-
1
-
-
0037417817
-
Modular organization of cellular networks
-
Rives AW, Galitski T: Modular organization of cellular networks. Proc Natl Acad Sci USA 2003, 100:1128-1133.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 1128-1133
-
-
Rives, A.W.1
Galitski, T.2
-
2
-
-
0037199968
-
Hierarchical organization of modularity in metabolic networks
-
Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabási A-L: Hierarchical organization of modularity in metabolic networks. Science 2002, 297:1551-1555.
-
(2002)
Science
, vol.297
, pp. 1551-1555
-
-
Ravasz, E.1
Somera, A.L.2
Mongru, D.A.3
Oltvai, Z.N.4
Barabási, A.-L.5
-
3
-
-
14644396645
-
Functional cartography of complex metabolic networks
-
Gimera R, Amaral LAN: Functional cartography of complex metabolic networks. Nature 2005, 433:895-900.
-
(2005)
Nature
, vol.433
, pp. 895-900
-
-
Gimera, R.1
Amaral, L.A.N.2
-
4
-
-
22744439567
-
The evolution of connectivity in metabolic networks
-
Pfeiffer T, Soyer OS, Bonhoeffer S: The evolution of connectivity in metabolic networks. PLOS Biology 2005, 3:1269-1275.
-
(2005)
PLOS Biology
, vol.3
, pp. 1269-1275
-
-
Pfeiffer, T.1
Soyer, O.S.2
Bonhoeffer, S.3
-
5
-
-
0029125284
-
No soup for starters? Autotrophy and the origins of metabolism
-
Maden BEH: No soup for starters? Autotrophy and the origins of metabolism. Trends Biochem Sci 1995, 20:337-341.
-
(1995)
Trends Biochem Sci
, vol.20
, pp. 337-341
-
-
Maden, B.E.H.1
-
6
-
-
0021277007
-
On the origin of enzyme species by means of natural selection
-
Kacser H, Beeby R: On the origin of enzyme species by means of natural selection. J Mol Evol 1984, 20:38-51.
-
(1984)
J Mol Evol
, vol.20
, pp. 38-51
-
-
Kacser, H.1
Beeby, R.2
-
7
-
-
0032829506
-
On the origin of metabolic pathways
-
Lazcano A, Miller SL: On the origin of metabolic pathways. J Mol Evol 1999, 49:424-431.
-
(1999)
J Mol Evol
, vol.49
, pp. 424-431
-
-
Lazcano, A.1
Miller, S.L.2
-
8
-
-
0038434059
-
Metabolites: A helping hand for pathway evolution?
-
Schmidt S, Sunyaev S, Bork P, Dandekar T: Metabolites: a helping hand for pathway evolution? Trends Biochem Sci 2003, 28:336-341.
-
(2003)
Trends Biochem Sci
, vol.28
, pp. 336-341
-
-
Schmidt, S.1
Sunyaev, S.2
Bork, P.3
Dandekar, T.4
-
9
-
-
0001260894
-
On the evolution of biochemical syntheses
-
Horowitz NH: On the evolution of biochemical syntheses. Proc Natl Acad Sci USA 1945, 31:153-157.
-
(1945)
Proc Natl Acad Sci USA
, vol.31
, pp. 153-157
-
-
Horowitz, N.H.1
-
11
-
-
0017272554
-
Enzyme recruitment in evolution of new function
-
Jensen RA. Enzyme recruitment in evolution of new function. Ann Rev Microbiol 1976, 30:409-425.
-
(1976)
Ann Rev Microbiol
, vol.30
, pp. 409-425
-
-
Jensen, R.A.1
-
12
-
-
0034601917
-
8 barrels: Implications for the evolution of metabolic pathways
-
8 barrels: implications for the evolution of metabolic pathways. J Mol Biol 2000, 303:627-640.
-
(2000)
J Mol Biol
, vol.303
, pp. 627-640
-
-
Copley, R.R.1
Bork, P.2
-
13
-
-
0035575588
-
Small-molecule metabolism: An enzyme mosaic
-
Teichmann SA, Rison SCG, Thornton JM, Riley M, Gough J, Chothia C: Small-molecule metabolism: an enzyme mosaic. Trends Biotech 2001, 19:482-486.
-
(2001)
Trends Biotech
, vol.19
, pp. 482-486
-
-
Teichmann, S.A.1
Rison, S.C.G.2
Thornton, J.M.3
Riley, M.4
Gough, J.5
Chothia, C.6
-
14
-
-
0035943351
-
The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli
-
Teichmann SA, Rison SC, Thornton JM, Riley M, Gough J, Cothia C: The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli. J Mol Biol 2001, 311:693-708.
-
(2001)
J Mol Biol
, vol.311
, pp. 693-708
-
-
Teichmann, S.A.1
Rison, S.C.2
Thornton, J.M.3
Riley, M.4
Gough, J.5
Cothia, C.6
-
15
-
-
0036303685
-
Evolution of enzymes in metabolism: A network perspective
-
Alves R, Chaleil RAG, Sternberg MJE: Evolution of enzymes in metabolism: A network perspective. J Mol Biol 2002, 320:751-770.
-
(2002)
J Mol Biol
, vol.320
, pp. 751-770
-
-
Alves, R.1
Chaleil, R.A.G.2
Sternberg, M.J.E.3
-
16
-
-
2942604422
-
Network analysis of metabolic enzyme evolution in Escherichia coli
-
Light S, Kraulis P: Network analysis of metabolic enzyme evolution in Escherichia coli. BMC Bioinformatics 2004, 5:15.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 15
-
-
Light, S.1
Kraulis, P.2
-
17
-
-
0031584266
-
Protein evolution viewed through Esherichia coli protein sequences: Introducing the notion of a structural segment of homology, the module
-
Riley M, Labedan B: Protein evolution viewed through Esherichia coli protein sequences: Introducing the notion of a structural segment of homology, the module. J Mol Biol 1997, 268:857-868.
-
(1997)
J Mol Biol
, vol.268
, pp. 857-868
-
-
Riley, M.1
Labedan, B.2
-
18
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin AG, Brenner SE, Hubbard T, Chothia C: SCOP: A structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995, 247:536-540.
-
(1995)
J Mol Biol
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
19
-
-
0030777303
-
CATH: A hierarchic classification of protein domain structures
-
Orengo CA, Michie AD, Jones S, Jones DJ, Swindells MB, Thornton JM: CATH: a hierarchic classification of protein domain structures. Structure 1997, 5:1093-1108.
-
(1997)
Structure
, vol.5
, pp. 1093-1108
-
-
Orengo, C.A.1
Michie, A.D.2
Jones, S.3
Jones, D.J.4
Swindells, M.B.5
Thornton, J.M.6
-
20
-
-
0037841804
-
Evolution of the protein repertoire
-
Chothia C, Gough J, Vogel C, Teichmann SA: Evolution of the protein repertoire. Science 2003, 300:1701-1703.
-
(2003)
Science
, vol.300
, pp. 1701-1703
-
-
Chothia, C.1
Gough, J.2
Vogel, C.3
Teichmann, S.A.4
-
21
-
-
0027122748
-
Proteins-1000 families for the molecular biologist
-
Chothia C: Proteins-1000 families for the molecular biologist. Nature 1992, 357:543-544.
-
(1992)
Nature
, vol.357
, pp. 543-544
-
-
Chothia, C.1
-
22
-
-
0028593509
-
Protein superfamilies and domain superfolds
-
Orengo CA, Jones DT, Thornton JM: Protein superfamilies and domain superfolds. Nature 1994, 372:631-634.
-
(1994)
Nature
, vol.372
, pp. 631-634
-
-
Orengo, C.A.1
Jones, D.T.2
Thornton, J.M.3
-
23
-
-
0031734751
-
Comparing genomes in terms of protein structure: Surveys of a finite parts list
-
Gerstein M, Hegyi H: Comparing genomes in terms of protein structure: Surveys of a finite parts list. FEMS Microbiol Rev 1998, 22:277-304.
-
(1998)
FEMS Microbiol Rev
, vol.22
, pp. 277-304
-
-
Gerstein, M.1
Hegyi, H.2
-
24
-
-
0032387685
-
Patterns of protein-fold usage in eight microbial genomes: A comprehensive structural census
-
Gerstein M: Patterns of protein-fold usage in eight microbial genomes: A comprehensive structural census. Proteins 1998, 33:518-534.
-
(1998)
Proteins
, vol.33
, pp. 518-534
-
-
Gerstein, M.1
-
25
-
-
0033008596
-
Distribution of protein folds in the three superkingdoms of life
-
Wolf YI, Brenner SE, Bash PA, Koonin EV: Distribution of protein folds in the three superkingdoms of life. Genome Res 1999, 9:17-26.
-
(1999)
Genome Res
, vol.9
, pp. 17-26
-
-
Wolf, Y.I.1
Brenner, S.E.2
Bash, P.A.3
Koonin, E.V.4
-
26
-
-
0033918311
-
Whole-genome trees based on the folds and orthologs: Implications for comparing genomes on different levels
-
Lin J, Gerstein M: Whole-genome trees based on the folds and orthologs: Implications for comparing genomes on different levels. Genome Res 2000, 10:808-818.
-
(2000)
Genome Res
, vol.10
, pp. 808-818
-
-
Lin, J.1
Gerstein, M.2
-
27
-
-
0038486929
-
An evolutionarily structured universe of protein architecture
-
Caetano-Anollés G, Caetano-Anollés D: An evolutionarily structured universe of protein architecture. Genome Res 2003, 13:1563-1571.
-
(2003)
Genome Res
, vol.13
, pp. 1563-1571
-
-
Caetano-Anollés, G.1
Caetano-Anollés, D.2
-
28
-
-
15544380021
-
Prokaryotic phylogenies inferred from protein structural domains
-
Deeds EJ, Hennessey H, Shakhnovich EI: Prokaryotic phylogenies inferred from protein structural domains. Genome Res 2005, 15:393-402.
-
(2005)
Genome Res
, vol.15
, pp. 393-402
-
-
Deeds, E.J.1
Hennessey, H.2
Shakhnovich, E.I.3
-
30
-
-
19944393249
-
Universal sharing patterns in proteomes and evolution of protein fold architecture and life
-
Caetano-Anollés G, Caetano-Anollés D: Universal sharing patterns in proteomes and evolution of protein fold architecture and life. J Mol Evol 2005, 60:484-498.
-
(2005)
J Mol Evol
, vol.60
, pp. 484-498
-
-
Caetano-Anollés, G.1
Caetano-Anollés, D.2
-
31
-
-
33748311638
-
A phylogenomic reconstruction of the protein world based on a genomic census of protein fold architecture
-
in press
-
Wang M, Boca SM, Kalelkar R, Mittenthal JE, Caetano-Anollés D: A phylogenomic reconstruction of the protein world based on a genomic census of protein fold architecture. Complexity 2006 in press.
-
(2006)
Complexity
-
-
Wang, M.1
Boca, S.M.2
Kalelkar, R.3
Mittenthal, J.E.4
Caetano-Anollés, D.5
-
33
-
-
0033597176
-
The relationship between protein structure and function: A comprehensive survey with application to the yeast genome
-
Hegyi H, Gerstein M: The relationship between protein structure and function: a comprehensive survey with application to the yeast genome. J Mol Biol 1999, 288:147-164.
-
(1999)
J Mol Biol
, vol.288
, pp. 147-164
-
-
Hegyi, H.1
Gerstein, M.2
-
35
-
-
0345863935
-
The KEGG resources for deciphering the genome
-
Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M: The KEGG resources for deciphering the genome. Nucleic Acids Res 2004, 32:D277-D280.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Kanehisa, M.1
Goto, S.2
Kawashima, S.3
Okuno, Y.4
Hattori, M.5
-
36
-
-
84874653588
-
-
Superfamily
-
Superfamily [http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY]
-
-
-
-
37
-
-
0035798406
-
Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
-
Gough J, Karplus K, Hughey R, Chothia C: Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol 2001, 313:903-919.
-
(2001)
J Mol Biol
, vol.313
, pp. 903-919
-
-
Gough, J.1
Karplus, K.2
Hughey, R.3
Chothia, C.4
-
39
-
-
0000461280
-
Confidence limits on phylogenies: An approach using the bootstrap
-
Felsenstein J: Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39:783-791.
-
(1985)
Evolution
, vol.39
, pp. 783-791
-
-
Felsenstein, J.1
-
40
-
-
84874667787
-
-
Kyoto Encyclopedia of Genes and Genomes [ftp://ftp.genome.ad.jp/pub/kegg]
-
Kyoto Encyclopedia of Genes and Genomes [ftp://ftp.genome.ad.jp/pub/ kegg].
-
-
-
-
41
-
-
84874659001
-
-
Structural Classification of Proteins
-
Structural Classification of Proteins [http://scop.mrc-lmb.cam.ac.uk/ scop/parse/index.html].
-
-
-
-
42
-
-
4043050799
-
-
SAS: Cary, NC: SAS Institute Inc
-
SAS: OnlineDoc®, version 8 Cary, NC: SAS Institute Inc; 1999.
-
(1999)
OnlineDoc®, Version 8
-
-
-
44
-
-
0036306663
-
Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli
-
Rison SCG, Teichmann SA, Thornton JM: Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli. J Mol Biol 2002, 318:911-932.
-
(2002)
J Mol Biol
, vol.318
, pp. 911-932
-
-
Rison, S.C.G.1
Teichmann, S.A.2
Thornton, J.M.3
-
45
-
-
0035834499
-
A structural census of metabolic networks for E. coli
-
Saqui MAS, Sternberg JE: A structural census of metabolic networks for E. coli. J Mol Biol 2001, 313:1195-1206.
-
(2001)
J Mol Biol
, vol.313
, pp. 1195-1206
-
-
Saqui, M.A.S.1
Sternberg, J.E.2
-
46
-
-
14644429634
-
A ligand-centric analysis of the diversity and evolution of protein-ligand relationships in E. coli
-
Nobeli I, Spriggs RV, George RA, Thornton JML: A ligand-centric analysis of the diversity and evolution of protein-ligand relationships in E. coli. J Mol Biol 2005, 347:415-436.
-
(2005)
J Mol Biol
, vol.347
, pp. 415-436
-
-
Nobeli, I.1
Spriggs, R.V.2
George, R.A.3
Thornton, J.M.L.4
-
47
-
-
0037350415
-
The phylogenetic extent of metabolic enzymes and pathways
-
Peregrin-Alvarez JM, Tsoka S, Ouzounis CA. The phylogenetic extent of metabolic enzymes and pathways. Genome Res 2003, 13:422-427.
-
(2003)
Genome Res
, vol.13
, pp. 422-427
-
-
Peregrin-Alvarez, J.M.1
Tsoka, S.2
Ouzounis, C.A.3
-
48
-
-
0033753685
-
Visualizing large hierarchical clusters in hyperbolic space
-
Bingham J, Sudarsanam S: Visualizing large hierarchical clusters in hyperbolic space. Bioinformatics 2000, 16:660-661.
-
(2000)
Bioinformatics
, vol.16
, pp. 660-661
-
-
Bingham, J.1
Sudarsanam, S.2
-
49
-
-
0036084625
-
SCOP database in 2002: Refinements accommodate structural genomics
-
Lo Conte L, Brenner SE, Hubbard TJP, Chothia C, Murzin A: SCOP database in 2002: Refinements accommodate structural genomics. Nucleic Acids Res 2002, 30:264-267.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 264-267
-
-
Lo Conte, L.1
Brenner, S.E.2
Hubbard, T.J.P.3
Chothia, C.4
Murzin, A.5
-
50
-
-
0036428739
-
Quantifying the similarities within fold space
-
Harrison A, Pearl F, Mott R, Thornton J, Orengo C: Quantifying the similarities within fold space. J Mol Biol 2002, 323:909-929.
-
(2002)
J Mol Biol
, vol.323
, pp. 909-929
-
-
Harrison, A.1
Pearl, F.2
Mott, R.3
Thornton, J.4
Orengo, C.5
-
51
-
-
0036384350
-
One fold with many functions: The evolutionary relationships between TIM barrel families based on their sequences, structures and functions
-
Nagano N, Orengo CA, Thornton JM: One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J Mol Biol 2002, 321:741-765.
-
(2002)
J Mol Biol
, vol.321
, pp. 741-765
-
-
Nagano, N.1
Orengo, C.A.2
Thornton, J.M.3
-
52
-
-
0348129526
-
The ASTRAL compendium in 2004
-
Chandonia JM, Hon G, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE: The ASTRAL compendium in 2004. Nucleic Acids Res 2004, 32:D189-D192.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Chandonia, J.M.1
Hon, G.2
Walker, N.S.3
Lo Conte, L.4
Koehl, P.5
Levitt, M.6
Brenner, S.E.7
-
53
-
-
76649085598
-
A theory of biochemical organization, metabolic pathways, and evolution
-
Morowitz H: A theory of biochemical organization, metabolic pathways, and evolution. Complexity 1999, 4:39-53.
-
(1999)
Complexity
, vol.4
, pp. 39-53
-
-
Morowitz, H.1
-
54
-
-
0034608818
-
The origin of intermediary metabolism
-
Morowitz HJ, Kostelnik JD, Yang J, Ody GD: The origin of intermediary metabolism. Proc Natl Acad Sci USA 2000, 97:7704-7708.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 7704-7708
-
-
Morowitz, H.J.1
Kostelnik, J.D.2
Yang, J.3
Ody, G.D.4
|