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Patil GroupPublications

Computational tools for modeling xenometabolism of the human gut microbiota.
Klunemann, M., Schmid, M. & Patil, K.R.
This is a review article.
Trends Biotechnol. 2014 Feb 13. pii: S0167-7799(14)00018-3. doi:10.1016/j.tibtech.2014.01.005. Europe PMC

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. Europe PMC

Identification of Metabolic Engineering Targets through Analysis of Optimal and Sub-Optimal Routes.
Soons, Z.I., Ferreira, E.C., Patil, K.R. & Rocha, I.
PLoS One. 2013 Apr 23;8(4):e61648. doi: 10.1371/journal.pone.0061648. Print 2013. Europe PMC

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. Europe PMC

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. Europe PMC

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. Europe PMC

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. Europe PMC

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. Europe PMC

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. Europe PMC

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. Europe PMC

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. Europe PMC

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. doi: 10.1186/1471-2180-11-202. Europe PMC

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. Europe PMC

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. Europe PMC

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. Europe PMC

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. Europe PMC

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. Europe PMC

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. Europe PMC

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. Europe PMC

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. Europe PMC

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. Europe PMC

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

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 Physiol. 2007 Jan;143(1):312-25. Epub 2006 Nov 22. Europe PMC

Global transcriptional and physiological responses of Saccharomyces cerevisiae to ammonium, L-alanine, or L-glutamine limitation.
Usaite, R., Patil, K.R., Grotkjaer, T., Nielsen, J. & Regenberg, B.
Appl Environ Microbiol. 2006 Sep;72(9):6194-203. Europe PMC

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. 2006 May 5;281(18):12308-14. Epub 2006 Mar 7. Europe PMC

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. Europe PMC

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. Europe PMC

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. Europe PMC

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. 2004 Feb;15(1):64-9. Europe PMC