-
1
-
-
0345863935
-
The KEGG resource for deciphering the genome
-
Kanehisa,M., Goto,S., Kawashima,S., Okuno,Y. and Hattori,M. (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res., 32, D277-D280.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Kanehisa, M.1
Goto, S.2
Kawashima, S.3
Okuno, Y.4
Hattori, M.5
-
2
-
-
27244436714
-
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes
-
Karp,P.D., Ouzounis,C.A., Moore-Kochlacs,C., Goldovsky,L., Kaipa,P., Ahren,D., Tsoka,S., Darzentas,N., Kunin,V. and Lopez-Bigas,N. (2005) Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res., 33, 6083-6089.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 6083-6089
-
-
Karp, P.D.1
Ouzounis, C.A.2
Moore-Kochlacs, C.3
Goldovsky, L.4
Kaipa, P.5
Ahren, D.6
Tsoka, S.7
Darzentas, N.8
Kunin, V.9
Lopez-Bigas, N.10
-
3
-
-
11244328060
-
The pathway tools software
-
Karp,P.D., Paley,S. and Romero,P. (2002) The pathway tools software. Bioinformatics, 18, S225-S232.
-
(2002)
Bioinformatics
, vol.18
-
-
Karp, P.D.1
Paley, S.2
Romero, P.3
-
4
-
-
4644231028
-
Prolinks: A database of protein functional linkages derived from coevolution
-
Bowers,P., Pellegrini,M., Thompson,M., Fierro,J., Yeates,T. and Eisenberg,D. (2004) Prolinks: A database of protein functional linkages derived from coevolution. Genome Biol., 5, R35.
-
(2004)
Genome Biol.
, vol.5
-
-
Bowers, P.1
Pellegrini, M.2
Thompson, M.3
Fierro, J.4
Yeates, T.5
Eisenberg, D.6
-
5
-
-
3342925846
-
Comparison of network-based pathway analysis methods
-
Papin,J.A., Stelling,J., Price,N.D., Klamt,S., Schuster,S. and Palsson,B.O. (2004) Comparison of network-based pathway analysis methods. Trends Biotechnol., 22, 400-405.
-
(2004)
Trends Biotechnol.
, vol.22
, pp. 400-405
-
-
Papin, J.A.1
Stelling, J.2
Price, N.D.3
Klamt, S.4
Schuster, S.5
Palsson, B.O.6
-
6
-
-
0033523989
-
Protein interaction maps for complete genomes based on gene fusion events
-
Enright,A.J., Iliopoulos,I., Kyrpides,N.C. and Ouzounis,C.A. (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature, 402, 86-90.
-
(1999)
Nature
, vol.402
, pp. 86-90
-
-
Enright, A.J.1
Iliopoulos, I.2
Kyrpides, N.C.3
Ouzounis, C.A.4
-
7
-
-
0033780375
-
Prediction of protein interactions: Metabolic enzymes are frequently involved in gene fusion
-
Tsoka,S. and Ouzounis,C.A. (2000) Prediction of protein interactions: metabolic enzymes are frequently involved in gene fusion. Nature Genet., 26, 141-142.
-
(2000)
Nature Genet.
, vol.26
, pp. 141-142
-
-
Tsoka, S.1
Ouzounis, C.A.2
-
8
-
-
0032169271
-
Conservation of gene order: A fingerprint of proteins that physically interact
-
Dandekar,T., Snel,B., Huynen,M. and Bork,P. (1998) Conservation of gene order: A fingerprint of proteins that physically interact. Trends Biochem. Sci., 23, 324-328.
-
(1998)
Trends Biochem. Sci.
, vol.23
, pp. 324-328
-
-
Dandekar, T.1
Snel, B.2
Huynen, M.3
Bork, P.4
-
9
-
-
2442423854
-
Prediction of protein function and pathways in the genome era
-
Gabaldon,T. and Huynen,M.A. (2004) Prediction of protein function and pathways in the genome era. Cell Mol. Life Sci., 61, 930-944.
-
(2004)
Cell Mol. Life Sci.
, vol.61
, pp. 930-944
-
-
Gabaldon, T.1
Huynen, M.A.2
-
10
-
-
0033055062
-
The use of gene clusters to infer functional coupling
-
Overbeek,R., Fonstein,M., D'Souza,M., Pusch,G.D. and Maltsev,N. (1999) The use of gene clusters to infer functional coupling. Proc. Natl Acad. Sci. USA, 96, 2896-2901.
-
(1999)
Proc. Natl Acad. Sci. USA
, vol.96
, pp. 2896-2901
-
-
Overbeek, R.1
Fonstein, M.2
D'Souza, M.3
Pusch, G.D.4
Maltsev, N.5
-
11
-
-
0033301555
-
Use of contiguity on the chromosome to predict functional coupling
-
Overbeek,R., Fonstein,M., D'Souza,M., Pusch,G.D. and Maltsev,N. (1998) Use of contiguity on the chromosome to predict functional coupling. In Silico Biol., 1, 93-108.
-
(1998)
In Silico Biol.
, vol.1
, pp. 93-108
-
-
Overbeek, R.1
Fonstein, M.2
D'Souza, M.3
Pusch, G.D.4
Maltsev, N.5
-
12
-
-
0033551248
-
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
-
Pellegrini,M., Marcotte,E.M., Thompson,M.J., Eisenberg,D. and Yeates,T.O. (1999) Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. Proc. Natl Acad. Sci. USA, 96, 4285-4288.
-
(1999)
Proc. Natl Acad. Sci. USA
, vol.96
, pp. 4285-4288
-
-
Pellegrini, M.1
Marcotte, E.M.2
Thompson, M.J.3
Eisenberg, D.4
Yeates, T.O.5
-
13
-
-
13444249988
-
STRING: Known and predicted protein-protein associations, integrated and transferred across organisms
-
von Mering,C., Jensen,L.J., Snel,B., Hooper,S.D., Krupp,M., Foglierini,M., Jouffre,N., Huynen,M.A. and Bork,P. (2005) STRING: Known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res., 33, D433-D437.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
von Mering, C.1
Jensen, L.J.2
Snel, B.3
Hooper, S.D.4
Krupp, M.5
Foglierini, M.6
Jouffre, N.7
Huynen, M.A.8
Bork, P.9
-
14
-
-
0347364646
-
Genome evolution reveals biochemical networks and functional modules
-
von Mering,C., Zdobnov,E.M., Tsoka,S., Ciccarelli,F.D., Pereira-Leal,J.B., Ouzounis,C.A. and Bork,P. (2003) Genome evolution reveals biochemical networks and functional modules. Proc. Natl Acad. Sci. USA, 100, 15428-15433.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 15428-15433
-
-
von Mering, C.1
Zdobnov, E.M.2
Tsoka, S.3
Ciccarelli, F.D.4
Pereira-Leal, J.B.5
Ouzounis, C.A.6
Bork, P.7
-
15
-
-
0042889111
-
Identification of functional links between genes using phylogenetic profiles
-
Wu,J., Kasif,S. and DeLisi,C. (2003) Identification of functional links between genes using phylogenetic profiles. Bioinformatics, 19, 1524-1530.
-
(2003)
Bioinformatics
, vol.19
, pp. 1524-1530
-
-
Wu, J.1
Kasif, S.2
DeLisi, C.3
-
16
-
-
0037174738
-
The society of genes: Networks of functional links between genes from comparative genomics
-
Research 0064
-
Yanai,I. and DeLisi,C. (2002) The society of genes: Networks of functional links between genes from comparative genomics. Genome Biol., 3, Research 0064.
-
(2002)
Genome Biol.
, vol.3
-
-
Yanai, I.1
DeLisi, C.2
-
17
-
-
0036533931
-
Identifying functional links between genes using conserved chromosomal proximity
-
Yanai,I., Mellor,J.C. and DeLisi,C. (2002) Identifying functional links between genes using conserved chromosomal proximity. Trends Genet., 18, 176-179.
-
(2002)
Trends Genet.
, vol.18
, pp. 176-179
-
-
Yanai, I.1
Mellor, J.C.2
DeLisi, C.3
-
18
-
-
0036046771
-
Evolution of gene fusions: Horizontal transfer versus independent events
-
Research 0024
-
Yanai,I., Wolf,Y.I. and Koonin,E.V. (2002) Evolution of gene fusions: horizontal transfer versus independent events. Genome Biol., 3, Research 0024.
-
(2002)
Genome Biol.
, vol.3
-
-
Yanai, I.1
Wolf, Y.I.2
Koonin, E.V.3
-
19
-
-
0032242111
-
Microbial genescapes: Phyletic and functional patterns of ORF distribution among prokaryotes
-
Gaasterland,T. and Ragan,M.A. (1998) Microbial genescapes: Phyletic and functional patterns of ORF distribution among prokaryotes. Microb. Comp. Genomics, 3, 199-217.
-
(1998)
Microb. Comp. Genomics
, vol.3
, pp. 199-217
-
-
Gaasterland, T.1
Ragan, M.A.2
-
20
-
-
0036160526
-
Computational method to assign microbial genes to pathways
-
Pellegrini,M., Thompson,M., Fierro,J. and Bowers,P. (2001) Computational method to assign microbial genes to pathways. J. Cell Biochem., (Suppl. 37), 106-109.
-
(2001)
J. Cell Biochem.
, Issue.SUPPL. 37
, pp. 106-109
-
-
Pellegrini, M.1
Thompson, M.2
Fierro, J.3
Bowers, P.4
-
21
-
-
0033618555
-
Detecting protein function and protein-protein interactions from genome sequences
-
Marcotte,E.M., Pellegrini,M., Ng,H.L., Rice,D.W., Yeates,T.O. and Eisenberg,D. (1999) Detecting protein function and protein-protein interactions from genome sequences. Science, 285, 751-753.
-
(1999)
Science
, vol.285
, pp. 751-753
-
-
Marcotte, E.M.1
Pellegrini, M.2
Ng, H.L.3
Rice, D.W.4
Yeates, T.O.5
Eisenberg, D.6
-
22
-
-
0033523854
-
A combined algorithm for genome-wide prediction of protein function
-
Marcotte,E.M., Pellegrini,M., Thompson,M.J., Yeates,T.O. and Eisenberg,D. (1999) A combined algorithm for genome-wide prediction of protein function. Nature, 402, 83-86.
-
(1999)
Nature
, vol.402
, pp. 83-86
-
-
Marcotte, E.M.1
Pellegrini, M.2
Thompson, M.J.3
Yeates, T.O.4
Eisenberg, D.5
-
23
-
-
13244268322
-
A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases
-
Green,M.L. and Karp,P.D. (2004) A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics, 5, 76.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 76
-
-
Green, M.L.1
Karp, P.D.2
-
24
-
-
19244366327
-
Call for an enzyme genomics initiative
-
Karp,P.D. (2004) Call for an enzyme genomics initiative. Genome Biol., 5, 401.
-
(2004)
Genome Biol.
, vol.5
, pp. 401
-
-
Karp, P.D.1
-
25
-
-
19344377263
-
Identifying protein function - A call for community action
-
Roberts,R.J. (2004) Identifying protein function - a call for community action. PLoS Biol., 2, E42.
-
(2004)
PLoS Biol.
, vol.2
-
-
Roberts, R.J.1
-
26
-
-
0033168258
-
Integrated pathway-genome databases and their role in drug discovery
-
Karp,P.D., Krummenacker,M., Paley,S. and Wagg,J. (1999) Integrated pathway-genome databases and their role in drug discovery. Trends Biotechnol., 17, 275-281.
-
(1999)
Trends Biotechnol.
, vol.17
, pp. 275-281
-
-
Karp, P.D.1
Krummenacker, M.2
Paley, S.3
Wagg, J.4
-
27
-
-
0036578644
-
GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways
-
Dahlquist,K.D., Salomonis,N., Vranizan,K., Lawlor,S.C. and Conklin,B.R. (2002) GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nature Genet., 31, 19-20.
-
(2002)
Nature Genet.
, vol.31
, pp. 19-20
-
-
Dahlquist, K.D.1
Salomonis, N.2
Vranizan, K.3
Lawlor, S.C.4
Conklin, B.R.5
-
28
-
-
33645958298
-
BioWarehouse: A bioinformatics database warehouse toolkit
-
Lee,T.J., Pouliot,Y., Wagner,V., Gupta,P., Stringer-Calvert,D.W., Tenenbaum,J.D. and Karp,P.D. (2006) BioWarehouse: A bioinformatics database warehouse toolkit. BMC Bioinformatics, 7, 170.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 170
-
-
Lee, T.J.1
Pouliot, Y.2
Wagner, V.3
Gupta, P.4
Stringer-Calvert, D.W.5
Tenenbaum, J.D.6
Karp, P.D.7
-
29
-
-
21544461263
-
PAX of mind for pathway researchers
-
Luciano,J.S. (2005) PAX of mind for pathway researchers. Drug Discov. Today, 10, 937-942.
-
(2005)
Drug Discov. Today
, vol.10
, pp. 937-942
-
-
Luciano, J.S.1
-
30
-
-
28944444766
-
Representations of molecular pathways: An evaluation of SBML, PSI MI and BioPAX
-
Stromback,L. and Lambrix,P. (2005) Representations of molecular pathways: An evaluation of SBML, PSI MI and BioPAX. Bioinformatics, 21, 4401-4407.
-
(2005)
Bioinformatics
, vol.21
, pp. 4401-4407
-
-
Stromback, L.1
Lambrix, P.2
-
31
-
-
0348049802
-
Systems biology markup language: Level 2 and beyond
-
Finney,A. and Hucka,M. (2003) Systems biology markup language: Level 2 and beyond. Biochem. Soc. Trans., 31, 1472-1473.
-
(2003)
Biochem. Soc. Trans.
, vol.31
, pp. 1472-1473
-
-
Finney, A.1
Hucka, M.2
|