-
1
-
-
77951640946
-
A method and server for predicting damaging missense mutations
-
Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. 2010. A method and server for predicting damaging missense mutations. Nat Methods 7:248-249.
-
(2010)
Nat Methods
, vol.7
, pp. 248-249
-
-
Adzhubei, I.A.1
Schmidt, S.2
Peshkin, L.3
Ramensky, V.E.4
Gerasimova, A.5
Bork, P.6
Kondrashov, A.S.7
Sunyaev, S.R.8
-
2
-
-
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
-
3
-
-
16244401676
-
Sequence variation in Gprotein-coupled receptors: analysis of single nucleotide polymorphisms
-
Balasubramanian S, Xia Y, Freinkman E, Gerstein M. 2005. Sequence variation in Gprotein-coupled receptors: analysis of single nucleotide polymorphisms. Nucleic Acids Res 33:1710-1721.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 1710-1721
-
-
Balasubramanian, S.1
Xia, Y.2
Freinkman, E.3
Gerstein, M.4
-
4
-
-
19544392545
-
Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information
-
Bao L, Cui Y. 2005. Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information. Bioinformatics 21:2185-2190.
-
(2005)
Bioinformatics
, vol.21
, pp. 2185-2190
-
-
Bao, L.1
Cui, Y.2
-
5
-
-
44349130366
-
Statistical geometry based prediction of nonsynonymous SNP functional effects using random forest and neuro-fuzzy classifiers
-
Barenboim M, Masso M, Vaisman I, Jamison DC. 2008. Statistical geometry based prediction of nonsynonymous SNP functional effects using random forest and neuro-fuzzy classifiers. Proteins 71:1930-1939.
-
(2008)
Proteins
, vol.71
, pp. 1930-1939
-
-
Barenboim, M.1
Masso, M.2
Vaisman, I.3
Jamison, D.C.4
-
6
-
-
2542458612
-
Classification of nuclear receptors based on amino acid composition and dipeptide composition
-
Bhasin M, Raghava GP. 2004. Classification of nuclear receptors based on amino acid composition and dipeptide composition. J Biol Chem 279:23262-23266.
-
(2004)
J Biol Chem
, vol.279
, pp. 23262-23266
-
-
Bhasin, M.1
Raghava, G.P.2
-
7
-
-
34547100092
-
SNAP: predict effect of non-synonymous polymorphisms on function
-
Bromberg Y, Rost B. 2007. SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Res 35:3823-3835.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 3823-3835
-
-
Bromberg, Y.1
Rost, B.2
-
8
-
-
3442888250
-
Bayesian approach to discovering pathogenic SNPs in conserved protein domains
-
Cai Z, Tsung EF, Marinescu VD, Ramoni MF, Riva A, Kohane IS. 2004. Bayesian approach to discovering pathogenic SNPs in conserved protein domains. Hum Mutat 24:178-184.
-
(2004)
Hum Mutat
, vol.24
, pp. 178-184
-
-
Cai, Z.1
Tsung, E.F.2
Marinescu, V.D.3
Ramoni, M.F.4
Riva, A.5
Kohane, I.S.6
-
9
-
-
33751013750
-
Predicting the insurgence of human genetic diseases associated to single point proteinmutationswith support vectormachines and evolutionary information
-
Capriotti E, Calabrese R, Casadio R. 2006. Predicting the insurgence of human genetic diseases associated to single point proteinmutationswith support vectormachines and evolutionary information. Bioinformatics 22:2729-2734.
-
(2006)
Bioinformatics
, vol.22
, pp. 2729-2734
-
-
Capriotti, E.1
Calabrese, R.2
Casadio, R.3
-
10
-
-
0032991552
-
Characterization of single-nucleotide polymorphisms in coding regions of human genes
-
Cargill M, Altshuler D, Ireland J, Sklar P, Ardlie K, Patil N, Shaw N, Lane CR, Lim EP, Kalyanaraman N, Nemesh J, Ziaugra L, Friedland L, Rolfe A, Warrington J, Lipshutz R, Daley GQ, Lander ES. 1999. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat Genet 22:231-238.
-
(1999)
Nat Genet
, vol.22
, pp. 231-238
-
-
Cargill, M.1
Altshuler, D.2
Ireland, J.3
Sklar, P.4
Ardlie, K.5
Patil, N.6
Shaw, N.7
Lane, C.R.8
Lim, E.P.9
Kalyanaraman, N.10
Nemesh, J.11
Ziaugra, L.12
Friedland, L.13
Rolfe, A.14
Warrington, J.15
Lipshutz, R.16
Daley, G.Q.17
Lander, E.S.18
-
11
-
-
84857794681
-
-
LIBSVM: a library for support vector machines Available at
-
Chang CC, Lin CJ. 2001. LIBSVM: a library for support vector machines. Available at http://www.csie.ntu.edu.tw/~cjlin/libsvm
-
(2001)
-
-
Chang, C.C.1
Lin, C.J.2
-
12
-
-
0035937259
-
Predicting the functional consequences of nonsynonymous single nucleotide polymorphisms: structure-based assessment of amino acid variation
-
Chasman D, Adams RM. 2001. Predicting the functional consequences of nonsynonymous single nucleotide polymorphisms: structure-based assessment of amino acid variation. J Mol Biol 307:683-706.
-
(2001)
J Mol Biol
, vol.307
, pp. 683-706
-
-
Chasman, D.1
Adams, R.M.2
-
14
-
-
0042121237
-
Multiple sequence alignment with the Clustal series of programs
-
Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. 2003. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31:3497-3500.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3497-3500
-
-
Chenna, R.1
Sugawara, H.2
Koike, T.3
Lopez, R.4
Gibson, T.J.5
Higgins, D.G.6
Thompson, J.D.7
-
15
-
-
0032429154
-
A DNA polymorphism discovery resource for research on human genetic variation
-
Collins FS, Brooks LD, Chakravarti A. 1998. A DNA polymorphism discovery resource for research on human genetic variation. Genome Res 8:1229-1231.
-
(1998)
Genome Res
, vol.8
, pp. 1229-1231
-
-
Collins, F.S.1
Brooks, L.D.2
Chakravarti, A.3
-
17
-
-
0034924997
-
Positive and negative selection on the human genome
-
Fay JC, WyckoffGJ, Wu CI. 2001. Positive and negative selection on the human genome. Genetics 158:1227-1234.
-
(2001)
Genetics
, vol.158
, pp. 1227-1234
-
-
Fay, J.C.1
Wyckoff, G.J.2
Wu, C.I.3
-
18
-
-
0036300807
-
Characterization of disease-associated single amino acid polymorphisms in terms of sequence and structure properties
-
Ferrer-Costa C, Orozco M, de la Cruz X. 2002. Characterization of disease-associated single amino acid polymorphisms in terms of sequence and structure properties. J Mol Biol 315:771-786.
-
(2002)
J Mol Biol
, vol.315
, pp. 771-786
-
-
Ferrer-Costa, C.1
Orozco, M.2
de la Cruz, X.3
-
19
-
-
10344242920
-
Sequence-based prediction of pathological mutations
-
Ferrer-Costa C, Orozco M, de la Cruz X. 2004. Sequence-based prediction of pathological mutations. Proteins 57:811-819.
-
(2004)
Proteins
, vol.57
, pp. 811-819
-
-
Ferrer-Costa, C.1
Orozco, M.2
de la Cruz, X.3
-
20
-
-
28644445533
-
Use of bioinformatics tools for the annotation of disease-associated mutations in animal models
-
Ferrer-Costa C, Orozco M, de la Cruz X. 2005. Use of bioinformatics tools for the annotation of disease-associated mutations in animal models. Proteins 61:878-887.
-
(2005)
Proteins
, vol.61
, pp. 878-887
-
-
Ferrer-Costa, C.1
Orozco, M.2
de la Cruz, X.3
-
21
-
-
0036081484
-
HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources
-
Fredman D, Siegfried M, Yuan YP, Bork P, Lehvaslaiho H, Brookes AJ. 2002. HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources. Nucleic Acids Res 30:387-391.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 387-391
-
-
Fredman, D.1
Siegfried, M.2
Yuan, Y.P.3
Bork, P.4
Lehvaslaiho, H.5
Brookes, A.J.6
-
23
-
-
13444266370
-
OnlineMendelian inheritance in man (OMIM), a knowledgebase of human genes and genetic disorders
-
Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusickVA. 2005. OnlineMendelian inheritance in man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 33:D514-D517.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Hamosh, A.1
Scott, A.F.2
Amberger, J.S.3
Bocchini, C.A.4
McKusick, V.A.5
-
24
-
-
79957621519
-
Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed
-
Hicks S, Wheeler DA, Plon SE, Kimmel M. 2011. Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed. Hum Mutat 32:661-668.
-
(2011)
Hum Mutat
, vol.32
, pp. 661-668
-
-
Hicks, S.1
Wheeler, D.A.2
Plon, S.E.3
Kimmel, M.4
-
25
-
-
0018784438
-
Surface and inside volumes in globular proteins
-
Janin J. 1979. Surface and inside volumes in globular proteins. Nature 277:491-492.
-
(1979)
Nature
, vol.277
, pp. 491-492
-
-
Janin, J.1
-
26
-
-
0344033683
-
A comparative study of machine-learning methods to predict the effects of single nucleotide polymorphisms on protein function
-
Krishnan VG, Westhead DR. 2003. A comparative study of machine-learning methods to predict the effects of single nucleotide polymorphisms on protein function. Bioinformatics 19:2199-2209.
-
(2003)
Bioinformatics
, vol.19
, pp. 2199-2209
-
-
Krishnan, V.G.1
Westhead, D.R.2
-
27
-
-
17244367767
-
Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis
-
Mooney S. 2005. Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis. Brief Bioinform 6:44-56.
-
(2005)
Brief Bioinform
, vol.6
, pp. 44-56
-
-
Mooney, S.1
-
28
-
-
33749430068
-
Predicting the effect of missensemutations on protein function: analysis with Bayesian networks
-
Needham CJ, Bradford JR, Bulpitt AJ, Care MA, Westhead DR. 2006. Predicting the effect of missensemutations on protein function: analysis with Bayesian networks. BMC Bioinformatics 7:405.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 405
-
-
Needham, C.J.1
Bradford, J.R.2
Bulpitt, A.J.3
Care, M.A.4
Westhead, D.R.5
-
29
-
-
0035026704
-
Predicting pathogenic amino acid substitutions
-
Ng PC, Henikoff S. 2001. Predicting pathogenic amino acid substitutions. Genome Res 11:863-874.
-
(2001)
Genome Res
, vol.11
, pp. 863-874
-
-
Ng, P.C.1
Henikoff, S.2
-
30
-
-
33750353461
-
Predicting the effects of amino acid substitutions on protein function. Annu Rev Genomics
-
Ng PC, Henikoff S. 2006. Predicting the effects of amino acid substitutions on protein function. Annu Rev Genomics Hum Genet 7:61-80.
-
(2006)
Hum Genet
, vol.7
, pp. 61-80
-
-
Ng, P.C.1
Henikoff, S.2
-
31
-
-
0043122919
-
SIFT: Predicting amino acid changes that affect protein function
-
Ng PC, Henikoff S. 2003. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acid Res 31:3812-3814.
-
(2003)
Nucleic Acid Res
, vol.31
, pp. 3812-3814
-
-
Ng, P.C.1
Henikoff, S.2
-
32
-
-
0036713510
-
Human non-synonymous SNPs: server and survey
-
Ramensky V, Bork P, Sunyaev S. 2002. Human non-synonymous SNPs: server and survey. Nucleic Acids Res 30:3894-3900.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 3894-3900
-
-
Ramensky, V.1
Bork, P.2
Sunyaev, S.3
-
33
-
-
0034201441
-
EMBOSS: the European molecular biology open software suite
-
Rice P, Longden I, Bleasby A. 2000. EMBOSS: the European molecular biology open software suite. Trends Genet 16:276-277.
-
(2000)
Trends Genet
, vol.16
, pp. 276-277
-
-
Rice, P.1
Longden, I.2
Bleasby, A.3
-
34
-
-
0036387236
-
Evaluation of structural and evolutionary contributions to pathogenic mutation prediction
-
Saunders CT, Baker D. 2002. Evaluation of structural and evolutionary contributions to pathogenic mutation prediction. J Mol Biol 322:891-901.
-
(2002)
J Mol Biol
, vol.322
, pp. 891-901
-
-
Saunders, C.T.1
Baker, D.2
-
35
-
-
77955151784
-
MutationTaster evaluates disease-causing potential of sequencealterations
-
Schwarz JM, R̈odelsperger C, Schuelke M, Seelow D. 2010. MutationTaster evaluates disease-causing potential of sequence alterations. Nat Methods 7:575-576.
-
(2010)
Nat Methods
, vol.7
, pp. 575-576
-
-
Schwarz, J.M.1
Rödelsperger, C.2
Schuelke, M.3
Seelow, D.4
-
36
-
-
0000120520
-
ProDom: automated clustering of homologous domains
-
Servant F, Bru C, Carr'ere S, Courcelle E, Gouzy J, Peyruc D, Kahn D. 2002. ProDom: automated clustering of homologous domains. Brief Bioinform 3:246-251.
-
(2002)
Brief Bioinform
, vol.3
, pp. 246-251
-
-
Servant, F.1
Bru, C.2
Carr'ere, S.3
Courcelle, E.4
Gouzy, J.5
Peyruc, D.6
Kahn, D.7
-
37
-
-
0032876978
-
dbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation
-
Sherry ST, Ward M, Sirotkin K. 1999. dbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation. Genome Res 9:677-679.
-
(1999)
Genome Res
, vol.9
, pp. 677-679
-
-
Sherry, S.T.1
Ward, M.2
Sirotkin, K.3
-
38
-
-
0001290045
-
PROSITE: a documented database using patterns and profiles as motif descriptors
-
Sigrist CJ, Cerutti L, Hulo N, Gattiker A, Falquet L, Pagni M, Bairoch A, Bucher P. 2002. PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform 3:265-274.
-
(2002)
Brief Bioinform
, vol.3
, pp. 265-274
-
-
Sigrist, C.J.1
Cerutti, L.2
Hulo, N.3
Gattiker, A.4
Falquet, L.5
Pagni, M.6
Bairoch, A.7
Bucher, P.8
-
40
-
-
0029906607
-
Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology
-
Sjolander K, Karplus K, Brown M, Hughey R, Krogh A, Mian IS, Haussler D. 1996. Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. Comput Appl Biosci 12:327-345.
-
(1996)
Comput Appl Biosci
, vol.12
, pp. 327-345
-
-
Sjolander, K.1
Karplus, K.2
Brown, M.3
Hughey, R.4
Krogh, A.5
Mian, I.S.6
Haussler, D.7
-
41
-
-
0037903275
-
Human Gene Mutation Database (HGMD): 2003 update
-
Stenson PD, Ball EV, Mort M, Phillips AD, Shiel JA, Thomas NS, Abeysinghe S, Krawczak M, Cooper DN. 2003. Human Gene Mutation Database (HGMD): 2003 update. Hum Mutat 21:577-581.
-
(2003)
Hum Mutat
, vol.21
, pp. 577-581
-
-
Stenson, P.D.1
Ball, E.V.2
Mort, M.3
Phillips, A.D.4
Shiel, J.A.5
Thomas, N.S.6
Abeysinghe, S.7
Krawczak, M.8
Cooper, D.N.9
-
42
-
-
0035869223
-
Prediction of pathogenic human alleles
-
Sunyaev S, RamenskyV, Koch I, Lathe W, 3rd, Kondrashov AS, Bork P. 2001. Prediction of pathogenic human alleles. Hum Mol Genet 10:591-597.
-
(2001)
Hum Mol Genet
, vol.10
, pp. 591-597
-
-
Sunyaev, S.1
Ramensky, V.2
Koch, I.3
Lathe III, W.4
Kondrashov, A.S.5
Bork, P.6
-
43
-
-
55549145156
-
In silico analysis of missense substitutions using sequence-alignment based methods
-
Tavtigian SV, Greenblatt MS, Lesueur F, Byrnes GB. 2008. In silico analysis of missense substitutions using sequence-alignment based methods. Hum Mutat 29:1327-1336.
-
(2008)
Hum Mutat
, vol.29
, pp. 1327-1336
-
-
Tavtigian, S.V.1
Greenblatt, M.S.2
Lesueur, F.3
Byrnes, G.B.4
-
44
-
-
0037250403
-
The SNP Consortium website: past, present and future
-
Thorisson GA, Stein LD. 2003. The SNP Consortium website: past, present and future. Nucleic Acids Res 31:124-127.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 124-127
-
-
Thorisson, G.A.1
Stein, L.D.2
-
45
-
-
65649108490
-
Pathogenic or not? And if so, then how? Studying the effects ofmissense mutations using bioinformatics methods
-
Thusberg J, Vihinen M. 2009. Pathogenic or not? And if so, then how? Studying the effects ofmissense mutations using bioinformatics methods. Hum Mutat 30:703-714.
-
(2009)
Hum Mutat
, vol.30
, pp. 703-714
-
-
Thusberg, J.1
Vihinen, M.2
-
46
-
-
38649091045
-
Predicting the phenotypic effects of non-synonymous single nucleotide polymorphisms based on support vector machines
-
Tian J, Wu N, Guo X, Guo J, Zhang J, Fan Y. 2007. Predicting the phenotypic effects of non-synonymous single nucleotide polymorphisms based on support vector machines. BMC Bioinformatics 8:450.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 450
-
-
Tian, J.1
Wu, N.2
Guo, X.3
Guo, J.4
Zhang, J.5
Fan, Y.6
-
47
-
-
36448935249
-
Accurate prediction of pathogenic protein kinase polymorphisms
-
Torkamani A, Schork NJ. 2007. Accurate prediction of pathogenic protein kinase polymorphisms. Bioinformatics 23:2918-2925.
-
(2007)
Bioinformatics
, vol.23
, pp. 2918-2925
-
-
Torkamani, A.1
Schork, N.J.2
-
49
-
-
1542577828
-
The amino-acidmutational spectrumof human genetic disease
-
Vitkup D, Sander C, ChurchGM. 2003. The amino-acidmutational spectrumof human genetic disease. Genome Biol 4:R72.
-
(2003)
Genome Biol
, vol.4
-
-
Vitkup, D.1
Sander, C.2
Church, G.M.3
-
50
-
-
25144523127
-
Loss of protein structure stability as a major causative factor in monogenic disease
-
Yue P, Li Z, Moult J. 2005. Loss of protein structure stability as a major causative factor in monogenic disease. J Mol Biol 353:459-473.
-
(2005)
J Mol Biol
, vol.353
, pp. 459-473
-
-
Yue, P.1
Li, Z.2
Moult, J.3
-
51
-
-
33645764714
-
SNPs3D: candidate gene and SNP selection for association studies
-
Yue P, Melamud E, Moult J. 2006. SNPs3D: candidate gene and SNP selection for association studies. BMC Bioinformatics 7:166.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 166
-
-
Yue, P.1
Melamud, E.2
Moult, J.3
-
52
-
-
32044453591
-
Identification and analysis of pathogenic human SNPs
-
Yue P, Moult J. 2006. Identification and analysis of pathogenic human SNPs. JMol Biol 356:1263-1274.
-
(2006)
JMol Biol
, vol.356
, pp. 1263-1274
-
-
Yue, P.1
Moult, J.2
|