-
1
-
-
17744394753
-
Phylogenomics and the reconstruction of the tree of life
-
Delsuc F, Brinkmann H, Philippe H (2005) Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 6: 361-375.
-
(2005)
Nat Rev Genet
, vol.6
, pp. 361-375
-
-
Delsuc, F.1
Brinkmann, H.2
Philippe, H.3
-
2
-
-
0031976258
-
Phylogenomics: Improving functional predictions for uncharacterized genes by evolutionary analysis
-
Eisen JA (1998) Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res 8: 163-167.
-
(1998)
Genome Res
, vol.8
, pp. 163-167
-
-
Eisen, J.A.1
-
3
-
-
1042280957
-
Phylogenomic inference of protein molecular function: Advances and challenges
-
Sjölander K (2004) Phylogenomic inference of protein molecular function: advances and challenges. Bioinformatics 20: 170-179.
-
(2004)
Bioinformatics
, vol.20
, pp. 170-179
-
-
Sjölander, K.1
-
4
-
-
33745630672
-
Functional classification using phylogenomic inference
-
doi:10.1371/journal. pcbi.0020077
-
Brown D, Sjölander K (2006) Functional classification using phylogenomic inference. PLoS Comput Biol 2: e77. doi:10.1371/journal. pcbi.0020077.
-
(2006)
PLoS Comput Biol
, vol.2
-
-
Brown, D.1
Sjölander, K.2
-
5
-
-
0032229196
-
Sources of systematic error in functional annotation of genomes: Domain rearrangement, non-orthologous gene displacement and operon disruption
-
Galperin MY, Koonin EV (1998) Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption. In Silico Biol 1: 55-67.
-
(1998)
In Silico Biol
, vol.1
, pp. 55-67
-
-
Galperin, M.Y.1
Koonin, E.V.2
-
6
-
-
0033119399
-
Errors in genome annotation
-
Brenner SE (1999) Errors in genome annotation. Trends Genet 15: 132-133.
-
(1999)
Trends Genet
, vol.15
, pp. 132-133
-
-
Brenner, S.E.1
-
7
-
-
23044485115
-
Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers
-
Green ML, Karp PD (2005) Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers. Nucleic Acids Res 33: 4035-4039.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 4035-4039
-
-
Green, M.L.1
Karp, P.D.2
-
8
-
-
34250790725
-
Estimating the annotation error rate of curated GO database sequence annotations
-
Jones CE, Brown AL, Baumann U (2007) Estimating the annotation error rate of curated GO database sequence annotations. BMC Bioinformatics 8: 170.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 170
-
-
Jones, C.E.1
Brown, A.L.2
Baumann, U.3
-
9
-
-
34248145506
-
FlowerPower: Clustering proteins into domain architecture classes for phylogenomic inference of protein function
-
Krishnamurthy N, Brown D, Sjölander K (2007) FlowerPower: Clustering proteins into domain architecture classes for phylogenomic inference of protein function. BMC Evol Biol 7 Suppl 1: S12.
-
(2007)
BMC Evol Biol
, vol.7
, Issue.SUPPL. 1
-
-
Krishnamurthy, N.1
Brown, D.2
Sjölander, K.3
-
10
-
-
41849110846
-
Structural evolution of the protein kinase-like superfamily
-
Scheeff ED, Bourne PE (2005) Structural evolution of the protein kinase-like superfamily. PLoS Comput Biol 1: e49.
-
(2005)
PLoS Comput Biol
, vol.1
-
-
Scheeff, E.D.1
Bourne, P.E.2
-
11
-
-
33750474439
-
PhyloFacts: An online structural phylogenomic encyclopedia for protein functional and structural classification
-
Krishnamurthy N, Brown DP, Kirshner D, Sjölander K (2006) PhyloFacts: An online structural phylogenomic encyclopedia for protein functional and structural classification. Genome Biol 7: R83.
-
(2006)
Genome Biol
, vol.7
-
-
Krishnamurthy, N.1
Brown, D.P.2
Kirshner, D.3
Sjölander, K.4
-
12
-
-
0013017592
-
RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs
-
Zmasek CM, Eddy SR (2002) RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinformatics 3: 14.
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 14
-
-
Zmasek, C.M.1
Eddy, S.R.2
-
13
-
-
0036699481
-
Increased taxon sampling greatly reduces phylogenetic error
-
Zwickl DJ, Hillis DM (2002) Increased taxon sampling greatly reduces phylogenetic error. Syst Biol 51: 588-598.
-
(2002)
Syst Biol
, vol.51
, pp. 588-598
-
-
Zwickl, D.J.1
Hillis, D.M.2
-
14
-
-
0035812694
-
Protein structure prediction and structural genomics
-
Baker D, Sali A (2001) Protein structure prediction and structural genomics. Science 294: 93-96.
-
(2001)
Science
, vol.294
, pp. 93-96
-
-
Baker, D.1
Sali, A.2
-
15
-
-
0042594474
-
SATCHMO: Sequence alignment and tree construction using hidden Markov models
-
Edgar RC, Sjölander K (2003) SATCHMO: Sequence alignment and tree construction using hidden Markov models. Bioinformatics 19: 1404-1411.
-
(2003)
Bioinformatics
, vol.19
, pp. 1404-1411
-
-
Edgar, R.C.1
Sjölander, K.2
-
16
-
-
57049150788
-
The ConSurf-DB: Pre-calculated evolutionary conservation profiles of protein structures
-
Goldenberg O, Erez E, Nimrod G, Ben-Tal N (2009) The ConSurf-DB: Pre-calculated evolutionary conservation profiles of protein structures. Nucleic Acids Res 37: D323-327.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Goldenberg, O.1
Erez, E.2
Nimrod, G.3
Ben-Tal, N.4
-
17
-
-
54949145058
-
INTREPID-INformation-theoretic TREe traversal for Protein functional site IDentification
-
Sankararaman S, Sjölander K (2008) INTREPID-INformation-theoretic TREe traversal for Protein functional site IDentification. Bioinformatics 24: 2445-2452.
-
(2008)
Bioinformatics
, vol.24
, pp. 2445-2452
-
-
Sankararaman, S.1
Sjölander, K.2
-
18
-
-
0030601801
-
Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses
-
Goldman N, Thorne JL, Jones DT (1996) Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses. J Mol Biol 263: 196-208.
-
(1996)
J Mol Biol
, vol.263
, pp. 196-208
-
-
Goldman, N.1
Thorne, J.L.2
Jones, D.T.3
-
19
-
-
0041671089
-
Detecting distant homologs using phylogenetic tree-based HMMs
-
Qian B, Goldstein RA (2003) Detecting distant homologs using phylogenetic tree-based HMMs. Proteins 52: 446-453.
-
(2003)
Proteins
, vol.52
, pp. 446-453
-
-
Qian, B.1
Goldstein, R.A.2
-
20
-
-
33748776559
-
Automated protein function prediction-the genomic challenge
-
Friedberg I (2006) Automated protein function prediction-the genomic challenge. Brief Bioinform 7: 225-242.
-
(2006)
Brief Bioinform
, vol.7
, pp. 225-242
-
-
Friedberg, I.1
|