Lista naših publikacija

• Davor Juretić, Juraj Simunić: Design of α-helical antimicrobial peptides with a high selectivity index. Expert Opin Drug Discov. 2019 Jul 16:1-11. doi: 10.1080/17460441.2019.1642322. [Epub ahead of print] PubMed PMID: 31311351.
• Davor Juretić, Željana Bonačić Lošić, Domagoj Kuić, Juraj Simunić, Andrej Dobovišek: The maximum entropy production requirement for proton transfers enhances catalytic efficiency for β-lactamases. Biophys Chem. 2019 Jan;244:11-21. doi: 10.1016/j.bpc.2018.10.004. Epub 2018 Oct 17. PubMed PMID: 30448627.
• Punit Saron, Ingrid Grozavu, Igor Štagljar: Saraon P, Grozavu I, Stagljar I. Testing cancer inhibitors at scale. Nat Biomed Eng. 2018 Apr;2(4):203-204. doi: 10.1038/s41551-018-0226-x. PubMed PMID: 30936440.
• E. Santiago-Cartagena, S González-Crespo, V Vélez, N Martínez, J Snider, M Jessulat, H Aoki, Z Minic, P Akamine, I Mejías, LM Pérez, BC Rymond, M Babu, Igor Štagljar: Santiago-Cartagena E, González-Crespo S, Vélez V, Martínez N, Snider J, Jessulat M, Aoki H, Minic Z, Akamine P, Mejías I, Pérez LM, Rymond BC, Babu M, Stagljar I, Rodríguez-Medina JR. Identification and Functional Testing of Novel Interacting Protein Partners for the Stress Sensors Wsc1p and Mid2p of Saccharomyces cerevisiae. G3 (Bethesda). 2019 Feb 7. pii: g3.200985.2018. doi: 10.1534/g3.118.200985. [Epub ahead of print] PubMed PMID: 30733383
• Cinizia Colombo, Anna Roberto, Karmela Krleža-Jerić, Elena Parmelli, Rita Banzi: Sharing individual participant data from clinical studies: a cross-sectional online survey among Italian patient and citizen groups BMJ Open 2019;9:e024863. doi:10.1136/bmjopen-2018-024863
• Marina Musa, Matea Kanunnikau, Peter Bou Dib, Sandra Sobočanec, Ana Šarić, Anita Lovrić, Marina Rudan, Andrea Nikolić, Ira Milošević, Krisijan Vlahoviček, Nuno Raimundo, Anita Kriško: Heat-induced longevity in budding yeast requires respiratory metabolism and glutathione recycling. Aging (Albany NY). 2018 Sep 17;10(9):2407-2427. doi: 10.18632/aging.101560. PubMed PMID: 30227387.
• Davor Juretić, Yogesh Sonavane, Nada Ilić, Goran Gajski, Ivana Goić-Barišić, Matea Kanunnikau, Marija Tonkić, Mara Kozic, Ana Maravić, François-Xavier Pellay, Larisa Zoranić: Designed peptide with a flexible central motif from ranatuerins adapts its conformation to bacterial membranes. Biochim Biophys Acta Biomembr. 2018 Dec;1860(12):2655-2668. doi: 10.1016/j.bbamem.2018.10.005. Epub 2018 Oct 4. PubMed PMID: 30292398
• M Mahmić-Kaknjo, Josip Šimić, Karmela Krleža-Jerić: Setting the IMPACT (IMProve Access to Clinical Trial data) Observatory baseline. Biochem Med (Zagreb). 2018 Feb 15;28(1):010201. doi: 10.11613/BM.2018.010201. Review. PubMed PMID: 29472799; PubMed Central PMCID: PMC5806612.
• Tomislav Rončević, Damir Vukičević, Nada Ilić, Lucija Krce, Goran Gajski, Marija Tonkić, Ivana Goić-Barišić, Larisa Zoranić, Yogesh Sonavane, Monica Benincasa, Davor Juretić, Ana Maravić, Alessandro Tossi: Antibacterial Activity Affected by the Conformational Flexibility in Glycine-Lysine Based α-Helical Antimicrobial Peptides. J Med Chem. 2018 Mar 29. doi: 10.1021/acs.jmedchem.7b01831. [Epub ahead of print] PubMed PMID: 29553266.
• Marina Rudan, Peter Bou Dib, Marina Musa, Matea Kanunnikau, Sandra Sobočanec, David Rueda, Tobias Warnecke, Anita Kriško: Normal mitochondrial function in Saccharomyces cerevisiae has become dependent on inefficient splicing. Elife. 2018 Mar 23;7. pii: e35330. doi: 10.7554/eLife.35330. [Epub ahead of print] PubMed PMID: 29570052
• Nuno Raimundo, Anita Kriško: Raimundo N, Kriško A. Cross-organelle communication at the core of longevity. Aging (Albany NY). 2018 Jan 22;10(1):15-16. doi: 10.18632/aging.101373. PubMed PMID: 29362289; PubMed Central PMCID: PMC5811256
• Matea Kanunnikau, Anita Lovrić, Ana Šarić, Marina Musa, Peter Bou Dib, Marina Rudan, Andrea Nikolić, Sandra Sobočanec, Ana-Matea Mikecin, Sven Dennerlein, Ira Milošević, Krisijan Vlahoviček, Nuno Raimundo, Anita Kriško: TORC1-mediated sensing of chaperone activity alters glucose metabolism and extends lifespan. Aging Cell. 2017 Oct;16(5):994-1005. doi: 10.1111/acel.12623. Epub 2017 Jun 14. PubMed PMID: 28613034; PubMed Central PMCID: PMC5595670.
• Kristina Ames, Dayse S. Da Cunha, Brenda Gonzalez, Marina Konta, Feng Lin, Gabriel Shechter, Lev Starikov, Sara Wong, Hannes E. Bulow, Alicia Melendez: A Non-Cell-Autonomous Role of BEC-1/BECN1/Beclin1 in Coordinating Cell-Cycle Progression and Stem Cell Proliferation during Germline Development
• Davor Juretić, Damir Vukičević, Alessandro Tossi: Tools for Designing Amphipathic Helical Antimicrobial Peptides. Methods Mol Biol. 2017;1548:23-34. doi: 10.1007/978-1-4939-6737-7_2. PubMed PMID: 28013494
• Željana Bonačić Lošić, Tomislav Donđivić, Davor Juretić: Is the catalytic activity of triosephosphate isomerase fully optimized? An investigation based on maximization of entropy production. J Biol Phys. 2017 Mar;43(1):69-86. doi: 10.1007/s10867-016-9434-3. Epub 2017 Jan 3. PubMed PMID: 28050739; PubMed Central PMCID: PMC5323346.
• Tomislav Rončević, Goran Gajski, Nada Ilić, Ivana Goić-Barišić, Marija Tonkić, Larisa Zoranić, Juraj Simunić, Monica Benincasa, Marijana Mijaković, Alessandro Tossi, Davor Juretić: PGLa-H tandem-repeat peptides active against multidrug resistant clinical bacterial isolates. Biochimica et Biophysica Acta 1859 (2017) 228–237
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• Mira Kuzmić, Helene Javot, Jean-Marc Bonzom, Catherine Lecomte-Pradines, Miroslav Radman, Jacqueline Garnier-Laplacea, Sandrine Frelon: In situ visualization of carbonylation and its co-localization with proteins, lipids, DNA and RNA in Caenorhabditis elegans : Free Radic Biol Med. 2016 Nov 10. pii: S0891-5849(16)31029-2. doi: 10.1016/j.freeradbiomed.2016.11.004
• Matea Kanunnikau, Peter Bou Dib, Sven Dennerlein, Marina Musa, Marina Rudan, Anita Lovrić, Andrea Nikolić, Ana Šarić, Sandra Sobočanec, Željka Mačak, Nuno Raimundo, Anita Kriško: Crosstalk between cellular compartments protects against proteotoxicity and extends lifespan. Sci Rep. 2016 Jun 27;6:28751. doi: 10.1038/srep28751. PubMed PMID: 27346163; PubMed Central PMCID: PMC4921836.
• Andrea Nikolić, Matea Kanunnikau, Romain Ladouce, Ana-Matea Mikecin, Fernando A. Martin , Marijeta Kralj, Anita Kriško, Miroslav Radman: Death by UVC Light Correlates with Protein Damage in Isogenic Human Tumor Cells: Primary Tumor SW480 versus its Metastasis SW620. Journal of Proteomics and Computational Biology (2016), 2 (1): 12.
• Marina Musa, Miroslav Radman, Anita Kriško: Decreasing translation error rate in Escherichia coli increases protein function. BMC Biotechnol 2016; 16 (1): 28.
• Miroslav Radman: Mismatch repair earns Nobel Prize in Chemistry 2015 to Paul Modrich for a biochemical tour de force. / DNA Repair 37 (2016) A22–A28
• Maria Brbic, Tobias Warnecke, Anita Kriško, Fran Supek: Global shifts in genome and proteome composition are very tightly coupled. 2015. Genome Biol. Evol. 7(6):1519–1532.
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• Marina Rudan, Dominique Schneider, Tobias Warnecke, Anita Kriško: RNA chaperones buffer deleterious mutations in E. coli. Elife. 2015 Mar 25;4. doi: 10.7554/eLife.04745. PubMed PMID: 25806682; PubMed Central PMCID: PMC4402597.
• Anita Lovrić, Fran Supek, Andrea Nikolić, Anita Kriško: Signatures of conformational stability and oxidation resistance in proteomes of pathogenic bacteria. Cell Rep 2014; 7: 1393-1400
• Anita Kriško, Tea Copić, Toni Gabaldón, Ben Lehner, Fran Supek: Inferring gene function from evolutionary change in signatures of translation efficiency. Genome Biol 2014; 15:R44.
• Marion Girod, Quentin Enjalbert, Claire Brunet, Rodolphe Antoine, Jerome Lemoine, Iva Lukac, Miroslav Radman, Anita Kriško, Philippe Dugourd: Structural basis of protein oxidation resistance: a lysozyme study. Plos One 2014; 9: e101642.
• Manière X, Anita Kriško, François-Xavier Pellay, Di Meglio JM, Hersen P, Ivan Matic: High transcript levels of heat-shock genes are associated with shorter lifespan of Caenorhabditis elegans. Experimental Gerontology 2014, 60C: 12-17.
• Anita Kriško, Miroslav Radman: Phenotypic and genetic consequences of protein damage. Plos Genetics 2013; 9(9): e1003810.
• Anita Kriško, Miroslav Radman: Biology of Extreme Radiation Resistance: The Way of Deinococcus radiodurans. Cold Spring Harb Perspect Biol. 2013; 5(7).
• Nives Skunca, Matko Bosnjak, Anita Kriško, Pance Panov, Sašo Džeroski, Tomislav Šmuc: Phyletic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships. PLoS Comput Biol. 2013;9(1):e1002852.
• Miroslav Radman: [Aging: the chemistry of a flexible biological clock]. Med Sci (Paris). 2012 Mar;28(3):231-3. doi: 10.1051/medsci/2012283001. Epub 2012 Apr 6. French. PubMed PMID:
• Anita Kriško, Magali Leroy, Miroslav Radman, Matthew Meselson: Extreme anti-oxidant protection against ionizing radiation in bdelloid rotifers. Proc Natl Acad Sci U S A. 2012;109(7): 2354-2357.
• Nela Nikolic, Zlatko Smole, Anita Kriško: Proteomic properties reveal phyloecological clusters of Archaea. PLoS One. 2012; 7(10):e48231.
• Marina Elez, Miroslav Radman, Ivan Matic: Stoichiometry of MutS and MutL at unrepaired mismatches in vivo suggests a mechanism of repair. Nucleic Acids Research, 2012, Vol. 40, No. 9 3929–3938
• Dea Slade, Miroslav Radman: Oxidative stress resistance in Deinococcus radiodurans. Microbiol Mol Biol Rev. 2011;75(1):133-91.
• Zlatko Smole, Nela Nikolic, Fran Supek, Tomislav Šmuc, Ivo Sbalzarini, Anita Kriško: Proteome sequence features carry signatures of the environmental niche of prokaryotes. BMC Evol Biol. 2011;11:26.
• Marina Elez, Andrew W. Murray, Li-Jun Bi, Xian-En Zhang, Ivan Matic, Miroslav Radman: Seeing mutations in living cells. Curr Biol. 2010;20(16):1432-7.
• Anita Kriško, Miroslav Radman: Protein damage and death by radiation in Escherichia coli and Deinococcus radiodurans. Proc Natl Acad Sci U S A. 2010; 107(32): 14373-14377.
• Anita Kriško, Zlatko Smole, Gaelle Debret, Nela Nikolic, Miroslav Radman: Unstructured hydrophilic sequences in prokaryotic proteomes correlate with dehydration tolerance and host association. J Mol Biol 402: 775-82. (2010)
• Jelena Repar, Svjetlana Cvjetan, Dea Slade, Miroslav Radman, Ksenija Zahradka: RecA protein assures fidelity of DNA repair and genome stability in Deinococcus radiodurans. DNA Repair 9: 1151-1161. (2010)
• Omar Awile, Anita Kriško, Ivo Sbalzarini: Intrinsically disordered regions may lower the hydration free energy in proteins: a case study of nudix hydrolase in the bacterium Deinococcus radiodurans. Plos Comput Biol, 6 (7):e1000854. (2010)
• Mario Hlevnjak, Gordan Zitkovic, Bojan Žagrović: Hydrophilicity matching - a potential prerequisite for the formation of protein-protein complexes in the cell. PLoS One. 2010; 5(6):e11169.
• Antonija Kuzmanić, Bojan Žagrović: Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors. Biophys J. 2010; 98(5):861-71
• Ivana Novak, Vladimir Kirkin, David G. McEwan , Philipp Wild , Alexis Rozenknop, Vladimir Rogov, Doris Popović, Angelo Occhipinti, Andreas S. Reichert, Janos Terzic, Volker Dotsch, Paul A. Ney, Ivan Đikić: Nix is a selective autophagy receptor for mitochondrial clearance, EMBO reports (2010) 11, 45 – 51
• Vanja Nagy, Ivan Đikić: Ubiquitin ligase complexes: from substrate selectivity to conjugational specificity. Biol Chem. 2010, 391(2-3):163-9.
• Dea Slade, Ariel B. Lindner, Gregory Paul, Miroslav Radman: "Recombination and replication in DNA repair of heavily irradiated Deinococcus radiodurans", Cell (2009) 136:1044-1055; IF 31.3
• Christian L. Müller, Ivo Sbalzarini, Wilfred F. van Gunsteren, Bojan Žagrović, Philippe H. Hünenberger: “In the eye of the beholder: inhomogeneous distribution of high-resolution shapes within the random-walk ensemble“, Journal of Chemical Physics, 130, 21, 214904; IF 3.149 (2009)
• Daniela Kruschel, Bojan Žagrović: “Conformational averaging in structural biology: issues, challenges and computational solutions”, Molecular Biosystems, (2009) DOI: 10.1039/b917186j; IF 4.236
• Tomasz Wlodarski, Bojan Žagrović: “Conformational selection and induced fit mechanism underlie specificity in non-covalent interactions with ubiquitin”,(2009) DOI:10.1073/pnas.0906966106
• JT Martinsohn, Miroslav Radman, MA Petit: The lambda red proteins promote efficient ecombination between diverged sequences: implications for bacteriophage genome mosaicism. PLoS Genet. 2008 May 2;4(5):e1000065. doi: 10.1371/journal.pgen.1000065. PubMed PMID: 18451987; PubMed Central PMCID: PMC2327257.
• A Babić, Ariel B. Lindner, M Vulić, EJ Stewart, Miroslav Radman: Direct visualization of horizontal gene transfer. Science. 2008 Mar 14;319(5869):1533-6. doi: 10.1126/science.1153498. PubMed PMID: 18339941.
• Marina Elez, Miroslav Radman, Ivan Matic: The frequency and structure of recombinant products is determined by the cellular level of MutL. Proc Natl Acad Sci U S A. 2007 May 22;104(21):8935-40. Epub 2007 May 14. PubMed PMID: 17502621; PubMed Central PMCID: PMC1885606
• Ksenija Zahradka, Dea Slade, A Bailone, S Sommer, D Averbeck, M Petranović, Ariel B. Lindner, Miroslav Radman: Reassembly of shattered chromosomes in Deinococcus radiodurans. Nature. 2006 Oct 5;443(7111):569-73. Epub 2006 Sep 27. PubMed PMID: 17006450
• Ivan Matic, D Ekiert, Miroslav Radman, M Kohiyama: Generation of DNA-free Escherichia coli cells by 2-aminopurine requires mismatch repair and nonmethylated DNA. J Bacteriol. 2006 Jan;188(1):339-42. PubMed PMID: 16352851; PubMed Central PMCID: PMC1317583
• W Banzhaf, G Belson, S Christensen, JA Foster, F Képès, V Lefort, JF Miller, Miroslav Radman, JJ Ramsden: Guidelines: From artificial evolution to computational evolution: a research agenda. Nat Rev Genet. 2006 Sep;7(9):729-35. Epub 2006 Aug 8. PubMed PMID: 16894364
• EC Friedberg, R Wagner, Miroslav Radman: Specialized DNA polymerases, cellular survival, and the genesis of mutations. Science. 2002 May 31;296(5573):1627-30. Review. PubMed PMID: 12040171.
• M Vulić, RE Lenski, Miroslav Radman: Mutation, recombination, and incipient speciation of bacteria in the laboratory. Proc Natl Acad Sci U S A. 1999 Jun 22;96(13):7348-51. PubMed PMID: 10377417; PubMed Central PMCID: PMC22088.
• François Taddei, H Hayakawa, M Bouton, A Cirinesi, Ivan Matic, M Sekiguchi , Miroslav Radman: Counteraction by MutT protein of transcriptional errors caused by oxidative damage. Science. 1997 Oct 3;278(5335):128-30. PubMed PMID: 9311918.
• François Taddei, Miroslav Radman, J Maynard-Smith, B Toupance, PH Gouyon: Role of mutator alleles in adaptive evolution. Nature. 1997 Jun 12;387(6634):700-2. PubMed PMID: 9192893.
• N de Wind, M Dekker, A Berns, Miroslav Radman, H te Riele: Inactivation of the mouse Msh2 gene results in mismatch repair deficiency, methylation tolerance, hyperrecombination, and predisposition to cancer. Cell. 1995 Jul 28;82(2):321-30. PubMed PMID: 7628020
• Ivan Matic, C Rayssiguier, Miroslav Radman: Interspecies gene exchange in bacteria: the role of SOS and mismatch repair systems in evolution of species. Cell. 1995 Feb 10;80(3):507-15. PubMed PMID: 7859291
• MC Kricker, JW Drake, Miroslav Radman: Duplication-targeted DNA methylation and mutagenesis in the evolution of eukaryotic chromosomes. Proc Natl Acad Sci U S A. 1992 Feb 1;89(3):1075-9. PubMed PMID: 1736289; PubMed Central PMCID: PMC48388.
• C Rayssiguier, DS Thaler, Miroslav Radman: The barrier to recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch-repair mutants. Nature. 1989 Nov 23;342(6248):396-401. PubMed PMID: 2555716.
• M Jones, R Wagner, Miroslav Radman: Mismatch repair and recombination in E. coli. Cell. 1987 Aug 14;50(4):621-6. PubMed PMID: 2955904.
• Glickman BW, Miroslav Radman: Escherichia coli mutator mutants deficient in methylation-instructed DNA mismatch correction. Proc Natl Acad Sci U S A. 1980 Feb;77(2):1063-7. PubMed PMID: 6987663; PubMed Central PMCID: PMC348424.
• Miroslav Radman: An endonuclease from Escherichia coli that introduces single polynucleotide chain scissions in ultraviolet-irradiated DNA. J Biol Chem. 1976 Mar 10;251(5):1438-45. PubMed PMID: 3498.
• Miroslav Radman: SOS repair hypothesis: phenomenology of an inducible DNA repair which is accompanied by mutagenesis. Basic Life Sci. 1975;5A:355-67. Review. PubMed PMID: 1103845.