Other Organisms

Supplementary Table 1: Available predictive genome-scale metabolic network reconstructions

Adam M. Feist, Markus J. Herrgard, Ines Thiele, Jennie L. Reed, Bernhard Ø. Palsson "Reconstruction of Biochemical Networks in Microbial Organisms", Nat. Rev. Microbiol. 2009 Feb;7(2):129-43.

Supplementary Table 2 - Common issues encountered during metabolic network reconstruction

This list includes genome-scale metabolic network reconstructions that have been converted into predictive genome-scale models and whose predictive power has been validated against experimental data.

This table is managed and updated by Jonathan Monk (jmonk@ucsd.edu). Please send me an email with any missing information.

[ Bacteria ] [ Archaea] [ Eukaryota ]

Bacteria

Organism Strain Organism Genes Version Model Genes Metabolites Reactions Compartments Reference Journal Date
1 Acinetobacter baumannii AYE 3760 AbyMBEL891 650 778 891 2 (c,e) Kim et al. Mol Biosyst 2010/01/23
2 Acinetobacter baylyi ADP1 3287 iAbaylyiV4 774 701 875 3 (c,e,p) Durot et al. BMC Syst Biol 2008/10/09
3 Amycolatopsis balhimycina 8585 583 647 1363 Vongsangnak et al. Biotechnol Bioeng 2012/01/19
4 Bacillus megaterium WSH002 1055 993 1112 Zou et al. J Biotechnol 2013/03/05
5 Bacillus subtilis 168 4114 iBsu1103 1103 1138 1437 2 (c,e) Henry et al. Genome Biol 2009/06/27
6 Bacillus subtilis 4114 model_v3 844 988 1020 2 (c,e) Oh et al. J Biol Chem 2007/06/19
7 Blattabacterium cuenoti Bge iCG238 364 238 296 Gonzalez-Domenech et al. BMC Microbiol 2012/03/02
8 Blattabacterium cuenoti Pam iCG230 358 230 289 Gonzalez-Domenech et al. BMC Microbiol 2012/03/02
9 Bordetella pertussis 10536 Budman et al. Biotechnol Prog 2012/12/12
10 Buchnera aphidicola APS 574 iGT196 196 240 263 2 (c,e) Thomas et al. BMC Syst Biol 2009/02/24
11 Burkholderia cenocepacia J2315 iKF1028 1028 834 859 Fang et al. BMC Syst Biol 2011/05/26
12 Campylobacter jejuni NCTC 11168 388 467 536 Metris et al. BMC Genomics 2011/11/03
13 Chromohalobacter salexigens DSM 3352 iOA584 584 1411 1386 2 (c,e) Ates et al. BMC Syst Biol 2011/01/22
14 Clostridium acetobutylicum ATCC 824 3848 474 422 552 2 (c,e) Senger and Papoutsakis Biotechnol Bioeng 2008/09/04
15 Clostridium acetobutylicum ATCC 824 3848 432 479 502 2 (c,e) Lee et al. Appl Microbiol Biotechnol 2008/09/02
16 Clostridium beijerinckii NCIMB 8052 5243 iCB925 925 881 938 2(c,e) Milne et al. BMC Syst Biol 2011/08/19
17 Clostridium difficile 630 3968 iMLTC806cdf 806 703 769 Larocque et al. BMC Syst Biol 2014/10/16
18 Clostridium ljungdahlii iHN637 637 698 785 Nagarajan et al. Microb Cell Fact 2013/11/28
19 Clostridium thermocellum ATCC 27405 3307 iSR432 432 525 577 2 (c,e) Roberts et al. BMC Syst Biol 2010/03/24
20 Corynebacterium glutamicum ATCC 13032 3002 411 446 2 (c,e) Kjeldsen and Nielsen Biotechnol Bioeng 2008/11/06
21 Corynebacterium glutamicum ATCC 13032 3002 227 423 502 2 (c,e) Shinfuku et al. Microb Cell Fact 2009/08/04
22 Cyanothece sp. ATCC 51142 iCce806 806 667 Vu et al. PLoS Comput Biol 2012/04/25
23 Cyanothece sp. ATCC 51142 iCyt773 Saha et al. PLoS One 2012/11/08
24 Cyanothece sp. PCC 6803 iSyn731 Saha et al. PLoS One 2012/11/08
25 Dehalococcoides ethenogenes 2061 iAI549 549 549 518 2 (c,e) Ahsanul et al. PLoS Comput Biol 2010/09/03
26 Escherichia coli K-12 4405 iJR904 904 625 931 2 (c,e) Reed et al. Genome Biol 2003/09/04
27 Escherichia coli K-12 MG1655 4405 iJE660 660 438 627 2 (c,e) Edwards and Palsson Proc Natl Acad Sci U S A 2000/05/11
28 Escherichia coli K-12 MG1655 4405 iAF1260 1260 1039 2077 3 (c,e,p) Feist et al. Mol Syst Biol 2007/06/28
29 Escherichia coli K-12 MG1655 4405 iJO1366 1366 1136 2251 3 (c, e, p) Orth et al. Mol Syst Biol 2011/10/13
30 Escherichia coli W (ATCC 9637) 4764 iCA1273 1273 1111 2477 3 (c,e,p) Archer et al. BMC Genomics 2011/01/07
31 Francisella tularensis LVS 1802 iRS605 683 586 605 2 (c,e) Raghunathan et al. BMC Syst Biol 2010/08/25
32 Geobacter metallireducens 3532 747 769 697 2 (c,e) Sun et al. BMC Syst Biol 2009/01/30
33 Geobacter sulfurreducens 3530 588 541 523 2 (c,e) Mahadevan et al. Appl Environ Microbiol 2006/02/08
34 Gluconobacter oxydans 621H iXW433 433 985 859 Wu et al. Biosystems 2014/01/15
35 Haemophilus influenzae Rd 1775 iJE296 296 343 488 2 (c,e) Edwards and Palsson J Biol Chem 1999/06/11
36 Haemophilus influenzae Rd 1775 iCS400 400 451 461 2 (c,e) Schilling and Palsson J Theor Biol 2000/03/16
37 Helicobacter pylori 26695 1632 iCS291 291 340 388 2 (c,e) Schilling et al. J Bacteriol 2002/07/27
38 Helicobacter pylori 26695 1632 iIT341 341 485 476 2 (c,e) Thiele et al. J Bacteriol 2005/08/04
39 Ketogulonicigenium vulgare WSH-001 iWZ663 663 649 830 Zou et al. J Biotechnol 2012/06/26
40 Klebsiella oxytoca KoxGSC1457 1099 1457 Park et al. Microb Cell Fact 2013/02/26
41 Klebsiella pneumoniae MGH 78578 5186 iYL1228 1228 1658 1970 3 (c,e,p) Liao et al. J Bacteriol 2011/02/08
42 Kluyveromyces lactis iOD907 907 1476 1867 Dias et al. Biotechnol J 2014/04/30
43 Lactobacillus plantarum WCFS1 3009 721 531 643 2 (c,e) Teusink et al. J Biol Chem 2006/10/26
44 Lactococcus lactis ssp. lactisIL1403 2310 358 422 621 2 (c,e) Oliveira et al. BMC Microbiol 2005/06/29
45 Lactococcus lactis subsp. cremoris MG1363 2563 518 650 754 2 (c,e) Flahaut et al. Appl Microbiol Biotechnol 2013/08/27
46 Mannheimia succiniciproducens MBEL55E 2384 425 519 686 2 (c,e) Kim et al. Biotechnol Bioeng 2007/04/04
47 Mannheimia succiniciproducens MBEL55E 2384 335 332 373 2 (c,e) Hong et al. Nat Biotechnol 2004/09/21
48 Mycobacterium tuberculosis H37Rv 4402 iNJ661 661 828 939 2 (c,e) Jamshidi and Palsson BMC Syst Biol 2007/06/09
49 Mycobacterium tuberculosis H37Rv 4402 GSMN-TB 726 739 849 2 (c,e) Beste et al. Genome Biol 2007/05/25
50 Mycobacterium tuberculosis H37Rv 4402 iNJ661m 663 838 1049 2 (c,e) Fang et al. BMC Syst Biol 2010/11/26
51 Mycoplasma genitalium G-37 521 iPS189 189 274 262 2 (c,e) Suthers et al. PLoS Comput Biol 2009/02/14
52 Mycoplasma pneumoniae iJW145 145 Wodke et al. Mol Syst Biol 2013/04/04
53 Neisseria meningitidis serogroup B 2226 555 471 496 2 (c,e) Baart et al. Genome Biol 2007/07/10
54 Penicillium chrysogenum Wisconsin 54-1255 1006 1471 Agren et al. PLoS Comput Biol 2013/04/05
55 Porphyromonas gingivalis W83 2015 iVM679 564 679 2 (c,e) Mazumdar et al. J Bacteriol 2008/10/22
56 Pseudomonas aeruginosa PA01 5640 iMO1056 1056 760 883 2 (c,e) Oberhardt et al. J Bacteriol 2008/01/15
57 Pseudomonas fluorescens SBW25 iSB1139 1139 1194 1012 Borgos et al. BMC Syst Biol 2013/03/19
58 Pseudomonas putida KT2440 5350 PpuMBEL1071 900 1044 1071 2 (c,e) Sohn et al. Biotechnol J 2010/06/12
59 Pseudomonas putida KT2440 5350 iJN746 746 911 950 3 (c,p,e) Nogales et al. BMC Syst Biol 2008/09/17
60 Pseudomonas putida KT2440 5350 iJP815 815 886 877 3 (c,p,e) Puchalka et al. PLoS Comput Biol 2008/11/01
61 Ralstonia eutropha H16 RehMBEL1391 1171 1391 Park et al. BMC Syst Biol 2011/06/30
62 Rhizobium etli iOR450 450 377 402 Resendis-Antonio et al. PLoS Comput Biol 2012/10/17
63 Rhizobium etli CFN42 3168 iOR363 363 371 387 2 (c,e) Resendis-Antonio et al. PLoS Comput Biol 2007/10/10
64 Rhodobacter sphaeroides 2.4.1 iRsp1095 1095 796 1158 Imam et al. BMC Syst Biol 2011/07/23
65 Rhodococcus erythropolis Aggarwal et al. Mol Biosyst 2011/09/14
66 Rhodoferax ferrireducens 4770 744 790 762 2 (c,e) Risso et al. BMC Genomics 2009/09/24
67 Saccharopolyspora erythraea NRRL23338 2075 1646 1482 Licona-Cassani et al. Antonie Van Leeuwenhoek 2012/08/01
68 Salmonella enterica LT2 4489 STM_v1.0 1270 1119 2201 3 (c,e,p) Thiele et al. BMC Syst Biol 2011/01/20
69 Salmonella enterica LT2 4489 iRR1083 1083 774 1087 2 (c,e) Raghunathan et al. BMC Syst Biol 2009/04/10
70 Salmonella enterica LT2 4489 iMA945 945 1036 1964 2 (c,e) AbuOun et al. J Biol Chem 2009/08/20
71 Shewanella oneidensis MR-1 5066 iSO783 783 634 774 2 (c,e) Pinchuk et al. PLoS Comput Biol 2010/07/01
72 Sinorhizobium meliloti iHZ565 565 522 503 Zhao et al. PLoS One 2012/02/10
73 Sodalis glossinidius 668 690 741 Belda et al. PLoS One 2012/02/01
74 Spirulina platensis C1 PCC9438 iAK692 692 837 875 Klanchui et al. BMC Syst Biol 2012/06/19
75 Staphylococcus aureus Many 2588 546 1431 1493 2 (c,e) Lee et al. J Bacteriol 2009/04/21
76 Staphylococcus aureus N315 2588 iSB619 619 571 641 2 (c,e) Becker and Palsson BMC Microbiol 2005/03/09
77 Staphylococcus aureus N315 2588 iMH551 551 604 712 2 (c,e) Heinemann et al. Biotechnol Bioeng 2005/09/13
78 Streptococcus thermophilus LMG18311 1889 429 522 2 (c,e) Pastink et al. Appl Environ Microbiol 2009/04/07
79 Streptomyces coelicolor A3(2) 7825 789 759 1015 2 (c,e) Alam et al. BMC Genomics 2010/03/27
80 Streptomyces coelicolor A3(2) 7825 700 500 700 2 (c,e) Borodina et al. Genome Res 2005/06/03
81 Streptomyces lividans TK24 602 702 D'Huys et al. J Biotechnol 2012/05/30
82 Sulfolobus solfataricus P2 2977 705 718 Ulas et al. PLoS One 2012/09/07
83 Synechococcus sp PCC 7002 Vu et al. Biotechnol J 2013/04/25
84 Synechocystis sp. PCC6803 PCC6803 3221 iJN678 678 795 863 3(c,p,e) Nogales et al. Proc Natl Acad Sci U S A 2012/02/07
85 Synechocystis sp. PCC6803 PCC6803 3221 iSyn669 669 790 882 2 (c,e) Montagud et al. BMC Syst Biol 2010/11/19
86 Thermoanaerobacter tengcongensis 236 227 253 Tong et al. Mol Biosyst 2013/02/12
87 Thermotoga maritima MSB8 1917 478 503 562 2 (c,e) Zhang et al. Science 2009/09/19
88 Vibrio vulnificus CMCP6 2896 VvuMBEL943 673 792 943 2 (c,e) Kim et al. Mol Syst Biol 2011/01/20
89 Xanthomonas campestris pv. campestris B100 352 338 437 Schatschneider et al. J Biotechnol 2013/02/12
90 Yersinia pestis 91001 4037 iAN818m 818 825 1020 2 (c,e) Navid and Almaas Mol Biosyst 2009/04/28
91 Yersinia pestis CO92 4306 iPC815 815 963 1678 3 (c,e,p) Charusanti et al. BMC Syst Biol 2011/10/15
92 Zymomonas mobilis ZM4 1808 iZM363 363 704 747 2 (c,e) Widiastuti et al. Biotechnol Bioeng 2010/10/23
93 Zymomonas mobilis ZM4 1808 ZmobMBEL601 347 579 601 2 (c,e) Lee et al. Microb Cell Fact 2010/11/26

Eukaryota

Organism Strain Organism Genes Version Model Genes Metabolites Reactions Compartments Reference Journal Date
1 Arabidopsis thaliana 27379 AraGEM 1419 1748 1567 6 (c,e,m, de et al. Plant Physiol 2010/01/02
2 Aspergillus nidulans 9451 iHD666 666 732 794 4 (c,e,m,o) David et al. BMC Genomics 2008/04/15
3 Aspergillus niger CBS 513.88 14165 iMA871 871 1045 1190 3 (c,e,m) Andersen et al. Mol Syst Biol 2008/03/28
4 Aspergillus oryzae RIB40 12074 1314 1073 1053 3 (c,e,m,x) Vongsangnak et al. BMC Genomics 2008/05/27
5 Aspergillus terreus NIH2624 10406 iJL1454 1454 1155 1451 3 (c,e,m) Liu et al. Mol Biosyst 2013/04/30
6 Brassica napus 262 313 Pilalis et al. Biotechnol Bioeng 2011/02/22
7 Candida glabrata iNX804 804 1025 1287 Xu et al. Mol Biosyst 2012/11/23
8 Chlamydomonas reinhardtii 16709 iRC1080 1080 1068 2190 10 (c, e, h, s, f, x, g, m, n, u) Chang et al. Mol Syst Biol 2011/08/04
9 Cryptosporidium hominis 3884 iNV213 213 540 2 (c,e) Vanee et al. Chem Biodivers 2010/05/22
10 Drosophila Melongaster 15431 fly_model Feala et al. BMC Syst Biol 2009/09/11
11 Homo sapiens 28783 Recon 1 1496 2766 3311 8 (c,e,m,x Duarte et al. Proc Natl Acad Sci U S A 2007/02/03
12 Homo sapiens 28783 Recon 2 1789 5063 7440 Thiele et al. Nat Biotechnol 2013/03/05
13 Leishmania major Friedlin 8370 iAC560 560 1101 1112 8 (a,f,y,c, Chavali et al. Mol Syst Biol 2008/03/28
14 Mus musculus 28287 473 872 1220 3 (c,e,m) Sheikh et al. Biotechnol Prog 2005/05/21
15 Mus musculus 28287 724 1287 1494 3 (c,e,m) Selvarasu et al. Mol Biosyst 2009/12/22
16 Mus musculus 28287 iMM1415 1415 2774 3726 8 (c,e,g,l, Sigurdsson et al. BMC Syst Biol 2010/10/21
17 Mus musculus 28287 1399 2179 2037 3 (c,e,m) Quek and Nielsen Genome Inform 2008/01/01
18 Pichia pastoris DSMZ 70382 5450 PpaMBEL1254 540 1147 1254 8 (c,e,g,m Sohn et al. Biotechnol J 2010/05/27
19 Pichia pastoris GS115 5313 iLC915 915 899 1423 7 (c,m,p,v,r,g,n) Caspeta et al. BMC Syst Biol 2012/04/05
20 Pichia stipitis CBS 6054 5841 iSS884 884 992 1332 4 (c,m,p,v) Caspeta et al. BMC Syst Biol 2012/04/05
21 Pichia pastoris GS115 5313 iPP668 668 1177 1361 8 (c,e,g,m Chung et al. Microb Cell Fact 2010/07/03
22 Plasmodium falciparum 3D7 5615 579 1622 1375 6 (c,i,m,n,r,v) Huthmacher et al. BMC Syst Biol 2010/09/03
23 Plasmodium falciparum 3D7 5615 366 616 1001 4 (c,e,i,m) Plata et al. Mol Syst Biol 2010/09/09
24 Saccharomyces cerevisiae Sc288 6183 iFF708 708 584 1175 3 (c,e,m) Forster et al. Genome Res 2003/02/05
25 Saccharomyces cerevisiae Sc288 6183 iMM904 904 713 1412 8(c,e,m,x Mo et al. BMC Syst Biol 2009/03/27
26 Saccharomyces cerevisiae Sc288 6183 iND750 750 646 1149 8 (c,e,m, Duarte et al. Genome Res 2004/06/16
27 Saccharomyces cerevisiae Sc288 6183 iIN800 800 1013 1446 3(c,e,m) Nookaew et al. BMC Syst Biol 2008/08/09
28 Saccharomyces cerevisiae Sc288 6183 iLL672 672 636 1038 3 (c,e,m) Kuepfer et al. Genome Res 2005/10/06
29 Saccharomyces cerevisiae Sc288 6183 iMH805/775 832 1168 1857 15(c,e,g,m,n, r Herrgard et al. Nat Biotechnol 2008/10/11
30 Saccharomyces cerevisiae Sc288 6183 iTO977 977 1353 1566 4 Osterlund et al. BMC Syst Biol 2013/05/02
31 Saccharomyces pombe Sz-0205 4940 SpoMBEL1693 605 1744 1693 8(c,e,m,x Sohn et al. Biotechnol J 2010/06/12
32 Scheffersomyces stipitis CBS 6054 5816 iTL885 885 589 1240 3(c,e,m) Liu et al. Biotechnol Biofuels 2012/09/25
33 Schizosaccharomyces pombe Sz-0205 4940 SpoMBEL1693 605 1744 1693 8(c,e,m,x Sohn et al. BMC Syst Biol 2012/05/29
34 Toxoplasma gondii 382 382 384 571 5 (a,c, rm, m, mm) Song et al. Mol Syst Biol 2013/11/20
35 Yarrowia lipolytica iNL895 895 1847 2002 16 Loira et al. BMC Syst Biol 2012/05/09
36 Yarrowia lipolytica iYL619_PCP 619 843 1142 Pan and Hua PLoS One 2012/12/14
37 Zea mays iRS1563 1563 1825 1985 Saha et al. PLoS One 2011/07/15

Archaea

Organism Strain Organism Genes Version Model Genes Metabolites Reactions Compartments Reference Journal Date
1 Halobacterium salinarum R-1 2867 490 557 711 2 (c,e) Gonzalez et al. Mol Biosyst 2008/01/24
2 Methanosarcina acetivorans C2A 4540 iVS941 941 708 705 2 (c,e) Satish et al. BMC Syst Biol 2011/02/18
3 Methanosarcina acetivorans C2A 4540 iMB745 745 715 756 2 (c,e) Benedict et al. J Bacteriol 2011/12/06
4 Methanosarcina barkeri Fusaro 5072 iAF692 692 558 619 2 (c,e) Feist et al. Mol Syst Biol 2006/06/02
5 Methanosarcina barkeri Fusaro 5072 iMG746 746 719 741 2 (c,e) Gonnerman et al. Biotechnol J 2013/02/20
6 Natronomonas pharaonis DSM 2160 2892 654 597 683 2 (c,e) Gonzalez et al. PLoS Comput Biol 2010/06/15

Reconstruction status: 

P = In progress, D = draft, F = Finish

Compartment abbreviations:

* a: acidocalcisome * c: cytoplasm * e: extra-organism/extracellular * f: flagellum * g: golgi * h: chloroplast * i: apicoplast * l: lysosome * m: mitochondrion * n: nucleus * o: glyoxysomes * p: periplasm * r: ER * s: plastid *u: thykaloid lumen * v: vacuole * x: peroxisome * y: glycosome * gm: golgi membrane * mm: mitochondrial membrane * nm: nuclear membrane * pm: plasma membrane * rm: ER membrane * vm: vacuolar membrane * xm: peroxisomal membrane

Multiple cell type interaction models

Human alveolar macrophage and M. tuburculosis: Bordbar A, Lewis NE, Schellenberger J, Palsson BØ, Jamshidi N. *Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions*. Mol Syst Biol. 2010 Oct 19;6:422. PMID: [20959820]
Mesophyll and bundle sheath cells in C4 plants: de Oliveira Dal'molin CG, Quek LE, Palfreyman RW, Brumbley SM, Nielsen LK. C4GEM, *a Genome-Scale Metabolic Model to Study C4 Plant Metabolism*. Plant Physiol. 2010 Dec;154(4):1871-85. PMID: [20974891
Human brain cells: Lewis NE, Schramm G, Bordbar A, Schellenberger J, Andersen MP, Cheng JK, Patel N, Yee A, Lewis RA, Eils R, König R, Palsson BØ. *Large-scale in silico modeling of metabolic interactions between cell types in the human brain*. Nat Biotechnol. 2010 Dec;28(12):1279-85. PMID: [21102456]

Smaller scale reconstructions/models

Aspergillus niger: David H, Akesson M, Nielsen J, "Reconstruction of the central metabolism of Aspergillus niger", European Journal of Biochemistry, 270(21):4243-4253 (2003). PMID: [14622289].
Chlamydomonas rheinhardtii: Boyle NR, Morgan JA. "Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii.",BMC Syst Biol. 2009 Jan 7;3(1):4. PMID: [19128495].
Desulfovibrio vulgaris/Methanococcus maripaludis: 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. PMID: [17353934
Pichia pastoris: Tortajada M, Llaneras F, Pico J. "Validation of a constraint-based model of Pichia pastors metabolism under data scarcity", BMC Syst Biol, 4:115 (2010). PMID: [20716335
Synechocystis sp PCC 6803: Shastri AA, Morgan JA, “Flux balance analysis of photoautotrophic metabolism”, Biotechnol Prog, 21(6):1617-1626 (2005). PMID: [16321043].
Synechocystis sp PCC 6803: Hong SJ, Lee CG. “Evaluation of Central Metabolism Based on a Genomic Database of Synechocystis PCC6803”, Biotechnol Bioprocess Eng, 12:165-173 (2007). 
Trypanosoma cruzi: Roberts SB, Robichaux JL, Chavali AK, Manque PA, Lee V, Lara AM, Papin JA, Buck GA. "Proteomic and network analysis characterize stage-specific metabolism in Trypanosoma cruzi". BMC Syst Biol. 2009 May 16;3:52. PMID: [19445715]. 
Zymomonas mobilis: Tsantili IC, Karim MN, Klapa MI. “Quantifying the metabolic capabilities of engineered Zymomonas mobilis using linear programming analysis.” Microb. Cell Fact. 6:8 (2007). PMID: [17349037].

Metabolic reconstructions with no modeling:

Mannheimia succiniproducens: Hong SH, Kim JS, Lee SY, In YH, Choi SS, Rih JK, Kim CH, Jeong H, Hur CG, Kim JJ, "The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens" Nature Biotechnology, 22:1275-1281 (2004). PMID: [15378067]
Plasmodium falciparum: Yeh I, Hanekamp T, Tsoka S, Karp PD, Altman RB, "Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery" Genome Research, 14:917-924 (2004). PMID: [15078855]
Human: Romero P, Wagg J, Green ML, Kaiser D, Krummenacker M, Karp PD, "Computational prediction of human metabolic pathways from the complete human genome" Genome Biology, 6:R2.1-R2.17 (2004). PMID: [15642094]
Methanococcus jannaschii: Tsoka S, Simon D, Ouzounis CA, "Automated metabolic reconstruction for Methanococcus jannaschii" Archaea, 1:223-229 (2004). PMID: [15810431]
Bos taurus: Soh S, Lewin HA, *Reconstruction of metabolic pathways for the cattle genome BMC Systems Biology*. 2009 Mar 12;3:33. PMID: [19284618]
Fish (5 species: Zebrafish, Medaka, Takifugu, Tetraodon, Stickleback) Li S, Pozhitkov A, Ryan RA, Manning CS, Brown-Peterson N, Brouwer M. *Constructing a fish metabolic network model*. Genome Biol. 2010 Nov 29;11(11):R115. PMID: [21114829]

Reconstructions and models of other cellular networks:

Jak-Stat signaling network: Papin, J.A. and Palsson, B.Ø., "The JAK-STAT Signaling Network in the Human B-Cell: An Extreme Signaling Pathway Analysis ", Biophysical Journal, 87: 37-46(2004). PMID: [15240442]
Toll-like receptor signaling network: Li, F., Thiele, I., Jamshidi, N., and Palsson, B.Ø.,"Identification of Potential Pathway Mediation Targets in Toll-Like Receptor Signaling", PLoS Comp Biol. PMID:[19229310]
Transcriptional and translational machinery: Thiele, I., Jamshidi, N., Fleming, M.T., Palsson, B.Ø., "Genome-scale reconstruction of E. coli 's transcriptional and translational machinery: A knowledge-base, its mathematical formulation, and its functional characterization.", PLoS Comp Biol. PMID: [19282977]

Integrated networks and models:

Metabolism and transcriptional regulation

  • Covert MW, Knight EM, Reed JL, Herrgård MJ, Palsson BØ. "Integrating high-throughput and computational data elucidates bacterial networks." Nature. 2004. 429(6987): 92-6. PMID: [15129285]
  • Goelzer A, Bekkal Brikci F, Martin-Verstraete I, Noirot P, Bessières P, Aymerich S, Fromion V. "Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis." BMC Syst Biol. 2008 Feb 26;2:20. PMID: [18302748]
  • Chandrasekaran S, Price ND. "Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis." Proc Natl Acad Sci U S A. 2010 Oct 12;107(41):17845-50. PMID: [20876091]
  • Barua D, Kim J, Reed JL. "An automated phenotype-driven approach (GeneForce) for refining metabolic and regulatory models." PLoS Comput Biol. 2010 Oct 28;6(10):e1000970. PMID: [21060853]

Metabolism, signaling, transcriptional regulation 

  • Covert MW, Xiao N, Chen TJ, and Karr JR. "Integrated Flux Balance Analysis Model of Escherichia coli" Bioinformatics. 2008. 24(18): 2044-2050. PMID: [18621757]
  • Min Lee J, Gianchandani EP, Eddy JA, Papin JA. " Dynamic analysis of integrated signaling, metabolic, and regulatory networks." PLoS Comput Biol. 2008 May 23;4(5):e1000086. [18483615]

Additional Review Articles on Metabolic Reconstructions and Methods

Computational Modeling Software and Tools

  • Grafahrend-Belau E, Klukas C, Junker BH, Schreiber F. "FBA-SimVis Interactive visualisation of constraint-based metabolic models." Bioinformatics. 2009 Jul 3 [19578041]
  • Le Fèvre F, Smidtas S, Combe C, Durot M, d'Alché-Buc F, Schachter V. "CycSim-an online tool for exploring and experimenting with genome-scale metabolic models." Bioinformatics. 2009 Aug 1;25(15):1987-8. [19420054]
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