-
1
-
-
0036327988
-
Clustering of proximal sequence space for the identification of protein families
-
Abascal, F. and Valencia, A. 2002. Clustering of proximal sequence space for the identification of protein families. Bioinformatics 18: 908-921.
-
(2002)
Bioinformatics
, vol.18
, pp. 908-921
-
-
Abascal, F.1
Valencia, A.2
-
2
-
-
0034069495
-
Gene ontology: Tool for the unification of biology
-
Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., et al. 2000. Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25: 25-29.
-
(2000)
The Gene Ontology Consortium. Nat. Genet.
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
-
3
-
-
0037246674
-
PlasmoDB: The Plasmodium Genome Resource. A database integrating experimental and computational data
-
Bahl, A., Brunk, B., Crabtree, J., Fraunholz, M.J., Gajria, B., Grant, G.R., Ginsburg, H., Gupta, D., Kissinger, J.C., Labo, P., et al. 2003. PlasmoDB: The Plasmodium Genome Resource. A database integrating experimental and computational data. Nucleic Acids Res. 31: 212-215.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 212-215
-
-
Bahl, A.1
Brunk, B.2
Crabtree, J.3
Fraunholz, M.J.4
Gajria, B.5
Grant, G.R.6
Ginsburg, H.7
Gupta, D.8
Kissinger, J.C.9
Labo, P.10
-
4
-
-
0037015592
-
Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii
-
Carlton, J.M., Angiuoli, S.V., Sub, B.B., Kooij, T.W., Pertea, M., Silva, J.C., Ermolaeva, M.D., Allen, J.E., Selengut, J.D., Koo, H.L., et al. 2002. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature 419: 512-519.
-
(2002)
Nature
, vol.419
, pp. 512-519
-
-
Carlton, J.M.1
Angiuoli, S.V.2
Sub, B.B.3
Kooij, T.W.4
Pertea, M.5
Silva, J.C.6
Ermolaeva, M.D.7
Allen, J.E.8
Selengut, J.D.9
Koo, H.L.10
-
5
-
-
0032509179
-
Comparison of the complete protein sets of worm and yeast: Orthology and divergence
-
Chervitz, S.A., Aravind, L., Sherlock, G., Ball, C.A., Koonin, E.V., Dwight, S.S., Harris, M.A., Dolinski, K., Mohr, S., Smith, T., et al. 1998. Comparison of the complete protein sets of worm and yeast: Orthology and divergence. Science 282: 2022-2028.
-
(1998)
Science
, vol.282
, pp. 2022-2028
-
-
Chervitz, S.A.1
Aravind, L.2
Sherlock, G.3
Ball, C.A.4
Koonin, E.V.5
Dwight, S.S.6
Harris, M.A.7
Dolinski, K.8
Mohr, S.9
Smith, T.10
-
6
-
-
0034957542
-
K2/Kleisi and GUS: Experiments in integrated access to genomic data sources
-
Davidson, S. B., Crabtree, J., Brunk, B.P., Schug, J., Tannen, V., Overton, G.C., and Stoekert, C.J. 2001. K2/Kleisi and GUS: Experiments in integrated access to genomic data sources. IBM Systems J. 40: 512-531.
-
(2001)
IBM Systems J.
, vol.40
, pp. 512-531
-
-
Davidson, S.B.1
Crabtree, J.2
Brunk, B.P.3
Schug, J.4
Tannen, V.5
Overton, G.C.6
Stoekert, C.J.7
-
7
-
-
0029006062
-
The multiplicity of domains in proteins
-
Doolittle, R.F. 1995. The multiplicity of domains in proteins. Annu. Rev. Biochem. 64: 287-314.
-
(1995)
Annu. Rev. Biochem.
, vol.64
, pp. 287-314
-
-
Doolittle, R.F.1
-
8
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
Enright, A.J., Van Dongen, S., and Ouzounis, C.A. 2002. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30: 1575-1584.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 1575-1584
-
-
Enright, A.J.1
Van Dongen, S.2
Ouzounis, C.A.3
-
9
-
-
0031444101
-
A plastid organelle as a drug target in apicomplexan parasites
-
Fichera, M.E. and Roos, D.S. 1997. A plastid organelle as a drug target in apicomplexan parasites. Nature 390: 407-409.
-
(1997)
Nature
, vol.390
, pp. 407-409
-
-
Fichera, M.E.1
Roos, D.S.2
-
10
-
-
0014800108
-
Distinguishing homologous from analogous proteins
-
Fitch, W.M. 1970. Distinguishing homologous from analogous proteins. Syst. Zool. 19: 99-113.
-
(1970)
Syst. Zool.
, vol.19
, pp. 99-113
-
-
Fitch, W.M.1
-
11
-
-
0034178257
-
Homology, a personal view on some of the problems
-
Fitch, W.M. 2000. Homology, a personal view on some of the problems. Trends Genet. 16: 227-231.
-
(2000)
Trends Genet.
, vol.16
, pp. 227-231
-
-
Fitch, W.M.1
-
12
-
-
0036574857
-
A hot story from comparative genomics: Reverse gyrase is the only hyperthermophile-specific protein
-
Forterre, P. 2002. A hot story from comparative genomics: Reverse gyrase is the only hyperthermophile-specific protein. Trends Genet. 18: 236-237.
-
(2002)
Trends Genet.
, vol.18
, pp. 236-237
-
-
Forterre, P.1
-
13
-
-
0032728399
-
Searching for drug targets in microbial genomes
-
Galperin, M.Y. and Koonin, E.V. 1999. Searching for drug targets in microbial genomes. Curr. Opin. Biotechnol. 10: 571-578.
-
(1999)
Curr. Opin. Biotechnol.
, vol.10
, pp. 571-578
-
-
Galperin, M.Y.1
Koonin, E.V.2
-
14
-
-
0037015614
-
Genome sequence of the human malaria parasite Plasmodium falciparum
-
Gardner, M.J., Hall, N., Fung, E., White, O., Berriman, M., Hyman, R.W., Carlton, J.M., Pain, A., Nelson, K.E., Bowman, S., et al. 2002. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419: 498-511.
-
(2002)
Nature
, vol.419
, pp. 498-511
-
-
Gardner, M.J.1
Hall, N.2
Fung, E.3
White, O.4
Berriman, M.5
Hyman, R.W.6
Carlton, J.M.7
Pain, A.8
Nelson, K.E.9
Bowman, S.10
-
15
-
-
0034887203
-
Creating the gene ontology resource: Design and implementation
-
The Gene Ontology Consortium
-
The Gene Ontology Consortium. 2001. Creating the gene ontology resource: Design and implementation. Genome Res. 11: 1425-1433.
-
(2001)
Genome Res.
, vol.11
, pp. 1425-1433
-
-
-
16
-
-
0035253864
-
A plastid segregation defect in the protozoan parasite Toxoplasma gondii
-
He, C.Y., Shaw, M.K., Pletcher, C.H., Striepen, B., Tilney, L.G., and Roos, D.S. 2001. A plastid segregation defect in the protozoan parasite Toxoplasma gondii. EMBO J. 20: 330-339.
-
(2001)
EMBO J.
, vol.20
, pp. 330-339
-
-
He, C.Y.1
Shaw, M.K.2
Pletcher, C.H.3
Striepen, B.4
Tilney, L.G.5
Roos, D.S.6
-
17
-
-
0030660580
-
Gene families: The taxonomy of protein paralogs and chimeras
-
Henikoff, S., Greene, E.A., Pietrokovski, S., Bork, P., Attwood, T.K., and Hood, L. 1997. Gene families: The taxonomy of protein paralogs and chimeras. Science 278: 609-614.
-
(1997)
Science
, vol.278
, pp. 609-614
-
-
Henikoff, S.1
Greene, E.A.2
Pietrokovski, S.3
Bork, P.4
Attwood, T.K.5
Hood, L.6
-
18
-
-
0037015621
-
The Plasmodium genome database
-
Kissinger, J.C., Brunk, B. P., Crabtree, J., Fraunholz, M.J., Gajria, B., Milgram, A.J., Pearson, D.S., Schug, J., Bahl, A., Diskin, S.J., et al. 2002. The Plasmodium genome database. Nature 419: 490-492.
-
(2002)
Nature
, vol.419
, pp. 490-492
-
-
Kissinger, J.C.1
Brunk, B.P.2
Crabtree, J.3
Fraunholz, M.J.4
Gajria, B.5
Milgram, A.J.6
Pearson, D.S.7
Schug, J.8
Bahl, A.9
Diskin, S.J.10
-
19
-
-
0040982083
-
A plastid of probable green algal origin in Apicomplexan parasites
-
Kohler, S., Delwiche, C.F., Denny, P.W., Tilney, L.G., Webster, P., Wilson, R.J., Palmer, J.D., and Roos, D.S. 1997. A plastid of probable green algal origin in Apicomplexan parasites. Science 275: 1485-1489.
-
(1997)
Science
, vol.275
, pp. 1485-1489
-
-
Kohler, S.1
Delwiche, C.F.2
Denny, P.W.3
Tilney, L.G.4
Webster, P.5
Wilson, R.J.6
Palmer, J.D.7
Roos, D.S.8
-
20
-
-
0036125446
-
Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA)
-
Lee, Y., Sultana, R., Pertea, G., Cho, J., Karamycheva, S., Tsai, J., Parvizi, B., Cheung, F., Antonescu, V., White, J., et al. 2002. Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA). Genome Res. 12: 493-502.
-
(2002)
Genome Res.
, vol.12
, pp. 493-502
-
-
Lee, Y.1
Sultana, R.2
Pertea, G.3
Cho, J.4
Karamycheva, S.5
Tsai, J.6
Parvizi, B.7
Cheung, F.8
Antonescu, V.9
White, J.10
-
21
-
-
0031877893
-
Large-scale taxonomic profiling of eukaryotic model organisms: A comparison of orthologous proteins encoded by the human, fly, nematode, and yeast genomes
-
Mushegian, A.R., Garey, J.R., Martin, J., and Liu, L.X. 1998. Large-scale taxonomic profiling of eukaryotic model organisms: A comparison of orthologous proteins encoded by the human, fly, nematode, and yeast genomes. Genome Res. 8:590-598.
-
(1998)
Genome Res.
, vol.8
, pp. 590-598
-
-
Mushegian, A.R.1
Garey, J.R.2
Martin, J.3
Liu, L.X.4
-
22
-
-
0034530835
-
Using the COG database to improve gene recognition in complete genomes
-
Natale, D.A., Galperin, M.Y., Tatusov, R.L., and Koonin, E.V. 2000a. Using the COG database to improve gene recognition in complete genomes. Genetica 108: 9-17.
-
(2000)
Genetica
, vol.108
, pp. 9-17
-
-
Natale, D.A.1
Galperin, M.Y.2
Tatusov, R.L.3
Koonin, E.V.4
-
23
-
-
0034572821
-
Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs)
-
research0009.1-0009.19
-
Natale, D.A., Shankavaram, U.T., Galperin, M.Y., Wolf, Y.I., Aravind, I., and Koonin, E.V. 2000b. Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs). Genome Biol. 1:research0009.1-0009.19.
-
(2000)
Genome Biol.
, vol.1
-
-
Natale, D.A.1
Shankavaram, U.T.2
Galperin, M.Y.3
Wolf, Y.I.4
Aravind, I.5
Koonin, E.V.6
-
24
-
-
0033965855
-
The TIGR gene indices: Reconstruction and representation of expressed gene sequences
-
Quackenbush, J., Liang, F., Holt, I., Pertea, G., and Upton, J. 2000. The TIGR gene indices: Reconstruction and representation of expressed gene sequences. Nucleic Acids Res. 28: 141-145.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 141-145
-
-
Quackenbush, J.1
Liang, F.2
Holt, I.3
Pertea, G.4
Upton, J.5
-
25
-
-
0035165581
-
The TIGR Gene Indices: Analysis of gene transcript sequences in highly sampled eukaryotic species
-
Quackenbush, J., Cho, J., Lee, D., Liang, F., Holt, I., Karamycheva, S., Parvizi, B., Pertea, G., Sultana, R., and White, J. 2001. The TIGR Gene Indices: Analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res. 29: 159-164.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 159-164
-
-
Quackenbush, J.1
Cho, J.2
Lee, D.3
Liang, F.4
Holt, I.5
Karamycheva, S.6
Parvizi, B.7
Pertea, G.8
Sultana, R.9
White, J.10
-
26
-
-
0035861990
-
Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
-
Remm, M., Storm, C.E., and Sonnhammer, E.L. 2001. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol. 314: 1041-1052.
-
(2001)
J. Mol. Biol.
, vol.314
, pp. 1041-1052
-
-
Remm, M.1
Storm, C.E.2
Sonnhammer, E.L.3
-
27
-
-
0032988608
-
The apicoplast as a potential therapeutic target in Toxoplasma and other apicomplexan parasites: Some additional thoughts
-
Roos, D.S. 1999. The apicoplast as a potential therapeutic target in Toxoplasma and other apicomplexan parasites: Some additional thoughts. Parasitol Today 15: 41.
-
(1999)
Parasitol. Today
, vol.15
, pp. 41
-
-
Roos, D.S.1
-
28
-
-
0034708444
-
Comparative genomics of the eukaryotes
-
Rubin, G.M., Yandell, M.D., Wortman, J.R., Gabor Miklos, G.L., Nelson, C.R., Hariharan, I.K., Fortini, M.E., Li, P.W., Apweiler, R., Fleischmann, W., et al. 2000. Comparative genomics of the eukaryotes. Science 287: 2204-2215.
-
(2000)
Science
, vol.287
, pp. 2204-2215
-
-
Rubin, G.M.1
Yandell, M.D.2
Wortman, J.R.3
Gabor Miklos, G.L.4
Nelson, C.R.5
Hariharan, I.K.6
Fortini, M.E.7
Li, P.W.8
Apweiler, R.9
Fleischmann, W.10
-
29
-
-
0036228634
-
Predicting gene ontology functions from ProDom and CDD protein domains
-
Schug, J., Diskin, S., Mazzarelli, J., Brunk, B.P., and Stoeckert Jr., C.J. 2002. Predicting gene ontology functions from ProDom and CDD protein domains. Genorne Res. 12: 648-655.
-
(2002)
Genorne Res.
, vol.12
, pp. 648-655
-
-
Schug, J.1
Diskin, S.2
Mazzarelli, J.3
Brunk, B.P.4
Stoeckert C.J., Jr.5
-
31
-
-
0030660581
-
A genomic perspective on protein families
-
Tatusov, R.L., Koonin, E.V., and Lipman, D.J. 1997. A genomic perspective on protein families. Science 278: 631-637.
-
(1997)
Science
, vol.278
, pp. 631-637
-
-
Tatusov, R.L.1
Koonin, E.V.2
Lipman, D.J.3
-
32
-
-
0033956060
-
The COG database: A tool for genome-scale analysis of protein functions and evolution
-
Tatusov, R.L., Galperin, M.Y., Natale, D.A., and Koonin, E.V. 2000. The COG database: A tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28: 33-36.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 33-36
-
-
Tatusov, R.L.1
Galperin, M.Y.2
Natale, D.A.3
Koonin, E.V.4
-
33
-
-
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., and Koonin, E.V. 2001. The COG database: New developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29: 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
-
34
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
35
-
-
0005924596
-
"Graph clustering by flow simulation"
-
Ph.D thesis, University of Utrecht, The Netherlands
-
Van Dongen, S. 2000. "Graph clustering by flow simulation." Ph.D thesis, University of Utrecht, The Netherlands.
-
(2000)
-
-
Van Dongen, S.1
-
36
-
-
0032835248
-
Human and nematode orthologs-Lessons from the analysis of 1800 human genes and the proteome of Caenorhabditis elegans
-
Wheelan, S.J., Boguski, M.S., Duret, L., and Makalowski, W. 1999. Human and nematode orthologs-Lessons from the analysis of 1800 human genes and the proteome of Caenorhabditis elegans. Gene 238: 163-170.
-
(1999)
Gene
, vol.238
, pp. 163-170
-
-
Wheelan, S.J.1
Boguski, M.S.2
Duret, L.3
Makalowski, W.4
|