Research IT (Podvinec)

Kolloff, Christopher et al. (2022) ‘Motional clustering in supra-τ; c; conformational exchange influences NOE cross-relaxation rate’, Journal of Magnetic Resonance, 338, p. 107196. Available at: https://doi.org/10.1016/j.jmr.2022.107196.

Gray, Declan A. et al. (2021) ‘Insights into SusCD-mediated glycan import by a prominent gut symbiont’, Nature Communications, 12(1), p. 44. Available at: https://doi.org/10.1038/s41467-020-20285-y.

Burmann, Björn M. et al. (2020) ‘Regulation of α-synuclein by chaperones in mammalian cells’, Nature, 577(7788), pp. 127–132. Available at: https://doi.org/10.1038/s41586-019-1808-9.

Mazur, Adam, Broz, Petr and Hiller, Sebastian (2019) ‘An integrative protocol for the structure determination of the mouse ASC-PYD filament’, in Sohn, Jungsan (ed.) Methods in Enzymology. New York: Elsevier (Methods in Enzymology), pp. 205–222. Available at: https://doi.org/10.1016/bs.mie.2019.04.033.

Benning, Friederike M. C. et al. (2017) ‘High-Speed Atomic Force Microscopy Visualization of the Dynamics of the Multienzyme Fatty Acid Synthase’, ACS Nano, 11(11), pp. 10852–10859. Available at: https://doi.org/10.1021/acsnano.7b04216.

Morgado, Leonor et al. (2017) ‘The dynamic dimer structure of the chaperone Trigger Factor’, Nature Communications, 8(1), p. 1992. Available at: https://doi.org/10.1038/s41467-017-02196-7.

He, Lichun et al. (2016) ‘A molecular mechanism of chaperone-client recognition’, Science Advances, 2(11), p. e1601625. Available at: https://doi.org/10.1126/sciadv.1601625.

Hoi Tik Alvin Leung et al. (2016) ‘A Rigorous and Efficient Method To Reweight Very Large Conformational Ensembles Using Average Experimental Data and To Determine Their Relative Information Content’, Journal of chemical theory and computation, 12(1), pp. 383–394. Available at: https://doi.org/10.1021/acs.jctc.5b00759.

Ravotti, Francesco et al. (2016) ‘Sequence-specific solid-state NMR assignments of the mouse ASC PYRIN domain in its filament form’, Biomolecular NMR Assignments, 10(1), pp. 107–15. Available at: https://doi.org/10.1007/s12104-015-9647-6.

Reinders, Alberto et al. (2016) ‘Expression and Genetic Activation of Cyclic Di-GMP-Specific Phosphodiesterases in Escherichia coli’, Journal of Bacteriology, 198(3), pp. 448–62. Available at: https://doi.org/10.1128/jb.00604-15.

Sakiyama, Yusuke et al. (2016) ‘Spatiotemporal dynamics of the nuclear pore complex transport barrier resolved by high-speed atomic force microscopy’, Nature Nanotechnology, 11(8), pp. 719–23. Available at: https://doi.org/10.1038/nnano.2016.62.

Stanger, Frédéric V. et al. (2016) ‘Intrinsic regulation of FIC-domain AMP-transferases by oligomerization and automodification’, Proceedings of the National Academy of Sciences of the United States of America, 113(5), pp. E529–37. Available at: https://doi.org/10.1073/pnas.1516930113.

Swiss Institute of Bioinformatics Members, SIB and Swiss Institute of Bioinformatics Members, SIB (2016) ‘The SIB Swiss Institute of Bioinformatics” resources: focus on curated databases’, Nucleic acids research, 44(D1), pp. D27–D37. Available at: https://doi.org/10.1093/nar/gkv1310.

Sborgi, Lorenzo et al. (2015) ‘Structure and assembly of the mouse ASC inflammasome by combined NMR spectroscopy and cryo-electron microscopy’, Proceedings of the National Academy of Sciences of the United States of America, 112(43), pp. 13237–42. Available at: https://doi.org/10.1073/pnas.1507579112.

Rämö, Pauli et al. (2014) ‘Simultaneous analysis of large-scale RNAi screens for pathogen entry’, BMC Genomics, 15(1), p. 1162. Available at: https://doi.org/10.1186/1471-2164-15-1162.

Rouilly, Vincent et al. (2012) ‘iBRAIN2: automated analysis and data handling for RNAi screens’, Studies in health technology and informatics, 175, pp. 205–213. Available at: https://doi.org/10.3233/978-1-61499-054-3-205.

Podvinec, Michael et al. (2010) ‘Novel Inhibitors of Dengue Virus Methyltransferase : discovery by in vitro-driven virtual screening on a Desktop Computer Grid’, Journal of Medicinal Chemistry, 53(4), pp. 1483–95. Available at: https://doi.org/10.1021/jm900776m.

Arnold, K. et al. (2009) ‘The protein model portal’, Journal of structural and functional genomics, 10(1), pp. 1–8. Available at: https://doi.org/10.1007/s10969-008-9048-5.

Berman, H. M. et al. (2009) ‘The protein structure initiative structural genomics knowledgebase’, Nucleic Acids Research, 37(1 Supplement), pp. D365–D368. Available at: https://doi.org/10.1093/nar/gkn790.

Moehren, Udo et al. (2008) ‘Identification of androgen-selective androgen-response elements in the human aquaporin-5 and Rad9 genes’, The Biochemical Journal, 411(3), pp. 679–86. Available at: https://doi.org/10.1042/bj20071352.

Podvinec, M., Schwede, T. and Peitsch, M. C. (2008) ‘Docking for neglected diseases as community efforts’, in Schwede T,; Peitsch MC, (ed.) Computational structural biology. Singapore: World Scientific Publishing (Computational structural biology), p. S. 683–704. Available at: https://doi.org/10.1142/9789812778789_0025.

Scarsi, Marco et al. (2007) ‘Sulfonylureas and glinides exhibit peroxisome proliferator-activated receptor gamma activity : a combined virtual screening and biological assay approach’, Molecular pharmacology, 71(2), pp. 398–406. Available at: https://doi.org/10.1124/mol.106.024596.

Zosso, D. et al. (2007) ‘SWISS-TANDEM : a Web-based workspace for MS/MS protein identification on PC grid’, in Kokol, P; Podgorelec, V; MiceticTurk, D; Zorman, M; Verlic, M (ed.). IEEE Computer Society: IEEE Computer Society. Available at: https://doi.org/10.1109/cbms.2007.103.

Zosso, D et al. (2007) ‘Tandem mass spectrometry protein identification on a PC grid’, Studies in health technology and informatics, 126, pp. 3–12.

Podvinec, Michael and Meyer, Urs A (2006) ‘Prediction of cis-regulatory elements for drug-activated transcription factors in the regulation of drug-metabolising enzymes and drug transporters’, Expert Opinion on Drug Metabolism & Toxicology, 2(3), pp. 367–79. Available at: https://doi.org/10.1517/17425255.2.3.367.

Podvinec, M. et al. (2006) ‘The SwissBioGrid Project : objectives, preliminary results and lessons learned’. IEEE Computer Society: IEEE Computer Society. Available at: https://doi.org/10.1109/e-science.2006.261081.

Gnerre, C. et al. (2005) ‘LXR deficiency and cholesterol feeding affect the expression and phenobarbital-mediated induction of cytochromes P450 in mouse liver’, Journal of Lipid Research, 46(8), pp. 1633–42. Available at: https://doi.org/10.1194/jlr.m400453-jlr200.

Dietrich, Fred S et al. (2004) ‘The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome’, Science, 304(5668), pp. 304–7. Available at: https://doi.org/10.1126/science.1095781.

Handschin, Christoph et al. (2004) ‘The evolution of drug-activated nuclear receptors : one ancestral gene diverged into two xenosensor genes in mammals’, Nuclear Receptor, 2(1), p. 7. Available at: https://doi.org/10.1186/1478-1336-2-7.

Podvinec, M. et al. (2004) ‘Identification of the xenosensors regulating human 5-aminolevulinate synthase’, Proceedings of the National Academy of Sciences of the United States of America, 101(24), pp. 9127–32. Available at: https://doi.org/10.1073/pnas.0401845101.

Schreiber, Sylvia N et al. (2004) ‘The estrogen-related receptor α (ERRα) functions in PPARγ coactivator 1α (PGC-1α)-induced mitochondrial biogenesis’, Proceedings of the National Academy of Sciences of the United States of America, 101(17), pp. 6472–7. Available at: https://doi.org/10.1073/pnas.0308686101.

Handschin, Christoph, Podvinec, Michael and Meyer, Urs A. (2003) ‘In silico approaches, and in vitro and in vivo experiments to predict induction of drug metabolism’, Drug news & perspectives, 16(7), pp. 423–434. Available at: https://doi.org/10.1358/dnp.2003.16.7.829354.

Sanyal, S. et al. (2003) ‘Molecular cloning and characterization of chicken orphan nuclear receptor cTR2’, General and Comparative Endocrinology, 132(3), pp. 474–84. Available at: https://doi.org/10.1016/s0016-6480(03)00116-3.

Fraser, David J et al. (2002) ‘Drugs mediate the transcriptional activation of the 5-aminolevulinic acid synthase (ALAS1) gene via the chicken xenobiotic-sensing nuclear receptor (CXR)’, Journal of biological chemistry, 277(38), pp. 34717–26. Available at: https://doi.org/10.1074/jbc.m204699200.

Handschin, C. et al. (2002) ‘Cholesterol and bile acids regulate xenosensor signaling in drug-mediated induction of cytochromes P450’, Journal of Biological Chemistry, 277(33), pp. 29561–7. Available at: https://doi.org/10.1074/jbc.m202739200.

Jung, D et al. (2002) ‘Human organic anion transporting polypeptide 8 promoter is transactivated by the farnesoid X receptor/bile acid receptorw’, Gastroenterology, 122(7), pp. 1954–1966. Available at: https://doi.org/10.1053/gast.2002.33583.

Meyer, Ralf Peter et al. (2002) ‘Cytochrome P450 CYP1A1 accumulates in the cytosol of kidney and brain and is activated by heme’, Molecular pharmacology, 62(5), pp. 1061–7. Available at: https://doi.org/10.1124/mol.62.5.1061.

Podvinec, Michael et al. (2002) ‘NUBIScan, an in silico approach for prediction of nuclear receptor response elements’, Molecular endocrinology, 16(6), pp. 1269–79. Available at: https://doi.org/10.1210/mend.16.6.0851.

Handschin, C. et al. (2001) ‘Multiple enhancer units mediate drug induction of CYP2H1 by xenobiotic-sensing orphan nuclear receptor chicken xenobiotic receptor’, Molecular pharmacology, 60(4), pp. 681–9.

Handschin, C et al. (2001) ‘Conservation of signaling pathways of xenobiotic-sensing orphan nuclear receptors, chicken xenobiotic receptor, constitutive androstane receptor, and pregnane X receptor, from birds to humans’, Molecular endocrinology, 15(9), pp. 1571–85. Available at: https://doi.org/10.1210/mend.15.9.0701.

Brachat, A. et al. (2000) ‘Analysis of deletion phenotypes and GFP fusions of 21 novel Saccharomyces cerevisiae open reading frames’, Yeast, 16(3), pp. 241–253. Available at: https://doi.org/10.1002/(sici)1097-0061(200002)16:33.0.co;2-t.

Handschin, C, Podvinec, M and Meyer, U A (2000) ‘CXR, a chicken xenobiotic-sensing orphan nuclear receptor, is related to both mammalian pregnane X receptor (PXR) and constitutive androstane receptor (CAR)’, Proceedings of the National Academy of Sciences of the United States of America, 97(20), pp. 10769–74. Available at: https://doi.org/10.1073/pnas.97.20.10769.

Wendland, J et al. (1999) ‘Compact organization of rRNA genes in the filamentous fungus Ashbya gossypii’, Current Genetics, 35(6), pp. 618–25. Available at: https://doi.org/10.1007/s002940050460.

Philippsen, P et al. (1997) ‘The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications’, Nature, 387(6632 Suppl), pp. 93–8.

Pöhlmann, R and Philippsen, P (1996) ‘Sequencing a cosmid clone of Saccharomyces cerevisiae chromosome XIV reveals 12 new open reading frames (ORFs) and an ancient duplication of six ORFs’, Yeast, 12(4), pp. 391–402. Available at: https://doi.org/10.1002/(sici)1097-0061(19960330)12:43.0.co;2-n.