-
1
-
-
34447344620
-
Divergent paralogous in Uniref50 enriched-COG clusters depicted by Phylip neighbor trees rooted with Taxbrowser tables
-
Retrieved September 30, 2006 from
-
Barnosa,D. et al. (2006) Divergent paralogous in Uniref50 enriched-COG clusters depicted by Phylip neighbor trees rooted with Taxbrowser tables. Abstract ISMB2006, Retrieved September 30, 2006 from http://ismb2006.cbi.cnptia.embrapa.br/ poster_abstract_lb.php?id=LB-56.
-
(2006)
Abstract ISMB2006
-
-
Barnosa, D.1
-
2
-
-
27244448022
-
Databases and information integration for the Medicago truncatula genome and transcriptome
-
Cannon,S.B. et al. (2005) Databases and information integration for the Medicago truncatula genome and transcriptome. Plant Physiol. 138, 38-46.
-
(2005)
Plant Physiol
, vol.138
, pp. 38-46
-
-
Cannon, S.B.1
-
3
-
-
33644843469
-
On single and multiple models of protein families for the detection of remote sequence relationships
-
Casbon,J.A. and Saqi,M.A. (2006) On single and multiple models of protein families for the detection of remote sequence relationships. BMC Bioinformatics, 7, 48.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 48
-
-
Casbon, J.A.1
Saqi, M.A.2
-
4
-
-
33750979817
-
Proteomic and bioinformatic characterization of the biogenesis and function of melanosomes
-
Chi,A. et al. (2006) Proteomic and bioinformatic characterization of the biogenesis and function of melanosomes. J. Proteome Res., 5, 3135-3144.
-
(2006)
J. Proteome Res
, vol.5
, pp. 3135-3144
-
-
Chi, A.1
-
5
-
-
33846059234
-
The TIGR Plant Transcript Assemblies database
-
Childs,K.L. et al. (2007) The TIGR Plant Transcript Assemblies database. Nucleic Acids Res., 35, D846-D851.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Childs, K.L.1
-
6
-
-
0033944826
-
GeneRAGE: A robust algorithm for sequence clustering and domain detection
-
Enright,A.J. and Ouzounis,C.A. (2000) GeneRAGE: A robust algorithm for sequence clustering and domain detection. Bioinformatics, 16 451-457.
-
(2000)
Bioinformatics
, vol.16
, pp. 451-457
-
-
Enright, A.J.1
Ouzounis, C.A.2
-
7
-
-
33748959731
-
Saturating representation of loop conformational fragments in structure databanks
-
Fernandez-Fuentes,N. and Fiser,A. (2006) Saturating representation of loop conformational fragments in structure databanks. BMC Struct. Biol., 6, 15.
-
(2006)
BMC Struct. Biol
, vol.6
, pp. 15
-
-
Fernandez-Fuentes, N.1
Fiser, A.2
-
8
-
-
33745122231
-
Identification of multiple distinct Snf2 subfamilies with conserved structural motifs
-
Flaus,A. et al. (2006) Identification of multiple distinct Snf2 subfamilies with conserved structural motifs. Nucleic Acids Res., 34, 2887-2905.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 2887-2905
-
-
Flaus, A.1
-
9
-
-
33646483032
-
The abundance of short proteins in the mammalian proteome
-
Frith,M.C. et al. (2006) The abundance of short proteins in the mammalian proteome. PLoS Genet., 2, e52.
-
(2006)
PLoS Genet
, vol.2
-
-
Frith, M.C.1
-
10
-
-
22744452105
-
Proteome profiling of human epithelial ovarian cancer cell line TOV-112D
-
Gagne,J.P. et al. (2005) Proteome profiling of human epithelial ovarian cancer cell line TOV-112D. Mol. Cell. Biochem., 275, 25-55.
-
(2005)
Mol. Cell. Biochem
, vol.275
, pp. 25-55
-
-
Gagne, J.P.1
-
11
-
-
0027092678
-
Selection of representative protein data sets
-
Hobohm,U. et al. (1992) Selection of representative protein data sets. Protein Sci., 1, 409-417.
-
(1992)
Protein Sci
, vol.1
, pp. 409-417
-
-
Hobohm, U.1
-
12
-
-
33750632498
-
Comparative bioinformatics analyses and profiling of lysosome-related organelle proteomes
-
Hu,Z.Z. et al. (2007) Comparative bioinformatics analyses and profiling of lysosome-related organelle proteomes. Int. J. Mass Spectrom., 259, 147-160.
-
(2007)
Int. J. Mass Spectrom
, vol.259
, pp. 147-160
-
-
Hu, Z.Z.1
-
13
-
-
33947652045
-
Challenges and solutions in proteomics
-
Huang,H. et al. (2007) Challenges and solutions in proteomics. Curr. Genomics, 8, 21-28.
-
(2007)
Curr. Genomics
, vol.8
, pp. 21-28
-
-
Huang, H.1
-
14
-
-
33846039019
-
-
Hubbard,T.J. et al. (2007) Ensembl 2007. Nucleic Acids Res., 35, D610-D617.
-
Hubbard,T.J. et al. (2007) Ensembl 2007. Nucleic Acids Res., 35, D610-D617.
-
-
-
-
15
-
-
33644652570
-
Structure of human semicarbazide-sensitive amine oxidase/vascular adhesion protein-1
-
Jakobsson,E. et al. (2005) Structure of human semicarbazide-sensitive amine oxidase/vascular adhesion protein-1. Acta Crystallogr. D. Biol. Crystallogr., 61, 1550-1562.
-
(2005)
Acta Crystallogr. D. Biol. Crystallogr
, vol.61
, pp. 1550-1562
-
-
Jakobsson, E.1
-
16
-
-
33748901660
-
-
Joron,M. et al. (2006) A conserved supergene locus controls colour pattern diversity in heliconius butterflies. PLoS Biol., 4.
-
Joron,M. et al. (2006) A conserved supergene locus controls colour pattern diversity in heliconius butterflies. PLoS Biol., 4.
-
-
-
-
17
-
-
33749357045
-
CRNPRED: Highly accurate prediction of one-dimensional protein structures by large-scale critical random networks
-
Kinjo,A.R. and Nishikawa,K. (2006) CRNPRED: Highly accurate prediction of one-dimensional protein structures by large-scale critical random networks. BMC Bioinformatics, 7, 401.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 401
-
-
Kinjo, A.R.1
Nishikawa, K.2
-
18
-
-
25444458848
-
AutoFACT: An automatic functional annotation and classification tool
-
Koski,L.B. et al. (2005) AutoFACT: An automatic functional annotation and classification tool. BMC Bioinformatics, 6, 151.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 151
-
-
Koski, L.B.1
-
19
-
-
33644873706
-
The RCSB PDB information portal for structural genomics
-
Kouranov,A. et al. (2006) The RCSB PDB information portal for structural genomics. Nucleic Acids Res., 34, D302-D305.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Kouranov, A.1
-
20
-
-
10244251690
-
UniProt archive
-
Leinonen,R. et al. (2004) UniProt archive. Bioinformatics, 20, 3236-3237.
-
(2004)
Bioinformatics
, vol.20
, pp. 3236-3237
-
-
Leinonen, R.1
-
21
-
-
33745634395
-
Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
-
Li,W. and Godzik,A. (2006) Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
-
(2006)
Bioinformatics
, vol.22
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
22
-
-
0035072551
-
Clustering of highly homologous sequences to reduce the size of large protein databases
-
Li,W. et al. (2001) Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics, 17 282-283.
-
(2001)
Bioinformatics
, vol.17
, pp. 282-283
-
-
Li, W.1
-
23
-
-
0242713700
-
The dominance of the population by a selected few: Power-law behaviour applies to a wide variety of genomic properties
-
RESEARCH0040
-
Luscombe,N.M. et al. (2002) The dominance of the population by a selected few: Power-law behaviour applies to a wide variety of genomic properties. Genome Biol., 3, RESEARCH0040.
-
(2002)
Genome Biol
, vol.3
-
-
Luscombe, N.M.1
-
24
-
-
33646366606
-
Refinement and prediction of protein prenylation motifs
-
Maurer-Stroh,S. and Eisenhaber,F. (2005) Refinement and prediction of protein prenylation motifs. Genome Biol., 6, R55.
-
(2005)
Genome Biol
, vol.6
-
-
Maurer-Stroh, S.1
Eisenhaber, F.2
-
25
-
-
33746358516
-
High throughput profile-profile based fold recognition for the entire human proteome
-
McGuffin,L.J. et al. (2006) High throughput profile-profile based fold recognition for the entire human proteome. BMC Bioinformatics 7, 288.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 288
-
-
McGuffin, L.J.1
-
26
-
-
0043122933
-
UniqueProt: Creating representative protein sequence sets
-
Mika,S. and Rost,B. (2003) UniqueProt: Creating representative protein sequence sets. Nucleic Acids Res., 31, 3789-3791.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3789-3791
-
-
Mika, S.1
Rost, B.2
-
27
-
-
24944485529
-
Highly syntenic regions in the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana
-
Mudge,J. et al. (2005) Highly syntenic regions in the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana. BMC Plant Biol., 5, 15.
-
(2005)
BMC Plant Biol
, vol.5
, pp. 15
-
-
Mudge, J.1
-
28
-
-
33644875750
-
pSTIING: A 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer
-
Ng,A. et al. (2006) pSTIING: A 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer. Nucleic Acids Res. 34, D527-D534.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Ng, A.1
-
29
-
-
33747825726
-
DOUTfinder - identification of distant domain outliers using subsignificant sequence similarity
-
Novatchkova,M. et al. (2006) DOUTfinder - identification of distant domain outliers using subsignificant sequence similarity. Nucleic Acids Res., 34, W214-W218.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Novatchkova, M.1
-
30
-
-
33745431550
-
A normalised scale for structural genomics target ranking: The OB-Score
-
Overton,I.M. and Barton,G.J. (2006) A normalised scale for structural genomics target ranking: The OB-Score. FEBS Lett., 580, 4005-4009.
-
(2006)
FEBS Lett
, vol.580
, pp. 4005-4009
-
-
Overton, I.M.1
Barton, G.J.2
-
31
-
-
33645523636
-
Spectral clustering of protein sequences
-
Paccanaro,A. et al. (2006) Spectral clustering of protein sequences. Nucleic Acids Res., 34, 1571-1580.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 1571-1580
-
-
Paccanaro, A.1
-
32
-
-
0033940118
-
RSDB: Representative protein sequence databases have high information content
-
Park,J. et al. (2000) RSDB: Representative protein sequence databases have high information content. Bioinformatics, 16, 458-464.
-
(2000)
Bioinformatics
, vol.16
, pp. 458-464
-
-
Park, J.1
-
33
-
-
27744527781
-
Generation, annotation, analysis and database integration of 16 500 white spruce EST clusters
-
Pavy,N. et al. (2005) Generation, annotation, analysis and database integration of 16 500 white spruce EST clusters. BMC Genomics, 6, 144.
-
(2005)
BMC Genomics
, vol.6
, pp. 144
-
-
Pavy, N.1
-
34
-
-
33748126341
-
Automated SNP detection from a large collection of white spruce expressed sequences: Contributing factors and approaches for the categorization of SNPs
-
Pavy,N. et al. (2006) Automated SNP detection from a large collection of white spruce expressed sequences: Contributing factors and approaches for the categorization of SNPs. BMC Genomics, 7, 174.
-
(2006)
BMC Genomics
, vol.7
, pp. 174
-
-
Pavy, N.1
-
35
-
-
33745289067
-
Length-dependent prediction of protein intrinsic disorder
-
Peng,K. et al. (2006) Length-dependent prediction of protein intrinsic disorder. BMC Bioinformatics, 7, 208.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 208
-
-
Peng, K.1
-
36
-
-
34447312595
-
-
online help manual, Retrieved November 28, 2006, from
-
Perkins,D.N. et al. (2006) Mascot online help manual, Retrieved November 28, 2006, from http://www.matrixscience.com/help/ seq_db_setup_uniref.html
-
(2006)
Mascot
-
-
Perkins, D.N.1
-
37
-
-
24644474560
-
The predictive power of the CluSTr database
-
Petryszak,R. et al. (2005) The predictive power of the CluSTr database. Bioinformatics, 21, 3604-3609.
-
(2005)
Bioinformatics
, vol.21
, pp. 3604-3609
-
-
Petryszak, R.1
-
38
-
-
0346652457
-
ProClust: Improved clustering of protein sequences with an extended graph-based approach
-
Pipenbacher,P. et al. (2002) ProClust: Improved clustering of protein sequences with an extended graph-based approach. Bioinformatics, 18 (Suppl. 2), S182-S191.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 2
-
-
Pipenbacher, P.1
-
39
-
-
33846057724
-
NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
-
Pruitt,K.D. et al. (2007) NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 35, D61-D65.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Pruitt, K.D.1
-
40
-
-
20444490755
-
Sequencing and analysis of common bean ESTs. Building a foundation for functional genomics
-
Ramirez,M. et al. (2005) Sequencing and analysis of common bean ESTs. Building a foundation for functional genomics. Plant Physiol. 137, 1211-1227.
-
(2005)
Plant Physiol
, vol.137
, pp. 1211-1227
-
-
Ramirez, M.1
-
41
-
-
22544457600
-
Death inducer obliterator protein 1 in the context of DNA regulation. Sequence analyses of distant homologues point to a novel functional role
-
Rojas,A.M. et al. (2005) Death inducer obliterator protein 1 in the context of DNA regulation. Sequence analyses of distant homologues point to a novel functional role. FEBS J., 272, 3505-3511.
-
(2005)
FEBS J
, vol.272
, pp. 3505-3511
-
-
Rojas, A.M.1
-
42
-
-
33646547906
-
Comprehensive structural analysis of the genome of red clover (Trifolium pratense L.)
-
Sato,S. et al. (2005) Comprehensive structural analysis of the genome of red clover (Trifolium pratense L.). DNA Res., 12, 301-364.
-
(2005)
DNA Res
, vol.12
, pp. 301-364
-
-
Sato, S.1
-
43
-
-
26944500600
-
Genome organization of more than 300 defensin-like genes in Arabidopsis
-
Silverstein,K.A. et al. (2005) Genome organization of more than 300 defensin-like genes in Arabidopsis. Plant Physiol., 138, 600-610.
-
(2005)
Plant Physiol
, vol.138
, pp. 600-610
-
-
Silverstein, K.A.1
-
44
-
-
33644877178
-
Tetrahymena Genome Database (TGD): A new genomic resource for Tetrahymena thermophila research
-
Stover,N.A. et al. (2006) Tetrahymena Genome Database (TGD): A new genomic resource for Tetrahymena thermophila research. Nucleic Acids Res., 34, D500-D503.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Stover, N.A.1
-
45
-
-
33846041078
-
The Universal Protein Resource (UniProt)
-
The UniProt Consortium
-
The UniProt Consortium (2007) The Universal Protein Resource (UniProt). Nucleic Acids Res., 35, D193-D197.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
-
46
-
-
33646227211
-
+ binding site in NADH:qUinone oxidoreductase from Klebsiella pneumoniae with dicyclohexylcarbodiimide
-
+ binding site in NADH:qUinone oxidoreductase from Klebsiella pneumoniae with dicyclohexylcarbodiimide. J. Bacteriol., 188, 3264-3272.
-
(2006)
J. Bacteriol
, vol.188
, pp. 3264-3272
-
-
Vgenopoulou, I.1
-
47
-
-
33748505263
-
Incorporating background frequency improves entropy-based residue conservation measures
-
Wang,K. and Samudrala,R. (2006) Incorporating background frequency improves entropy-based residue conservation measures. BMC Bioinformatics, 7, 385.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 385
-
-
Wang, K.1
Samudrala, R.2
-
48
-
-
33846062023
-
Database resources of the national center for biotechnology information
-
Wheeler,D.L. et al. (2007) Database resources of the national center for biotechnology information. Nucleic Acids Res., 35 D5-D12.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Wheeler, D.L.1
-
49
-
-
33644873213
-
The Universal Protein Resource (UniProt): An expanding universe of protein information
-
Wu,C.H. et al. (2006) The Universal Protein Resource (UniProt): An expanding universe of protein information. Nucleic Acids Res., 34, D187-D191.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Wu, C.H.1
-
50
-
-
33749263896
-
Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromere
-
Yan,H. et al. (2006) Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromere. Plant Cell, 18, 2123-2133.
-
(2006)
Plant Cell
, vol.18
, pp. 2123-2133
-
-
Yan, H.1
|