-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
2
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25-29.
-
(2000)
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
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
3
-
-
27844536541
-
A rigorous method for multigenic families' functional annotation: The peptidyl arginine deiminase (PADs) proteins family example
-
Balandraud N, Gouret P, Danchin EG, Blanc M, Zinn D, Roudier J, Pontarotti P. 2005. A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example. BMC Genomics 6:153.
-
(2005)
BMC Genomics
, vol.6
, pp. 153
-
-
Balandraud, N.1
Gouret, P.2
Danchin, E.G.3
Blanc, M.4
Zinn, D.5
Roudier, J.6
Pontarotti, P.7
-
4
-
-
0033976458
-
The Pfam protein families database
-
Bateman A, Birney E, Durbin R, Eddy SR, Howe KL, Sonnhammer EL. 2000. The Pfam protein families database. Nucleic Acids Res 28:263-266.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 263-266
-
-
Bateman, A.1
Birney, E.2
Durbin, R.3
Eddy, S.R.4
Howe, K.L.5
Sonnhammer, E.L.6
-
5
-
-
9144257886
-
The Pfam protein families database
-
Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR. 2004. The Pfam protein families database. Nucleic Acids Res 32:D138-141.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Bateman, A.1
Coin, L.2
Durbin, R.3
Finn, R.D.4
Hollich, V.5
Griffiths-Jones, S.6
Khanna, A.7
Marshall, M.8
Moxon, S.9
Sonnhammer, E.L.10
Studholme, D.J.11
Yeats, C.12
Eddy, S.R.13
-
6
-
-
1842609703
-
Differential enzyme targeting as an evolutionary adaptation to herbivory in carnivora
-
Birdsey GM, Lewin J, Cunningham AA, Bruford MW, Danpure CJ. 2004. Differential enzyme targeting as an evolutionary adaptation to herbivory in carnivora. Mol Biol Evol 21:632-646.
-
(2004)
Mol Biol Evol
, vol.21
, pp. 632-646
-
-
Birdsey, G.M.1
Lewin, J.2
Cunningham, A.A.3
Bruford, M.W.4
Danpure, C.J.5
-
7
-
-
16444378220
-
Natural selection during functional divergence to LMP7 and proteasome subunit X (PSMB5) following gene duplication
-
Bos DH. 2005. Natural selection during functional divergence to LMP7 and proteasome subunit X (PSMB5) following gene duplication. J Mol Evol 60:221-228.
-
(2005)
J Mol Evol
, vol.60
, pp. 221-228
-
-
Bos, D.H.1
-
8
-
-
0038305140
-
A co-evolution perspective of the TNFSF and TNFRSF families in the immune system
-
Collette Y, Gilles A, Pontarotti P, Olive D. 2003. A co-evolution perspective of the TNFSF and TNFRSF families in the immune system. Trends Immunol 24:387-394.
-
(2003)
Trends Immunol
, vol.24
, pp. 387-394
-
-
Collette, Y.1
Gilles, A.2
Pontarotti, P.3
Olive, D.4
-
9
-
-
0031024921
-
Of worms and men: An evolutionary perspective on the fibroblast growth factor (FGF) and FGF receptor families
-
Coulier F, Pontarotti P, Roubin R, Haetung H, Goldfarb M, Birnbaum D. 1997. Of worms and men: an evolutionary perspective on the fibroblast growth factor (FGF) and FGF receptor families. J Mol Evol 44:43-56.
-
(1997)
J Mol Evol
, vol.44
, pp. 43-56
-
-
Coulier, F.1
Pontarotti, P.2
Roubin, R.3
Haetung, H.4
Goldfarb, M.5
Birnbaum, D.6
-
10
-
-
1642504712
-
The major histocompatibility complex origin
-
Danchin E, Vitiello V, Vienne A, Richard O, Gouret P, McDermott MF, Pontarotti P. 2004. The major histocompatibility complex origin. Immunol Rev 198:216-232.
-
(2004)
Immunol Rev
, vol.198
, pp. 216-232
-
-
Danchin, E.1
Vitiello, V.2
Vienne, A.3
Richard, O.4
Gouret, P.5
McDermott, M.F.6
Pontarotti, P.7
-
11
-
-
33644557410
-
Eleven ancestral gene families lost in mammals and vertebrates while otherwise universally conserved in animals
-
Danchin EG, Gouret P, Pontarotti P. 2006. Eleven ancestral gene families lost in mammals and vertebrates while otherwise universally conserved in animals. BMC Evol Biol 6:5.
-
(2006)
BMC Evol Biol
, vol.6
, pp. 5
-
-
Danchin, E.G.1
Gouret, P.2
Pontarotti, P.3
-
12
-
-
20744436518
-
Tree pattern matching in phylogenetic trees: Automatic search for orthologs or paralogs in homologous gene sequence databases
-
Dufayard JF, Duret L, Penel S, Gouy M, Rechenmann F, Perriere G. 2005. Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases. Bioinformatics 21:2596-2603.
-
(2005)
Bioinformatics
, vol.21
, pp. 2596-2603
-
-
Dufayard, J.F.1
Duret, L.2
Penel, S.3
Gouy, M.4
Rechenmann, F.5
Perriere, G.6
-
13
-
-
0033977618
-
Determinants of substitution rates in mammalian genes: Expression pattern affects selection intensity but not mutation rate
-
Duret L, Mouchiroud D. 2000. Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Mol Biol Evol 17:68-74.
-
(2000)
Mol Biol Evol
, vol.17
, pp. 68-74
-
-
Duret, L.1
Mouchiroud, D.2
-
14
-
-
13244255415
-
MUSCLE: A multiple sequence alignment method with reduced time and space complexity
-
Edgar RC. 2004a. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 113
-
-
Edgar, R.C.1
-
15
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar RC. 2004b. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792-1797.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
16
-
-
33645310990
-
-
Engelhardt BE, Jordan MI, Muratore KE, Brenner SE. 2005. Protein molecular function prediction by Bayesian phylogenomics. PLoS Comput Biol 1:e45.
-
Engelhardt BE, Jordan MI, Muratore KE, Brenner SE. 2005. Protein molecular function prediction by Bayesian phylogenomics. PLoS Comput Biol 1:e45.
-
-
-
-
17
-
-
0032893932
-
Preservation of duplicate genes by complementary, degenerative mutations
-
Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531-1545.
-
(1999)
Genetics
, vol.151
, pp. 1531-1545
-
-
Force, A.1
Lynch, M.2
Pickett, F.B.3
Amores, A.4
Yan, Y.L.5
Postlethwait, J.6
-
18
-
-
0345161806
-
Generation of evolutionary novelty by functional shift
-
Ganfornina MD, Sanchez D. 1999. Generation of evolutionary novelty by functional shift. Bioessays 21:432-439.
-
(1999)
Bioessays
, vol.21
, pp. 432-439
-
-
Ganfornina, M.D.1
Sanchez, D.2
-
19
-
-
0036606898
-
Predicting functional divergence in protein evolution by site-specific rate shifts
-
Gaucher EA, Gu X, Miyamoto MM, Benner SA. 2002. Predicting functional divergence in protein evolution by site-specific rate shifts. Trends Biochem Sci 27:315-321.
-
(2002)
Trends Biochem Sci
, vol.27
, pp. 315-321
-
-
Gaucher, E.A.1
Gu, X.2
Miyamoto, M.M.3
Benner, S.A.4
-
20
-
-
25444473119
-
FIGENIX: Intelligent automation of genomic annotation: expertise integration in a new software platform
-
Gouret P, Vitiello V, Balandraud N, Gilles A, Pontarotti P, Danchin EGJ. 2005. FIGENIX: Intelligent automation of genomic annotation: expertise integration in a new software platform. BMC Bioinformatics 6:198.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 198
-
-
Gouret, P.1
Vitiello, V.2
Balandraud, N.3
Gilles, A.4
Pontarotti, P.5
Danchin, E.G.J.6
-
21
-
-
0036205440
-
DIVERGE: Phylogeny-based analysis for functional-structural divergence of a protein family
-
Gu X, Vander Velden K. 2002. DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family. Bioinformatics 18:500-501.
-
(2002)
Bioinformatics
, vol.18
, pp. 500-501
-
-
Gu, X.1
Vander Velden, K.2
-
22
-
-
0029888297
-
Strong evolutionary conservation of broadly expressed protein isoforms in the troponin I gene family and other vertebrate gene families
-
Hastings KE. 1996. Strong evolutionary conservation of broadly expressed protein isoforms in the troponin I gene family and other vertebrate gene families. J Mol Evol 42:631-640.
-
(1996)
J Mol Evol
, vol.42
, pp. 631-640
-
-
Hastings, K.E.1
-
23
-
-
0024307824
-
Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea
-
Kishino H, Hasegawa M. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J Mol Evol 29:170-179.
-
(1989)
J Mol Evol
, vol.29
, pp. 170-179
-
-
Kishino, H.1
Hasegawa, M.2
-
24
-
-
17744376961
-
Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions
-
Lemos B, Bettencourt BR, Meiklejohn CD, Hartl DL. 2005. Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions. Mol Biol Evol 22:1345-1354.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 1345-1354
-
-
Lemos, B.1
Bettencourt, B.R.2
Meiklejohn, C.D.3
Hartl, D.L.4
-
25
-
-
0036796369
-
Current methods of gene prediction, their strengths and weaknesses
-
Mathe C, Sagot MF, Schiex T, Rouze P. 2002. Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res 30:4103-4117.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 4103-4117
-
-
Mathe, C.1
Sagot, M.F.2
Schiex, T.3
Rouze, P.4
-
26
-
-
0019134329
-
Molecular evolution of mRNA: A method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application
-
Miyata T, Yasunaga T. 1980. Molecular evolution of mRNA: a method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application. J Mol Evol 16:23-36.
-
(1980)
J Mol Evol
, vol.16
, pp. 23-36
-
-
Miyata, T.1
Yasunaga, T.2
-
27
-
-
0035861990
-
Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
-
Remm M, Storm CE, Sonnhammer EL. 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
-
28
-
-
0344824014
-
Convergent neofunctionalization by positive Darwinian selection after ancient recurrent duplications of the xanthine dehydrogenase gene
-
Rodriguez-Trelles F, Tarrio R, Ayala FJ. 2003. Convergent neofunctionalization by positive Darwinian selection after ancient recurrent duplications of the xanthine dehydrogenase gene. Proc Natl Acad Sci USA 100:13413-13417.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 13413-13417
-
-
Rodriguez-Trelles, F.1
Tarrio, R.2
Ayala, F.J.3
-
29
-
-
0036205377
-
TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing
-
Schmidt HA, Strimmer K, Vingron M, von Haeseler A. 2002. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504.
-
(2002)
Bioinformatics
, vol.18
, pp. 502-504
-
-
Schmidt, H.A.1
Strimmer, K.2
Vingron, M.3
von Haeseler, A.4
-
30
-
-
0041884765
-
Retention of a duplicate gene through changes in subcellular targeting: An electron transport protein homologue localizes to the golgi
-
Schmidt TR, Doan JW, Goodman M, Grossman LI. 2003. Retention of a duplicate gene through changes in subcellular targeting: an electron transport protein homologue localizes to the golgi. J Mol Evol 57:222-228.
-
(2003)
J Mol Evol
, vol.57
, pp. 222-228
-
-
Schmidt, T.R.1
Doan, J.W.2
Goodman, M.3
Grossman, L.I.4
-
31
-
-
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
-
32
-
-
0036173130
-
Automated ortholog inference from phylogenetic trees and calculation of orthology reliability
-
Storm CE, Sonnhammer EL. 2002. Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics 18:92-99.
-
(2002)
Bioinformatics
, vol.18
, pp. 92-99
-
-
Storm, C.E.1
Sonnhammer, E.L.2
-
33
-
-
24644457706
-
BALIBASE 3.0-latest developments of the multiple alignment benchmark
-
Thompson JD, Koehl P, Ripp R, Poch O. 2005. BALIBASE 3.0-latest developments of the multiple alignment benchmark. Proteins 61:127-136.
-
(2005)
Proteins
, vol.61
, pp. 127-136
-
-
Thompson, J.D.1
Koehl, P.2
Ripp, R.3
Poch, O.4
-
34
-
-
0036439421
-
Gene co-option in physiological and morphological evolution
-
True JR, Carroll SB. 2002. Gene co-option in physiological and morphological evolution. Annu Rev Cell Dev Biol 18:53-80.
-
(2002)
Annu Rev Cell Dev Biol
, vol.18
, pp. 53-80
-
-
True, J.R.1
Carroll, S.B.2
-
35
-
-
0030683599
-
PAML: A program package for phylogenetic analysis by maximum likelihood
-
Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555-556.
-
(1997)
Comput Appl Biosci
, vol.13
, pp. 555-556
-
-
Yang, Z.1
-
36
-
-
0031897964
-
Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution
-
Yang Z. 1998. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol 15:568-573.
-
(1998)
Mol Biol Evol
, vol.15
, pp. 568-573
-
-
Yang, Z.1
-
37
-
-
0033639150
-
Statistical methods for detecting molecular adaptation
-
Yang Z, Bielawski JP. 2000. Statistical methods for detecting molecular adaptation. Trends Ecol Evol 15:496-503.
-
(2000)
Trends Ecol Evol
, vol.15
, pp. 496-503
-
-
Yang, Z.1
Bielawski, J.P.2
-
38
-
-
0036270185
-
Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages
-
Yang Z, Nielsen R. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol 19:908-917.
-
(2002)
Mol Biol Evol
, vol.19
, pp. 908-917
-
-
Yang, Z.1
Nielsen, R.2
-
39
-
-
1542286776
-
Mammalian housekeeping genes evolve more slowly than tissue-specific genes
-
Zhang L, Li WH. 2004. Mammalian housekeeping genes evolve more slowly than tissue-specific genes. Mol Biol Evol 21:236-239.
-
(2004)
Mol Biol Evol
, vol.21
, pp. 236-239
-
-
Zhang, L.1
Li, W.H.2
-
40
-
-
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
|