-
1
-
-
0030660581
-
A genomic perspective on protein families
-
Tatusov R.L., Koonin E.V., Lipman D.J. A genomic perspective on protein families. Science. 278:1997;631-637.
-
(1997)
Science
, vol.278
, pp. 631-637
-
-
Tatusov, R.L.1
Koonin, E.V.2
Lipman, D.J.3
-
2
-
-
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
-
3
-
-
0034069495
-
Gene Ontology: Tool for the unification of biology
-
The Gene Ontology Consortium (2000) Gene Ontology: tool for the unification of biology. Nat. Genet. 25, 25-29.
-
(2000)
Nat. Genet.
, vol.25
, pp. 25-29
-
-
-
4
-
-
0037249497
-
The PEDANT genome database
-
Frishman D., Mokrejs M., Kosykh D., Kastenmuller G., Kolesov G., Zubrzycki I., Gruber C., Geier B., Kaps A., Albermann K., Volz A., Wagner C., Fellenberg M., Heumann K., Mewes H.W. The PEDANT genome database. Nucleic Acids Res. 31:2003;207-211.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 207-211
-
-
Frishman, D.1
Mokrejs, M.2
Kosykh, D.3
Kastenmuller, G.4
Kolesov, G.5
Zubrzycki, I.6
Gruber, C.7
Geier, B.8
Kaps, A.9
Albermann, K.10
Volz, A.11
Wagner, C.12
Fellenberg, M.13
Heumann, K.14
Mewes, H.W.15
-
5
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:1997;3389-3402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
6
-
-
0035166979
-
The Comprehensive Microbial Resource
-
Peterson J.D., Umayam L.A., Dickinson T.M., Hickey E.K., White O. The Comprehensive Microbial Resource. Nucleic Acids Res. 29:2001;123-125.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 123-125
-
-
Peterson, J.D.1
Umayam, L.A.2
Dickinson, T.M.3
Hickey, E.K.4
White, O.5
-
8
-
-
0033034745
-
Automated genome sequence and annotation
-
Andrade M.A., Brown N.P., Leroy C., Hoersch S., de Daruvar A., Reich C., Franchini A., Tamames J., Valencia A., Ouzounis C., Sander C. Automated genome sequence and annotation. Bioinformatics. 15:1999;391-412.
-
(1999)
Bioinformatics
, vol.15
, pp. 391-412
-
-
Andrade, M.A.1
Brown, N.P.2
Leroy, C.3
Hoersch, S.4
De Daruvar, A.5
Reich, C.6
Franchini, A.7
Tamames, J.8
Valencia, A.9
Ouzounis, C.10
Sander, C.11
-
9
-
-
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 Jr., E.5
Kyrpides, N.6
Fonstein, M.7
Maltsev, N.8
Selkov, E.9
-
10
-
-
0031764044
-
Indigo: A World-Wide-Web review of genomes and gene functions
-
Nitschké P., Guerdoux-Jamet P., Chiapello H., Faroux G., Hénaut C., Hénaut A., Danchin A. Indigo: a World-Wide-Web review of genomes and gene functions. FEMS Microbiol. Rev. 22:1998;207-227.
-
(1998)
FEMS Microbiol. Rev.
, vol.22
, pp. 207-227
-
-
Nitschké, P.1
Guerdoux-Jamet, P.2
Chiapello, H.3
Faroux, G.4
Hénaut, C.5
Hénaut, A.6
Danchin, A.7
-
11
-
-
0034007992
-
Gene content and organization of a 281-kbp contig from the genome of the extremely thermophilic archaeon, Sulfolobus solfataricus P2
-
Charlebois R.L., Singh R.K., Chan-Weiher C.C.-Y., Allard G., Chow C., Confalonieri F., Curtis B., Duguet M., Erauso G., Faguy D., Gaasterland T., Garrett R.A., Gordon P., Jeffries A.C., Kozera C., Kushwaha N., Lafleur É., Medina N., Peng X., Penny S.L., She Q., St. Jean A., van der Oost J., Young F., Zivanovic Y., Doolittle W.F., Ragan M.A., Sensen C.W. Gene content and organization of a 281-kbp contig from the genome of the extremely thermophilic archaeon, Sulfolobus solfataricus P2. Genome. 43:2000;116-136.
-
(2000)
Genome
, vol.43
, pp. 116-136
-
-
Charlebois, R.L.1
Singh, R.K.2
Chan-Weiher, C.C.-Y.3
Allard, G.4
Chow, C.5
Confalonieri, F.6
Curtis, B.7
Duguet, M.8
Erauso, G.9
Faguy, D.10
Gaasterland, T.11
Garrett, R.A.12
Gordon, P.13
Jeffries, A.C.14
Kozera, C.15
Kushwaha, N.16
Lafleur, É.17
Medina, N.18
Peng, X.19
Penny, S.L.20
She, Q.21
St. Jean, A.22
Van Der Oost, J.23
Young, F.24
Zivanovic, Y.25
Doolittle, W.F.26
Ragan, M.A.27
Sensen, C.W.28
more..
-
13
-
-
1642287184
-
Genome phylogenies
-
(Hirt, R.P. and Horner, D.S., Eds.), in press. Taylor and Francis Group, London.
-
Charlebois, R.L., Beiko, R.G. and Ragan, M.A. (2003) Genome phylogenies. In: Organelles, Genomes and Eukaryote Evolution: An Evolutionary Perspective in the Age of Genomics (Hirt, R.P. and Horner, D.S., Eds.), in press. Taylor and Francis Group, London.
-
(2003)
Organelles, Genomes and Eukaryote Evolution: An Evolutionary Perspective in the Age of Genomics
-
-
Charlebois, R.L.1
Beiko, R.G.2
Ragan, M.A.3
-
14
-
-
0036210883
-
Inferring genome trees using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores
-
Clarke G.D.P., Beiko R.G., Ragan M.A., Charlebois R.L. Inferring genome trees using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores. J. Bacteriol. 184:2002;2072-2080.
-
(2002)
J. Bacteriol.
, vol.184
, pp. 2072-2080
-
-
Clarke, G.D.P.1
Beiko, R.G.2
Ragan, M.A.3
Charlebois, R.L.4
-
15
-
-
0035989433
-
Distributional profiles of homologous open reading frames among bacterial phyla: Implications for vertical and lateral transmission
-
Ragan M.A., Charlebois R.L. Distributional profiles of homologous open reading frames among bacterial phyla: implications for vertical and lateral transmission. Int. J. Syst. Evol. Microbiol. 52:2002;777-787.
-
(2002)
Int. J. Syst. Evol. Microbiol.
, vol.52
, pp. 777-787
-
-
Ragan, M.A.1
Charlebois, R.L.2
-
16
-
-
0034831587
-
Defining the core of nontransferable prokaryotic genes: The euryarchaeal core
-
Nesbø C.L., Boucher Y., Doolittle W.F. Defining the core of nontransferable prokaryotic genes: the euryarchaeal core. J. Mol. Evol. 53:2001;340-350.
-
(2001)
J. Mol. Evol.
, vol.53
, pp. 340-350
-
-
Nesbø, C.L.1
Boucher, Y.2
Doolittle, W.F.3
-
17
-
-
0035943134
-
On surrogate methods for detecting lateral gene transfer
-
Ragan M.A. On surrogate methods for detecting lateral gene transfer. FEMS Microbiol. Lett. 201:2001;187-191.
-
(2001)
FEMS Microbiol. Lett.
, vol.201
, pp. 187-191
-
-
Ragan, M.A.1
-
18
-
-
0029894792
-
The yeast genome project: What did we learn?
-
Dujon B. The yeast genome project: what did we learn? Trends Genet. 12:1996;263-270.
-
(1996)
Trends Genet.
, vol.12
, pp. 263-270
-
-
Dujon, B.1
-
19
-
-
0032871834
-
Finding families for genomic ORFans
-
Fischer D., Eisenberg D. Finding families for genomic ORFans. Bioinformatics. 15:1999;759-762.
-
(1999)
Bioinformatics
, vol.15
, pp. 759-762
-
-
Fischer, D.1
Eisenberg, D.2
-
20
-
-
0037228878
-
Twenty thousand ORFan microbial protein families for the biologist?
-
Siew N., Fischer D. Twenty thousand ORFan microbial protein families for the biologist? Structure. 11:2003;7-9.
-
(2003)
Structure
, vol.11
, pp. 7-9
-
-
Siew, N.1
Fischer, D.2
-
22
-
-
0033198828
-
Origin and properties of non-coding ORFs in the yeast genome
-
Mackiewicz P., Kowalczuk M., Gierlik A., Dudek M.R., Cebrat S. Origin and properties of non-coding ORFs in the yeast genome. Nucleic Acids Res. 17:1999;3503-3509.
-
(1999)
Nucleic Acids Res.
, vol.17
, pp. 3503-3509
-
-
MacKiewicz, P.1
Kowalczuk, M.2
Gierlik, A.3
Dudek, M.R.4
Cebrat, S.5
-
23
-
-
0035424711
-
On the total number of genes and their length distribution in complete microbial genomes
-
Skovgaard M., Jensen L.J., Brunak S., Ussery D., Krogh A. On the total number of genes and their length distribution in complete microbial genomes. Trends Genet. 17:2001;425-428.
-
(2001)
Trends Genet.
, vol.17
, pp. 425-428
-
-
Skovgaard, M.1
Jensen, L.J.2
Brunak, S.3
Ussery, D.4
Krogh, A.5
-
24
-
-
0034754788
-
The evolutionary analysis of 'orphans' from the Drosophila genome identifies rapidly diverging and incorrectly annotated genes
-
Schmid K.J., Aquadro C.F. The evolutionary analysis of 'orphans' from the Drosophila genome identifies rapidly diverging and incorrectly annotated genes. Genetics. 159:2001;589-598.
-
(2001)
Genetics
, vol.159
, pp. 589-598
-
-
Schmid, K.J.1
Aquadro, C.F.2
-
25
-
-
0034956159
-
A re-annotation of the Saccharomyces cerevisiae genome
-
Wood V., Rutherford K.M., Ivens A., Rajandream M.-A., Barrell B. A re-annotation of the Saccharomyces cerevisiae genome. Comp. Funct. Genom. 2:2001;143-154.
-
(2001)
Comp. Funct. Genom.
, vol.2
, pp. 143-154
-
-
Wood, V.1
Rutherford, K.M.2
Ivens, A.3
Rajandream, M.-A.4
Barrell, B.5
-
26
-
-
0032740153
-
Searching for frameshift evolutionary relationships between protein sequence families
-
Pellegrini M., Yeates T.O. Searching for frameshift evolutionary relationships between protein sequence families. Proteins. 37:1999;278-283.
-
(1999)
Proteins
, vol.37
, pp. 278-283
-
-
Pellegrini, M.1
Yeates, T.O.2
-
27
-
-
0034704256
-
Genomic exploration of the hemiascomycetous yeasts: 19. Ascomycetes-specific genes
-
Malpertuy A., Tekaia F., Casarégola S., Aigle M., Artiguenave F., Blandin G., Bolotin-Fukuhara M., Bon E., Brottier P., de Montigny J., Durrens P., Gaillardin C., Lépingle A., Llorente B., Neuvéglise C., Ozier-Kalogeropoulos O., Potier S., Saurin W., Toffano-Nioche C., Wésolowski-Louvel M., Wincker P., Weissenbach J., Souciet J.-L., Dujon B. Genomic exploration of the hemiascomycetous yeasts: 19. Ascomycetes-specific genes. FEBS Lett. 487:2000;113-121.
-
(2000)
FEBS Lett.
, vol.487
, pp. 113-121
-
-
Malpertuy, A.1
Tekaia, F.2
Casarégola, S.3
Aigle, M.4
Artiguenave, F.5
Blandin, G.6
Bolotin-Fukuhara, M.7
Bon, E.8
Brottier, P.9
De Montigny, J.10
Durrens, P.11
Gaillardin, C.12
Lépingle, A.13
Llorente, B.14
Neuvéglise, C.15
Ozier-Kalogeropoulos, O.16
Potier, S.17
Saurin, W.18
Toffano-Nioche, C.19
Wésolowski-Louvel, M.20
Wincker, P.21
Weissenbach, J.22
Souciet, J.-L.23
Dujon, B.24
more..
-
28
-
-
0030928758
-
A screen for fast evolving genes from Drosophila
-
Schmid K.J., Tautz D. A screen for fast evolving genes from Drosophila. Proc. Natl. Acad. Sci. USA. 94:1997;9746-9750.
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 9746-9750
-
-
Schmid, K.J.1
Tautz, D.2
-
29
-
-
0032764518
-
Global transposon mutagenesis and a minimal Mycoplasma genome
-
Hutchison C.A. III, Peterson S.N., Gill S.R., Cline R.T., White O., Fraser C.M., Smith H.O., Venter J.C. Global transposon mutagenesis and a minimal Mycoplasma genome. Science. 286:1999;2165-2169.
-
(1999)
Science
, vol.286
, pp. 2165-2169
-
-
Hutchison III, C.A.1
Peterson, S.N.2
Gill, S.R.3
Cline, R.T.4
White, O.5
Fraser, C.M.6
Smith, H.O.7
Venter, J.C.8
-
30
-
-
0033865920
-
Reverse transcriptase-polymerase chain reaction validation of 25 'Orphan' genes from Escherichia coli K-12 MG1655
-
Alimi J.-P., Poirot O., Lopez F., Claverie J.-M. Reverse transcriptase-polymerase chain reaction validation of 25 'Orphan' genes from Escherichia coli K-12 MG1655. Genome Res. 10:2000;959-966.
-
(2000)
Genome Res.
, vol.10
, pp. 959-966
-
-
Alimi, J.-P.1
Poirot, O.2
Lopez, F.3
Claverie, J.-M.4
-
31
-
-
0035947615
-
Escherichia coli ykfE ORFan gene encodes a potent inhibitor of C-type lysozyme
-
Monchois V., Abergel C., Sturgis J., Jeudy S., Claverie J.-M. Escherichia coli ykfE ORFan gene encodes a potent inhibitor of C-type lysozyme. J. Biol. Chem. 276:2001;18437-18441.
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 18437-18441
-
-
Monchois, V.1
Abergel, C.2
Sturgis, J.3
Jeudy, S.4
Claverie, J.-M.5
-
32
-
-
0035076532
-
Conserved 'hypothetical' proteins: New hints and new puzzles
-
Galperin M.Y. Conserved 'hypothetical' proteins: new hints and new puzzles. Comp. Funct. Genom. 2:2001;14-18.
-
(2001)
Comp. Funct. Genom.
, vol.2
, pp. 14-18
-
-
Galperin, M.Y.1
-
33
-
-
0004287255
-
-
The Iowa State University Press, Ames, IA.
-
Ostle, B. and Mensing, R.W. (1975) Statistics in Research, 3rd edn., 596 pp. The Iowa State University Press, Ames, IA.
-
(1975)
Statistics in Research, 3rd Edn.
-
-
Ostle, B.1
Mensing, R.W.2
|