Lista naših publikacija

• Punit Saron, J Snider, Yannis Kalaidzidis, Leanne E. Wybenga-Groot, Konstantin Weiss, Ankit Rai, Nikolina Radulovich, Luka Drecun, Nika Vučković, Adriana Vučetić, Victoria Wong, Brigiitte Theriault, Nhu-An Pham, Jin H. Park, Alessandro Datti, Jenny Wang, Shivanthy Pathmanathan, Farzaneh Aboualizadeh, Anna Lyakisheva, Zhong Yao, Yuhui Wang, Babu Joseph, Ahmed Aman, Michael F. Moran, Michael Prakesch, Gennady Poda, Richard Marcellus, David Uehling, Miroslav Samržija, Marko Jakopović, Ming-Sound Tsao, Frances A. Shepherd, Adrian Sacher, Natasha Leighi, Anna Akhmanova, Rima Al-awar, Marino Zerial, Igor Štagljar: A drug discovery platform to identify compounds that inhibit EGFR triple mutants
• Albi Celaj, Marinella Gebbia, Loaui Musa, Atina G. Cote, J Snider, Vanja Nagy, Minjeong Ko, Tiffany Fong, Paul Bansal, Joseph C. Mellor, Gireesh Seesankar, Marija Nguyen, Sašo Džeroski, Liangxi Wang, Nishka Kishore, Igor Štagljar, Yo Suzuki, Nozomu Yachie, Frederick P Roth: Highly Combinatorial Genetic Interaction Analysis Reveals a Multi-Drug Transporter Influence Network
• Miroslav Radman: Ecobiological approach to research regarding ageing and diseases. Eur J Dermatol. 2019;29(S1):11–14. doi:10.1684/ejd.2019.3534
• Anita Kriško, Miroslav Radman: Protein damage, ageing and age-related diseases Open Biol. 2019;9(3):180249. doi:10.1098/rsob.180249
• Miroslav Radman: Cellular parabiosis and the latency of age-related diseases Open Biol. 2019;9(3):180250. doi:10.1098/rsob.180250
• 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: 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.