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For: Yus E, Maier T, Michalodimitrakis K, van Noort V, Yamada T, Chen WH, Wodke JAH, Güell M, Martínez S, Bourgeois R, Kühner S, Raineri E, Letunic I, Kalinina OV, Rode M, Herrmann R, Gutiérrez-Gallego R, Russell RB, Gavin AC, Bork P, Serrano L. Impact of genome reduction on bacterial metabolism and its regulation. Science 2009;326:1263-8. [PMID: 19965476 DOI: 10.1126/science.1177263] [Citation(s) in RCA: 223] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Number Cited by Other Article(s)
101
de la Escosura A, Briones C, Ruiz-Mirazo K. The systems perspective at the crossroads between chemistry and biology. J Theor Biol 2015;381:11-22. [DOI: 10.1016/j.jtbi.2015.04.036] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 04/26/2015] [Indexed: 01/21/2023]
102
Xiao L, Ptacek T, Osborne JD, Crabb DM, Simmons WL, Lefkowitz EJ, Waites KB, Atkinson TP, Dybvig K. Comparative genome analysis of Mycoplasma pneumoniae. BMC Genomics 2015;16:610. [PMID: 26275904 PMCID: PMC4537597 DOI: 10.1186/s12864-015-1801-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 07/29/2015] [Indexed: 12/30/2022]  Open
103
Systems biology perspectives on minimal and simpler cells. Microbiol Mol Biol Rev 2015;78:487-509. [PMID: 25184563 DOI: 10.1128/mmbr.00050-13] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
104
Feig M, Harada R, Mori T, Yu I, Takahashi K, Sugita Y. Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology. J Mol Graph Model 2015;58:1-9. [PMID: 25765281 DOI: 10.1016/j.jmgm.2015.02.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/18/2015] [Accepted: 02/22/2015] [Indexed: 01/10/2023]
105
Caufield JH, Abreu M, Wimble C, Uetz P. Protein complexes in bacteria. PLoS Comput Biol 2015;11:e1004107. [PMID: 25723151 PMCID: PMC4344305 DOI: 10.1371/journal.pcbi.1004107] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 01/02/2015] [Indexed: 01/26/2023]  Open
106
Lluch-Senar M, Delgado J, Chen WH, Lloréns-Rico V, O'Reilly FJ, Wodke JA, Unal EB, Yus E, Martínez S, Nichols RJ, Ferrar T, Vivancos A, Schmeisky A, Stülke J, van Noort V, Gavin AC, Bork P, Serrano L. Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium. Mol Syst Biol 2015;11:780. [PMID: 25609650 PMCID: PMC4332154 DOI: 10.15252/msb.20145558] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]  Open
107
Baverstock K, Rönkkö M. The evolutionary origin of form and function. J Physiol 2015;592:2261-5. [PMID: 24882811 DOI: 10.1113/jphysiol.2014.271775] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
108
Wium M, Botes A, Bellstedt DU. The identification of oppA gene homologues as part of the oligopeptide transport system in mycoplasmas. Gene 2014;558:31-40. [PMID: 25528211 DOI: 10.1016/j.gene.2014.12.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/03/2014] [Accepted: 12/16/2014] [Indexed: 11/27/2022]
109
Hansen AK, Degnan PH. Widespread expression of conserved small RNAs in small symbiont genomes. THE ISME JOURNAL 2014;8:2490-502. [PMID: 25012903 PMCID: PMC4260695 DOI: 10.1038/ismej.2014.121] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 06/02/2014] [Accepted: 06/05/2014] [Indexed: 12/17/2022]
110
Wodke JAH, Alibés A, Cozzuto L, Hermoso A, Yus E, Lluch-Senar M, Serrano L, Roma G. MyMpn: a database for the systems biology model organism Mycoplasma pneumoniae. Nucleic Acids Res 2014;43:D618-23. [PMID: 25378328 PMCID: PMC4383923 DOI: 10.1093/nar/gku1105] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
111
Nuñez PA, Romero H, Farber MD, Rocha EPC. Natural selection for operons depends on genome size. Genome Biol Evol 2014;5:2242-54. [PMID: 24201372 PMCID: PMC3845653 DOI: 10.1093/gbe/evt174] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
112
Bohlin J, Brynildsrud OB, Sekse C, Snipen L. An evolutionary analysis of genome expansion and pathogenicity in Escherichia coli. BMC Genomics 2014;15:882. [PMID: 25297974 PMCID: PMC4200225 DOI: 10.1186/1471-2164-15-882] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 09/29/2014] [Indexed: 12/27/2022]  Open
113
Schmidt R, Waschina S, Boettger-Schmidt D, Kost C, Kaleta C. Computing autocatalytic sets to unravel inconsistencies in metabolic network reconstructions. ACTA ACUST UNITED AC 2014;31:373-81. [PMID: 25286919 DOI: 10.1093/bioinformatics/btu658] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
114
Hydrogen peroxide production from glycerol metabolism is dispensable for virulence of Mycoplasma gallisepticum in the tracheas of chickens. Infect Immun 2014;82:4915-20. [PMID: 25156740 DOI: 10.1128/iai.02208-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
115
Pritchard RE, Prassinos AJ, Osborne JD, Raviv Z, Balish MF. Reduction of hydrogen peroxide accumulation and toxicity by a catalase from Mycoplasma iowae. PLoS One 2014;9:e105188. [PMID: 25127127 PMCID: PMC4134286 DOI: 10.1371/journal.pone.0105188] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 07/19/2014] [Indexed: 12/02/2022]  Open
116
Yugi K, Kubota H, Toyoshima Y, Noguchi R, Kawata K, Komori Y, Uda S, Kunida K, Tomizawa Y, Funato Y, Miki H, Matsumoto M, Nakayama KI, Kashikura K, Endo K, Ikeda K, Soga T, Kuroda S. Reconstruction of insulin signal flow from phosphoproteome and metabolome data. Cell Rep 2014;8:1171-83. [PMID: 25131207 DOI: 10.1016/j.celrep.2014.07.021] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 06/13/2014] [Accepted: 07/15/2014] [Indexed: 12/20/2022]  Open
117
do Nascimento NC, dos Santos AP, Chu Y, Guimaraes AMS, Baird AN, Weil AB, Messick JB. Microscopy and genomic analysis of Mycoplasma parvum strain Indiana. Vet Res 2014;45:86. [PMID: 25113534 PMCID: PMC4423628 DOI: 10.1186/s13567-014-0086-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 08/06/2014] [Indexed: 11/21/2022]  Open
118
Essential plasticity and redundancy of metabolism unveiled by synthetic lethality analysis. PLoS Comput Biol 2014;10:e1003637. [PMID: 24854166 PMCID: PMC4031049 DOI: 10.1371/journal.pcbi.1003637] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 04/04/2014] [Indexed: 01/18/2023]  Open
119
Grosjean H, Breton M, Sirand-Pugnet P, Tardy F, Thiaucourt F, Citti C, Barré A, Yoshizawa S, Fourmy D, de Crécy-Lagard V, Blanchard A. Predicting the minimal translation apparatus: lessons from the reductive evolution of mollicutes. PLoS Genet 2014;10:e1004363. [PMID: 24809820 PMCID: PMC4014445 DOI: 10.1371/journal.pgen.1004363] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 03/24/2014] [Indexed: 11/18/2022]  Open
120
Phylogeny and evolution of RNA structure. Methods Mol Biol 2014. [PMID: 24639167 DOI: 10.1007/978-1-62703-709-9_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
121
Guimaraes AMS, Santos AP, do Nascimento NC, Timenetsky J, Messick JB. Comparative genomics and phylogenomics of hemotrophic mycoplasmas. PLoS One 2014;9:e91445. [PMID: 24642917 PMCID: PMC3958358 DOI: 10.1371/journal.pone.0091445] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 02/10/2014] [Indexed: 11/18/2022]  Open
122
Vanyushkina AA, Fisunov GY, Gorbachev AY, Kamashev DE, Govorun VM. Metabolomic analysis of three Mollicute species. PLoS One 2014;9:e89312. [PMID: 24595068 PMCID: PMC3942410 DOI: 10.1371/journal.pone.0089312] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 01/22/2014] [Indexed: 01/19/2023]  Open
123
Macklin DN, Ruggero NA, Covert MW. The future of whole-cell modeling. Curr Opin Biotechnol 2014;28:111-5. [PMID: 24556244 DOI: 10.1016/j.copbio.2014.01.012] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 01/19/2014] [Accepted: 01/20/2014] [Indexed: 12/21/2022]
124
Porcar M, Peretó J. Synthetic Biology in Action. Synth Biol (Oxf) 2014. [DOI: 10.1007/978-94-017-9382-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]  Open
125
Mapping condition-dependent regulation of lipid metabolism in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2013;3:1979-95. [PMID: 24062529 PMCID: PMC3815060 DOI: 10.1534/g3.113.006601] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
126
Jordan DS, Daubenspeck JM, Laube AH, Renfrow MB, Dybvig K. O-linked protein glycosylation in Mycoplasma. Mol Microbiol 2013;90:1046-53. [PMID: 24118505 DOI: 10.1111/mmi.12415] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2013] [Indexed: 01/06/2023]
127
Use of a global metabolic network to curate organismal metabolic networks. Sci Rep 2013;3:1695. [PMID: 23603845 PMCID: PMC3631772 DOI: 10.1038/srep01695] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 04/04/2013] [Indexed: 12/18/2022]  Open
128
Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling. Mol Syst Biol 2013;9:653. [PMID: 23549481 PMCID: PMC3658275 DOI: 10.1038/msb.2013.6] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 02/20/2013] [Indexed: 12/15/2022]  Open
129
Semi-automated curation of metabolic models via flux balance analysis: a case study with Mycoplasma gallisepticum. PLoS Comput Biol 2013;9:e1003208. [PMID: 24039564 PMCID: PMC3764002 DOI: 10.1371/journal.pcbi.1003208] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 07/19/2013] [Indexed: 11/19/2022]  Open
130
Krishnakumar R, Prat L, Aerni HR, Ling J, Merryman C, Glass JI, Rinehart J, Söll D. Transfer RNA misidentification scrambles sense codon recoding. Chembiochem 2013;14:1967-72. [PMID: 24000185 DOI: 10.1002/cbic.201300444] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Indexed: 12/22/2022]
131
Feig M, Sugita Y. Reaching new levels of realism in modeling biological macromolecules in cellular environments. J Mol Graph Model 2013;45:144-56. [PMID: 24036504 DOI: 10.1016/j.jmgm.2013.08.017] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 08/14/2013] [Accepted: 08/19/2013] [Indexed: 12/21/2022]
132
Sun R, Wang L. Inhibition of Mycoplasma pneumoniae growth by FDA-approved anticancer and antiviral nucleoside and nucleobase analogs. BMC Microbiol 2013;13:184. [PMID: 23919755 PMCID: PMC3750255 DOI: 10.1186/1471-2180-13-184] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 07/24/2013] [Indexed: 11/11/2022]  Open
133
Martínez-Núñez MA, Poot-Hernandez AC, Rodríguez-Vázquez K, Perez-Rueda E. Increments and duplication events of enzymes and transcription factors influence metabolic and regulatory diversity in prokaryotes. PLoS One 2013;8:e69707. [PMID: 23922780 PMCID: PMC3726781 DOI: 10.1371/journal.pone.0069707] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 06/13/2013] [Indexed: 11/18/2022]  Open
134
Jordan DS, Daubenspeck JM, Dybvig K. Rhamnose biosynthesis in mycoplasmas requires precursor glycans larger than monosaccharide. Mol Microbiol 2013;89:918-28. [PMID: 23826905 DOI: 10.1111/mmi.12320] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2013] [Indexed: 11/30/2022]
135
Carvalhais LC, Dennis PG, Fan B, Fedoseyenko D, Kierul K, Becker A, von Wiren N, Borriss R. Linking plant nutritional status to plant-microbe interactions. PLoS One 2013;8:e68555. [PMID: 23874669 PMCID: PMC3713015 DOI: 10.1371/journal.pone.0068555] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Accepted: 05/30/2013] [Indexed: 11/17/2022]  Open
136
Characterization of free exopolysaccharides secreted by Mycoplasma mycoides subsp. mycoides. PLoS One 2013;8:e68373. [PMID: 23869216 PMCID: PMC3711806 DOI: 10.1371/journal.pone.0068373] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 05/29/2013] [Indexed: 12/25/2022]  Open
137
Maier T, Marcos J, Wodke JAH, Paetzold B, Liebeke M, Gutiérrez-Gallego R, Serrano L. Large-scale metabolome analysis and quantitative integration with genomics and proteomics data in Mycoplasma pneumoniae. MOLECULAR BIOSYSTEMS 2013;9:1743-55. [PMID: 23598864 DOI: 10.1039/c3mb70113a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
138
Designing de novo: interdisciplinary debates in synthetic biology. SYSTEMS AND SYNTHETIC BIOLOGY 2013;7:41-50. [PMID: 24432141 DOI: 10.1007/s11693-013-9106-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 03/27/2013] [Accepted: 03/30/2013] [Indexed: 12/11/2022]
139
Abu Kwaik Y, Bumann D. Microbial quest for food in vivo: 'nutritional virulence' as an emerging paradigm. Cell Microbiol 2013;15:882-90. [PMID: 23490329 DOI: 10.1111/cmi.12138] [Citation(s) in RCA: 141] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 03/05/2013] [Accepted: 03/07/2013] [Indexed: 12/14/2022]
140
Life as physics and chemistry: A system view of biology. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013;111:108-15. [DOI: 10.1016/j.pbiomolbio.2012.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Revised: 09/13/2012] [Accepted: 09/17/2012] [Indexed: 11/17/2022]
141
Xu Y, Wang H, Nussinov R, Ma B. Protein charge and mass contribute to the spatio-temporal dynamics of protein-protein interactions in a minimal proteome. Proteomics 2013;13:1339-51. [PMID: 23420643 PMCID: PMC3762602 DOI: 10.1002/pmic.201100540] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 12/10/2012] [Accepted: 01/31/2013] [Indexed: 11/07/2022]
142
Geyer T. Modeling metabolic processes between molecular and systems biology. Curr Opin Struct Biol 2013;23:218-23. [DOI: 10.1016/j.sbi.2012.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 12/03/2012] [Indexed: 10/27/2022]
143
Silicon dreams of cells into symbols. Nat Biotechnol 2013;30:838-40. [PMID: 22965055 DOI: 10.1038/nbt.2358] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
144
Gancedo JM. Biological roles of cAMP: variations on a theme in the different kingdoms of life. Biol Rev Camb Philos Soc 2013;88:645-68. [PMID: 23356492 DOI: 10.1111/brv.12020] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 12/19/2012] [Accepted: 12/20/2012] [Indexed: 12/18/2022]
145
Lluch-Senar M, Luong K, Lloréns-Rico V, Delgado J, Fang G, Spittle K, Clark TA, Schadt E, Turner SW, Korlach J, Serrano L. Comprehensive methylome characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at single-base resolution. PLoS Genet 2013;9:e1003191. [PMID: 23300489 PMCID: PMC3536716 DOI: 10.1371/journal.pgen.1003191] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 11/08/2012] [Indexed: 11/18/2022]  Open
146
Present Day Biology seen in the Looking Glass of Physics of Complexity. UNDERSTANDING COMPLEX SYSTEMS 2013. [DOI: 10.1007/978-3-642-34070-3_44] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
147
From essential to persistent genes: a functional approach to constructing synthetic life. Trends Genet 2012;29:273-9. [PMID: 23219343 PMCID: PMC3642372 DOI: 10.1016/j.tig.2012.11.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 10/14/2012] [Accepted: 11/01/2012] [Indexed: 11/21/2022]
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Krüger B, Liang C, Prell F, Fieselmann A, Moya A, Schuster S, Völker U, Dandekar T. Metabolic adaptation and protein complexes in prokaryotes. Metabolites 2012;2:940-958. [PMID: 24957769 PMCID: PMC3901225 DOI: 10.3390/metabo2040940] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Revised: 11/10/2012] [Accepted: 11/12/2012] [Indexed: 02/07/2023]  Open
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A whole-cell computational model predicts phenotype from genotype. Cell 2012;150:389-401. [PMID: 22817898 DOI: 10.1016/j.cell.2012.05.044] [Citation(s) in RCA: 785] [Impact Index Per Article: 60.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 04/20/2012] [Accepted: 05/14/2012] [Indexed: 11/20/2022]
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Leprince A, van Passel MWJ, dos Santos VAPM. Streamlining genomes: toward the generation of simplified and stabilized microbial systems. Curr Opin Biotechnol 2012;23:651-8. [DOI: 10.1016/j.copbio.2012.05.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 05/01/2012] [Accepted: 05/02/2012] [Indexed: 02/07/2023]
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