Items where Division is "05 Faculty of Science > Departement Biozentrum > Services Biozentrum > Research IT (Podvinec)"

4 January 2016

Swiss Institute of Bioinformatics Members, SIB. (2016) The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. Nucleic acids research, 44 (D1). D27-D37.

January 2016

Leung, Hoi Tik Alvin and Bignucolo, Olivier and Aregger, Regula and Dames, Sonja A. and Mazur, Adam and Bernèche, Simon and Grzesiek, Stephan. (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.

2016

Ravotti, Francesco and Sborgi, Lorenzo and Cadalbert, Riccardo and Huber, Matthias and Mazur, Adam and Broz, Petr and Hiller, Sebastian and Meier, Beat H. and Böckmann, Anja. (2016) Sequence-specific solid-state NMR assignments of the mouse ASC PYRIN domain in its filament form. Biomolecular NMR Assignments, 10 (1). pp. 107-115.

27 October 2015

Sborgi, Lorenzo and Ravotti, Francesco and Dandey, Venkata Prasad and Dick, Mathias S. and Mazur, Adam and Reckel, Sina and Chami, Mohamed and Scherer, Sebastian and Huber, Matthias and Böckmann, Anja and Egelman, Edward H. and Stahlberg, Henning and Broz, Petr and Meier, Beat H. and Hiller, Sebastian. (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. 13237-13242.

December 2014

Rämö, Pauli and Drewek, Anna and Arrieumerlou, Cécile and Beerenwinkel, Niko and Ben-Tekaya, Houchaïma and Cardel, Bettina and Casanova, Alain and Conde-Alvarez, Raquel and Cossart, Pascale and Csúcs, Gábor and Eicher, Simone and Emmenlauer, Mario and Greber, Urs and Hardt, Wolf-Dietrich and Helenius, Ari and Kasper, Christoph and Kaufmann, Andreas and Kreibich, Saskia and Kühbacher, Andreas and Kunszt, Peter and Low, Shyan Huey and Mercer, Jason and Mudrak, Daria and Muntwiler, Simone and Pelkmans, Lucas and Pizarro-Cerdá, Javier and Podvinec, Michael and Pujadas, Eva and Rinn, Bernd and Rouilly, Vincent and Schmich, Fabian and Siebourg-Polster, Juliane and Snijder, Berend and Stebler, Michael and Studer, Gabriel and Szczurek, Ewa and Truttmann, Matthias and von Mering, Christian and Vonderheit, Andreas and Yakimovich, Artur and Bühlmann, Peter and Dehio, Christoph. (2014) Simultaneous analysis of large-scale RNAi screens for pathogen entry. BMC Genomics, 15 (1). p. 1162.

2012

Rouilly, Vincent and Pujadas, Eva and Hullár, Béla and Balázs, Csaba and Kunszt, Peter and Podvinec, Michael. (2012) iBRAIN2: automated analysis and data handling for RNAi screens. Studies in health technology and informatics, Vol. 175. pp. 205-213.

2010

Podvinec, M. and Lim, S. P. and Schmidt, T. B. and Scarsi, M. and Wen, D. and Sonntag, L. S. and Sanschagrin, P. and Shenkin, P. S. and Schwede, T.. (2010) Novel Inhibitors of Dengue Virus Methyltransferase : discovery by in vitro-driven virtual screening on a Desktop Computer Grid. Journal of Medicinal Chemistry, Vol. 53, H. 4. pp. 1483-1495.

2009

Berman, H. M. and Westbrook, J. D. and Gabanyi, M. J. and Tao, W. and Shah, R. and Kouranov, A. and Schwede, T. and Arnold, K. and Kiefer, F. and Bordoli, L. and Kopp, J. and Podvinec, M. and Adams, P. D. and Carter, L. G. and Minor, W. and Nair, R. and Baer, J. L.. (2009) The protein structure initiative structural genomics knowledgebase. Nucleic Acids Research, 37 (1 Supplement). D365-D368.

2008

Moehren, U. and Denayer, S. and Podvinec, M. and Verrijdt, G. and Claessens, F.. (2008) Identification of androgen-selective androgen-response elements in the human aquaporin-5 and Rad9 genes. The Biochemical Journal, Vol. 411, Pt. 3. pp. 679-686.

Podvinec, M. and Schwede, T. and Peitsch, M. C.. (2008) Docking for neglected diseases as community efforts. In: Computational structural biology. Singapore, pp. 683-704.

2007

Scarsi, M. and Podvinec, M. and Roth, A. and Hug, H. and Kersten, S. and Albrecht, H. and Schwede, T. and Meyer, U. A. and Rucker, C.. (2007) Sulfonylureas and glinides exhibit peroxisome proliferator-activated receptor gamma activity : a combined virtual screening and biological assay approach. Molecular pharmacology, Vol. 71, H. 2. pp. 398-406.

Zosso, D. and Arnold, K. and Schwede, T. and Podvinec, M.. (2007) SWISS-TANDEM : a Web-based workspace for MS/MS protein identification on PC grid. In: Twentieth IEEE international symposium on computer-based medical systems, CBMS 2007. Los Alamitos, Calif., pp. 406-411.

Zosso, D. and Podvinec, M. and Muller, M. and Aebersold, R. and Peitsch, M. C. and Schwede, T.. (2007) Tandem mass spectrometry protein identification on a PC grid. Studies in health technology and informatics, Vol. 126. pp. 3-12.

2006

Podvinec, M. and Maffioletti, S. and Kunszt, P. and Arnold, K. and Cerutti, L. and Nyffeler, B. and Schlapbach, R. and Turker, C. and Stockinger, H. and Thomas, A. J. and Peitsch, M. C. and Schwede, T.. (2006) The SwissBioGrid Project : objectives, preliminary results and lessons learned. In: e-Science 2006 : 2nd IEEE International Conference on e-Science and Grid Computing, e-Science 2006, 148. Los Alamitos, Calif..

Podvinec, M. and Meyer, U. 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, Vol. 2, H. 3. pp. 367-379.

2005

Gnerre, C. and Schuster, G. U. and Roth, A. and Handschin, C. and Johansson, L. and Looser, R. and Parini, P. and Podvinec, M. and Robertsson, K. and Gustafsson, J. -A. and Meyer, U. A.. (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. 1633-1642.

2004

Dietrich, F. S. and Voegeli, S. and Brachat, S. and Lerch, A. and Gates, K. and Steiner, S. and Mohr, C. and Pohlmann, R. and Luedi, P. and Choi, S. and Wing, R. A. and Flavier, A. and Gaffney, T. D. and Philippsen, P.. (2004) The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science, Vol. 304, no. 5668. pp. 304-307.

Handschin, C. and Blattler, S. and Roth, A. and Looser, R. and Oscarson, M. and Kaufmann, M. R. and Podvinec, M. and Gnerre, C. and Meyer, U. A.. (2004) The evolution of drug-activated nuclear receptors : one ancestral gene diverged into two xenosensor genes in mammals. Nuclear Receptor, Vol. 2, H. 1. p. 7.

Podvinec, M. and Handschin, C. and Looser, R. and Meyer, U. A.. (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. 9127-9132.

Schreiber, S. N. and Emter, R. and Hock, M. B. and Knutti, D. and Cardenas, J. and Podvinec, M. and Oakeley, E. J. and Kralli, A.. (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, Vol. 101, H. 17. pp. 6472-6477.

2003

Handschin, Christoph and 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.

Sanyal, S. and Handschin, C. and Podvinec, M. and Song, K. -H. and Kim, H. -J. and Kim, J. -Y. and Seo, Y. -W. and Kim, S. -A. and Kwon, H. -B. and Lee, K. and Kim, W. -S. and Meyer, U. A. and Choi, H. -S.. (2003) Molecular cloning and characterization of chicken orphan nuclear receptor cTR2. General and Comparative Endocrinology, 132 (3). pp. 474-484.

2002

Fraser, D. J. and Podvinec, M. and Kaufmann, M. R. and Meyer, U. A.. (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, Vol. 277 , no. 38. pp. 34717-34726.

Handschin, C. and Podvinec, M. and Amherd, R. and Looser, R. and Ourlin, J. -C. and Meyer, U. A.. (2002) Cholesterol and bile acids regulate xenosensor signaling in drug-mediated induction of cytochromes P450. Journal of Biological Chemistry, 277 (33). pp. 29561-29567.

Jung, Diana and Podvinec, Michael and Meyer, Urs A. and Mangelsdorf, David J. and Fried, Michael and Meier, Peter J. and Kullak-Ublick, Gerd A.. (2002) Human organic anion transporting polypeptide 8 promoter is transactivated by the farnesoid X receptor/bile acid receptorw. Gastroenterology, Vol. 122, H. 7. pp. 1954-1966.

Meyer, R. P. and Podvinec, M. and Meyer, U. A.. (2002) Cytochrome P450 CYP1A1 accumulates in the cytosol of kidney and brain and is activated by heme. Molecular pharmacology, Vol. 62, H. 5. pp. 1061-1067.

Podvinec, M. and Kaufmann, M. R. and Handschin, C. and Meyer, U. A.. (2002) NUBIScan, an in silico approach for prediction of nuclear receptor response elements. Molecular endocrinology, Vol. 16, H. 6. pp. 1269-1279.

2001

Handschin, C. and Podvinec, M. and Looser, R. and Amherd, R. and Meyer, U. A.. (2001) Multiple enhancer units mediate drug induction of CYP2H1 by xenobiotic-sensing orphan nuclear receptor chicken xenobiotic receptor. Molecular pharmacology, 60 (4). pp. 681-689.

Handschin, C. and Podvinec, M. and Stockli, J. and Hoffmann, K. and Meyer, U. A.. (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, Vol. 15, H. 9. pp. 1571-1585.

2000

Brachat, A. and Liebundguth, N. and Rebischung, C. and Lemire, S. and Scharer, F. and Hoepfner, D. and Demchyshyn, V. and Howald, I. and Dusterhoft, A. and Mostl, D. and Pohlmann, R. and Kotter, P. and Hall, M. N. and Wach, A. and Philippsen, P.. (2000) Analysis of deletion phenotypes and GFP fusions of 21 novel Saccharomyces cerevisiae open reading frames. Yeast, 16 (3). pp. 241-253.

Handschin, C. and 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, Vol. 97, No. 20. pp. 10769-10774.

1999

Wendland, J. and Pohlmann, R. and Dietrich, F. and Steiner, S. and Mohr, C. and Philippsen, P.. (1999) Compact organization of rRNA genes in the filamentous fungus Ashbya gossypii. Current Genetics, Vol. 35, H. 6. pp. 618-625.

1997

Philippsen, P. and Kleine, K. and Pohlmann, R. and Dusterhoft, A. and Hamberg, K. and Hegemann, J. H. and Obermaier, B. and Urrestarazu, L. A. and Aert, R. and Albermann, K. and Altmann, R. and Andre, B. and Baladron, V. and Ballesta, J. P. and Becam, A. M. and Beinhauer, J. and Boskovic, J. and Buitrago, M. J. and Bussereau, F. and Coster, F. and Crouzet, M. and D'Angelo, M. and Dal Pero, F. and De Antoni, A. and Hani, J.. (1997) The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications. Nature, Vol. 387, no. 6632, Suppl.. pp. 93-98.

1996

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, Vol. 12, H. 4. pp. 391-402.