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DomovPredmetiBioinformacijska orodja in podatkovne zbirke

Bioinformacijska orodja in podatkovne zbirke

Vrsta predmeta: teoretični

Število kreditnih točk: 10

Semester izvajanja: Celoletni

Opis predmeta

– Bioinformacijske podatkovne zbirke: zaporedja nukleinskih kislin, proteinov, strukturne podatkovne zbirke, bibliografske podatkovne zbirke. Orodja za analizo zaporedij in struktur.

– Genomski projekti modelnih organizmov, primerjalna genomika, določevanje genov in regulatornih regij v genomih, SNP analize, genske mreže.

– Orodja v transkriptomiki in visoko-zmogljivostni genetiki.

– Bioinformacijska orodja v proteomiki in interaktomiki.

– Integrativna genomika.

– Aplikacije: bioinformatika v okoljski genomiki, farmakogenomiki.

– Ontologije in zbirke znanj v bioinformatiki.

– Bioinformacijski pristopi v kemogenomiki.

– Projektno delo s specifičnimi programskimi orodji med predavanji in v okviru seminarske naloge.

Cilji in kompetence

Seznanitev s celotnim področjem bioinformatike in trenutnimi trendi v razvoju bioinformatike. Predmet daje študentu pregled nad celotnim področjem bioinformatike in ga uvaja v raziskovalno delo na glavnih toriščih raziskav v bioinformatiki.

Metode poučevanja in učenja

Predavanja, projektno delom, praktične vaje z računalniki.

Predvideni študijski rezultati

Znanje in razumevanje:

Študenti bodo spoznali specifična bioinformacijska orodja, njihove omejitve in potrebe po njihovem izboljšanju glede na razvoj raziskav v genetiki, genomiki, proteomiki, sistemski in strukturni biologiji ter v evolucijskih študijah. Študenti se bodo tudi seznanili z naravo podatkov v bioloških raziskavah in z najpomembnejšimi biološkimi podatkovnimi zbirkami ter njihovo uporabo.

Reference nosilca

Jernej Jakše

  1. PRENTOUT, Djivan, ŠTAJNER, Nataša, ČERENAK, Andreja, TRICOU, Theo, BROCHIER-ARMANET, Céline, JAKŠE, Jernej, KÄFER, Jos, MARAIS, Gabriel A. B. Plant genera Cannabis and Humulus share the same pair of well-differentiated sex chromosomes. The New phytologist, ISSN 0028-646X, 2021, vol. , iss. , str., doi: 10.1111/nph.17456. [COBISS.SI-ID 63536131]
  2. GONZALEZ, Francisco, JIBIN, Johny, WALKER III, William B., GUAN, Qingtian, MFARREJ, Sara, JAKŠE, Jernej, MONTAGNÉ, Nicolas, JACQUIN-JOLY, Emmanuelle, ALQARNI, Abdulaziz A., MOHAMMED ALI, Al-Saleh, PAIN, Arnab, ANTONY, Binu. Antennal transcriptome sequencing and identification of candidate chemoreceptor proteins from an invasive pest, the American palm weevil, Rhynchophorus palmarum. Scientific reports, ISSN 2045-2322, 2021, vol. 11, str. 1-14 (8334), ilustr. https://www.nature.com/articles/s41598-021-87348-y, doi: 10.1038/s41598-021-87348-y. [COBISS.SI-ID 60452099]
  3. ŠTAJNER, Nataša, RADIŠEK, Sebastjan, KUMAR MISHRA, Ajay, NATH, Vishnu Sukumari, MATOUŠEK, Jaroslav, JAKŠE, Jernej. Evaluation of Disease Severity and Global Transcriptome response Induced by Citrus bark cracking viroid, Hop latent viroid, and their co-infection in hop (Humulus lupulus L.). International journal of molecular sciences, ISSN 1422-0067, 2019, vol. 20, no. 13, str. 1-21 (3154), doi: 10.3390/ijms20133154. [COBISS.SI-ID 9268089]
  4. JESENIČNIK, Taja, ŠTAJNER, Nataša, RADIŠEK, Sebastjan, JAKŠE, Jernej. RNA interference core components identified and characterised in Verticillium nonalfalfae, a vascular wilt pathogenic plant fungi of hops. Scientific reports, ISSN 2045-2322, 2019, vol. 9, str. 1-12 (8651), ilustr. https://doi.org/10.1038/s41598-019-44494-8, doi: 10.1038/s41598-019-44494-8. [COBISS.SI-ID 9242233]
  5. NATH, Vishnu Sukumari, KUMAR MISHRA, Ajay, KUMAR, Atul, MATOUŠEK, Jaroslav, JAKŠE, Jernej. Revisiting the role of transcription factors in coordinating the defense response against citrus bark cracking viroid infection in commercial hop (Humulus Lupulus L.). Viruses, ISSN 1999-4915, 2019, vol. 11, iss. 5: 419, str. 1-19. https://doi.org/10.3390/v11050419. [COBISS.SI-ID 9229433]
  6. POKORN, Tine, RADIŠEK, Sebastjan, JAVORNIK, Branka, ŠTAJNER, Nataša, JAKŠE, Jernej. Development of hop transcriptome to support research into host-viroid interactions. PloS one, ISSN 1932-6203, Sep. 2017, vol. 12, iss. 9, 0184528. https://doi.org/10.1371/journal.pone.0184528. [COBISS.SI-ID 8793977]

 

Roman Jerala:

  1. GRADIŠAR, Helena, BOŽIČ, Sabina, DOLES, Tibor, VENGUST, Damjan, HAFNER BRATKOVIČ, Iva, MERTELJ, Alenka, WEBB, Ben, ŠALI, Andrej, KLAVŽAR, Sandi, JERALA, Roman. Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments. Nature chemical biology, ISSN 1552-4450, 2013, vol. 9, issue 6, str. 362-366, doi: 10.1038/nCHeMBIO.1248. [COBISS.SI-ID 5222682
  2. FEKONJA, Ota, AVBELJ, Monika, JERALA, Roman. Suppression of TLR signaling by targeting TIR domain-containing proteins. Current protein and peptide science, ISSN 1389-2037, 2012, vol. 13, no. 8, str. 776-788, doi: 10.2174/1389203711213080007. [COBISS.SI-ID 5167898]
  3. MANČEK KEBER, Mateja, BENČINA, Mojca, JAPELJ, Boštjan, PANTER, Gabriela, ANDRÄ, Jörg, BRANDENBURG, Klaus, TRIANTAFILOU, Martha, TRIANTAFILOU, Kathy, JERALA, Roman. MARCKS as a negative regulator of lipopolysaccharide signaling. The journal of immunology, ISSN 0022-1767, 2012, vol. 188, no. 8, str. 3893-3902. http://www.jimmunol.org/content/early/2012/03/16/jimmunol.1003605.abstract, doi: 10.4049/jimmunol.1003605. [COBISS.SI-ID 4930586]
  4. CONRADO, Robert J., LEBAR, Tina, TURNŠEK, Jernej, TOMŠIČ, Nejc, AVBELJ, Monika, GABER, Rok, KOPRIVNJAK, Tomaž, MORI, Jerneja, GLAVNIK, Vesna, VOVK, Irena, BENČINA, Mojca, HODNIK, Vesna, ANDERLUH, Gregor, JERALA, Roman, et al. DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency. Nucleic acids research, ISSN 0305-1048, 2012, vol. 40, no. 4, str. 1879-1889, ilustr. http://nar.oxfordjournals.org/content/early/2011/10/22/nar.gkr888.full.pdf+html, doi: 10.1093/nar/gkr888. [COBISS.SI-ID 4824602]
  5. MORI, Jerneja, VRANAC, Tanja, SMREKAR, Boštjan, ČERNILEC, Maja, ČURIN-ŠERBEC, Vladka, HORVAT, Simon, IHAN, Alojz, BENČINA, Mojca, JERALA, Roman. Chimeric flagellin as the self-adjuvanting antigen for the activation of immune response against Helicobacter pylori. Vaccine, ISSN 0264-410X. [Print ed.], 2012, vol. 30, issue 40, str. 5856-5863. http://www.sciencedirect.com/science/article/pii/S0264410X12010134, doi: 10.1016/j.vaccine.2012.07.011. [COBISS.SI-ID 5023770]
  6. PANTER, Gabriela, JERALA, Roman. Ectodomain of the toll-like receptor 4 prevents constitutive receptor activation. The Journal of biological chemistry, ISSN 0021-9258, 2011, vol. 286, no. 26, str. 23334-23344, doi: 10.1074/jbc.M110.205419. [COBISS.SI-ID 4652570]

 

Tanja Kunej:

  1. ŠKRLJ, Blaž, ERŽEN, Nika, LAVRAČ, Nada, KUNEJ, Tanja, KONC, Janez. CaNDis: a web server for investigation of causal relationships between diseases, drugs, and drug targets. Bioinformatics, ISSN 1367-4803, 2021, vol. 36, no. 6, str. 885-887. doi: 10.1093/bioinformatics/btaa762. [COBISS.SI-ID 27212035]
  2. ŠKRLJ, Blaž, KUNEJ, Tanja, KONC, Janez. Insights from ion binding site network analysis into evolution and functions of proteins. Molecular informatics, ISSN 1868-1743, 2018, vol. 37, 1700144, str. 1-11. doi: 10.1002/minf.201700144. [COBISS.SI-ID 4043912]
  3. ROZMAN, Vita, KUNEJ, Tanja. Harnessing omics big data in nine vertebrate species by genome-wide prioritization of sequence variants with the highest predicted deleterious effect on protein function. Omics: a journal of integrative biology, ISSN 1536-2310, 2018, vol. 22, no. 6, str. 410-421. doi: 10.1089/omi.2018.0046. [COBISS.SI-ID 4072584]
  4. URH, Kristian, KUNEJ, Tanja. Genome-wide screening for smallest regions of overlaps in cryptorchidism. Reproductive biomedicine online, ISSN 1472-6491, 2018, vol. 37, no. 1, str. 85-99. doi: 10.1016/j.rbmo.2018.02.008. [COBISS.SI-ID 4061320]
  5.  ŠKRLJ, Blaž, KONC, Janez, KUNEJ, Tanja. Identification of sequence variants within experimentally validated protein interaction sites provides new insights into molecular mechanisms of disease development. Molecular informatics, ISSN 1868-1743, 2017, vol. 36, no. 9, str. 1-8. doi: 10.1002/minf.201700017. [COBISS.SI-ID 3888008]
  6. KONC, Janez, ŠKRLJ, Blaž, ERŽEN, Nika, KUNEJ, Tanja, JANEŽIČ, Dušanka. GenProBiS: web server for mapping of sequence variants to protein binding sites. Nucleic acids research, ISSN 0305-1048, 2017, vol. 45, no. W1, str. W253-W259. doi: 10.1093/nar/gkx420. [COBISS.SI-ID 3897736]

 

Uroš Petrovič:

1.     GODEC, Primož, PANČUR, Matjaž, ILENIČ, Nejc, ČOPAR, Andrej, STRAŽAR, Martin, ERJAVEC, Aleš, PRETNAR, Ajda, DEMŠAR, Janez, STARIČ, Anže, TOPLAK, Marko, ŽAGAR, Lan, HARTMAN, Jan, HAMILTON, Wang, BELLAZZI, Riccardo, PETROVIČ, Uroš, GARAGNA, Silvia, ZUCCOTTI, Maurizio, PARK, Dongsu, SHAULSKY, Gad, ZUPAN, Blaž. Democratized image analytics by visual programming through integration of deep models and small-scale machine learning. Nature communications. 2019, vol. 10, str. 4551-1-4551-7. ISSN 2041-1723. DOI: 10.1038/s41467-019-12397-x. [COBISS.SI-ID 32755751]    

2.     ARHAR, Simon, GOGG-FASSOLTER, Gabriela, BRLOŽNIK, Mojca, PAČNIK, Klavdija, SCHWAIGER, Katharina, ŽGANJAR, Mia, PETROVIČ, Uroš, NATTER, Klaus. Engineering of Saccharomyces cerevisiae for the accumulation of high amounts of triacylglycerol. Microbial cell factories. 2021, no. 20, issue 1, str. 147-1-147-15. ISSN 1475-2859. DOI: 10.1186/s12934-021-01640-0. [COBISS.SI-ID 71619331]    

3.     MEIJNEN, Jean-Paul, RANDAZZO, Paola, FOULQUIÉ-MORENO, María R., BRINK, Joost van den, VANDECRUYS, Paul, STOJILJKOVIC, Marija, DUMORTIER, Françoise, ZALAR, Polona, BOEKHOUT, Teun, GUNDE-CIMERMAN, Nina, KOKOŠAR, Janez, ŠTAJDOHAR, Miha, CURK, Tomaž, PETROVIČ, Uroš, THEVELEIN, Johan M. Polygenic analysis and targeted improvement of the complex trait of high acetic acid tolerance in the yeast Saccharomyces cerevisiae. Biotechnology for biofuels. 2016, vol. 9, str. 1-18. ISSN 1754-6834. DOI: 10.1186/s13068-015-0421-x. [COBISS.SI-ID 29140775]    

4.     MATTIAZZI, Mojca, BRLOŽNIK, Mojca, KAFERLE, Petra, ŽITNIK, Marinka, WOLINSKI, Heimo, LEITNER, F., KOHLWEIN, Sepp D., ZUPAN, Blaž, PETROVIČ, Uroš. Genome-wide localization study of yeast Pex11 identifies peroxisome-mitochondria interactions through the ERMES complex. Journal of molecular biology. Jun. 2015, vol. 427, no. 11, str. 2072-2087, ilustr. ISSN 0022-2836. DOI: 10.1016/j.jmb.2015.03.004. [COBISS.SI-ID 28442663]    

5.     CURK, Tomaž, PETROVIČ, Uroš, SHAULSKY, Gad, ZUPAN, Blaž. Rule-based clustering for gene promoter structure discovery. Methods of information in medicine, ISSN 0026-1270, 2009, vol. 48, no. 3, str. 229-235. http://eprints.fri.uni-lj.si/897/. [COBISS.SI-ID 22605095]

6.     MATTIAZZI, Mojca, PRELEC, Metod, BRLOŽNIK, Mojca, PRIMO, Cecilia, CURK, Tomaž, ŠČANČAR, Janez, YENUSH, Lynne, PETROVIČ, Uroš. Yeast Saccharomyces cerevisiae adiponectin receptor homolog Izh2 is involved in the regulation of zinc, phospholipid and pH homeostasis. Metallomics. 2015, vol. 7, iss. 9, str. 1338-1351. ISSN 1756-5901. DOI: 10.1039/C5MT00095E. [COBISS.SI-ID 28620583]    

 

Cene Gostinčar:

  1. CONLON, Benjamin H., GOSTINČAR, Cene, FRICKE, Janis, KREUZENBECK, Nina B., DANIEL, Jan-Martin, SCHLOSSER, Malte S.L., PEEREBOOM, Nils, AANEN, Duur K., DE BEER, Z. Wilhelm, BEEMELMANNS, Christine, GUNDE-CIMERMAN, Nina, POULSEN, Michael. Genome reduction and relaxed selection is associated with the transition to symbiosis in the basidiomycete genus Podaxis. iScience. 2021, vol. 24, iss. 6, str. 1-20, ilustr. ISSN 2589-0042. https://www.sciencedirect.com/science/article/pii/S2589004221006489?via%3Dihub, DOI: 10.1016/j.isci.202102680. [COBISS.SI-ID 68516099], [JCR, SNIP, WoS, Scopus]
  2. TOUCHETTE, D., ALTSHULER, I., GOSTINČAR, Cene, ZALAR, Polona, RAYMOND-BOUCHARD, I., ZAJC, Janja, MCKAY, C. P., GUNDE-CIMERMAN, Nina, WHYTE, Lyle G. Novel Antarctic yeast adapts to cold by switching energy metabolism and increasing small RNA synthesis. The ISME journal. 2021, vol. , iss. , str. 1-12, ilustr. ISSN 1751-7370. https://www.nature.com/articles/s41396-021-01030-9, DOI: 10.1038/s41396-021-01030-9. [COBISS.SI-ID 72620035], [JCR, SNIP, WoS, Scopus]
  3. GOSTINČAR, Cene, STAJICH, Jason Eric, KEJŽAR, Anja, SINHA, Sunita, NISLOW, Corey, LENASSI, Metka, GUNDE-CIMERMAN, Nina. Seven years at high salinity – experimental evolution of the extremely halotolerant black yeast Hortaea werneckii. Journal of fungi. 2021, vol. 7, iss. 9, str. 1-22. ISSN 2309-608X. https://www.mdpi.com/2309-608X/7/9/723, DOI: 10.3390/jof709072 [COBISS.SI-ID 76085763], [JCR, SNIP, WoS, Scopus]
  4. SCHALK, Felix, GOSTINČAR, Cene, KREUZENBECK, Nina B., CONLON, Benjamin H., SOMMERWERK, Elisabeth, RABE, Patrick, BURKHARDT, Immo, KRÜGER, Thomas, KNIEMEYER, Olaf, BRAKHAGE, Axel A., GUNDE-CIMERMAN, Nina, DE BEER, Z. Wilhelm, DICKSCHAT, Jeroen S., POULSEN, Michael, BEEMELMANNS, Christine. The termite fungal cultivar Termitomyces combines diverse enzymes and oxidative reactions for plant biomass conversion. mBio. 2021, vol. 12, iss. 3, str. 1-17. ISSN 2150-7511. DOI: 10.1128/mBio.03551-20. [COBISS.SI-ID 68499459], [JCR, SNIP, WoS, Scopus]
  5. GOSTINČAR, Cene, TURK, Martina, ZAJC, Janja, GUNDE-CIMERMAN, Nina. Fifty Aureobasidium pullulans genomes reveal a recombining polyextremotolerant generalist. Environmental microbiology. [Print ed.]. 2019, vol. 21, iss. 10, str. 3638-3652. ISSN 1462-2912. https://doi.org/10.1111/1462-2920.14693, DOI: 10.1111/1462-2920.14693. [COBISS.SI-ID 5158991], [JCR, SNIP, WoS do 24. 9. 2021: št. citatov (TC): 7, čistih citatov (CI): 4, čistih citatov na avtorja (CIAu): 1,00, Scopus do 26. 10. 2021: št. citatov (TC): 8, čistih citatov (CI): 6, čistih citatov na avtorja (CIAu): 1,50]
  6. GOSTINČAR, Cene, SUN, Xiaohuan, ZAJC, Janja, FANG, Chao, YONG, Hou, LUO, Yonglun, GUNDE-CIMERMAN, Nina, SONG, Zewei. Population genomics of an obligately halophilic basidiomycete Wallemia ichthyophaga. Frontiers in microbiology. 2019, vol. 10, str. 1-12, ilustr. ISSN 1664-302X. DOI: 10.3389/fmicb.2019.02019. [COBISS.SI-ID 5158479], [JCR, SNIP, WoS do 19. 10. 2021: št. citatov (TC): 1, čistih citatov (CI): 0, čistih citatov na avtorja (CIAu): 0,00, Scopus do 20. 10. 2021: št. citatov (TC): 1, čistih citatov (CI): 0, čistih citatov na avtorja (CIAu): 0,00]

 

Tomaž Curk:

  1. OMANOVIĆ, Amra, KAZAN, Hilal, OBLAK, Polona, CURK, Tomaž. Sparse data embedding and prediction by tropical matrix factorization. BMC bioinformatics, ISSN 1471-2105, Feb. 2021, vol. 22, str. 1-18, graf. prikazi. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04023-9, doi: 10.1186/s12859-021-04023-9. [COBISS.SI-ID 53512451]
  2. PAČNIK, Klavdija, BRLOŽNIK, Mojca, DIEPOLD, Matthias, EISENBERG, Tobias, ŽGANJAR, Mia, ŽUN, Gašper, KUŽNIK, Beti, GOSTINČAR, Cene, CURK, Tomaž, PETROVIČ, Uroš, NATTER, Klaus. Identification of novel genes involved inneutral lipid storage by quantitative traitloci analysis of Saccharomyces cerevisiae. BMC genomics, ISSN 1471-2164, 2021, vol. 22, str. 110-1-110-15, doi: 10.1186/s12864-021-07417-4. [COBISS.SI-ID 50785539]
  3. EHRMANN, Ingrid, CRICHTON, James H., GAZZARA, Matthew R., JAMES, Katherine, LIU, Yilei, GRELLSCHEID, Sushma N., CURK, Tomaž, ROOIJ, Dirk de, STEYN, Jannetta S., COCKELL, Simon, ADAMS, Ian R., BARASH, Yoseph, ELLIOTT, David J. An ancient germ cell-specific RNA-binding protein protects the germline from cryptic splice site poisoning. eLife, ISSN 2050-084X, Jan. 2019, vol. 8, str. 1-26, ilustr. https://www.ncbi.nlm.nih.gov/pubmed/30674417, doi: 10.7554/eLife.39304. [COBISS.SI-ID 1538163395]
  4. BRIESE, Michael, HABERMAN, Nejc, SIBLEY, Christopher R., FARAWAY, Rupert, ELSER, Andrea S., CHAKRABARTI, Anob M., WANG, Zhen, KÖNIG, Julian, PERERA, David, WICKRAMASINGHE, Vihandha O., VENKITARAMAN, Ashok R., LUSCOMBE, Nicholas M., SAIEVA, Luciano, PELLIZZONI, Livio, SMITH, Christopher W. J., CURK, Tomaž, ULE, Jernej. A systems view of spliceosomal assembly and branchpoints with iCLIP. Nature structural & molecular biology, ISSN 1545-9985. Online ed., Oct. 2019, vol. 26, no. 10, str. 930-940, ilustr. https://www.nature.com/articles/s41594-019-0300-4, doi: 10.1038/s41594-019-0300- [COBISS.SI-ID 1538384323]
  5. KOVANDA, Anja, LEONARDIS, Lea, ZIDAR, Janez, KORITNIK, Blaž, DOLENC-GROŠELJ, Leja, RISTIĆ KOVAČIČ, Stanislava, CURK, Tomaž, ROGELJ, Boris. Differential expression of microRNAs and other small RNAs in muscle tissue of patients with ALS and healthy age-matched controls. Scientific reports, ISSN 2045-2322, 2018, vol. 8, str. 1-14. https://www.nature.com/articles/s41598-018-23139-2, doi: 10.1038/s41598-018-23139-2. [COBISS.SI-ID 4730540]
  6. ROT, Gregor, WANG, Zhen, HUPPERTZ, Ina, MODIC, Miha, LENČE, Tina, HALLEGGER, Martina, HABERMAN, Nejc, CURK, Tomaž, MERING, Christian von, ULE, Jernej. High-resolution RNA maps suggest common principles of splicing and polyadenylation regulation by TDP-43. Cell reports, ISSN 2211-1247, May 2017, vol. 19, iss. 5, str. 1056-1067, graf. prikazi. http://www.cell.com/cell-reports/fulltext/S2211-1247(17)30522-3, doi: 10.1016/j.celrep.2017.04.028. [COBISS.SI-ID 1537665475]

 

Blaž Stres:

  1. MUROVEC, Boštjan, DEUTSCH, Leon, STRES, Blaž. General Unified Microbiome Profiling Pipeline (GUMPP) for large scale, streamlined and reproducible analysis of bacterial 16S rRNA data to predicted microbial metagenomes, enzymatic reactions and metabolic pathways. Metabolites. 2021, vol. 11, no. 6, str. 1-15, 336, ilustr. ISSN 2218-1989. https://www.mdpi.com/2218-1989/11/6/336, DOI: 10.3390/metabo11060336.
  2. MUROVEC, Boštjan, DEUTSCH, Leon, STRES, Blaž. Computational framework for high-quality production and large-scale evolutionary analysis of metagenome assembled genomes. Molecular biology and evolution, ISSN 0737-4038, 2020, doi: 10.1093/molbev/msz237
  3. ŠKET, Robert, DEBEVEC, Tadej, KUBLIK, Susanne, SCHLOTER, Michael, SCHOELLER, Anne, MUROVEC, Boštjan, VOGEL-MIKUŠ, Katarina, MAKUC, Damjan, PEČNIK, Klemen, PLAVEC, Janez, MEKJAVIĆ, Igor B., EIKEN, Ola, PREVORŠEK, Zala, STRES, Blaž. Intestinal metagenomes and metabolomes in healthy young males : inactivity and hypoxia generated negative physiological symptoms precede microbial dysbiosis. Frontiers in physiology, ISSN 1664-042X, 2018, doi: 10.3389/fphys.2018.00198.
  4. ŠKET, Robert, DEBEVEC, Tadej, MEKJAVIĆ, Igor B., MUROVEC, Boštjan, PREVORŠEK, Zala, STRES, Blaž, et al. Hypoxia and inactivity related physiological changes (constipation, inflammation) are not reflected at the level of gut metabolites and butyrate producing microbial community : the PlanHab study. Frontiers in physiology. 2017, vol. 8, art. no. 250, str. 1-16. ISSN 1664-042X. DOI: 10.3389/fphys.2017.00250.
  5. ŠKET, Robert, TREICHEL, Nicole S., KUBLIK, Susanne, DEBEVEC, Tadej, EIKEN, Ola, MEKJAVIĆ, Igor B., SCHLOTER, Michael, VITAL, Marius, CHANDLER, Jenna, TIEDJE, James M., MUROVEC, Boštjan, PREVORŠEK, Zala, LIKAR, Matevž, STRES, Blaž. Hypoxia and inactivity related physiological changes precede or take place in absence of significant rearrangements in bacterial community structure : the PlanHab randomized trial pilot study. PloS one. 2017, vol. 12, no. 12, str.1-26, e0188556. ISSN 1932-6203. http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0188556&type=printable, DOI: 10.1371/journal.pone.0188556.
  6. NICOLA, Lidia, INSAM, Heribert, PERTOT, Ilaria, STRES, Blaž. Reanalysis of microbiomes in soils affected by apple replant disease (ARD) : old foes and novel suspects lead to the proposal of extended model of disease development. Applied soil ecology. avg. 2018, vol. 129, str. 24-33, ilustr. ISSN 0929-1393. https://www.sciencedirect.com/science/article/pii/S0929139317312556, DOI: 10.1016/j.apsoil.2018.04.010.

Temeljni viri in literatura

– Jonathan Pevsner (2015) Bioinformatics and Functional Genomics, 3rd Edition, ISBN 9781118581780

– David W. Mount (2004) Bioinformatics. Sequence and Genome Analysis. Cold Spring Harbor Laboratory Press, USA, 2nd edition, ISBN 0879697121.

– pregledni in originalni znanstveni članki s širšega področja bioinformatike.

Bodi na tekočem

Univerza v Ljubljani, Fakulteta za elektrotehniko, Tržaška cesta 25, 1000 Ljubljana

E:  dekanat@fe.uni-lj.si T:  01 4768 411

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