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Patil GroupPublications

Total: 33 publication(s)


Xavier JC, Patil KR, Rocha I. (2014)
Systems Biology Perspectives on Minimal and Simpler Cells
Microbiol. Mol. Biol. Rev. 78(3):487-509. doi:10.1128/MMBR.00050-13
Europe PMC | doi

Zelezniak A, Sheridan S, Patil KR. (2014)
Contribution of network connectivity in determining the relationship between gene expression and metabolite concentration changes.
PLoS Comput. Biol. 10(4) doi:10.1371/journal.pcbi.1003572
Europe PMC | doi

Klünemann M, Schmid M, Patil KR. (2014)
Computational tools for modeling xenometabolism of the human gut microbiota
Trends Biotechnol. 32(3):157-165. doi:10.1016/j.tibtech.2014.01.005
Europe PMC | doi

Brochado AR, Patil KR. (2014)
Model-guided identification of gene deletion targets for metabolic engineering in Saccharomyces cerevisiae.
Methods Mol. Biol. 1152:281-294. doi:10.1007/978-1-4939-0563-8_17
Europe PMC | doi


Brochado AR, Patil KR. (2013)
Overexpression of O-methyltransferase leads to improved vanillin production in baker's yeast only when complemented with model-guided network engineering
Biotechnol. Bioeng. 110(2):656-659. doi:10.1002/bit.24731
Europe PMC | doi

Soons ZI, Ferreira EC, Patil KR, Rocha I. (2013)
Identification of metabolic engineering targets through analysis of optimal and sub-optimal routes
PLoS ONE 8(4):e61648. doi:10.1371/journal.pone.0061648
Europe PMC | doi

Otero JM, Cimini D, Patil KR, Poulsen SG, Olsson L, Nielsen J. (2013)
Industrial systems biology of Saccharomyces cerevisiae enables novel succinic acid cell factory
PLoS ONE 8(1):e54144. doi:10.1371/journal.pone.0054144
Europe PMC | doi


Machado D, Soons Z, Patil KR, Ferreira EC, Rocha I. (2012)
Random sampling of elementary flux modes in large-scale metabolic networks
Bioinformatics 28(18):i515-i521. doi:10.1093/bioinformatics/bts401
Europe PMC | doi

Hansen BG, Mnich E, Nielsen KF, Nielsen JB, Nielsen MT, Mortensen UH, Larsen TO, Patil KR. (2012)
Involvement of a natural fusion of a cytochrome P450 and a hydrolase in mycophenolic acid biosynthesis
Appl. Environ. Microbiol. 78(14):4908-4913. doi:10.1128/aem.07955-11
Europe PMC | doi

Brochado AR, Andrejev S, Maranas CD, Patil KR. (2012)
Impact of stoichiometry representation on simulation of genotype-phenotype relationships in metabolic networks
PLoS Comput. Biol. 8(11):e1002758. doi:10.1371/journal.pcbi.1002758
Europe PMC | doi

Yamada T, Waller AS, Raes J, Zelezniak A, Perchat N, Perret A, Salanoubat M, Patil KR, Weissenbach J, Bork P. (2012)
Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours
Mol. Syst. Biol. 8:581. doi:10.1038/msb.2012.13
Europe PMC | doi


Olsen LR, Hansen NB, Bonde MT, Genee HJ, Holm DK, Carlsen S, Hansen BG, Patil KR, Mortensen UH, Wernersson R. (2011)
PHUSER (Primer Help for USER): a novel tool for USER fusion primer design
Nucleic Acids Res. 39(Web Server issue):W61-7. doi:10.1093/nar/gkr394
Europe PMC | doi

Hansen BG, Salomonsen B, Nielsen MT, Nielsen JB, Hansen NB, Nielsen KF, Regueira TB, Nielsen J, Patil KR, Mortensen UH. (2011)
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
Appl. Environ. Microbiol. 77(9):3044-3051. doi:10.1128/aem.01768-10
Europe PMC | doi

Montagud A, Zelezniak A, Navarro E, de Córdoba PF, Urchueguía JF, Patil KR. (2011)
Flux coupling and transcriptional regulation within the metabolic network of the photosynthetic bacterium Synechocystis sp. PCC6803
Biotechnol J 6(3):330-342. doi:10.1002/biot.201000109
Europe PMC | doi

Hansen BG, Genee HJ, Kaas CS, Nielsen JB, Regueira TB, Mortensen UH, Frisvad JC, Patil KR. (2011)
A new class of IMP dehydrogenase with a role in self-resistance of mycophenolic acid producing fungi
BMC Microbiol. 11:202. doi:10.1186/1471-2180-11-202
Europe PMC | doi


Cvijovic M, Olivares-Hernández R, Agren R, Dahr N, Vongsangnak W, Nookaew I, Patil KR, Nielsen J. (2010)
BioMet Toolbox: genome-wide analysis of metabolism
Nucleic Acids Res. 38(Web Server issue):W144-9. doi:10.1093/nar/gkq404
Europe PMC | doi

Zelezniak A, Pers TH, Soares S, Patti ME, Patil KR. (2010)
Metabolic network topology reveals transcriptional regulatory signatures of type 2 diabetes
PLoS Comput. Biol. 6(4):e1000729. doi:10.1371/journal.pcbi.1000729
Europe PMC | doi

Brochado AR, Matos C, Møller BL, Hansen J, Mortensen UH, Patil KR. (2010)
Improved vanillin production in baker's yeast through in silico design
Microb. Cell Fact. 9:84. doi:10.1186/1475-2859-9-84
Europe PMC | doi

Rocha I, Maia P, Evangelista P, Vilaça P, Soares S, Pinto JP, Nielsen J, Patil KR, Ferreira EC, Rocha M. (2010)
OptFlux: an open-source software platform for in silico metabolic engineering
BMC Syst Biol 4:45. doi:10.1186/1752-0509-4-45
Europe PMC | doi

Montagud A, Navarro E, Fernández de Córdoba P, Urchueguía JF, Patil KR. (2010)
Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium
BMC Syst Biol 4:156. doi:10.1186/1752-0509-4-156
Europe PMC | doi


Asadollahi MA, Maury J, Patil KR, Schalk M, Clark A, Nielsen J. (2009)
Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering
Metab. Eng. 11(6):328-334. doi:10.1016/j.ymben.2009.07.001
Europe PMC | doi

Cimini D, Patil KR, Schiraldi C, Nielsen J. (2009)
Global transcriptional response of Saccharomyces cerevisiae to the deletion of SDH3
BMC Syst Biol 3:17. doi:10.1186/1752-0509-3-17
Europe PMC | doi


Oliveira AP, Patil KR, Nielsen J. (2008)
Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks
BMC Syst Biol 2:17. doi:10.1186/1752-0509-2-17
Europe PMC | doi

Rocha M, Maia P, Mendes R, Pinto JP, Ferreira EC, Nielsen J, Patil KR, Rocha I. (2008)
Natural computation meta-heuristics for the in silico optimization of microbial strains
BMC Bioinformatics 9:499. doi:10.1186/1471-2105-9-499
Europe PMC | doi


Villadsen J, Patil KR. (2007)
Optimal fed-batch cultivation when mass transfer becomes limiting
Biotechnol. Bioeng. 98(3):706-710. doi:10.1002/bit.21451
Europe PMC | doi

Baxter CJ, Redestig H, Schauer N, Repsilber D, Patil KR, Nielsen J, Selbig J, Liu J, Fernie AR, Sweetlove LJ. (2007)
The metabolic response of heterotrophic Arabidopsis cells to oxidative stress
Plant Physiol. 143(1):312-325. doi:10.1104/pp.106.090431
Europe PMC | doi


Usaite R, Patil KR, Grotkjaer T, Nielsen J, Regenberg B. (2006)
Global transcriptional and physiological responses of Saccharomyces cerevisiae to ammonium, L-alanine, or L-glutamine limitation
Appl. Environ. Microbiol. 72(9):6194-6203. doi:10.1128/aem.00548-06
Europe PMC | doi

Raghevendran V, Patil KR, Olsson L, Nielsen J. (2006)
Hap4 is not essential for activation of respiration at low specific growth rates in Saccharomyces cerevisiae
J. Biol. Chem. 281(18):12308-12314. doi:10.1074/jbc.m512972200
Europe PMC | doi

Cakir T, Patil KR, Onsan Zi, Ulgen KO, Kirdar B, Nielsen J. (2006)
Integration of metabolome data with metabolic networks reveals reporter reactions
Mol. Syst. Biol. 2:50. doi:10.1038/msb4100085
Europe PMC | doi


Jewett MC, Oliveira AP, Patil KR, Nielsen J. (2005)
The role of high-throughput transcriptome analysis in metabolic engineering

Patil KR, Nielsen J. (2005)
Uncovering transcriptional regulation of metabolism by using metabolic network topology
Proc. Natl. Acad. Sci. U.S.A. 102(8):2685-2689. doi:10.1073/pnas.0406811102
Europe PMC | doi

Patil KR, Rocha I, Förster J, Nielsen J. (2005)
Evolutionary programming as a platform for in silico metabolic engineering
BMC Bioinformatics 6:308. doi:10.1186/1471-2105-6-308
Europe PMC | doi


Patil KR, Akesson M, Nielsen J. (2004)
Use of genome-scale microbial models for metabolic engineering
Curr. Opin. Biotechnol. 15(1):64-69. doi:10.1016/j.copbio.2003.11.003
Europe PMC | doi