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

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

Metab Eng. 2018 Mar 10. pii: S1096-7176(17)30403-2. doi: 10.1016/j.ymben.2018.03.006. [Epub ahead of print]


Evaluation of non-negative matrix factorization of grey matter in age prediction.

Varikuti DP, Genon S, Sotiras A, Schwender H, Hoffstaedter F, Patil KR, Jockwitz C, Caspers S, Moebus S, Amunts K, Davatzikos C, Eickhoff SB.

Neuroimage. 2018 Mar 6;173:394-410. doi: 10.1016/j.neuroimage.2018.03.007. [Epub ahead of print]


A simple plug-in bagging ensemble based on threshold-moving for classifying binary and multiclass imbalanced data.

Collell G, Prelec D, Patil KR.

Neurocomputing. 2018 Jan 31;275:330-340. doi: 10.1016/j.neucom.2017.08.035.


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

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

Mol Microbiol. 2018 Mar;107(5):639-658. doi: 10.1111/mmi.13905. Epub 2018 Jan 18.


Towards standards for human fecal sample processing in metagenomic studies.

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.

Nat Biotechnol. 2017 Nov;35(11):1069-1076. doi: 10.1038/nbt.3960. Epub 2017 Oct 2.


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

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

Cell Syst. 2017 Oct 25;5(4):345-357.e6. doi: 10.1016/j.cels.2017.09.002. Epub 2017 Sep 27.


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

Kim Y, Blasche S, Patil KR.

Genome Announc. 2017 Sep 28;5(39). pii: e00869-17. doi: 10.1128/genomeA.00869-17.


Integration and Segregation of Default Mode Network Resting-State Functional Connectivity in Transition-Age Males with High-Functioning Autism Spectrum Disorder: A Proof-of-Concept Study.

Joshi G, Arnold Anteraper S, Patil KR, Semwal M, Goldin RL, Furtak SL, Chai XJ, Saygin ZM, Gabrieli JDE, Biederman J, Whitfield-Gabrieli S.

Brain Connect. 2017 Nov;7(9):558-573. doi: 10.1089/brain.2016.0483.


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

Blasche S, Kim Y, Patil KR.

Genome Announc. 2017 Sep 14;5(37). pii: e00877-17. doi: 10.1128/genomeA.00877-17.


Past and current perspective on new therapeutic targets for Type-II diabetes.

Patil PD, Mahajan UB, Patil KR, Chaudhari S, Patil CR, Agrawal YO, Ojha S, Goyal SN.

Drug Des Devel Ther. 2017 May 22;11:1567-1583. doi: 10.2147/DDDT.S133453. eCollection 2017. Review.


Metabolic shifts in residual breast cancer drive tumor recurrence.

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.

J Clin Invest. 2017 Jun 1;127(6):2091-2105. doi: 10.1172/JCI89914. Epub 2017 May 15.


Metabolic anchor reactions for robust biorefining.

Jouhten P, Huerta-Cepas J, Bork P, Patil KR.

Metab Eng. 2017 Mar;40:1-4. doi: 10.1016/j.ymben.2017.02.010. Epub 2017 Feb 21.


Anti-inflammatory activity of bartogenic acid containing fraction of fruits of Barringtonia racemosa Roxb. in acute and chronic animal models of inflammation.

Patil KR, Patil CR.

J Tradit Complement Med. 2016 Apr 4;7(1):86-93. doi: 10.1016/j.jtcme.2016.02.001. eCollection 2017 Jan.


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

Xavier JC, Patil KR, Rocha I.

Metab Eng. 2017 Jan;39:200-208. doi: 10.1016/j.ymben.2016.12.002. Epub 2016 Dec 8.


Chemomodulatory Potential of Bartogenic Acid Against DMBA/Croton Oil Induced Two-Step Skin Carcinogenesis in Mice.

Patil CR, Sonara BM, Mahajan UB, Patil KR, Patil DD, Jadhav RB, Goyal SN, Ojha S.

J Cancer. 2016 Oct 23;7(14):2139-2147. eCollection 2016.


Saccharomyces cerevisiae metabolism in ecological context.

Jouhten P, Ponomarova O, Gonzalez R, Patil KR.

FEMS Yeast Res. 2016 Nov;16(7). pii: fow080. Epub 2016 Sep 14. Review.


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

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

Nat Microbiol. 2016 Feb 1;1:15030. doi: 10.1038/nmicrobiol.2015.30.


Yeast metabolic chassis designs for diverse biotechnological products.

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

Sci Rep. 2016 Jul 19;6:29694. doi: 10.1038/srep29694.


Midterm survivorship and clinical outcome of INDUS knee prosthesis: 5 year followup study.

Sancheti KH, Sancheti PK, Joshi RS, Patil KR, Shyam AK, Bhaskar RR.

Indian J Orthop. 2016 Mar-Apr;50(2):131-5. doi: 10.4103/0019-5413.177583.


Chitinases and Imaginal disc growth factors organize the extracellular matrix formation at barrier tissues in insects.

Pesch YY, Riedel D, Patil KR, Loch G, Behr M.

Sci Rep. 2016 Feb 3;6:18340. doi: 10.1038/srep18340.


Challenges and issues with streptozotocin-induced diabetes - A clinically relevant animal model to understand the diabetes pathogenesis and evaluate therapeutics.

Goyal SN, Reddy NM, Patil KR, Nakhate KT, Ojha S, Patil CR, Agrawal YO.

Chem Biol Interact. 2016 Jan 25;244:49-63. doi: 10.1016/j.cbi.2015.11.032. Epub 2015 Dec 2. Review.


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

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.

Mol Syst Biol. 2015 Oct 14;11(10):831. doi: 10.15252/msb.20156157. No abstract available.


Architecturally designed Pt-MoS2 and Pt-graphene composites for electrocatalytic methanol oxidation.

Patil SH, Anothumakkool B, Sathaye SD, Patil KR.

Phys Chem Chem Phys. 2015 Oct 21;17(39):26101-10. doi: 10.1039/c5cp04141d. Epub 2015 Sep 17.


Metabolic interactions in microbial communities: untangling the Gordian knot.

Ponomarova O, Patil KR.

Curr Opin Microbiol. 2015 Oct;27:37-44. doi: 10.1016/j.mib.2015.06.014. Epub 2015 Jul 24. Review.


Phytocannabinoids for Cancer Therapeutics: Recent Updates and Future Prospects.

Patil KR, Goyal SN, Sharma C, Patil CR, Ojha S.

Curr Med Chem. 2015;22(30):3472-501. Review.


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

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

Proc Natl Acad Sci U S A. 2015 May 19;112(20):6449-54. doi: 10.1073/pnas.1421834112. Epub 2015 May 4. Erratum in: Proc Natl Acad Sci U S A. 2015 Dec 22;112(51):E7156.


Pentacyclic Triterpenoids Inhibit IKKβ Mediated Activation of NF-κB Pathway: In Silico and In Vitro Evidences.

Patil KR, Mohapatra P, Patel HM, Goyal SN, Ojha S, Kundu CN, Patil CR.

PLoS One. 2015 May 4;10(5):e0125709. doi: 10.1371/journal.pone.0125709. eCollection 2015.


Shape-selective oriented cerium oxide nanocrystals permit assessment of the effect of the exposed facets on catalytic activity and oxygen storage capacity.

Sreeremya TS, Krishnan A, Remani KC, Patil KR, Brougham DF, Ghosh S.

ACS Appl Mater Interfaces. 2015 Apr 29;7(16):8545-55. doi: 10.1021/acsami.5b00298. Epub 2015 Apr 17.


A method to form semiconductor quantum dot (QD) thin films by igniting a flame at air-liquid interface: CdS and WO3.

Jadhav AH, Patil SH, Sathaye SD, Patil KR.

J Colloid Interface Sci. 2015 Feb 1;439:121-8. doi: 10.1016/j.jcis.2014.10.029. Epub 2014 Oct 30.


Systems biology perspectives on minimal and simpler cells.

Xavier JC, Patil KR, Rocha I.

Microbiol Mol Biol Rev. 2014 Sep;78(3):487-509. doi: 10.1128/MMBR.00050-13. Review.


Nitrogen-induced surface area and conductivity modulation of carbon nanohorn and its function as an efficient metal-free oxygen reduction electrocatalyst for anion-exchange membrane fuel cells.

Unni SM, Bhange SN, Illathvalappil R, Mutneja N, Patil KR, Kurungot S.

Small. 2015 Jan 21;11(3):352-60. doi: 10.1002/smll.201303892. Epub 2014 Aug 22.


Contribution of network connectivity in determining the relationship between gene expression and metabolite concentration changes.

Zelezniak A, Sheridan S, Patil KR.

PLoS Comput Biol. 2014 Apr 24;10(4):e1003572. doi: 10.1371/journal.pcbi.1003572. eCollection 2014 Apr.


Model-guided identification of gene deletion targets for metabolic engineering in Saccharomyces cerevisiae.

Brochado AR, Patil KR.

Methods Mol Biol. 2014;1152:281-94. doi: 10.1007/978-1-4939-0563-8_17.


Computational tools for modeling xenometabolism of the human gut microbiota.

Klünemann M, Schmid M, Patil KR.

Trends Biotechnol. 2014 Mar;32(3):157-65. doi: 10.1016/j.tibtech.2014.01.005. Epub 2014 Feb 13. Review.


Vapor-liquid-solid growth of one-dimensional tin sulfide (SnS) nanostructures with promising field emission behavior.

Suryawanshi SR, Warule SS, Patil SS, Patil KR, More MA.

ACS Appl Mater Interfaces. 2014 Feb 12;6(3):2018-25. doi: 10.1021/am405039j. Epub 2014 Jan 27.


Alignment-free genome tree inference by learning group-specific distance metrics.

Patil KR, McHardy AC.

Genome Biol Evol. 2013;5(8):1470-84. doi: 10.1093/gbe/evt105.


Oleanolic acid prevents progression of streptozotocin induced diabetic nephropathy and protects renal microstructures in Sprague Dawley rats.

Dubey VK, Patil CR, Kamble SM, Tidke PS, Patil KR, Maniya PJ, Jadhav RB, Patil SP.

J Pharmacol Pharmacother. 2013 Jan;4(1):47-52. doi: 10.4103/0976-500X.107678.


Identification of metabolic engineering targets through analysis of optimal and sub-optimal routes.

Soons ZI, Ferreira EC, Patil KR, Rocha I.

PLoS One. 2013 Apr 23;8(4):e61648. doi: 10.1371/journal.pone.0061648. Print 2013.


Industrial systems biology of Saccharomyces cerevisiae enables novel succinic acid cell factory.

Otero JM, Cimini D, Patil KR, Poulsen SG, Olsson L, Nielsen J.

PLoS One. 2013;8(1):e54144. doi: 10.1371/journal.pone.0054144. Epub 2013 Jan 21.


Impact of stoichiometry representation on simulation of genotype-phenotype relationships in metabolic networks.

Brochado AR, Andrejev S, Maranas CD, Patil KR.

PLoS Comput Biol. 2012;8(11):e1002758. doi: 10.1371/journal.pcbi.1002758. Epub 2012 Nov 1.


Overexpression of O-methyltransferase leads to improved vanillin production in baker's yeast only when complemented with model-guided network engineering.

Brochado AR, Patil KR.

Biotechnol Bioeng. 2013 Feb;110(2):656-9. doi: 10.1002/bit.24731. Epub 2012 Oct 23.


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

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

Bioinformatics. 2012 Sep 15;28(18):i515-i521. doi: 10.1093/bioinformatics/bts401.


Toxicodendron pubescens retains its anti-arthritic efficacy at 1M, 10M and CM homeopathic dilutions.

Patel DR, Ansari IA, Kachchhi YN, Patel RB, Patil KR, Jadhav RB, Patil CR.

Homeopathy. 2012 Jul;101(3):165-70. doi: 10.1016/j.homp.2012.02.007.


The PhyloPythiaS web server for taxonomic assignment of metagenome sequences.

Patil KR, Roune L, McHardy AC.

PLoS One. 2012;7(6):e38581. doi: 10.1371/journal.pone.0038581. Epub 2012 Jun 20.


Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours.

Yamada T, Waller AS, Raes J, Zelezniak A, Perchat N, Perret A, Salanoubat M, Patil KR, Weissenbach J, Bork P.

Mol Syst Biol. 2012 May 8;8:581. doi: 10.1038/msb.2012.13.


Involvement of a natural fusion of a cytochrome P450 and a hydrolase in mycophenolic acid biosynthesis.

Hansen BG, Mnich E, Nielsen KF, Nielsen JB, Nielsen MT, Mortensen UH, Larsen TO, Patil KR.

Appl Environ Microbiol. 2012 Jul;78(14):4908-13. doi: 10.1128/AEM.07955-11. Epub 2012 Apr 27.


A new class of IMP dehydrogenase with a role in self-resistance of mycophenolic acid producing fungi.

Hansen BG, Genee HJ, Kaas CS, Nielsen JB, Regueira TB, Mortensen UH, Frisvad JC, Patil KR.

BMC Microbiol. 2011 Sep 16;11:202. doi: 10.1186/1471-2180-11-202.


Modulation of arthritis in rats by Toxicodendron pubescens and its homeopathic dilutions.

Patil CR, Rambhade AD, Jadhav RB, Patil KR, Dubey VK, Sonara BM, Toshniwal SS.

Homeopathy. 2011 Jul;100(3):131-7. doi: 10.1016/j.homp.2011.01.001.


PHUSER (Primer Help for USER): a novel tool for USER fusion primer design.

Olsen LR, Hansen NB, Bonde MT, Genee HJ, Holm DK, Carlsen S, Hansen BG, Patil KR, Mortensen UH, Wernersson R.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W61-7. doi: 10.1093/nar/gkr394. Epub 2011 May 26.


One-step in situ synthesis of NHx-adsorbed rhodium nanocrystals at liquid-liquid interfaces for possible electrocatalytic applications.

Patil VS, Krishna SR, Hawaldar RR, Gaikwad AB, Sathaye SD, Patil KR.

J Colloid Interface Sci. 2011 Jun 1;358(1):238-44. doi: 10.1016/j.jcis.2011.02.065. Epub 2011 Mar 6.


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