Računska biologija

Opis predmeta

Biološka omrežja: gensko-regulatorna omrežja, signalna omrežja, metabolna omrežja.
Procesiranje informacij v bioloških sistemih.
Pristopi za računsko modeliranje bioloških sistemov: deterministično in stohastično modeliranje, agentno modeliranje, logično modeliranje, modeliranje na podlagi omejitev, modeliranje na nivoju genoma.
Simulacija dinamike bioloških sistemov.
Pristopi za računsko analizo bioloških sistemov: kvalitativna in kvantitativna analiza, preiskovanje prostora dopustnih vrednosti kinetičnih parametrov.
Hevristike za analizo in načrtovanje bioloških sistemov.
Kontekstno-specifično modeliranje in prilagajanje računskih modelov specifičnemu kontekstu.
Modeliranje populacij bioloških entitet z agentnimi modeli.
Dopolnjevanje eksperimentalnega dela z računalniškim modeliranjem in uporaba eksperimentalno pridobljenih podatkov pri postavitvi, dopolnjevanju in prilagajanju računskih modelov.
Uporaba računskih modelov pri interpretaciji eksperimentalnih podatkov.
Uporaba računskih modelov za generiranje novih podatkov in testiranje postavljenih hipotez.

Cilji in kompetence

Poznavanje računskih pristopov za modeliranje, simulacijo, analizo in načrtovanje bioloških sistemov. Sposobnost gradnje in prilagajanja računskih modelov pri reševanju specifičnih problemov. Uporaba računskih modelov v kombinaciji z eksperimentalnim delom za interpretacijo eksperimentalno-pridobljenih podatkov, generiranje novih podatkov in testiranje postavljenih hipotez.

Metode poučevanja in učenja

Seminarji, vaje, individualne konzultacije

Predvideni študijski rezultati

Znanje in razumevanje računskega modeliranja, analize in načrtovanja bioloških sistemov.

Reference nosilca

Miha Mraz

WALAKIRA, Andrew, ROZMAN, Damjana, REŽEN, Tadeja, MRAZ, Miha, MOŠKON, Miha. Guided extraction of genome-scale metabolic models for the integration and analysis of omics data. Computational and Structural Biotechnology Journal. 2021, vol. 19, str. 3521-3530, graf. prikazi. ISSN 2001-0370. https://www.sciencedirect.com/science/article/pii/S2001037021002476, DOI: 10.1016/j.csbj.2021.06.009. [COBISS.SI-ID 66227971]
MOŠKON, Miha, PUŠNIK, Žiga, ZIMIC, Nikolaj, MRAZ, Miha. Field-programmable biological circuits and configurable (bio)logic blocks for distributed biological computing. Computers in Biology and Medicine. [Print ed.]. Jan. 2021, vol. 128, str. 1-9, ilustr. ISSN 0010-4825. https://www.sciencedirect.com/science/article/abs/pii/S0010482520304406, DOI: 10.1016/j.compbiomed.2020.104109. [COBISS.SI-ID 37003267]
MOŠKON, Miha, KOMAC, Roman, ZIMIC, Nikolaj, MRAZ, Miha. Distributed biological computation : from oscillators, logic gates and switches to a multicellular processor and neural computing applications. Neural computing & applications. Aug. 2021, vol. 33, no. 15, str. 8923-8938, ilustr. ISSN 0941-0643. https://link.springer.com/article/10.1007/s00521-021-05711-6, DOI: 10.1007/s00521-021-05711-6. [COBISS.SI-ID 48415747]
BLAGOTINŠEK COKAN, Kaja, URLEP, Žiga, MOŠKON, Miha, MRAZ, Miha, KONG, Xiang Y., ESKILD, Winnie, ROZMAN, Damjana, JUVAN, Peter, REŽEN, Tadeja. Common transcriptional program of liver fibrosis in mouse genetic models and humans. International journal of molecular sciences. 2021, vol. 22, iss. 2, str. 1-21, ilustr. ISSN 1422-0067. https://www.mdpi.com/1422-0067/22/2/832, DOI: 10.3390/ijms22020832. [COBISS.SI-ID 47324419]
PUŠNIK, Žiga, MRAZ, Miha, ZIMIC, Nikolaj, MOŠKON, Miha. Computational analysis of viable parameter regions in models of synthetic biological systems. Journal of biological engineering. Sep. 2019, vol. 13, str. 1-21, graf. prikazi. ISSN 1754-1611. https://jbioleng.biomedcentral.com/articles/10.1186/s13036-019-0205-0, DOI: 10.1186/s13036-019-0205-0. [COBISS.SI-ID 1538345411]
MAGDEVSKA, Lidija, MRAZ, Miha, ZIMIC, Nikolaj, MOŠKON, Miha. Initial state perturbations as a validation method for data-driven fuzzy models of cellular networks. BMC bioinformatics. Sep. 2018, vol. 19, str. 1-7, graf. prikazi. ISSN 1471-2105. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2366-0, DOI: 10.1186/s12859-018-2366-0. [COBISS.SI-ID 1537917379]

Aleš Belič

KISS, Ádám, BELIČ, Aleš, et al. Phenoconversion of CYP2D6 by inhibitors modifies aripiprazole exposure. European archives of psychiatry and clinical neuroscience. 2020, vol. 270, str. 71-82. ISSN 0940-1334. DOI: 10.1007/s00406-018-0975-2. [COBISS.SI-ID 30244611]
BRINC, Matjaž, BELIČ, Aleš. Optimization of process conditions for mammalian fed-batch cell culture in automated micro-bioreactor system using genetic algorithm. Journal of biotechnology. [Print ed.]. 2019, vol. 300, str. 40-47. ISSN 0168-1656. DOI: 10.1016/j.jbiotec.2019.05.001. [COBISS.SI-ID 30237187]
TÓTH, Katalin, BELIČ, Aleš, et al. Potential role of patients' CYP3A-status in clozapine pharmacokinetics. The international journal of neuropsychopharmacology. 2017, vol. 20, issue 7, str. 529-537. ISSN 1461-1457. DOI: 10.1093/ijnp/pyx019. [COBISS.SI-ID 1358686]
KANDUŠER, Maša, BELIČ, Aleš, ČOROVIĆ, Selma, ŠKRJANC, Igor. Modular Serial Flow Through device for pulsed electric field treatment of the liquid samples. Scientific reports. 2017, 7, art. no. 8115, str. 1-12, ilustr. ISSN 2045-2322. https://www.nature.com/articles/s41598-017-08620-8, DOI: 10.1038/s41598-017-08620-8. [COBISS.SI-ID 11793492]

Miha Moškon

WALAKIRA, Andrew, ROZMAN, Damjana, REŽEN, Tadeja, MRAZ, Miha, MOŠKON, Miha. Guided extraction of genome-scale metabolic models for the integration and analysis of omics data. Computational and Structural Biotechnology Journal. 2021, vol. 19, str. 3521-3530, graf. prikazi. ISSN 2001-0370. https://www.sciencedirect.com/science/article/pii/S2001037021002476, DOI: 10.1016/j.csbj.2021.06.009. [COBISS.SI-ID 66227971]
MOŠKON, Miha, PUŠNIK, Žiga, ZIMIC, Nikolaj, MRAZ, Miha. Field-programmable biological circuits and configurable (bio)logic blocks for distributed biological computing. Computers in Biology and Medicine. [Print ed.]. Jan. 2021, vol. 128, str. 1-9, ilustr. ISSN 0010-4825. https://www.sciencedirect.com/science/article/abs/pii/S0010482520304406, DOI: 10.1016/j.compbiomed.2020.104109. [COBISS.SI-ID 37003267]
MOŠKON, Miha, KOMAC, Roman, ZIMIC, Nikolaj, MRAZ, Miha. Distributed biological computation : from oscillators, logic gates and switches to a multicellular processor and neural computing applications. Neural computing & applications. Aug. 2021, vol. 33, no. 15, str. 8923-8938, ilustr. ISSN 0941-0643. https://link.springer.com/article/10.1007/s00521-021-05711-6, DOI: 10.1007/s00521-021-05711-6. [COBISS.SI-ID 48415747]
BLAGOTINŠEK COKAN, Kaja, URLEP, Žiga, MOŠKON, Miha, MRAZ, Miha, KONG, Xiang Y., ESKILD, Winnie, ROZMAN, Damjana, JUVAN, Peter, REŽEN, Tadeja. Common transcriptional program of liver fibrosis in mouse genetic models and humans. International journal of molecular sciences. 2021, vol. 22, iss. 2, str. 1-21, ilustr. ISSN 1422-0067. https://www.mdpi.com/1422-0067/22/2/832, DOI: 10.3390/ijms22020832. [COBISS.SI-ID 47324419]
KOVAČ, Urša, ŽUŽEK, Zala, RASPOR DALL'OLIO, Lucija, POHAR, Katka, IHAN, Alojz, MOŠKON, Miha, ROZMAN, Damjana, STARČIČ ERJAVEC, Marjanca. Escherichia coli affects expression of circadian clock genes in human hepatoma cells. Microorganisms. 2021, vol. 9, iss. 4, str. 1-14. ISSN 2076-2607. https://www.mdpi.com/2076-2607/9/4/869, DOI: 10.3390/microorganisms9040869. [COBISS.SI-ID 61091843]
MOŠKON, Miha. CosinorPy : a Python package for cosinor-based rhythmometry. BMC bioinformatics. Oct. 2020, vol. 21, str. 1-12, graf. prikazi. ISSN 1471-2105. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03830-w, DOI: 10.1186/s12859-020-03830-w. [COBISS.SI-ID 34886403]

Temeljni viri in literatura

Alon, Uri. (2006) An introduction to systems biology: design principles of biological circuits. Chapman and Hall/CRC.
BØ, P. (2015) Systems Biology: Constraint-Based Reconstruction and Analysis. Cambridge University Press; 1st edition.
Ingalls, B. P. (2013). Mathematical modeling in systems biology: an introduction. MIT press.
Sneppen, K. (2014). Models of life. Cambridge University Press.
Klipp, E., Liebermeister, W., Wierling, C., & Kowald, A. (2016). Systems biology: a textbook. John Wiley & Sons.

Ostalo: revijski članki s področja, tekoča periodika in druga učna gradiva.