EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany


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


Total: 55 publication(s)


Xavier JC, Patil KR, Rocha I. (2018)

Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes.

PLoS Comput Biol 14(11) doi: 10.1371/journal.pcbi.1006556
Europe PMC | doi

Machado D, Andrejev S, Tramontano M, Patil KR. (2018)

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities.

Nucleic Acids Res. 46(15):7542-7553. doi: 10.1093/nar/gky537
Europe PMC | doi

Patil KR, Ralser M. (2018)

Freeing Yeast from Alcohol Addiction (Just) to Make (It) Fat Instead.

Cell 174(6):1342-1344. doi: 10.1016/j.cell.2018.08.024
Europe PMC | doi

Oatley M, Vargel O, Svensson V, Shvartsman M, Ganter K, Zirngibl K, Pavlovich PV, Milchevskaya V, Foteva VV, Natarajan KN, Baying B, Benes V, Patil KR, Teichmann SA, Lancrin C. (2018)

Single-cell transcriptomics identifies CD44 as a new marker and regulator of haematopoietic stem cells development.

bioRxiv 1-41. doi: 10.1101/338178

Strucko T, Zirngibl K, Pereira F, Kafkia E, Mohamed ET, Rettel M, Stein F, Feist AM, Jouhten P, Patil KR, Forster J. (2018)

Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae.

Metab Eng 47:73-82. doi: 10.1016/j.ymben.2018.03.006
Europe PMC | doi

Maier L, Pruteanu M, Kuhn M, Zeller G, Telzerow A, Anderson EE, Brochado AR, Fernandez KC, Dose H, Mori H, Patil KR, Bork P, Typas A. (2018)

Extensive impact of non-antibiotic drugs on human gut bacteria.

Nature 555(7698) doi: 10.1038/nature25979
Europe PMC | doi

Tramontano M, Andrejev S, Pruteanu M, Klünemann M, Kuhn M, Galardini M, Jouhten P, Zelezniak A, Zeller G, Bork P, Typas A, Patil KR. (2018)

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies.

Nat Microbiol 3(4) doi: 10.1038/s41564-018-0123-9
Europe PMC | doi

Lambertsen L, Rubio-Cosials A, Patil KR, Barabas O. (2018)

Conjugative transposition of the vancomycin resistance carrying Tn1549: enzymatic requirements and target site preferences.

Mol. Microbiol. 107(5) doi: 10.1111/mmi.13905
Europe PMC | doi

Machado D, Andrejev S, Tramontano M, Patil KR. (2018)

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

bioRxiv doi: 10.1101/223198


Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, Tramontano M, Driessen M, Hercog R, Jung FE, Kultima JR, Hayward MR, Coelho LP, Allen-Vercoe E, Bertrand L, Blaut M, Brown JRM, Carton T, Cools-Portier S, Daigneault M, Derrien M, Druesne A, de Vos WM, Finlay BB, Flint HJ, Guarner F, Hattori M, Heilig H, Luna RA, van Hylckama Vlieg J, Junick J, Klymiuk I, Langella P, Le Chatelier E, Mai V, Manichanh C, Martin JC, Mery C, Morita H, O'Toole PW, Orvain C, Patil KR, Penders J, Persson S, Pons N, Popova M, Salonen A, Saulnier D, Scott KP, Singh B, Slezak K, Veiga P, Versalovic J, Zhao L, Zoetendal EG, Ehrlich SD, Dore J, Bork P. (2017)

Towards standards for human fecal sample processing in metagenomic studies.

Nat Biotechnol. 35(11) doi: 10.1038/nbt.3960
Europe PMC | doi

Ponomarova O, Gabrielli N, Sévin DC, Mülleder M, Zirngibl K, Bulyha K, Andrejev S, Kafkia E, Typas A, Sauer U, Ralser M, Patil KR. (2017)

Yeast Creates a Niche for Symbiotic Lactic Acid Bacteria through Nitrogen Overflow.

Cell Syst S2405-4712(17):30390-30393. doi: 10.1016/j.cels.2017.09.002
Europe PMC | doi

Kim Y, Blasche S, Patil KR. (2017)

Draft Genome Sequences of Three Novel Low-Abundance Species Strains Isolated from Kefir Grain.

Genome Announc 5(39) doi: 10.1128/genomeA.00869-17
Europe PMC | doi

Blasche S, Kim Y, Patil KR. (2017)

Draft Genome Sequence of Corynebacterium kefirresidentii SB, Isolated from Kefir.

Genome Announc 5(37) doi: 10.1128/genomeA.00877-17
Europe PMC | doi

Havas KM, Milchevskaya V, Radic K, Alladin A, Kafkia E, Garcia M, Stolte J, Klaus B, Rotmensz N, Gibson TJ, Burwinkel B, Schneeweiss A, Pruneri G, Patil KR, Sotillo R, Jechlinger M. (2017)

Metabolic shifts in residual breast cancer drive tumor recurrence

J Clin Invest 127(6):2091-2105. doi: 10.1172/JCI89914
Europe PMC | doi

Jouhten P, Huerta-Cepas J, Bork P, Patil KR. (2017)

Metabolic anchor reactions for robust biorefining.

Metab. Eng. 40:1-4. doi: 10.1016/j.ymben.2017.02.010
Europe PMC | doi

Xavier JC, Patil KR, Rocha I. (2017)

Integration of Biomass Formulations of Genome-Scale Metabolic Models with Experimental Data Reveals Universally Essential Cofactors in Prokaryotes.

Metab. Eng. 39:200-208. doi: 10.1016/j.ymben.2016.12.002
Europe PMC | doi


Jouhten P, Ponomarova O, Gonzalez R, Patil KR. (2016)

Saccharomyces cerevisiae metabolism in ecological context.

FEMS Yeast Res. 16(7) doi: 10.1093/femsyr/fow080
Europe PMC | doi

Jouhten P, Boruta T, Andrejev S, Pereira F, Rocha I, Patil KR. (2016)

Yeast metabolic chassis designs for diverse biotechnological products.

Sci Rep 6:29694. doi: 10.1038/srep29694
Europe PMC | doi

Alam MT, Zelezniak A, Mülleder M, Shliaha P, Schwarz R, Capuano F, Vowinckel J, Radmaneshfar E, Krüger A, Calvani E, Michel S, Börno S, Christen S, Patil KR, Timmermann B, Lilley KS, Ralser M. (2016)

The metabolic background is a global player in Saccharomyces gene expression epistasis

Nat Microbiol 1(3) doi: 10.1038/nmicrobiol.2015.30
Europe PMC | doi


Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RM, Fong SS, Hatzimanikatis V, Herrgård MJ, Holder A, Hucka M, Hyduke D, Jamshidi N, Lee SY, Le Novère N, Lerman JA, Lewis NE, Ma D, Mahadevan R, Maranas C, Nagarajan H, Navid A, Nielsen J, Nielsen LK, Nogales J, Noronha A, Pal C, Palsson BO, Papin JA, Patil KR, Price ND, Reed JL, Saunders M, Senger RS, Sonnenschein N, Sun Y, Thiele I. (2015)

Do genome-scale models need exact solvers or clearer standards?

Mol Syst Biol 11(10):831. doi: 10.15252/msb.20156157
Europe PMC | doi

Ponomarova O, Patil KR. (2015)

Metabolic interactions in microbial communities: untangling the Gordian knot.

Curr. Opin. Microbiol. 27:37-44. doi: 10.1016/j.mib.2015.06.014
Europe PMC | doi

Zelezniak A, Andrejev S, Ponomarova O, Mende DR, Bork P, Patil KR. (2015)

Metabolic dependencies drive species co-occurrence in diverse microbial communities.

Proc. Natl. Acad. Sci. U.S.A. 112(20):6449-6454. doi: 10.1073/pnas.1421834112
Europe PMC | doi


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

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

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


Machado D, Soons Z, Patil KR, Ferreira EC, Rocha I. (2012)

Random sampling of elementary flux modes in large-scale metabolic networks

Paper presented at the 11th European Conference on Computational Biology (ECCB) / Conference of the Intelligent Systems in Molecular Biology (ISMB), Basel, SWITZERLAND, SEP 09-12, 2012.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

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

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


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

BIOTECHNOL BIOPROC E 10(5):385-399. doi: 10.1007/BF02989821

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