SummaryI am currently Head of the Research IT group at the Biozentrum of the University of Basel in Switzerland.
As a molecular biologist, I have researched how drugs affect the gene expression of drug-metabolizing enzymes in our body for several years. Combining my passion for biomedical research and my interest for computer science, I then was a post-doctoral fellow in structural bioinformatics, where I worked on the discovery of new drugs against tropical diseases using molecular modeling approaches and grid computing.
With 10 years of research experience in life science, I oscillate today between the worlds of experimental biology and bioinformatics and try to bring the two closer together. Lately, I have started introducing agile practices, Scrum in particular, in scientific projects.
SpecialtiesBioinformatics, Chemoinformatics, Scientific Computing, GRID computing, Docking and Virtual Screening, Biomedical Research, Signal Transduction, Transcriptional Regulation, Drug Metabolism, Scrum Master, Certified Scrum Practitioner, Agile
Research highlight:Our "Docking against Dengue" project aims to find small molecules with the potential to be developed as drugs against Dengue fever, a neglected disease affecting between 50 and 100 million people annually and claiming 25'000 lives per year. This large-scale project is only feasible using GRID computing on the SwissBioGrid platform (
http://www.swissbiogrid.org).
Through this project, I have become experienced in developing and deploying GRID middleware as a computational enabler and in porting existing applications to the GRID model, both within the university and in collaboration with pharmaceutical industry. Further applications from the fields of proteomics and molecular dynamics have now been successfully brought to the GRID platform. More information about these projects can be found at
http://www.biozentrum.unibas.ch/grid .
Strengths• Experienced in the planning and execution of research projects, strong conceptual and logical thinker. Excellent oral and written communication skills, experienced public speaker.
• Good knowledge of bioinformatics and software development, combined with a strong background in molecular biology, in particular in regard to gene regulation and receptor-ligand interactions. Several years of real-life laboratory experience.
• Experience in a clinically relevant field of biology, and in understanding the requirements and demands of industrial research partners.
• Comfortable in a diverse, multicultural team environment
Scientific profile: Conference lectures, peer-reviewed publications and patents ... in other words, all that stuff that goes in a scientific CV and is rarely read. The casual reader may choose to skip this part.
Selected lectures:
• 03/2008 Basel Computational Biology Conference, Basel: “Docking for neglected diseases as community effort”
• 08/2007 NorduGrid 2007, Copenhagen, Denmark: “Application examples and lessons learned from the SwissBioGrid initiative”
• 12/2006 eScience 2006, Amsterdam, The Netherlands: “The SwissBioGrid Project: Objectives, Preliminary Results and Lessons Learned”
• 06/2006 HealthGrid 2006, Valencia, Spain: “The Dengue Docking Project: Virtual Screening on the SwissBioGrid provides small-molecule candidates for in vitro inhibition testing of viral proteins”, contribution to the WISDOM workshop
• 01/2005 United Devices 2005 Grid Conference, Zürich, Switzerland: “Grid Technology: A Cure for Neglected Diseases?”
• 08/2004 7th International ISSX Meeting, Vancouver, Canada. Short course: “In Silico prediction of drug effects on the expression of drug-metabolizing enzymes and transporters”
• 10/2002 EUFEPS 2002, 7th European Congress of Pharmaceutical Sciences, Stockholm, Sweden: “Genomic screening of induction responses”
Publications, Book chapters and patents:• Moehren U, Denayer S, Podvinec M, Verrijdt G, Claessens F:
Identification of androgen-selective androgen-response elements in the human aquaporin-5 and Rad9 genes. Biochem J. (2008) 411(3):679-86
• Zosso D, Arnold K, Schwede T, Podvinec M:
SWISS-TANDEM: A Web-based Workspace for MS/MS Protein Identification on PC Grids. Proceedings of the 20th IEEE International Symposium on computer-based medical systems (2007).
• Zosso D, Podvinec M, Müller M, Aebersold R, Peitsch MC, Schwede T:
Tandem Mass Spectrometry Identification on a PC Grid. Stud. Health Technol Inform. (2007) 126:3-12
• Podvinec M, Scarsi M, Roth A, Hug H, Kersten S, Albrecht H, Schwede T, Meyer UA, Rücker C:
Sulfonylureas and Glinides Exhibit PPARγ Activity: A Combined Virtual Screening and Biological Assay Approach. Mol. Pharmacol. (2007) 71(2):398-406
• Podvinec M, Maffioletti S, Kunszt P, Arnold K, Cerutti L, Nyffeler B, Schlapbach R, Türker C, Stockinger H, Thomas AJ, Peitsch MC, Schwede T:
The SwissBioGrid Project: Objectives, Preliminary Results and Lessons Learned. 2nd IEEE International Conference on e-Science and Grid Computing, IEEE Computer Society Press, Amsterdam, The Netherlands (2006)
• Podvinec M, Meyer UA:
Prediction of cis-regulatory elements for drug-activated transcription factors in the regulation of drug-metabolizing enzymes and drug transporters. Expert Opin. Drug Metab. Toxicol. (2006) 2(3) 367-79
• Gnerre C, Schuster GU, Roth A, Handschin C, Johansson L, Looser R, Parini P, Podvinec M, Robertsson K, Gustafsson JA, Meyer UA:
LXR deficiency and cholesterol feeding affect the expression and phenobarbital-mediated induction of cytochromes P450 in mouse liver. J Lipid Res. 2005 Aug;46(8):1633-42.
• Handschin C, Blattler S, Roth A, Looser R, Oscarson M, Kaufmann MR, Podvinec M, Gnerre C, Meyer UA.:
The evolution of drug-activated nuclear receptors: one ancestral gene diverged into two xenosensor genes in mammals. Nucl Recept. 2004 Oct 12;2(1):7.
• Podvinec M, Handschin C, Looser R, Meyer UA.:
Identification of the xenosensors regulat¬ing human 5-aminolevulinate synthase. Proc Natl Acad Sci U S A. 2004 Jun 15;101(24):9127-32
• Schreiber SN, Emter R, Hock MB, Knutti D, Cardenas J, Podvinec M, Oakeley EJ, Kralli A.:
The estrogen-related receptor alpha (ERRalpha) functions in PPARgamma coactivator 1alpha (PGC-1alpha)-induced mitochondrial biogenesis. Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6472-7.
• Handschin C, Podvinec M, Meyer UA.:
In silico approaches, and in vitro and in vivo experiments to predict induction of drug metabolism. Drug News Perspect. 2003 Sep;16(7):423-34.
• Sanyal S, Handschin C, Podvinec M, Song KH, Kim HJ, Kim JY, Seo YW, Kim SA, Kwon HB, Lee K, Kim WS, Meyer UA, Choi HS.:
Molecular cloning and characterization of chicken orphan nuclear receptor cTR2. Gen Comp Endocrinol. 2003 Jul;132(3):474-84.
• Meyer RP, Podvinec M, Meyer UA.:
Cytochrome P450 CYP1A1 accumulates in the cytosol of kidney and brain and is activated by heme. Mol Pharmacol. 2002 Nov;62(5):1061-7.
• Fraser DJ, Podvinec M, Kaufmann MR, Meyer UA.:
Drugs mediate the transcriptional activation of the 5-aminolevulinic acid synthase (ALAS1) gene via the chicken xenobiotic-sensing nuclear receptor (CXR). J Biol Chem. 2002 Sep 20;277(38):34717-26.
• Jung D, Podvinec M, Meyer UA, Mangelsdorf DJ, Fried M, Meier PJ, Kullak-Ublick GA.:
Human organic anion transporting polypeptide 8 promoter is transactivated by the farnesoid X receptor/bile acid receptor. Gastroenterology. 2002 Jun;122(7):1954-66.
• Handschin C, Podvinec M, Amherd R, Looser R, Ourlin JC, Meyer UA.:
Cholesterol and bile acids regulate xenosensor signaling in drug-mediated induction of cytochromes P450. J Biol Chem. 2002 Aug 16;277(33):29561-7.
• Podvinec M, Kaufmann MR, Handschin C, Meyer UA.:
NUBIScan, an in silico approach for prediction of nuclear receptor response elements. Mol Endocrinol. 2002 Jun;16(6):1269-79.
• Handschin C, Podvinec M, Looser R, Amherd R, Meyer UA.:
Multiple enhancer units mediate drug induction of CYP2H1 by xenobiotic-sensing orphan nuclear receptor chicken xenobiotic receptor. Mol Pharmacol. 2001 Oct;60(4):681-9.
• Handschin C, Podvinec M, Stockli J, Hoffmann K, Meyer UA.: Conservation of signaling pathways of xenobiotic-sensing orphan nuclear receptors, chicken xenobiotic receptor, constitutive androstane receptor, and pregnane X receptor, from birds to humans. Mol Endocrinol. 2001 Sep;15(9):1571-85.
• Handschin C, Podvinec M, Meyer UA.:
CXR, a chicken xenobiotic-sensing orphan nuclear receptor, is related to both mammalian pregnane X receptor (PXR) and constitutive androstane receptor (CAR). Proc Natl Acad Sci U S A. 2000 Sep 26;97(20):10769-74.
Book chapters:• Podvinec M, Schwede T., Peitsch M.C:
Docking for Neglected Diseases as Community Efforts. In: Computational Structural Biology: Methods and Applications, World Scientific Publishing Co. (2008)
Granted patents•
US Patent US2005118601: MEYER URS (CH); FRASER DAVID J (CH); KAUFMANN MICHEL R (CH); PODVINEC MICHAEL (CH); ZUMSTEG ADRIAN (CH):
Enhancer sequence of the 5-aminolevulinic acid synthase gene: Nucleic acid se¬quences mediating chemical compound induced 5-aminolevulinate synthase gene (ALAS1) expres¬sion are disclosed. Said sequences comprise at least a DR-4 binding site. Furthermore, in vitro methods for testing chemical compounds for modulation of heme and/or P 450 cytochromes syn¬thesis are described.
Publication date: June 2, 2005
