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Dynamics of the human skin mediator lipidome in response to dietary ω-3 fatty acid supplementation.

Kendall AC, Pilkington SM, Murphy SA, Del Carratore F, Sunarwidhi AL, Kiezel-Tsugunova M, Urquhart P, Watson REB, Breitling R, Rhodes LE, Nicolaou A.

FASEB J. 2019 Nov;33(11):13014-13027. doi: 10.1096/fj.201901501R. Epub 2019 Sep 13.


Integrated Probabilistic Annotation: A Bayesian-Based Annotation Method for Metabolomic Profiles Integrating Biochemical Connections, Isotope Patterns, and Adduct Relationships.

Del Carratore F, Schmidt K, Vinaixa M, Hollywood KA, Greenland-Bews C, Takano E, Rogers S, Breitling R.

Anal Chem. 2019 Oct 15;91(20):12799-12807. doi: 10.1021/acs.analchem.9b02354. Epub 2019 Sep 30.


Synthetic biology for fibres, adhesives and active camouflage materials in protection and aerospace.

Roberts AD, Finnigan W, Wolde-Michael E, Kelly P, Blaker JJ, Hay S, Breitling R, Takano E, Scrutton NS.

MRS Commun. 2019 May 15;9(2):486-504. doi: 10.1557/mrc.2019.35. Epub 2019 Apr 24.


SelProm: A Queryable and Predictive Expression Vector Selection Tool for Escherichia coli.

Jervis AJ, Carbonell P, Taylor S, Sung R, Dunstan MS, Robinson CJ, Breitling R, Takano E, Scrutton NS.

ACS Synth Biol. 2019 Jul 19;8(7):1478-1483. doi: 10.1021/acssynbio.8b00399. Epub 2019 Mar 18.


Computational identification of co-evolving multi-gene modules in microbial biosynthetic gene clusters.

Del Carratore F, Zych K, Cummings M, Takano E, Medema MH, Breitling R.

Commun Biol. 2019 Feb 28;2:83. doi: 10.1038/s42003-019-0333-6. eCollection 2019.


Machine Learning of Designed Translational Control Allows Predictive Pathway Optimization in Escherichia coli.

Jervis AJ, Carbonell P, Vinaixa M, Dunstan MS, Hollywood KA, Robinson CJ, Rattray NJW, Yan C, Swainston N, Currin A, Sung R, Toogood H, Taylor S, Faulon JL, Breitling R, Takano E, Scrutton NS.

ACS Synth Biol. 2019 Jan 18;8(1):127-136. doi: 10.1021/acssynbio.8b00398. Epub 2019 Jan 7.


Defining informative priors for ensemble modeling in systems biology.

Tsigkinopoulou A, Hawari A, Uttley M, Breitling R.

Nat Protoc. 2018 Nov;13(11):2643-2663. doi: 10.1038/s41596-018-0056-z.


An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals.

Carbonell P, Jervis AJ, Robinson CJ, Yan C, Dunstan M, Swainston N, Vinaixa M, Hollywood KA, Currin A, Rattray NJW, Taylor S, Spiess R, Sung R, Williams AR, Fellows D, Stanford NJ, Mulherin P, Le Feuvre R, Barran P, Goodacre R, Turner NJ, Goble C, Chen GG, Kell DB, Micklefield J, Breitling R, Takano E, Faulon JL, Scrutton NS.

Commun Biol. 2018 Jun 8;1:66. doi: 10.1038/s42003-018-0076-9. eCollection 2018.


Transduction and transfection of difficult-to-transfect cells: Systematic attempts for the transfection of protozoa Leishmania.

Keller AA, Scheiding B, Breitling R, Licht A, Hemmerich P, Lorkowski S, Reissmann S.

J Cell Biochem. 2019 Jan;120(1):14-27. doi: 10.1002/jcb.27463. Epub 2018 Sep 14.


Mobilising ion mobility mass spectrometry for metabolomics.

Sinclair E, Hollywood KA, Yan C, Blankley R, Breitling R, Barran P.

Analyst. 2018 Sep 24;143(19):4783-4788. doi: 10.1039/c8an00902c.


Insights on a putative aminoacyl-tRNA-protein transferase of Leishmania major.

Sharma R, Terrão MC, Castro FF, Breitling R, Faça V, Oliveira EB, Cruz AK.

PLoS One. 2018 Sep 12;13(9):e0203369. doi: 10.1371/journal.pone.0203369. eCollection 2018.


Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism.

Amara A, Takano E, Breitling R.

BMC Genomics. 2018 Jul 4;19(1):519. doi: 10.1186/s12864-018-4905-5.


Metabolomics tools for the synthetic biology of natural products.

Hollywood KA, Schmidt K, Takano E, Breitling R.

Curr Opin Biotechnol. 2018 Dec;54:114-120. doi: 10.1016/j.copbio.2018.02.015. Epub 2018 Mar 19. Review.


Orthogonal Regulatory Circuits for Escherichia coli Based on the γ-Butyrolactone System of Streptomyces coelicolor.

Biarnes-Carrera M, Lee CK, Nihira T, Breitling R, Takano E.

ACS Synth Biol. 2018 Apr 20;7(4):1043-1055. doi: 10.1021/acssynbio.7b00425. Epub 2018 Mar 19.


Rational cell culture optimization enhances experimental reproducibility in cancer cells.

Wright Muelas M, Ortega F, Breitling R, Bendtsen C, Westerhoff HV.

Sci Rep. 2018 Feb 14;8(1):3029. doi: 10.1038/s41598-018-21050-4.


Selenzyme: enzyme selection tool for pathway design.

Carbonell P, Wong J, Swainston N, Takano E, Turner NJ, Scrutton NS, Kell DB, Breitling R, Faulon JL.

Bioinformatics. 2018 Jun 15;34(12):2153-2154. doi: 10.1093/bioinformatics/bty065.


Translation Stress Positively Regulates MscL-Dependent Excretion of Cytoplasmic Proteins.

Morra R, Del Carratore F, Muhamadali H, Horga LG, Halliwell S, Goodacre R, Breitling R, Dixon N.

mBio. 2018 Jan 30;9(1). pii: e02118-17. doi: 10.1128/mBio.02118-17.


Output ordering and prioritisation system (OOPS): ranking biosynthetic gene clusters to enhance bioactive metabolite discovery.

Peña A, Del Carratore F, Cummings M, Takano E, Breitling R.

J Ind Microbiol Biotechnol. 2018 Jul;45(7):615-619. doi: 10.1007/s10295-017-1993-1. Epub 2017 Dec 18.


A transatlantic perspective on 20 emerging issues in biological engineering.

Wintle BC, Boehm CR, Rhodes C, Molloy JC, Millett P, Adam L, Breitling R, Carlson R, Casagrande R, Dando M, Doubleday R, Drexler E, Edwards B, Ellis T, Evans NG, Hammond R, Haseloff J, Kahl L, Kuiken T, Lichman BR, Matthewman CA, Napier JA, ÓhÉigeartaigh SS, Patron NJ, Perello E, Shapira P, Tait J, Takano E, Sutherland WJ.

Elife. 2017 Nov 14;6. pii: e30247. doi: 10.7554/eLife.30247.


Detection and Quantification of Butyrolactones from Streptomyces.

Biarnes-Carrera M, Breitling R, Takano E.

Methods Mol Biol. 2018;1673:117-128. doi: 10.1007/978-1-4939-7309-5_10.


biochem4j: Integrated and extensible biochemical knowledge through graph databases.

Swainston N, Batista-Navarro R, Carbonell P, Dobson PD, Dunstan M, Jervis AJ, Vinaixa M, Williams AR, Ananiadou S, Faulon JL, Mendes P, Kell DB, Scrutton NS, Breitling R.

PLoS One. 2017 Jul 14;12(7):e0179130. doi: 10.1371/journal.pone.0179130. eCollection 2017.


RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets.

Del Carratore F, Jankevics A, Eisinga R, Heskes T, Hong F, Breitling R.

Bioinformatics. 2017 Sep 1;33(17):2774-2775. doi: 10.1093/bioinformatics/btx292.


antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification.

Blin K, Wolf T, Chevrette MG, Lu X, Schwalen CJ, Kautsar SA, Suarez Duran HG, de Los Santos ELC, Kim HU, Nave M, Dickschat JS, Mitchell DA, Shelest E, Breitling R, Takano E, Lee SY, Weber T, Medema MH.

Nucleic Acids Res. 2017 Jul 3;45(W1):W36-W41. doi: 10.1093/nar/gkx319.


reGenotyper: Detecting mislabeled samples in genetic data.

Zych K, Snoek BL, Elvin M, Rodriguez M, Van der Velde KJ, Arends D, Westra HJ, Swertz MA, Poulin G, Kammenga JE, Breitling R, Jansen RC, Li Y.

PLoS One. 2017 Feb 13;12(2):e0171324. doi: 10.1371/journal.pone.0171324. eCollection 2017.


Respectful Modeling: Addressing Uncertainty in Dynamic System Models for Molecular Biology.

Tsigkinopoulou A, Baker SM, Breitling R.

Trends Biotechnol. 2017 Jun;35(6):518-529. doi: 10.1016/j.tibtech.2016.12.008. Epub 2017 Jan 13. Review.


SYNBIOCHEM Synthetic Biology Research Centre, Manchester - A UK foundry for fine and speciality chemicals production.

Ra LF, P C, A C, M D, D F, Aj J, Njw R, Cj R, N S, M V, A W, C Y, P B, R B, Gg C, Jl F, C G, R G, Db K, J M, Ns S, P S, E T, Nj T.

Synth Syst Biotechnol. 2016 Aug 25;1(4):271-275. doi: 10.1016/j.synbio.2016.07.001. eCollection 2016 Dec.


Synthetic Biology of Natural Products.

Breitling R, Takano E.

Cold Spring Harb Perspect Biol. 2016 Oct 3;8(10). pii: a023994. doi: 10.1101/cshperspect.a023994. Review.


Towards synthesis of monoterpenes and derivatives using synthetic biology.

Zebec Z, Wilkes J, Jervis AJ, Scrutton NS, Takano E, Breitling R.

Curr Opin Chem Biol. 2016 Oct;34:37-43. doi: 10.1016/j.cbpa.2016.06.002. Epub 2016 Jun 14. Review.


SYNBIOCHEM-a SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals.

Carbonell P, Currin A, Dunstan M, Fellows D, Jervis A, Rattray NJ, Robinson CJ, Swainston N, Vinaixa M, Williams A, Yan C, Barran P, Breitling R, Chen GG, Faulon JL, Goble C, Goodacre R, Kell DB, Feuvre RL, Micklefield J, Scrutton NS, Shapira P, Takano E, Turner NJ.

Biochem Soc Trans. 2016 Jun 15;44(3):675-7. doi: 10.1042/BST20160009.


Bioinformatics for the synthetic biology of natural products: integrating across the Design-Build-Test cycle.

Carbonell P, Currin A, Jervis AJ, Rattray NJ, Swainston N, Yan C, Takano E, Breitling R.

Nat Prod Rep. 2016 Aug 27;33(8):925-32. doi: 10.1039/c6np00018e. Epub 2016 May 17. Review.


LC-MS-based absolute metabolite quantification: application to metabolic flux measurement in trypanosomes.

Kim DH, Achcar F, Breitling R, Burgess KE, Barrett MP.

Metabolomics. 2015;11(6):1721-1732. Epub 2015 Jul 9.


Minimum Information about a Biosynthetic Gene cluster.

Medema MH, Kottmann R, Yilmaz P, Cummings M, Biggins JB, Blin K, de Bruijn I, Chooi YH, Claesen J, Coates RC, Cruz-Morales P, Duddela S, Düsterhus S, Edwards DJ, Fewer DP, Garg N, Geiger C, Gomez-Escribano JP, Greule A, Hadjithomas M, Haines AS, Helfrich EJ, Hillwig ML, Ishida K, Jones AC, Jones CS, Jungmann K, Kegler C, Kim HU, Kötter P, Krug D, Masschelein J, Melnik AV, Mantovani SM, Monroe EA, Moore M, Moss N, Nützmann HW, Pan G, Pati A, Petras D, Reen FJ, Rosconi F, Rui Z, Tian Z, Tobias NJ, Tsunematsu Y, Wiemann P, Wyckoff E, Yan X, Yim G, Yu F, Xie Y, Aigle B, Apel AK, Balibar CJ, Balskus EP, Barona-Gómez F, Bechthold A, Bode HB, Borriss R, Brady SF, Brakhage AA, Caffrey P, Cheng YQ, Clardy J, Cox RJ, De Mot R, Donadio S, Donia MS, van der Donk WA, Dorrestein PC, Doyle S, Driessen AJ, Ehling-Schulz M, Entian KD, Fischbach MA, Gerwick L, Gerwick WH, Gross H, Gust B, Hertweck C, Höfte M, Jensen SE, Ju J, Katz L, Kaysser L, Klassen JL, Keller NP, Kormanec J, Kuipers OP, Kuzuyama T, Kyrpides NC, Kwon HJ, Lautru S, Lavigne R, Lee CY, Linquan B, Liu X, Liu W, Luzhetskyy A, Mahmud T, Mast Y, Méndez C, Metsä-Ketelä M, Micklefield J, Mitchell DA, Moore BS, Moreira LM, Müller R, Neilan BA, Nett M, Nielsen J, O'Gara F, Oikawa H, Osbourn A, Osburne MS, Ostash B, Payne SM, Pernodet JL, Petricek M, Piel J, Ploux O, Raaijmakers JM, Salas JA, Schmitt EK, Scott B, Seipke RF, Shen B, Sherman DH, Sivonen K, Smanski MJ, Sosio M, Stegmann E, Süssmuth RD, Tahlan K, Thomas CM, Tang Y, Truman AW, Viaud M, Walton JD, Walsh CT, Weber T, van Wezel GP, Wilkinson B, Willey JM, Wohlleben W, Wright GD, Ziemert N, Zhang C, Zotchev SB, Breitling R, Takano E, Glöckner FO.

Nat Chem Biol. 2015 Sep;11(9):625-31. doi: 10.1038/nchembio.1890. No abstract available.


Butyrolactone signalling circuits for synthetic biology.

Biarnes-Carrera M, Breitling R, Takano E.

Curr Opin Chem Biol. 2015 Oct;28:91-8. doi: 10.1016/j.cbpa.2015.06.024. Epub 2015 Jul 9. Review.


antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters.

Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Müller R, Wohlleben W, Breitling R, Takano E, Medema MH.

Nucleic Acids Res. 2015 Jul 1;43(W1):W237-43. doi: 10.1093/nar/gkv437. Epub 2015 May 6.


Probing the metabolic network in bloodstream-form Trypanosoma brucei using untargeted metabolomics with stable isotope labelled glucose.

Creek DJ, Mazet M, Achcar F, Anderson J, Kim DH, Kamour R, Morand P, Millerioux Y, Biran M, Kerkhoven EJ, Chokkathukalam A, Weidt SK, Burgess KE, Breitling R, Watson DG, Bringaud F, Barrett MP.

PLoS Pathog. 2015 Mar 16;11(3):e1004689. doi: 10.1371/journal.ppat.1004689. eCollection 2015 Mar.


Synthetic biology advances for pharmaceutical production.

Breitling R, Takano E.

Curr Opin Biotechnol. 2015 Dec;35:46-51. doi: 10.1016/j.copbio.2015.02.004. Epub 2015 Mar 3. Review.


Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets.

Wandy J, Daly R, Breitling R, Rogers S.

Bioinformatics. 2015 Jun 15;31(12):1999-2006. doi: 10.1093/bioinformatics/btv072. Epub 2015 Feb 2.


Judging synthetic biology risks.

Breitling R, Takano E, Gardner TS.

Science. 2015 Jan 9;347(6218):107. doi: 10.1126/science.aaa5253. No abstract available.


A fast algorithm for determining bounds and accurate approximate p-values of the rank product statistic for replicate experiments.

Heskes T, Eisinga R, Breitling R.

BMC Bioinformatics. 2014 Nov 21;15:367. doi: 10.1186/s12859-014-0367-1.


TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei.

Shameer S, Logan-Klumpler FJ, Vinson F, Cottret L, Merlet B, Achcar F, Boshart M, Berriman M, Breitling R, Bringaud F, Bütikofer P, Cattanach AM, Bannerman-Chukualim B, Creek DJ, Crouch K, de Koning HP, Denise H, Ebikeme C, Fairlamb AH, Ferguson MA, Ginger ML, Hertz-Fowler C, Kerkhoven EJ, Mäser P, Michels PA, Nayak A, Nes DW, Nolan DP, Olsen C, Silva-Franco F, Smith TK, Taylor MC, Tielens AG, Urbaniak MD, van Hellemond JJ, Vincent IM, Wilkinson SR, Wyllie S, Opperdoes FR, Barrett MP, Jourdan F.

Nucleic Acids Res. 2015 Jan;43(Database issue):D637-44. doi: 10.1093/nar/gku944. Epub 2014 Oct 9.


Pep2Path: automated mass spectrometry-guided genome mining of peptidic natural products.

Medema MH, Paalvast Y, Nguyen DD, Melnik A, Dorrestein PC, Takano E, Breitling R.

PLoS Comput Biol. 2014 Sep 4;10(9):e1003822. doi: 10.1371/journal.pcbi.1003822. eCollection 2014 Sep.


MetAssign: probabilistic annotation of metabolites from LC-MS data using a Bayesian clustering approach.

Daly R, Rogers S, Wandy J, Jankevics A, Burgess KE, Breitling R.

Bioinformatics. 2014 Oct;30(19):2764-71. doi: 10.1093/bioinformatics/btu370. Epub 2014 Jun 9.


The silicon trypanosome: a test case of iterative model extension in systems biology.

Achcar F, Fadda A, Haanstra JR, Kerkhoven EJ, Kim DH, Leroux AE, Papamarkou T, Rojas F, Bakker BM, Barrett MP, Clayton C, Girolami M, Krauth-Siegel RL, Matthews KR, Breitling R.

Adv Microb Physiol. 2014;64:115-43. doi: 10.1016/B978-0-12-800143-1.00003-8. Review.


SecA is required for membrane targeting of the cell division protein DivIVA in vivo.

Halbedel S, Kawai M, Breitling R, Hamoen LW.

Front Microbiol. 2014 Feb 14;5:58. doi: 10.3389/fmicb.2014.00058. eCollection 2014.


Stable isotope-labeling studies in metabolomics: new insights into structure and dynamics of metabolic networks.

Chokkathukalam A, Kim DH, Barrett MP, Breitling R, Creek DJ.

Bioanalysis. 2014 Feb;6(4):511-24. doi: 10.4155/bio.13.348. Review.


Phosphoenolpyruvate carboxylase identified as a key enzyme in erythrocytic Plasmodium falciparum carbon metabolism.

Storm J, Sethia S, Blackburn GJ, Chokkathukalam A, Watson DG, Breitling R, Coombs GH, Müller S.

PLoS Pathog. 2014 Jan;10(1):e1003876. doi: 10.1371/journal.ppat.1003876. Epub 2014 Jan 16.


Steps towards the synthetic biology of polyketide biosynthesis.

Cummings M, Breitling R, Takano E.

FEMS Microbiol Lett. 2014 Feb;351(2):116-25. doi: 10.1111/1574-6968.12365. Epub 2014 Jan 7. Review.


Handling uncertainty in dynamic models: the pentose phosphate pathway in Trypanosoma brucei.

Kerkhoven EJ, Achcar F, Alibu VP, Burchmore RJ, Gilbert IH, Trybiło M, Driessen NN, Gilbert D, Breitling R, Bakker BM, Barrett MP.

PLoS Comput Biol. 2013;9(12):e1003371. doi: 10.1371/journal.pcbi.1003371. Epub 2013 Dec 5.


Relationships between Cargo, Cell Penetrating Peptides and Cell Type for Uptake of Non-Covalent Complexes into Live Cells.

Keller AA, Mussbach F, Breitling R, Hemmerich P, Schaefer B, Lorkowski S, Reissmann S.

Pharmaceuticals (Basel). 2013 Feb 6;6(2):184-203. doi: 10.3390/ph6020184.


Transduction of proteins into leishmania tarentolae by formation of non-covalent complexes with cell-penetrating peptides.

Keller AA, Breitling R, Hemmerich P, Kappe K, Braun M, Wittig B, Schaefer B, Lorkowski S, Reissmann S.

J Cell Biochem. 2014 Feb;115(2):243-52. doi: 10.1002/jcb.24654.


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