-
1
-
-
0032491377
-
Predicting function: From genes to genomes and back
-
Bork P., Dandekar T., Diaz-Lazcoz Y., Eisenhaber F., Huynen M., Yuan Y. Predicting function: from genes to genomes and back. J. Mol. Biol. 283:1998;707-725.
-
(1998)
J. Mol. Biol.
, vol.283
, pp. 707-725
-
-
Bork, P.1
Dandekar, T.2
Diaz-Lazcoz, Y.3
Eisenhaber, F.4
Huynen, M.5
Yuan, Y.6
-
2
-
-
0034628508
-
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
-
Uetz P., Giot L., Cagney G., Mansfield T.A., Judson R.S., Knight J.R., Lockshon D., Narayan V., Srinivasan M., Pochart P.et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature. 403:2000;623-627.
-
(2000)
Nature
, vol.403
, pp. 623-627
-
-
Uetz, P.1
Giot, L.2
Cagney, G.3
Mansfield, T.A.4
Judson, R.S.5
Knight, J.R.6
Lockshon, D.7
Narayan, V.8
Srinivasan, M.9
Pochart, P.10
-
3
-
-
0037050026
-
Functional organization of the yeast proteome by systematic analysis of protein complexes
-
Gavin A.C., Bosche M., Krause R., Grandi P., Marzioch M., Bauer A., Schultz J., Rick J.M., Michon A.M., Cruciat C.M.et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 415:2002;141-147.
-
(2002)
Nature
, vol.415
, pp. 141-147
-
-
Gavin, A.C.1
Bosche, M.2
Krause, R.3
Grandi, P.4
Marzioch, M.5
Bauer, A.6
Schultz, J.7
Rick, J.M.8
Michon, A.M.9
Cruciat, C.M.10
-
4
-
-
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., Eisenberg D. Detecting protein function and protein-protein interactions from genome sequences. Science. 285:1999;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
-
5
-
-
0033523989
-
Protein interaction maps for complete genomes based on gene fusion events
-
Enright A.J., Iliopoulos I., Kyrpides N.C., Ouzounis C.A. Protein interaction maps for complete genomes based on gene fusion events. Nature. 402:1999;86-90.
-
(1999)
Nature
, vol.402
, pp. 86-90
-
-
Enright, A.J.1
Iliopoulos, I.2
Kyrpides, N.C.3
Ouzounis, C.A.4
-
6
-
-
0033301555
-
Use of contiguity on the chromosome to predict functional coupling
-
Overbeek R., Fonstein M., D'Souza M., Pusch G.D., Maltsev N. Use of contiguity on the chromosome to predict functional coupling. In Silico Biol. 1:1998;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
-
7
-
-
0032169271
-
Conservation of gene order: A fingerprint of proteins that physically interact
-
Dandekar T., Snel B., Huynen M., Bork P. Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem. Sci. 23:1998;324-328.
-
(1998)
Trends Biochem. Sci.
, vol.23
, pp. 324-328
-
-
Dandekar, T.1
Snel, B.2
Huynen, M.3
Bork, P.4
-
8
-
-
0033551248
-
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
-
Pellegrini M., Marcotte E.M., Thompson M.J., Eisenberg D., Yeates T.O. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. USA. 96:1999;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
-
10
-
-
0035177259
-
Similarity of phylogenetic trees as indicator of protein-protein interaction
-
Pazos F., Valencia A. Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng. 14:2001;609-614.
-
(2001)
Protein Eng.
, vol.14
, pp. 609-614
-
-
Pazos, F.1
Valencia, A.2
-
11
-
-
0033918228
-
Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes
-
McGuire A.M., Hughes J.D., Church G.M. Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. Genome Res. 10:2000;744-757.
-
(2000)
Genome Res.
, vol.10
, pp. 744-757
-
-
McGuire, A.M.1
Hughes, J.D.2
Church, G.M.3
-
12
-
-
0037188521
-
Probabilistic clustering of sequences: Inferring new bacterial regulons by comparative genomics
-
A novel Bayesian clustering methodology for promotor prediction by comparative genome analysis, leading to the prediction of around 100 new regulons in E. coli. The paper argues that there are inherent mathematical limits to our ability to discover promoters in sequence data and that comparative genomic information may be crucial in this respect
-
van Nimwegen E., Zavolan M., Rajewsky N., Siggia E.D. Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics. Proc. Natl. Acad. Sci. USA. 99:2002;7323-7328 A novel Bayesian clustering methodology for promotor prediction by comparative genome analysis, leading to the prediction of around 100 new regulons in E. coli. The paper argues that there are inherent mathematical limits to our ability to discover promoters in sequence data and that comparative genomic information may be crucial in this respect.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 7323-7328
-
-
Van Nimwegen, E.1
Zavolan, M.2
Rajewsky, N.3
Siggia, E.D.4
-
13
-
-
0034027595
-
Computational genetics: Finding protein function by nonhomology methods
-
Marcotte E.M. Computational genetics: finding protein function by nonhomology methods. Curr. Opin. Struct. Biol. 10:2000;359-365.
-
(2000)
Curr. Opin. Struct. Biol.
, vol.10
, pp. 359-365
-
-
Marcotte, E.M.1
-
14
-
-
0034084865
-
Who's your neighbor? New computational approaches for functional genomics
-
Galperin M.Y., Koonin E.V. Who's your neighbor? New computational approaches for functional genomics. Nat. Biotechnol. 18:2000;609-613.
-
(2000)
Nat. Biotechnol.
, vol.18
, pp. 609-613
-
-
Galperin, M.Y.1
Koonin, E.V.2
-
15
-
-
0036601150
-
Computational methods for the prediction of protein interactions
-
Valencia A., Pazos F. Computational methods for the prediction of protein interactions. Curr. Opin. Struct. Biol. 12:2002;368-373.
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 368-373
-
-
Valencia, A.1
Pazos, F.2
-
17
-
-
0033832615
-
Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences
-
Huynen M., Snel B., Lathe W. III, Bork P. Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res. 10:2000;1204-1210.
-
(2000)
Genome Res.
, vol.10
, pp. 1204-1210
-
-
Huynen, M.1
Snel, B.2
Lathe W. III3
Bork, P.4
-
18
-
-
0034940467
-
Genes linked by fusion events are generally of the same functional category: A systematic analysis of 30 microbial genomes
-
Yanai I., Derti A., DeLisi C. Genes linked by fusion events are generally of the same functional category: a systematic analysis of 30 microbial genomes. Proc. Natl. Acad. Sci. USA. 98:2001;7940-7945.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 7940-7945
-
-
Yanai, I.1
Derti, A.2
DeLisi, C.3
-
19
-
-
0037250152
-
STRING: A database of predicted functional associations between proteins
-
von Mering C., Huynen M.A., Jaeggi D., Schmidt S., Bork P., Snel B. STRING: a database of predicted functional associations between proteins. Nucleic Acids Res. 31:2003;258-261.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 258-261
-
-
Von Mering, C.1
Huynen, M.A.2
Jaeggi, D.3
Schmidt, S.4
Bork, P.5
Snel, B.6
-
20
-
-
0036533931
-
Identifying functional links between genes using conserved chromosomal proximity
-
Yanai I., Mellor J.C., DeLisi C. Identifying functional links between genes using conserved chromosomal proximity. Trends Genet. 18:2002;176-179.
-
(2002)
Trends Genet.
, vol.18
, pp. 176-179
-
-
Yanai, I.1
Mellor, J.C.2
DeLisi, C.3
-
21
-
-
0033957834
-
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
-
Bairoch A., Apweiler R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28:2000;45-48.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 45-48
-
-
Bairoch, A.1
Apweiler, R.2
-
23
-
-
0037161731
-
Comparative assessment of large-scale data sets of protein-protein interactions
-
The paper summarizes protein interaction data in the yeast S. cerevisiae, and performs a rough quality assessment through several independent benchmarks. Interaction data are found to be largely complementary - having a surprisingly small overlap. The best accuracy is found for combined datasets
-
von Mering C., Krause R., Snel B., Cornell M., Oliver S.G., Fields S., Bork P. Comparative assessment of large-scale data sets of protein-protein interactions. Nature. 417:2002;399-403 The paper summarizes protein interaction data in the yeast S. cerevisiae, and performs a rough quality assessment through several independent benchmarks. Interaction data are found to be largely complementary - having a surprisingly small overlap. The best accuracy is found for combined datasets.
-
(2002)
Nature
, vol.417
, pp. 399-403
-
-
Von Mering, C.1
Krause, R.2
Snel, B.3
Cornell, M.4
Oliver, S.G.5
Fields, S.6
Bork, P.7
-
25
-
-
0012423648
-
Exploiting the variations in the genomic associations of genes to predict pathways and reconstruct their evolution
-
Edited by Galperin MY, Koonin EV. Norfolk: Caisters Academic Press
-
Huynen MA, Snel B: Exploiting the variations in the genomic associations of genes to predict pathways and reconstruct their evolution. In Frontiers in Computational Genomics. Edited by Galperin MY, Koonin EV. Norfolk: Caisters Academic Press; 2003:145-166.
-
(2003)
Frontiers in Computational Genomics
, pp. 145-166
-
-
Huynen, M.A.1
Snel, B.2
-
26
-
-
13344270899
-
Friedreich's ataxia: Autosomal recessive disease caused by an intronic GAA triplet repeat expansion
-
Campuzano V., Montermini L., Molto M.D., Pianese L., Cossee M., Cavalcanti F., Monros E., Rodius F., Duclos F., Monticelli A.et al. Friedreich's ataxia: autosomal recessive disease caused by an intronic GAA triplet repeat expansion. Science. 271:1996;1423-1427.
-
(1996)
Science
, vol.271
, pp. 1423-1427
-
-
Campuzano, V.1
Montermini, L.2
Molto, M.D.3
Pianese, L.4
Cossee, M.5
Cavalcanti, F.6
Monros, E.7
Rodius, F.8
Duclos, F.9
Monticelli, A.10
-
27
-
-
0035504444
-
The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly
-
Huynen M.A., Snel B., Bork P., Gibson T.J. The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly. Hum. Mol. Genet. 10:2001;2463-2468.
-
(2001)
Hum. Mol. Genet.
, vol.10
, pp. 2463-2468
-
-
Huynen, M.A.1
Snel, B.2
Bork, P.3
Gibson, T.J.4
-
28
-
-
0037101845
-
The yeast frataxin homolog Yfh1p plays a specific role in the maturation of cellular Fe/S proteins
-
Muhlenhoff U., Richhardt N., Ristow M., Kispal G., Lill R. The yeast frataxin homolog Yfh1p plays a specific role in the maturation of cellular Fe/S proteins. Hum. Mol. Genet. 11:2002;2025-2036.
-
(2002)
Hum. Mol. Genet.
, vol.11
, pp. 2025-2036
-
-
Muhlenhoff, U.1
Richhardt, N.2
Ristow, M.3
Kispal, G.4
Lill, R.5
-
29
-
-
0037126057
-
Inhibition of Fe-S cluster biosynthesis decreases mitochondrial iron export: Evidence that Yfh1p affects Fe-S cluster synthesis
-
Chen O.S., Hemenway S., Kaplan J. Inhibition of Fe-S cluster biosynthesis decreases mitochondrial iron export: Evidence that Yfh1p affects Fe-S cluster synthesis. Proc. Natl. Acad. Sci. USA. 99:2002;12321-12326.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 12321-12326
-
-
Chen, O.S.1
Hemenway, S.2
Kaplan, J.3
-
30
-
-
0036799372
-
A non-essential function for yeast frataxin in iron-sulfur cluster assembly
-
Duby G., Foury F., Ramazzotti A., Herrmann J., Lutz T. A non-essential function for yeast frataxin in iron-sulfur cluster assembly. Hum. Mol. Genet. 11:2002;2635-2643.
-
(2002)
Hum. Mol. Genet.
, vol.11
, pp. 2635-2643
-
-
Duby, G.1
Foury, F.2
Ramazzotti, A.3
Herrmann, J.4
Lutz, T.5
-
31
-
-
0035799707
-
Lethality and centrality in protein networks
-
This fresh and original study integrates data from yeast two-hybrids and lethal mutations in yeast to convincingly show that mutations in proteins central in the network of proteins interactions are indeed more lethal, as predicted by theory of scale-free networks
-
Jeong H., Mason S.P., Barabasi A.L., Oltvai Z.N. Lethality and centrality in protein networks. Nature. 411:2001;41-42 This fresh and original study integrates data from yeast two-hybrids and lethal mutations in yeast to convincingly show that mutations in proteins central in the network of proteins interactions are indeed more lethal, as predicted by theory of scale-free networks.
-
(2001)
Nature
, vol.411
, pp. 41-42
-
-
Jeong, H.1
Mason, S.P.2
Barabasi, A.L.3
Oltvai, Z.N.4
-
32
-
-
0037177560
-
Evolutionary rate in the protein interaction network
-
A rigorous statistical analysis of variations in evolutionary rates and their causes. Notably the authors can reject the hypothesis that the slow evolutionary rate of highly connected proteins is because these proteins are relatively essential for the organism. Instead it appears to be caused by co-evolutionary constraints that are caused by protein-protein interactions
-
Fraser H.B., Hirsh A.E., Steinmetz L.M., Scharfe C., Feldman M.W. Evolutionary rate in the protein interaction network. Science. 296:2002;750-752 A rigorous statistical analysis of variations in evolutionary rates and their causes. Notably the authors can reject the hypothesis that the slow evolutionary rate of highly connected proteins is because these proteins are relatively essential for the organism. Instead it appears to be caused by co-evolutionary constraints that are caused by protein-protein interactions.
-
(2002)
Science
, vol.296
, pp. 750-752
-
-
Fraser, H.B.1
Hirsh, A.E.2
Steinmetz, L.M.3
Scharfe, C.4
Feldman, M.W.5
-
33
-
-
0034609791
-
The large-scale organization of metabolic networks
-
Jeong H., Tombor B., Albert R., Oltvai Z.N., Barabasi A.L. The large-scale organization of metabolic networks. Nature. 407:2000;651-654.
-
(2000)
Nature
, vol.407
, pp. 651-654
-
-
Jeong, H.1
Tombor, B.2
Albert, R.3
Oltvai, Z.N.4
Barabasi, A.L.5
-
34
-
-
0036008543
-
Scale-free networks in biology: New insights into the fundamentals of evolution?
-
The authors give a clear exposition on findings on biological networks. They deem it trivial that the majority of the biological networks are scale-free networks because this is easily explained through slow evolutionary growth by preferential attachment. They conclude that most network studies have not yet 'crossed the line between abstract discourse and actual research tools and techniques'
-
Wolf Y.I., Karev G., Koonin E.V. Scale-free networks in biology: new insights into the fundamentals of evolution? Bioessays. 24:2002;105-109 The authors give a clear exposition on findings on biological networks. They deem it trivial that the majority of the biological networks are scale-free networks because this is easily explained through slow evolutionary growth by preferential attachment. They conclude that most network studies have not yet 'crossed the line between abstract discourse and actual research tools and techniques'.
-
(2002)
Bioessays
, vol.24
, pp. 105-109
-
-
Wolf, Y.I.1
Karev, G.2
Koonin, E.V.3
-
35
-
-
0037012880
-
Specificity and stability in topology of protein networks
-
Maslov S., Sneppen K. Specificity and stability in topology of protein networks. Science. 296:2002;910-913.
-
(2002)
Science
, vol.296
, pp. 910-913
-
-
Maslov, S.1
Sneppen, K.2
-
36
-
-
0037163883
-
Potential artefacts in protein-interaction networks
-
A detailed analysis of the asymmetry in the yeast two-hybrid experiments between situations where proteins act as 'prey' versus where they act as 'bait'. In the network of interactions, the most highly connected nodes (hubs) turn out to have a strong preference for being 'bait' rather than 'prey'. This systematic experimental bias explains why the hubs do not tend to interact with each other, and no unproven selection effect, as proposed by Maslov and Sneppen (2002) [35], is required to explain this bias in the network topology
-
Aloy P., Russell R.B. Potential artefacts in protein-interaction networks. FEBS Lett. 530:2002;253-254 A detailed analysis of the asymmetry in the yeast two-hybrid experiments between situations where proteins act as 'prey' versus where they act as 'bait'. In the network of interactions, the most highly connected nodes (hubs) turn out to have a strong preference for being 'bait' rather than 'prey'. This systematic experimental bias explains why the hubs do not tend to interact with each other, and no unproven selection effect, as proposed by Maslov and Sneppen (2002) [35], is required to explain this bias in the network topology.
-
(2002)
FEBS Lett.
, vol.530
, pp. 253-254
-
-
Aloy, P.1
Russell, R.B.2
-
37
-
-
0034745504
-
Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach
-
Koonin E.V., Wolf Y.I., Aravind L. Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach. Genome Res. 11:2001;240-252.
-
(2001)
Genome Res.
, vol.11
, pp. 240-252
-
-
Koonin, E.V.1
Wolf, Y.I.2
Aravind, L.3
-
38
-
-
0037197886
-
The identification of functional modules from the genomic association of genes
-
The network properties of a genomic-context network (based on conservation of gene order). The network is shown to be a scale-free network with a high clustering coefficient. Subclusters are separated from each other by 'cutting' at orthologous groups that are locally the only link between them. The subclusters are functionally homogeneous, and can be regarded as functional modules. Orthologous groups that link separate subclusters to each other tend to be multifunctional
-
Snel B., Bork P., Huynen M.A. The identification of functional modules from the genomic association of genes. Proc. Natl. Acad. Sci. USA. 99:2002;5890-5895 The network properties of a genomic-context network (based on conservation of gene order). The network is shown to be a scale-free network with a high clustering coefficient. Subclusters are separated from each other by 'cutting' at orthologous groups that are locally the only link between them. The subclusters are functionally homogeneous, and can be regarded as functional modules. Orthologous groups that link separate subclusters to each other tend to be multifunctional.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 5890-5895
-
-
Snel, B.1
Bork, P.2
Huynen, M.A.3
-
39
-
-
0037052935
-
Connected gene neighborhoods in prokaryotic genomes
-
This work outlines an approach to find clusters of gene arrays through connected trails of conserved gene pairs. It is successful in obtaining functionally coherent sets of genes. The authors coin the term genomic hitchhiking for those genes that associate themselves to other genes for what, to the human eye, seem unclear reasons
-
Rogozin I.B., Makarova K.S., Murvai J., Czabarka E., Wolf Y.I., Tatusov R.L., Szekely L.A., Koonin E.V. Connected gene neighborhoods in prokaryotic genomes. Nucleic Acids Res. 30:2002;2212-2223 This work outlines an approach to find clusters of gene arrays through connected trails of conserved gene pairs. It is successful in obtaining functionally coherent sets of genes. The authors coin the term genomic hitchhiking for those genes that associate themselves to other genes for what, to the human eye, seem unclear reasons.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 2212-2223
-
-
Rogozin, I.B.1
Makarova, K.S.2
Murvai, J.3
Czabarka, E.4
Wolf, Y.I.5
Tatusov, R.L.6
Szekely, L.A.7
Koonin, E.V.8
-
40
-
-
0033977576
-
WIT: Integrated system for high-throughput genome sequence analysis and metabolic reconstruction
-
Overbeek R., Larsen N., Pusch G.D., D'Souza M., Selkov E. Jr., Kyrpides N., Fonstein M., Maltsev N., Selkov E. WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res. 28:2000;123-125.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 123-125
-
-
Overbeek, R.1
Larsen, N.2
Pusch, G.D.3
D'Souza, M.4
Selkov E., Jr.5
Kyrpides, N.6
Fonstein, M.7
Maltsev, N.8
Selkov, E.9
-
41
-
-
0037199968
-
Hierarchical organization of modularity in metabolic networks
-
Ravasz E., Somera A.L., Mongru D.A., Oltvai Z.N., Barabasi A.L. Hierarchical organization of modularity in metabolic networks. Science. 297:2002;1551-1555.
-
(2002)
Science
, vol.297
, pp. 1551-1555
-
-
Ravasz, E.1
Somera, A.L.2
Mongru, D.A.3
Oltvai, Z.N.4
Barabasi, A.L.5
-
42
-
-
0036649020
-
Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters
-
Wu L.F., Hughes T.R., Davierwala A.P., Robinson M.D., Stoughton R., Altschuler S.J. Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nat. Genet. 31:2002;255-265.
-
(2002)
Nat. Genet.
, vol.31
, pp. 255-265
-
-
Wu, L.F.1
Hughes, T.R.2
Davierwala, A.P.3
Robinson, M.D.4
Stoughton, R.5
Altschuler, S.J.6
-
43
-
-
0036699526
-
Revealing modular organization in the yeast transcriptional network
-
The authors rightly point out that conventional hierarchical clustering of co-expression data often fails, because genes can play a role in multiple cellular processes and their common regulatory element can only be detected in a subset of experiments. They have therefore developed a method to detect genes that are co-expressed under a subset of conditions. This method finds a comprehensive set of overlapping 'transcriptional modules' that promise to be very useful for function prediction
-
Ihmels J., Friedlander G., Bergmann S., Sarig O., Ziv Y., Barkai N. Revealing modular organization in the yeast transcriptional network. Nat. Genet. 31:2002;370-377 The authors rightly point out that conventional hierarchical clustering of co-expression data often fails, because genes can play a role in multiple cellular processes and their common regulatory element can only be detected in a subset of experiments. They have therefore developed a method to detect genes that are co-expressed under a subset of conditions. This method finds a comprehensive set of overlapping 'transcriptional modules' that promise to be very useful for function prediction.
-
(2002)
Nat. Genet.
, vol.31
, pp. 370-377
-
-
Ihmels, J.1
Friedlander, G.2
Bergmann, S.3
Sarig, O.4
Ziv, Y.5
Barkai, N.6
-
44
-
-
0036772367
-
Conservation of gene co-regulation in prokaryotes and eukaryotes
-
Snel B., Bork P., Huynen M. Conservation of gene co-regulation in prokaryotes and eukaryotes. Trends Biotechnol. 20:2002;410.
-
(2002)
Trends Biotechnol.
, vol.20
, pp. 410
-
-
Snel, B.1
Bork, P.2
Huynen, M.3
-
45
-
-
0035813109
-
Identification of the human methylmalonyl-CoA racemase gene based on the analysis of prokaryotic gene arrangements. Implications for decoding the human genome
-
Bobik T.A., Rasche M.E. Identification of the human methylmalonyl-CoA racemase gene based on the analysis of prokaryotic gene arrangements. Implications for decoding the human genome. J. Biol. Chem. 276:2001;37194-37198.
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 37194-37198
-
-
Bobik, T.A.1
Rasche, M.E.2
-
46
-
-
0037031655
-
Identification of a DNA nonhomologous end-joining complex in bacteria
-
Weller G.R., Kysela B., Roy R., Tonkin L.M., Scanlan E., Della M., Devine S.K., Day J.P., Wilkinson A., di Fagagna F.et al. Identification of a DNA nonhomologous end-joining complex in bacteria. Science. 297:2002;1686-1689.
-
(2002)
Science
, vol.297
, pp. 1686-1689
-
-
Weller, G.R.1
Kysela, B.2
Roy, R.3
Tonkin, L.M.4
Scanlan, E.5
Della, M.6
Devine, S.K.7
Day, J.P.8
Wilkinson, A.9
Di Fagagna, F.10
-
47
-
-
0037142086
-
A global analysis of Caenorhabditis elegans operons
-
Direct experimental identification of the majority of polycistronic transcription units in the genome of C. elegans, yielding an estimate of 13%-15% of genes being operon members. Case studies hint at functional links within such operons - but the overall signal, if any, appears much weaker than in prokaryotes
-
Blumenthal T., Evans D., Link C.D., Guffanti A., Lawson D., Thierry-Mieg J., Thierry-Mieg D., Chiu W.L., Duke K., Kiraly M.et al. A global analysis of Caenorhabditis elegans operons. Nature. 417:2002;851-854 Direct experimental identification of the majority of polycistronic transcription units in the genome of C. elegans, yielding an estimate of 13%-15% of genes being operon members. Case studies hint at functional links within such operons - but the overall signal, if any, appears much weaker than in prokaryotes.
-
(2002)
Nature
, vol.417
, pp. 851-854
-
-
Blumenthal, T.1
Evans, D.2
Link, C.D.3
Guffanti, A.4
Lawson, D.5
Thierry-Mieg, J.6
Thierry-Mieg, D.7
Chiu, W.L.8
Duke, K.9
Kiraly, M.10
-
48
-
-
0037194732
-
Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans
-
Roy P.J., Stuart J.M., Lund J., Kim S.K. Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature. 418:2002;975-979.
-
(2002)
Nature
, vol.418
, pp. 975-979
-
-
Roy, P.J.1
Stuart, J.M.2
Lund, J.3
Kim, S.K.4
-
49
-
-
0035895502
-
The human transcriptome map: Clustering of highly expressed genes in chromosomal domains
-
Caron H., van Schaik B., van der Mee M., Baas F., Riggins G., van Sluis P., Hermus M.C., van Asperen R., Boon K., Voute P.A.et al. The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science. 291:2001;1289-1292.
-
(2001)
Science
, vol.291
, pp. 1289-1292
-
-
Caron, H.1
Van Schaik, B.2
Van der Mee, M.3
Baas, F.4
Riggins, G.5
Van Sluis, P.6
Hermus, M.C.7
Van Asperen, R.8
Boon, K.9
Voute, P.A.10
-
50
-
-
0036613754
-
Clustering of housekeeping genes provides a unified model of gene order in the human genome
-
The authors demonstrate through rigorous statistical analysis that the at-first-glance surprising finding of clustered highly expressed genes on human chromosomes can be completely explained through co-localization of housekeeping genes
-
Lercher M.J., Urrutia A.O., Hurst L.D. Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat. Genet. 31:2002;180-183 The authors demonstrate through rigorous statistical analysis that the at-first-glance surprising finding of clustered highly expressed genes on human chromosomes can be completely explained through co-localization of housekeeping genes.
-
(2002)
Nat. Genet.
, vol.31
, pp. 180-183
-
-
Lercher, M.J.1
Urrutia, A.O.2
Hurst, L.D.3
-
51
-
-
0036772367
-
Conservation of gene co-regulation in prokaryotes and eukaryotes
-
To our knowledge, this is the first comparative (i.e. between species) co-expression analysis. The results appear to suggest that very little co-expression is conserved, but those gene pairs that are conservedly co-expressed invariably are part of the same protein complex
-
Teichmann S., Babu M. Conservation of gene co-regulation in prokaryotes and eukaryotes. Trends Biotechnol. 20:2002;407 To our knowledge, this is the first comparative (i.e. between species) co-expression analysis. The results appear to suggest that very little co-expression is conserved, but those gene pairs that are conservedly co-expressed invariably are part of the same protein complex.
-
(2002)
Trends Biotechnol.
, vol.20
, pp. 407
-
-
Teichmann, S.1
Babu, M.2
-
52
-
-
0036890388
-
Natural selection promotes the conservation of linkage of co-expressed genes
-
First demonstration (together with Huynen and Snel [2003] [25]) that divergently transcribed, co-expressed genes in S. cerevisiae tend to have conserved gene order in C. albicans. Such conserved gene order of co-expressed genes hints at the usage of gene-order conservation for function prediction in fungi
-
Hurst L.D., Wiliams E.J.B., Pal C. Natural selection promotes the conservation of linkage of co-expressed genes. Trends Genet. 18:2002;604-606 First demonstration (together with Huynen and Snel [2003] [25]) that divergently transcribed, co-expressed genes in S. cerevisiae tend to have conserved gene order in C. albicans. Such conserved gene order of co-expressed genes hints at the usage of gene-order conservation for function prediction in fungi.
-
(2002)
Trends Genet.
, vol.18
, pp. 604-606
-
-
Hurst, L.D.1
Wiliams, E.J.B.2
Pal, C.3
-
53
-
-
0035085816
-
Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context
-
Wolf Y.I., Rogozin I.B., Kondrashov A.S., Koonin E.V. Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. Genome Res. 11:2001;356-372.
-
(2001)
Genome Res.
, vol.11
, pp. 356-372
-
-
Wolf, Y.I.1
Rogozin, I.B.2
Kondrashov, A.S.3
Koonin, E.V.4
-
54
-
-
0035162592
-
The COG database: New developments in phylogenetic classification of proteins from complete genomes
-
Tatusov R.L., Natale D.A., Garkavtsev I.V., Tatusova T.A., Shankavaram U.T., Rao B.S., Kiryutin B., Galperin M.Y., Fedorova N.D., Koonin E.V. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29:2001;22-28.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 22-28
-
-
Tatusov, R.L.1
Natale, D.A.2
Garkavtsev, I.V.3
Tatusova, T.A.4
Shankavaram, U.T.5
Rao, B.S.6
Kiryutin, B.7
Galperin, M.Y.8
Fedorova, N.D.9
Koonin, E.V.10
-
55
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
Lee T.I., Rinaldi N.J., Robert F., Odom D.T., Bar-Joseph Z., Gerber G.K., Hannett N.M., Harbison C.T., Thompson C.M., Simon I.et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science. 298:2002;799-804.
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.I.1
Rinaldi, N.J.2
Robert, F.3
Odom, D.T.4
Bar-Joseph, Z.5
Gerber, G.K.6
Hannett, N.M.7
Harbison, C.T.8
Thompson, C.M.9
Simon, I.10
-
56
-
-
0037174670
-
Network motifs: Simple building blocks of complex networks
-
Milo R., Shen-Orr S., Itzkovitz S., Kashtan N., Chklovskii D., Alon U. Network motifs: simple building blocks of complex networks. Science. 298:2002;824-827.
-
(2002)
Science
, vol.298
, pp. 824-827
-
-
Milo, R.1
Shen-Orr, S.2
Itzkovitz, S.3
Kashtan, N.4
Chklovskii, D.5
Alon, U.6
-
57
-
-
0033968928
-
The glnKamtB operon. A conserved gene pair in prkaryotes
-
Thomas G., Coutts G., Merrick M. The glnKamtB operon. A conserved gene pair in prkaryotes. Trends Genet. 16:2000;11-14.
-
(2000)
Trends Genet.
, vol.16
, pp. 11-14
-
-
Thomas, G.1
Coutts, G.2
Merrick, M.3
-
58
-
-
0037083882
-
Membrane sequestration of the signal transduction protein GlnK by the ammonium transporter AmtB
-
Coutts G., Thomas G., Blakey D., Merrick M. Membrane sequestration of the signal transduction protein GlnK by the ammonium transporter AmtB. EMBO J. 21:2002;536-545.
-
(2002)
EMBO J.
, vol.21
, pp. 536-545
-
-
Coutts, G.1
Thomas, G.2
Blakey, D.3
Merrick, M.4
-
59
-
-
0035901535
-
In vitro conversion of propionate to pyruvate by Salmonella enterica enzymes: 2-methylcitrate dehydratase (PrpD) and aconitase enzymes catalyze the conversion of 2-methylcitrate to 2-methylisocitrate
-
Horswill A.R., Escalante-Semerena J.C. In vitro conversion of propionate to pyruvate by Salmonella enterica enzymes: 2-methylcitrate dehydratase (PrpD) and aconitase enzymes catalyze the conversion of 2-methylcitrate to 2-methylisocitrate. Biochemistry. 40:2001;4703-4713.
-
(2001)
Biochemistry
, vol.40
, pp. 4703-4713
-
-
Horswill, A.R.1
Escalante-Semerena, J.C.2
-
60
-
-
0035180870
-
Archaeal shikimate kinase, a new member of the GHMP-kinase family
-
Daugherty M., Vonstein V., Overbeek R., Osterman A. Archaeal shikimate kinase, a new member of the GHMP-kinase family. J. Bacteriol. 183:2001;292-300.
-
(2001)
J. Bacteriol.
, vol.183
, pp. 292-300
-
-
Daugherty, M.1
Vonstein, V.2
Overbeek, R.3
Osterman, A.4
-
61
-
-
0034797059
-
Identification of coenzyme M biosynthetic 2-phosphosulfolactate phosphatase. A member of a new class of Mg(2+)-dependent acid phosphatases
-
Graham D.E., Graupner M., Xu H., White R.H. Identification of coenzyme M biosynthetic 2-phosphosulfolactate phosphatase. A member of a new class of Mg(2+)-dependent acid phosphatases. Eur. J. Biochem. 268:2001;5176-5188.
-
(2001)
Eur. J. Biochem.
, vol.268
, pp. 5176-5188
-
-
Graham, D.E.1
Graupner, M.2
Xu, H.3
White, R.H.4
-
62
-
-
0033964943
-
Biosynthesis of terpenoids: YchB protein of Escherichia coli phosphorylates the 2-hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol
-
Luttgen H., Rohdich F., Herz S., Wungsintaweekul J., Hecht S., Schuhr C.A., Fellermeier M., Sagner S., Zenk M.H., Bacher A.et al. Biosynthesis of terpenoids: YchB protein of Escherichia coli phosphorylates the 2-hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol. Proc. Natl. Acad. Sci. USA. 97:2000;1062-1067.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 1062-1067
-
-
Luttgen, H.1
Rohdich, F.2
Herz, S.3
Wungsintaweekul, J.4
Hecht, S.5
Schuhr, C.A.6
Fellermeier, M.7
Sagner, S.8
Zenk, M.H.9
Bacher, A.10
-
63
-
-
0345465673
-
SmpB, a unique RNA-binding protein essential for the peptide-tagging activity of SsrA (tmRNA)
-
Karzai A.W., Susskind M.M., Sauer R.T. SmpB, a unique RNA-binding protein essential for the peptide-tagging activity of SsrA (tmRNA). EMBO J. 18:1999;3793-3799.
-
(1999)
EMBO J.
, vol.18
, pp. 3793-3799
-
-
Karzai, A.W.1
Susskind, M.M.2
Sauer, R.T.3
-
64
-
-
0037025191
-
An alternative flavin-dependent mechanism for thymidylate synthesis
-
Myllykallio H., Lipowski G., Leduc D., Filee J., Forterre P., Liebl U. An alternative flavin-dependent mechanism for thymidylate synthesis. Science. 297:2002;105-107.
-
(2002)
Science
, vol.297
, pp. 105-107
-
-
Myllykallio, H.1
Lipowski, G.2
Leduc, D.3
Filee, J.4
Forterre, P.5
Liebl, U.6
-
65
-
-
0035202123
-
Isolation and characterization of a new peroxiredoxin from poplar sieve tubes that uses either glutaredoxin or thioredoxin as a proton donor
-
Rouhier N., Gelhaye E., Sautiere P.E., Brun A., Laurent P., Tagu D., Gerard J., de Fay E., Meyer Y., Jacquot J.P. Isolation and characterization of a new peroxiredoxin from poplar sieve tubes that uses either glutaredoxin or thioredoxin as a proton donor. Plant Physiol. 127:2001;1299-1309.
-
(2001)
Plant Physiol.
, vol.127
, pp. 1299-1309
-
-
Rouhier, N.1
Gelhaye, E.2
Sautiere, P.E.3
Brun, A.4
Laurent, P.5
Tagu, D.6
Gerard, J.7
De Fay, E.8
Meyer, Y.9
Jacquot, J.P.10
-
66
-
-
0034646297
-
Biosynthesis of terpenoids: YgbB protein converts 4-diphosphocytidyl-2C-methyl-D-erythritol 2-phosphate to 2C-methyl-D-erythritol 2,4-cyclodiphosphate
-
Herz S., Wungsintaweekul J., Schuhr C.A., Hecht S., Luttgen H., Sagner S., Fellermeier M., Eisenreich W., Zenk M.H., Bacher A.et al. Biosynthesis of terpenoids: YgbB protein converts 4-diphosphocytidyl-2C-methyl-D-erythritol 2-phosphate to 2C-methyl-D-erythritol 2,4-cyclodiphosphate. Proc. Natl. Acad. Sci. USA. 97:2000;2486-2490.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 2486-2490
-
-
Herz, S.1
Wungsintaweekul, J.2
Schuhr, C.A.3
Hecht, S.4
Luttgen, H.5
Sagner, S.6
Fellermeier, M.7
Eisenreich, W.8
Zenk, M.H.9
Bacher, A.10
-
67
-
-
0033832615
-
Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences
-
Huynen M., Snel B., Lathe W. III, Bork P. Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res. 10:2000;1204-1210.
-
(2000)
Genome Res.
, vol.10
, pp. 1204-1210
-
-
Huynen, M.1
Snel, B.2
Lathe W. III3
Bork, P.4
-
68
-
-
0037007089
-
Selenoprotein R is a zinc-containing stereo-specific methionine sulfoxide reductase
-
Kryukov G.V., Kumar R.A., Koc A., Sun Z., Gladyshev V.N. Selenoprotein R is a zinc-containing stereo-specific methionine sulfoxide reductase. Proc. Natl. Acad. Sci. USA. 99:2002;4245-4250.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 4245-4250
-
-
Kryukov, G.V.1
Kumar, R.A.2
Koc, A.3
Sun, Z.4
Gladyshev, V.N.5
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