Staff at EMBL

Dr. Kiran Raosaheb Patil

Group Leader
Patil Group

EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

Biography

M. tech. (Chemical engineering) 2002, Indian Institute of Technology, Bombay.
PhD 2006, Technical University of Denmark.
Assistant Professor, 2006-2010, Technical University of Denmark.
Group leader at EMBL since 2010.

Publications

Overexpression of O-methyltransferase leads to improved vanillin production in baker's yeast only when complemented with model-guided network engineering. Brochado, A.R. & Patil, K.R. Biotechnol Bioeng. 2013 Feb;110(2):656-9. doi: 10.1002/bit.24731. Epub 2012 Oct23. PubMed

Industrial Systems Biology of Saccharomyces cerevisiae Enables Novel Succinic Acid Cell Factory. Otero, J.M., Cimini, D., Patil, K.R., Poulsen, S.G., Olsson, L. & Nielsen, J. PLoS One. 2013;8(1):e54144. doi: 10.1371/journal.pone.0054144. Epub 2013 Jan 21. PubMed

Impact of stoichiometry representation on simulation of genotype-phenotype relationships in metabolic networks. Brochado, A.R., Andrejev, S., Maranas, C.D. & Patil, K.R. PLoS Comput Biol. 2012;8(11):e1002758. doi: 10.1371/journal.pcbi.1002758. Epub2012 Nov 1. PubMed

Random sampling of elementary flux modes in large-scale metabolic networks. Machado, D., Soons, Z., Patil, K.R., Ferreira, E.C. & Rocha, I. Bioinformatics. 2012 Sep 15;28(18):i515-i521. PubMed

Involvement of a natural fusion of a cytochrome P450 and a hydrolase in mycophenolic acid biosynthesis. Hansen, B.G., Mnich, E., Nielsen, K.F., Nielsen, J.B., Nielsen, M.T., Mortensen, U.H., Larsen, T.O. & Patil, K.R. Appl Environ Microbiol. 2012 Jul;78(14):4908-13. doi: 10.1128/AEM.07955-11. Epub2012 Apr 27. PubMed

Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours. Yamada, T., Waller, A.S., Raes, J., Zelezniak, A., Perchat, N., Perret, A., Salanoubat, M., Patil, K.R., Weissenbach, J. & Bork, P. Mol Syst Biol. 2012 May 8;8:581. doi: 10.1038/msb.2012.13. PubMed

A new class of IMP dehydrogenase with a role in self-resistance of mycophenolic acid producing fungi. Hansen, B.G., Genee, H.J., Kaas, C.S., Nielsen, J.B., Regueira, T.B., Mortensen, U.H., Frisvad, J.C. & Patil, K.R. BMC Microbiol. 2011 Sep 16;11:202. PubMed

PHUSER (Primer Help for USER): a novel tool for USER fusion primer design. Olsen, L.R., Hansen, N.B., Bonde, M.T., Genee, H.J., Holm, D.K., Carlsen, S., Hansen, B.G., Patil, K.R., Mortensen, U.H. & Wernersson, R. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W61-7. Epub 2011 May 26. PubMed

Versatile enzyme expression and characterization system for Aspergillus nidulans, with the Penicillium brevicompactum polyketide synthase gene from the mycophenolic acid gene cluster as a test case. Hansen, B.G., Salomonsen, B., Nielsen, M.T., Nielsen, J.B., Hansen, N.B., Nielsen, K.F., Regueira, T.B., Nielsen, J., Patil, K.R. & Mortensen, U.H. Appl Environ Microbiol. 2011 May;77(9):3044-51. doi: 10.1128/AEM.01768-10. Epub2011 Mar 11. PubMed

Flux coupling and transcriptional regulation within the metabolic network of the photosynthetic bacterium Synechocystis sp. PCC6803. Montagud, A., Zelezniak, A., Navarro, E., de Cordoba, P.F., Urchueguia, J.F. & Patil, K.R. Biotechnol J. 2011 Mar;6(3):330-42. doi: 10.1002/biot.201000109. Epub 2011 Jan11. PubMed

Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium. Montagud, A., Navarro, E., Fernandez de Cordoba, P., Urchueguia, J.F. & Patil, K.R. BMC Syst Biol. 2010 Nov 17;4:156. doi: 10.1186/1752-0509-4-156. PubMed

Improved vanillin production in baker's yeast through in silico design. Brochado, A.R., Matos, C., Moller, B.L., Hansen, J., Mortensen, U.H. & Patil, K.R. Microb Cell Fact. 2010 Nov 8;9(1):84. PubMed

BioMet Toolbox: genome-wide analysis of metabolism. Cvijovic, M., Olivares-Hernandez, R., Agren, R., Dahr, N., Vongsangnak, W., Nookaew, I., Patil, K.R. & Nielsen, J. Nucleic Acids Res. 2010 Jul 1;38 Suppl:W144-9. Epub 2010 May 18. PubMed

Metabolic network topology reveals transcriptional regulatory signatures of type 2 diabetes. Zelezniak, A., Pers, T.H., Soares, S., Patti, M.E. & Patil, K.R. PLoS Comput Biol. 2010 Apr 1;6(4):e1000729. PubMed

OptFlux: an open-source software platform for in silico metabolic engineering. Rocha, I., Maia, P., Evangelista, P., Vilaca, P., Soares, S., Pinto, J.P., Nielsen, J., Patil, K.R., Ferreira, E.C. & Rocha, M. BMC Syst Biol. 2010 Apr 19;4:45. PubMed

Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering. Asadollahi, M.A., Maury, J., Patil, K.R., Schalk, M., Clark, A. & Nielsen, J. Metab Eng. 2009 Nov;11(6):328-34. Epub 2009 Jul 18. PubMed

Global transcriptional response of Saccharomyces cerevisiae to the deletion of SDH3. Cimini, D., Patil, K.R., Schiraldi, C. & Nielsen, J. BMC Syst Biol. 2009 Feb 6;3:17. PubMed

Natural computation meta-heuristics for the in silico optimization of microbial strains. Rocha, M., Maia, P., Mendes, R., Pinto, J.P., Ferreira, E.C., Nielsen, J., Patil, K.R. & Rocha, I. BMC Bioinformatics. 2008 Nov 27;9:499. PubMed

Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks. Oliveira, A.P., Patil, K.R. & Nielsen, J. BMC Syst Biol. 2008 Feb 8;2:17. PubMed

Optimal fed-batch cultivation when mass transfer becomes limiting. Villadsen, J. & Patil, K.R. Biotechnol Bioeng. 2007 Oct 15;98(3):706-10. PubMed

The metabolic response of heterotrophic Arabidopsis cells to oxidative stress Baxter C.J., Redestig H., Schauer N., Repsilber D., Patil K.R., Nielsen J., Selbig J., Liu J., Fernie A.R. & Sweetlove L.J. Plant Physiology. 143 (1), 312-325 (2007).

Global transcriptional and physiological response of Saccharomyces cerevisiae to nitrogen limitation Usaite R., Patil K.R., Grotkjær T., Nielsen J. & Regenberg B. Appl. Env. Microbiol., 72 (9), 6194-6203 (2006).

Hap4 is not essential for activation of respiration at low specific growth rates in Saccharomyces cerevisiae Raghevendran V., Patil K.R., Olsson L. & Nielsen J. J. Biol. Chem., 281 (18), 12308-12314 (2006).

Integration of metabolome data with metabolic networks reveals reporter reactions. Cakir, T., Patil, K.R., Onsan, Z., Ulgen, K.O., Kirdar, B. & Nielsen, J. Mol Syst Biol. 2006;2:50. Epub 2006 Oct 3. PubMed

Evolutionary programming as a platform for in silico metabolic engineering. Patil, K.R., Rocha, I., Forster, J. & Nielsen, J. BMC Bioinformatics. 2005 Dec 23;6:308. PubMed

Uncovering transcriptional regulation of metabolism by using metabolic network topology. Patil, K.R. & Nielsen, J. Proc Natl Acad Sci U S A. 2005 Feb 22;102(8):2685-9. Epub 2005 Feb 14. PubMed

The role of high-throughput transcriptome analysis in metabolic engineering Jewett M., Oliveira A. P., Patil K.R. & Nielsen J. Biotechnol. Bioproc. Eng. 10, 385-399 (2005).

Use of genome-scale microbial models for metabolic engineering Patil K. R., Akesson M. & Nielsen J. Curr. Opin. Biotechnol. 15, 64-69 (2004).