MetRxn: A knowledgebase of metabolites and reactions spanning metabolic models and databases

BMC Bioinformatics

Volumn 13, Issue 1, 2012, Pages

  Kumar, Akhil ^a   Suthers, Patrick F ^b   Maranas, Costas D ^b  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b The Pennsylvania State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOTECHNOLOGICAL PRODUCTION; CONTENT REPRESENTATION; GENOME-SCALE METABOLIC MODELS; INTEGRATING INFORMATION; METABOLIC RECONSTRUCTION; REACTION STOICHIOMETRY; RELATIONAL DATABASE MODEL; STRUCTURAL COMPARISON;

BIOMOLECULES; DATA FLOW ANALYSIS; DATABASE SYSTEMS; GENES; INFORMATION USE; METABOLISM; METABOLITES;

ASSOCIATION REACTIONS;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; COMPUTER PROGRAM; FACTUAL DATABASE; HUMAN; INTERNET; KNOWLEDGE BASE; METABOLISM; METABOLOMICS;

ALGORITHMS; DATABASES, FACTUAL; HUMANS; INTERNET; KNOWLEDGE BASES; METABOLIC NETWORKS AND PATHWAYS; METABOLOMICS; MODELS, BIOLOGICAL; SOFTWARE;

EID: 84855499408     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-6     Document Type: Article

References (89)

1. Liolios K, Tavernarakis N, Hugenholtz P, Kyrpides NC. The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Res 2006, (34 database):D332-4.
2. Stolyar S, Van Dien S, Hillesland KL, Pinel N, Lie TJ, Leigh JA, Stahl DA. Metabolic modeling of a mutualistic microbial community. Mol Syst Biol 2007, 3:92. 1847946, 17353934.
3. Reed JL, Famili I, Thiele I, Palsson BO. Towards multidimensional genome annotation. Nat Rev Genet 2006, 7(2):130-41. 10.1038/nrg1769, 16418748.
4. Burgard AP, Pharkya P, Maranas CD. Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 2003, 84(6):647-57. 10.1002/bit.10803, 14595777.
5. Oliveira AP, Nielsen J, Forster J. Modeling Lactococcus lactis using a genome-scale flux model. BMC Microbiol 2005, 5:39. 10.1186/1471-2180-5-39, 1185544, 15982422.
6. Alper H, Jin YS, Moxley JF, Stephanopoulos G. Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli. Metab Eng 2005, 7(3):155-64. 10.1016/j.ymben.2004.12.003, 15885614.
7. Pharkya P, Maranas CD. An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems. Metab Eng 2006, 8(1):1-13. 10.1016/j.ymben.2005.08.003, 16199194.
8. Almaas E, Kovacs B, Vicsek T, Oltvai ZN, Barabasi AL. Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature 2004, 427(6977):839-43. 10.1038/nature02289, 14985762.
9. Burgard AP, Nikolaev EV, Schilling CH, Maranas CD. Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Res 2004, 14(2):301-12. 10.1101/gr.1926504, 327106, 14718379.
10. Motter AE, Gulbahce N, Almaas E, Barabasi AL. Predicting synthetic rescues in metabolic networks. Mol Syst Biol 2008, 4:168. 2267730, 18277384.
11. Jin YS, Jeffries TW. Stoichiometric network constraints on xylose metabolism by recombinant Saccharomyces cerevisiae. Metab Eng 2004, 6(3):229-38. 10.1016/j.ymben.2003.11.006, 15256213.
12. Lee DY, Fan LT, Park S, Lee SY, Shafie S, Bertok B, Friedler F. Complementary identification of multiple flux distributions and multiple metabolic pathways. Metab Eng 2005, 7(3):182-200. 10.1016/j.ymben.2005.02.002, 15885617.
13. Jamshidi N, Palsson BO. Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets. BMC Syst Biol 2007, 1:26. 10.1186/1752-0509-1-26, 1925256, 17555602.
14. Reed JL, Patel TR, Chen KH, Joyce AR, Applebee MK, Herring CD, Bui OT, Knight EM, Fong SS, Palsson BO. Systems approach to refining genome annotation. Proc Natl Acad Sci USA 2006, 103(46):17480-4. 10.1073/pnas.0603364103, 1859954, 17088549.
15. Scheer M, Grote A, Chang A, Schomburg I, Munaretto C, Rother M, Sohngen C, Stelzer M, Thiele J, Schomburg D. BRENDA, the enzyme information system in 2011. Nucleic Acids Res 2011, (39 database):D670-6.
16. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 2009, (38 database):D355-60.
17. Caspi R, Altman T, Dale JM, Dreher K, Fulcher CA, Gilham F, Kaipa P, Karthikeyan AS, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Paley S, Popescu L, Pujar A, Shearer AG, Zhang P, Karp PD. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 2009, (38 database):D473-9.
18. Lang M, Stelzer M, Schomburg D. BKM-react, an integrated biochemical reaction database. BMC Biochem 2011, 12:42. 10.1186/1471-2091-12-42, 3167764, 21824409.
19. Gao J, Ellis LB, Wackett LP. The University of Minnesota Biocatalysis/Biodegradation Database: improving public access. Nucleic Acids Res 2010, (38 database):D488-91.
20. Feist AM, Herrgard MJ, Thiele I, Reed JL, Palsson BO. Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol 2009, 7(2):129-43. 3119670, 19116616.
21. Gevorgyan A, Poolman MG, Fell DA. Detection of stoichiometric inconsistencies in biomolecular models. Bioinformatics 2008, 24(19):2245-51. 10.1093/bioinformatics/btn425, 18697772.
22. Notebaart RA, van Enckevort FH, Francke C, Siezen RJ, Teusink B. Accelerating the reconstruction of genome-scale metabolic networks. BMC Bioinformatics 2006, 7:296. 10.1186/1471-2105-7-296, 1550432, 16772023.
23. Ott MA, Vriend G. Correcting ligands, metabolites, and pathways. BMC Bioinformatics 2006, 7:517. 10.1186/1471-2105-7-517, 1686944, 17132165.
24. Fleischmann A, Darsow M, Degtyarenko K, Fleischmann W, Boyce S, Axelsen KB, Bairoch A, Schomburg D, Tipton KF, Apweiler R. IntEnz, the integrated relational enzyme database. Nucleic Acids Res 2004, (32 database):D434-7.
25. Bairoch A. The ENZYME database in 2000. Nucleic Acids Res 2000, 28(1):304-5. 10.1093/nar/28.1.304, 102465, 10592255.
26. Vastrik I, D'Eustachio P, Schmidt E, Gopinath G, Croft D, de Bono B, Gillespie M, Jassal B, Lewis S, Matthews L, Wu G, Birney E, Stein L. Reactome: a knowledge base of biologic pathways and processes. Genome Biol 2007, 8(3):R39. 10.1186/gb-2007-8-3-r39, 1868929, 17367534.
27. Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B, Kanapin A, Lewis S, Mahajan S, May B, Schmidt E, Vastrik I, Wu G, Birney E, Stein L, D'Eustachio P. Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res 2009, (37 database):D619-22.
28. Stobbe MD, Houten SM, Jansen GA, van Kampen AH, Moerland PD. Critical assessment of human metabolic pathway databases: a stepping stone for future integration. BMC Syst Biol 2011, 5:165. 10.1186/1752-0509-5-165, 21999653.
29. Bornstein BJ, Keating SM, Jouraku A, Hucka M. LibSBML: an API library for SBML. Bioinformatics 2008, 24(6):880-1. 10.1093/bioinformatics/btn051, 2517632, 18252737.
30. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novere N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003, 19(4):524-31. 10.1093/bioinformatics/btg015, 12611808.
31. Stromback L, Lambrix P. Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX. Bioinformatics 2005, 21(24):4401-7. 10.1093/bioinformatics/bti718, 16234320.
32. Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 2007, 3:121. 1911197, 17593909.
33. Radrich K, Tsuruoka Y, Dobson P, Gevorgyan A, Swainston N, Baart G, Schwartz JM. Integration of metabolic databases for the reconstruction of genome-scale metabolic networks. BMC Syst Biol 2010, 4:114. 10.1186/1752-0509-4-114, 2930596, 20712863.
34. Pitkanen E, Akerlund A, Rantanen A, Jouhten P, Ukkonen E. ReMatch: a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis. J Integr Bioinform 2008, 5(2).
35. Quek LE, Nielsen LK. On the reconstruction of the Mus musculus genome-scale metabolic network model. Genome Inform 2008, 21:89-100.
36. Gonzalez O, Gronau S, Falb M, Pfeiffer F, Mendoza E, Zimmer R, Oesterhelt D. Reconstruction, modeling & analysis of Halobacterium salinarum R-1 metabolism. Mol Biosyst 2008, 4(2):148-59. 10.1039/b715203e, 18213408.
37. Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL. High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol 2010, 28(9):977-82. 10.1038/nbt.1672, 20802497.
38. Weininger D. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. Journal of Chemical Information and Computer Sciences 1988, 28(1):31-36.
39. Weininger D, Weininger A, Weininger JL. SMILES. 2. Algorithm for generation of unique SMILES notation. Journal of Chemical Information and Computer Sciences 1989, 29(2):97-101.
40. Daylight Theory Manual. , http://www.daylight.com/dayhtml/doc/theory/
41. Weininger D. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. Journal of chemical information and computer sciences 1988, 28(1):31.
42. Weininger D, Weininger A, Weininger J. SMILES. 2. Algorithm for generation of unique SMILES notation. J Chem Inf Comput Sci 1989, 29:97-101.
43. Varma A, Palsson BO. Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl Environ Microbiol 1994, 60(10):3724-31. 201879, 7986045.
44. Kjeldsen KR, Nielsen J. In silico genome-scale reconstruction and validation of the Corynebacterium glutamicum metabolic network. Biotechnol Bioeng 2009, 102(2):583-97. 10.1002/bit.22067, 18985611.
45. Durot M, Le Fevre F, de Berardinis V, Kreimeyer A, Vallenet D, Combe C, Smidtas S, Salanoubat M, Weissenbach J, Schachter V. Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data. BMC Syst Biol 2008, 2:85. 10.1186/1752-0509-2-85, 2606687, 18840283.
46. Henry CS, Zinner JF, Cohoon MP, Stevens RL. iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations. Genome Biol 2009, 10(6):R69. 10.1186/gb-2009-10-6-r69, 2718503, 19555510.
47. David H, Ozcelik IS, Hofmann G, Nielsen J. Analysis of Aspergillus nidulans metabolism at the genome-scale. BMC Genomics 2008, 9:163. 10.1186/1471-2164-9-163, 2386489, 18405346.
48. Teusink B, Wiersma A, Molenaar D, Francke C, de Vos WM, Siezen RJ, Smid EJ. Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model. J Biol Chem 2006, 281(52):40041-8. 10.1074/jbc.M606263200, 17062565.
49. Oberhardt MA, Puchalka J, Fryer KE, Martins dos Santos VA, Papin JA. Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1. J Bacteriol 2008, 190(8):2790-803. 10.1128/JB.01583-07, 2293256, 18192387.
50. Becker SA, Palsson BO. Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation. BMC Microbiol 2005, 5:8. 10.1186/1471-2180-5-8, 1079855, 15752426.
51. Oh YK, Palsson BO, Park SM, Schilling CH, Mahadevan R. Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data. J Biol Chem 2007, 282(39):28791-9. 10.1074/jbc.M703759200, 17573341.
52. Nogales J, Palsson BO, Thiele I. A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst Biol 2008, 2:79. 10.1186/1752-0509-2-79, 2569920, 18793442.
53. JL R, Encarnacion S, Collado-Vides J, Palsson BO. Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli. PLoS Comput Biol 2007, 3(10):1887-95. 2000972, 17922569.
54. Duarte NC, Herrgard MJ, Palsson BO. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res 2004, 14(7):1298-309. 10.1101/gr.2250904, 442145, 15197165.
55. Herrgard MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Bluthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novere N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasic I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttila M, Klipp E, Palsson BO, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol 2008, 26(10):1155-60. 10.1038/nbt1492, 18846089.
56. Reed JL, Vo TD, Schilling CH, Palsson BO. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 2003, 4(9):R54. 10.1186/gb-2003-4-9-r54, 193654, 12952533.
57. Feist AM, Scholten JC, Palsson BO, Brockman FJ, Ideker T. Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Mol Syst Biol 2006, 2:2006 0004. 1681478, 16738551.
58. Edwards JS, Palsson BO. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc Natl Acad Sci USA 2000, 97(10):5528-33. 10.1073/pnas.97.10.5528, 25862, 10805808.
59. Sheikh K, Forster J, Nielsen LK. Modeling hybridoma cell metabolism using a generic genome-scale metabolic model of Mus musculus. Biotechnol Prog 2005, 21(1):112-21.
60. Kuepfer L, Sauer U, Blank LM. Metabolic functions of duplicate genes in Saccharomyces cerevisiae. Genome Res 2005, 15(10):1421-30. 10.1101/gr.3992505, 1240085, 16204195.
61. Forster J, Famili I, Fu P, Palsson BO, Nielsen J. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 2003, 13(2):244-53. 10.1101/gr.234503, 420374, 12566402.
62. Kim TY, Kim HU, Park JM, Song H, Kim JS, Lee SY. Genome-scale analysis of Mannheimia succiniciproducens metabolism. Biotechnol Bioeng 2007, 97(4):657-71. 10.1002/bit.21433, 17405177.
63. Borodina I, Krabben P, Nielsen J. Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism. Genome Res 2005, 15(6):820-9. 10.1101/gr.3364705, 1142472, 15930493.
64. Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, Palsson BO. Genome-scale metabolic model of Helicobacter pylori 26695. J Bacteriol 2002, 184(16):4582-93. 10.1128/JB.184.16.4582-4593.2002, 135230, 12142428.
65. Lee J, Yun H, Feist AM, Palsson BO, Lee SY. Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network. Appl Microbiol Biotechnol 2008, 80(5):849-62. 10.1007/s00253-008-1654-4, 18758767.
66. Roberts SB, Gowen CM, Brooks JP, Fong SS. Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production. BMC Syst Biol 2010, 4:31. 10.1186/1752-0509-4-31, 2852388, 20307315.
67. Bode HB, Muller R. The impact of bacterial genomics on natural product research. Angew Chem Int Ed Engl 2005, 44(42):6828-46. 10.1002/anie.200501080, 16249991.
68. Wenzel SC, Muller R. Recent developments towards the heterologous expression of complex bacterial natural product biosynthetic pathways. Curr Opin Biotechnol 2005, 16(6):594-606. 10.1016/j.copbio.2005.10.001, 16226455.
69. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y. KEGG for linking genomes to life and the environment. Nucleic Acids Res 2008, (36 database):D480-4.
70. Chang A, Scheer M, Grote A, Schomburg I, Schomburg D. BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009. Nucleic Acids Res 2009, (37 database):D588-92.
71. Pharkya P, Burgard AP, Maranas CD. OptStrain: a computational framework for redesign of microbial production systems. Genome Res 2004, 14(11):2367-76. 10.1101/gr.2872004, 525696, 15520298.
72. Hatzimanikatis V, Li C, Ionita JA, Henry CS, Jankowski MD, Broadbelt LJ. Exploring the diversity of complex metabolic networks. Bioinformatics 2005, 21(8):1603-9. 10.1093/bioinformatics/bti213, 15613400.
73. Henry CS, Broadbelt LJ, Hatzimanikatis V. Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-hydroxypropanoate. Biotechnol Bioeng 2010, 106(3):462-73.
74. Cho A, Yun H, Park JH, Lee SY, Park S. Prediction of novel synthetic pathways for the production of desired chemicals. BMC Systems Biology 2010, 4(35).
75. S R, Shah I. PathMiner: predicting metabolic pathways by heuristic search. Bioinformatics 2003, 19(13):1692-8. 10.1093/bioinformatics/btg217, 2709535, 12967966.
76. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 2006, (34 database):D354-7.
77. Karp PD, Paley S, Romero P. The Pathway Tools software. Bioinformatics 2002, 18(Suppl 1):S225-32. 10.1093/bioinformatics/18.suppl_1.S225, 12169551.
78. Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, Kaipa P, Gilham F, Spaulding A, Popescu L, Altman T, Paulsen I, Keseler IM, Caspi R. Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief Bioinform 2009,
79. Blum T, Kohlbacher O. MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization. Bioinformatics 2008, 24(18):2108-9. 10.1093/bioinformatics/btn360, 2530881, 18635573.
80. Goesmann A, Haubrock M, Meyer F, Kalinowski J, Giegerich R. PathFinder: reconstruction and dynamic visualization of metabolic pathways. Bioinformatics 2002, 18(1):124-9. 10.1093/bioinformatics/18.1.124, 11836220.
81. Ellis LB, Roe D, Wackett LP. The University of Minnesota Biocatalysis/Biodegradation Database: the first decade. Nucleic Acids Res 2006, (34 database):D517-21.
82. Ranganathan S, Maranas CD. Microbial 1-butanol production: Identification of non-native production routes and in silico engineering interventions. Biotechnol J 2010, 5(7):716-25. 10.1002/biot.201000171, 20665644.
83. Yen JY. Finding K Shortest Loopless Paths in a Network. Management Science Series a-Theory 1971, 17(11):712-716.
84. Atsumi S, Cann AF, Connor MR, Shen CR, Smith KM, Brynildsen MP, Chou KJY, Hanai T, Liao JC. Metabolic engineering of Escherichia coli for 1-butanol production. Metabolic Engineering 2008, 10(6):305-311. 10.1016/j.ymben.2007.08.003, 17942358.
85. Formanek J, Mackie R, Blaschek HP. Enhanced Butanol Production by Clostridium beijerinckii BA101 Grown in Semidefined P2 Medium Containing 6 Percent Maltodextrin or Glucose. Appl Environ Microbiol 1997, 63(6):2306-10. 1389183, 16535628.
86. Lee JY, Jang YS, Lee J, Papoutsakis ET, Lee SY. Metabolic engineering of Clostridium acetobutylicum M5 for highly selective butanol production. Biotechnol J 2009, 4(10):1432-40. 10.1002/biot.200900142, 19830716.
87. Shen CR, Liao JC. Metabolic engineering of Escherichia coli for 1-butanol and 1-propanol production via the keto-acid pathways. Metab Eng 2008, 10(6):312-20. 10.1016/j.ymben.2008.08.001, 18775501.
88. Sillers R, Chow A, Tracy B, Papoutsakis ET. Metabolic engineering of the non-sporulating, non-solventogenic Clostridium acetobutylicum strain M5 to produce butanol without acetone demonstrate the robustness of the acid-formation pathways and the importance of the electron balance. Metab Eng 2008, 10(6):321-32. 10.1016/j.ymben.2008.07.005, 18725313.
89. Atsumi S, Hanai T, Liao JC. Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 2008, 451(7174):86-9. 10.1038/nature06450, 18172501.