavitev ključnih spoznanj in spretnost argumentiranja. Metode poučevanja in učenja: Vodeno individualno raziskovalno delo. Intended learning outcomes: 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. 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. Learning and teaching methods: Guided individual research work. Načini ocenjevanja: Magistrska naloga Zagovor Delež (v %) / Weight (in %) 70% 30% Assessment: Master Thesis Presentation

Predmet: Course title: UČNI NAČRT PREDMETA / COURSE SYLLABUS Matematično modeliranje in simulacije v zdravstvu Mathematical Modeling and Simulations in Health Science Študijski program in stopnja Študijska smer Letnik Study programme and level Study field Academic year Bioinformatika 2. stopnja Bioinformatika 2 3 Bioinformatics 2nd degree Bologna Study programme Bioinformatics 2 3 Vrsta predmeta / Course type Izbirni predmet / Optional subject Univerzitetna koda predmeta / University course code: Predavanja Lectures Sem. vaje Tutorial Lab. vaje Laboratory work Teren. vaje Field work Samost. delo Individ. work 15 30 105 6 ECTS Nosilec predmeta / Lecturer: Doc. dr. Aleš Fajmut Jeziki / Languages: Predavanja / Lectures: slovenski/slovenian Vaje / Tutorial: slovenski/slovenian Pogoji za vključitev v delo oz. za opravljanje študijskih obveznosti: Ni pogojev. 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: Prerequisits: No prerequisites. Content (Syllabus outline): 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 - matematično modeliranje in računalniška

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 Temeljni literatura in viri / 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 Cilji in kompetence: 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. Predvideni študijski rezultati: 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. Objectives and competences: 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. Intended learning outcomes: 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. Metode poučevanja in učenja: Predavanja Laboratorijske vaje Načini ocenjevanja: Način (pisni izpit, ustno izpraševanje, naloge, projekt) Ustni izpit Praktično delo v laboratoriju in domače naloge Delež (v %) / Weight (in %) 50 50 Learning and teaching methods: Lectures Laboratory work Assessment: Type (examination, oral, coursework, project): Oral exam Practical work in laboratory and Homework Reference nosilca / Lecturer's references: 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 aspirinintolerant 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

UČNI NAČRT PREDMETA / COURSE SYLLABUS Predmet: Napredne raziskovalne metode v bioinformatiki Course title: Advanced research methodology in bioinformatics Študijski program in stopnja Study programme and level Študijska smer Study field Letnik Academic year Bioinformatika 2. stopnja Bioinformatika 2 4 Bioinformatics 2 nd degree Bologna Study programme Bioinformatics 2 4 Vrsta predmeta / Course type Obvezni predmet / Obligatory subject Univerzitetna koda predmeta / University course code: Predavanja Lectures Sem. vaje Tutorial Lab. vaje Laboratory work Teren. vaje Field work Samost. delo Individ. work ECTS 15 30 105 6 Nosilec predmeta / Lecturer: Izr. prof. dr. Gregor Štiglic Jeziki / Languages: Predavanja/Lectures: Vaje / Tutorial: Pogoji za vključitev v delo oz. za opravljanje študijskih obveznosti: Ni pogojev. 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. Prerequisits: None. Content (Syllabus outline): 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.

Temeljni literatura in viri / Readings: 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/). Cilji in kompetence: 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. Objectives and competences: 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. Predvideni študijski rezultati: Znanje in razumevanje: 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. Intended learning outcomes: Knowledge and understanding: 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.

Metode poučevanja in učenja: Predavanja, seminarji. Learning and teaching methods: Lectures, seminars. Načini ocenjevanja: Način (pisni izpit, ustno izpraševanje, naloge, projekt) Delež (v %) / Weight (in %) Projekt 100 Assessment: Type (examination, oral, coursework, project): Project Reference nosilca / Lecturer's references: 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.

UČNI NAČRT PREDMETA / COURSE SYLLABUS Predmet: Osnove molekularne in populacijske genetike Course title: Basics of molecular and population genetics Študijski program in stopnja Study programme and level Študijska smer Study field Letnik Academic year Bioinformatika 2. stopnja Bioinformatika 2 3 Bioinformatics 2 nd degree Bologna Study programme Bioinformatics 2 3 Vrsta predmeta / Course type Izbirni predmet/ Optional subject Univerzitetna koda predmeta / University course code: Predavanja Lectures Sem. vaje Tutorial Lab. vaje Laboratory work Teren. vaje Field work Samost. delo Individ. work ECTS 15 30 90 6 Nosilec predmeta / Lecturer: Izr. prof. dr. Uroš Potočnik Jeziki / Languages: Predavanja/Lectures: Vaje / Tutorial: Pogoji za vključitev v delo oz. za opravljanje študijskih obveznosti: Poznavanje osnov molekularne biologije. 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) Prerequisits: Understanding basics of molecular biology Content (Syllabus outline): 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 Temeljni literatura in viri / 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 Cilji in kompetence: 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. Predvideni študijski rezultati: Znanje in razumevanje: 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 Objectives and competences: 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. Intended learning outcomes: Knowledge and understanding: 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

Metode poučevanja in učenja: Predavanja ske vaje Learning and teaching methods: Lectures Tutorial Načini ocenjevanja: Način (pisni izpit, ustno izpraševanje, naloge, projekt) pisni in ustni izpit Delež (v %) / Weight (in %) 60 40 Assessment: 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

UČNI NAČRT PREDMETA / COURSE SYLLABUS Predmet: Proteinske strukture in proteomika Course title: Proteine structures and proteomics Študijski program in stopnja Study programme and level Študijska smer Study field Letnik Academic year Bioinformatika 2. stopnja Bioinformatika 2 3 Bioinformatics 2 nd degree Bologna Study programme Bioinformatics 2 3 Vrsta predmeta / Course type Izbirni predmet/ Optional subject Univerzitetna koda predmeta / University course code: Predavanja Lectures Sem. vaje Tutorial Lab. vaje Laboratory work Teren. vaje Field work Samost. delo Individ. work ECTS 15 30 30 6 Nosilec predmeta / Lecturer: Prof. dr. Damjan Glavač Jeziki / Languages: Predavanja/Lectures: Vaje / Tutorial: Pogoji za vključitev v delo oz. za opravljanje študijskih obveznosti: Poznavanje osnov molekularne biologije, biokemije, molekularne genetike in bioinformatike Prerequisits: 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 Content (Syllabus outline): 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