-
1
-
-
84878799611
-
Predicting functional effect of human missense mutations using PolyPhen-2
-
Chapter 7:Unit7 20.
-
Adzhubei I, Jordan DM, Sunyaev SR. 2013. Predicting functional effect of human missense mutations using PolyPhen-2. Curr Protoc Hum Genet Chapter 7:Unit7 20.
-
(2013)
Curr Protoc Hum Genet
-
-
Adzhubei, I.1
Jordan, D.M.2
Sunyaev, S.R.3
-
2
-
-
70349611306
-
Climate shaped the worldwide distribution of human mitochondrial DNA sequence variation
-
Balloux F, Handley LJ, Jombart T, Liu H, Manica A. 2009. Climate shaped the worldwide distribution of human mitochondrial DNA sequence variation. Proc Biol Sci 276:3447-55.
-
(2009)
Proc Biol Sci
, vol.276
, pp. 3447-3455
-
-
Balloux, F.1
Handley, L.J.2
Jombart, T.3
Liu, H.4
Manica, A.5
-
3
-
-
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 35:3823-35.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 3823-3835
-
-
Bromberg, Y.1
Rost, B.2
-
4
-
-
84880443165
-
Congruency in the prediction of pathogenic missense mutations: state-of-the-art web-based tools
-
Castellana S, Mazza T. 2013. Congruency in the prediction of pathogenic missense mutations: state-of-the-art web-based tools. Brief Bioinform 14:448-59.
-
(2013)
Brief Bioinform
, vol.14
, pp. 448-459
-
-
Castellana, S.1
Mazza, T.2
-
5
-
-
84858110655
-
Evolutionary patterns of the mitochondrial genome in Metazoa: exploring the role of mutation and selection in mitochondrial protein coding genes
-
Castellana S, Vicario S, Saccone C. 2011. Evolutionary patterns of the mitochondrial genome in Metazoa: exploring the role of mutation and selection in mitochondrial protein coding genes. Genome Biol Evol.
-
(2011)
Genome Biol Evol.
-
-
Castellana, S.1
Vicario, S.2
Saccone, C.3
-
6
-
-
84867301515
-
Predicting the functional effect of amino acid substitutions and indels
-
Choi Y, Sims GE, Murphy S, Miller JR, Chan AP. 2012. Predicting the functional effect of amino acid substitutions and indels. PLoS One 7:e46688.
-
(2012)
PLoS One
, vol.7
, pp. e46688
-
-
Choi, Y.1
Sims, G.E.2
Murphy, S.3
Miller, J.R.4
Chan, A.P.5
-
7
-
-
69749122314
-
Identification of deleterious mutations within three human genomes
-
Chun S, Fay JC. 2009. Identification of deleterious mutations within three human genomes. Genome Res 19:1553-61.
-
(2009)
Genome Res
, vol.19
, pp. 1553-1561
-
-
Chun, S.1
Fay, J.C.2
-
8
-
-
43349102636
-
The adaptive evolution of the mammalian mitochondrial genome
-
da Fonseca RR, Johnson WE, O'Brien SJ, Ramos MJ, Antunes A. 2008. The adaptive evolution of the mammalian mitochondrial genome. BMC Genomics 9:119.
-
(2008)
BMC Genomics
, vol.9
, pp. 119
-
-
da Fonseca, R.R.1
Johnson, W.E.2
O'Brien, S.J.3
Ramos, M.J.4
Antunes, A.5
-
9
-
-
84861090227
-
SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants
-
De Baets G, Van Durme J, Reumers J, Maurer-Stroh S, Vanhee P, Dopazo J, Schymkowitz J, Rousseau F. 2012. SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants. Nucleic Acids Res 40(Database issue):D935-9.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.DATABASE ISSUE
, pp. D935-D939
-
-
De Baets, G.1
Van Durme, J.2
Reumers, J.3
Maurer-Stroh, S.4
Vanhee, P.5
Dopazo, J.6
Schymkowitz, J.7
Rousseau, F.8
-
10
-
-
84874732372
-
CRAVAT: cancer-related analysis of variants toolkit
-
Douville C, Carter H, Kim R, Niknafs N, Diekhans M, Stenson PD, Cooper DN, Ryan M, Karchin R. 2013. CRAVAT: cancer-related analysis of variants toolkit. Bioinformatics 29:647-8.
-
(2013)
Bioinformatics
, vol.29
, pp. 647-648
-
-
Douville, C.1
Carter, H.2
Kim, R.3
Niknafs, N.4
Diekhans, M.5
Stenson, P.D.6
Cooper, D.N.7
Ryan, M.8
Karchin, R.9
-
11
-
-
79953715693
-
Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel
-
Gonzalez-Perez A, Lopez-Bigas N. 2011. Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel. Am J Hum Genet 88:440-9.
-
(2011)
Am J Hum Genet
, vol.88
, pp. 440-449
-
-
Gonzalez-Perez, A.1
Lopez-Bigas, N.2
-
12
-
-
80053371129
-
Non-neutral nonsynonymous single nucleotide polymorphisms in human ABC transporters: the first comparison of six prediction methods
-
Hao da C, Feng Y, Xiao R, Xiao PG. 2011. Non-neutral nonsynonymous single nucleotide polymorphisms in human ABC transporters: the first comparison of six prediction methods. Pharmacol Rep 63:924-34.
-
(2011)
Pharmacol Rep
, vol.63
, pp. 924-934
-
-
Hao da, C.1
Feng, Y.2
Xiao, R.3
Xiao, P.G.4
-
13
-
-
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 32:661-8.
-
(2011)
Hum Mutat
, vol.32
, pp. 661-668
-
-
Hicks, S.1
Wheeler, D.A.2
Plon, S.E.3
Kimmel, M.4
-
14
-
-
18444402182
-
The Ensembl genome database project
-
Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T and others. 2002. The Ensembl genome database project. Nucleic Acids Res 30:38-41.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 38-41
-
-
Hubbard, T.1
Barker, D.2
Birney, E.3
Cameron, G.4
Chen, Y.5
Clark, L.6
Cox, T.7
Cuff, J.8
Curwen, V.9
Down, T.10
-
15
-
-
0029965430
-
MITOMAP: a human mitochondrial genome database
-
Kogelnik AM, Lott MT, Brown MD, Navathe SB, Wallace DC. 1996. MITOMAP: a human mitochondrial genome database. Nucleic Acids Res 24:177-9.
-
(1996)
Nucleic Acids Res
, vol.24
, pp. 177-179
-
-
Kogelnik, A.M.1
Lott, M.T.2
Brown, M.D.3
Navathe, S.B.4
Wallace, D.C.5
-
16
-
-
84866111524
-
Evolutionary diagnosis method for variants in personal exomes
-
Kumar S, Sanderford M, Gray VE, Ye J, Liu L. 2012. Evolutionary diagnosis method for variants in personal exomes. Nat Methods 9:855-6.
-
(2012)
Nat Methods
, vol.9
, pp. 855-856
-
-
Kumar, S.1
Sanderford, M.2
Gray, V.E.3
Ye, J.4
Liu, L.5
-
17
-
-
70350671733
-
Automated inference of molecular mechanisms of disease from amino acid substitutions
-
Li B, Krishnan VG, Mort ME, Xin F, Kamati KK, Cooper DN, Mooney SD, Radivojac P. 2009. Automated inference of molecular mechanisms of disease from amino acid substitutions. Bioinformatics 25:2744-50.
-
(2009)
Bioinformatics
, vol.25
, pp. 2744-2750
-
-
Li, B.1
Krishnan, V.G.2
Mort, M.E.3
Xin, F.4
Kamati, K.K.5
Cooper, D.N.6
Mooney, S.D.7
Radivojac, P.8
-
18
-
-
79960763462
-
dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions
-
Liu X, Jian X, Boerwinkle E. 2011. dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions. Hum Mutat 32:894-9.
-
(2011)
Hum Mutat
, vol.32
, pp. 894-899
-
-
Liu, X.1
Jian, X.2
Boerwinkle, E.3
-
19
-
-
84855896680
-
A combined functional annotation score for non-synonymous variants
-
Lopes MC, Joyce C, Ritchie GR, John SL, Cunningham F, Asimit J, Zeggini E. 2012. A combined functional annotation score for non-synonymous variants. Hum Hered 73:47-51.
-
(2012)
Hum Hered
, vol.73
, pp. 47-51
-
-
Lopes, M.C.1
Joyce, C.2
Ritchie, G.R.3
John, S.L.4
Cunningham, F.5
Asimit, J.6
Zeggini, E.7
-
20
-
-
80052864956
-
In silico SNP analysis and bioinformatics tools: a review of the state of the art to aid drug discovery
-
Mah JT, Low ES, Lee E. 2011. In silico SNP analysis and bioinformatics tools: a review of the state of the art to aid drug discovery. Drug Discov Today 16:800-9.
-
(2011)
Drug Discov Today
, vol.16
, pp. 800-809
-
-
Mah, J.T.1
Low, E.S.2
Lee, E.3
-
21
-
-
50549201557
-
The Relation of Recombination to Mutational Advance
-
Muller HJ. 1964. The Relation of Recombination to Mutational Advance. Mutat Res 106:2-9.
-
(1964)
Mutat Res
, vol.106
, pp. 2-9
-
-
Muller, H.J.1
-
22
-
-
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 Acids Res 31:3812-4.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3812-3814
-
-
Ng, P.C.1
Henikoff, S.2
-
23
-
-
33144483078
-
Transitions to asexuality result in excess amino acid substitutions
-
Paland S, Lynch M. 2006. Transitions to asexuality result in excess amino acid substitutions. Science 311:990-2.
-
(2006)
Science
, vol.311
, pp. 990-992
-
-
Paland, S.1
Lynch, M.2
-
24
-
-
84861859734
-
The neglected genome
-
Pesole G, Allen JF, Lane N, Martin W, Rand DM, Schatz G, Saccone C. 2012. The neglected genome. EMBO Rep 13:473-4.
-
(2012)
EMBO Rep
, vol.13
, pp. 473-474
-
-
Pesole, G.1
Allen, J.F.2
Lane, N.3
Martin, W.4
Rand, D.M.5
Schatz, G.6
Saccone, C.7
-
25
-
-
0035108825
-
A novel method for estimating substitution rate variation among sites in a large dataset of homologous DNA sequences
-
Pesole G, Saccone C. 2001. A novel method for estimating substitution rate variation among sites in a large dataset of homologous DNA sequences. Genetics 157:859-65.
-
(2001)
Genetics
, vol.157
, pp. 859-865
-
-
Pesole, G.1
Saccone, C.2
-
27
-
-
34548082528
-
Accumulation of slightly deleterious mutations in mitochondrial protein-coding genes of large versus small mammals
-
Popadin K, Polishchuk LV, Mamirova L, Knorre D, Gunbin K. 2007. Accumulation of slightly deleterious mutations in mitochondrial protein-coding genes of large versus small mammals. Proc Natl Acad Sci U S A 104:13390-5.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 13390-13395
-
-
Popadin, K.1
Polishchuk, L.V.2
Mamirova, L.3
Knorre, D.4
Gunbin, K.5
-
28
-
-
80053189298
-
Predicting the functional impact of protein mutations: application to cancer genomics
-
Reva B, Antipin Y, Sander C. 2011. Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res 39:e118.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. e118
-
-
Reva, B.1
Antipin, Y.2
Sander, C.3
-
29
-
-
84862222737
-
HmtDB, a genomic resource for mitochondrion-based human variability studies
-
Rubino F, Piredda R, Calabrese FM, Simone D, Lang M, Calabrese C, Petruzzella V, Tommaseo-Ponzetta M, Gasparre G, Attimonelli M. 2012. HmtDB, a genomic resource for mitochondrion-based human variability studies. Nucleic Acids Res 40(Database issue):D1150-9.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.DATABASE ISSUE
, pp. D1150-D1159
-
-
Rubino, F.1
Piredda, R.2
Calabrese, F.M.3
Simone, D.4
Lang, M.5
Calabrese, C.6
Petruzzella, V.7
Tommaseo-Ponzetta, M.8
Gasparre, G.9
Attimonelli, M.10
-
31
-
-
77955151784
-
MutationTaster evaluates disease-causing potential of sequence alterations
-
Schwarz JM, Rodelsperger C, Schuelke M, Seelow D. 2010. MutationTaster evaluates disease-causing potential of sequence alterations. Nat Methods 7:575-6.
-
(2010)
Nat Methods
, vol.7
, pp. 575-576
-
-
Schwarz, J.M.1
Rodelsperger, C.2
Schuelke, M.3
Seelow, D.4
-
32
-
-
84871578629
-
Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models
-
Shihab HA, Gough J, Cooper DN, Stenson PD, Barker GL, Edwards KJ, Day IN, Gaunt TR. 2013. Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. Hum Mutat 34:57-65.
-
(2013)
Hum Mutat
, vol.34
, pp. 57-65
-
-
Shihab, H.A.1
Gough, J.2
Cooper, D.N.3
Stenson, P.D.4
Barker, G.L.5
Edwards, K.J.6
Day, I.N.7
Gaunt, T.R.8
-
33
-
-
38949091096
-
Strong purifying selection in transmission of mammalian mitochondrial DNA
-
Stewart JB, Freyer C, Elson JL, Wredenberg A, Cansu Z, Trifunovic A, Larsson NG. 2008. Strong purifying selection in transmission of mammalian mitochondrial DNA. PLoS Biol 6:e10.
-
(2008)
PLoS Biol
, vol.6
, pp. e10
-
-
Stewart, J.B.1
Freyer, C.2
Elson, J.L.3
Wredenberg, A.4
Cansu, Z.5
Trifunovic, A.6
Larsson, N.G.7
-
34
-
-
80052832184
-
Computational and statistical approaches to analyzing variants identified by exome sequencing
-
Stitziel NO, Kiezun A, Sunyaev S. 2011. Computational and statistical approaches to analyzing variants identified by exome sequencing. Genome Biol 12:227.
-
(2011)
Genome Biol
, vol.12
, pp. 227
-
-
Stitziel, N.O.1
Kiezun, A.2
Sunyaev, S.3
-
35
-
-
79952764520
-
Performance of mutation pathogenicity prediction methods on missense variants
-
Thusberg J, Olatubosun A, Vihinen M. 2011. Performance of mutation pathogenicity prediction methods on missense variants. Hum Mutat 32:358-68.
-
(2011)
Hum Mutat
, vol.32
, pp. 358-368
-
-
Thusberg, J.1
Olatubosun, A.2
Vihinen, M.3
-
37
-
-
84860833500
-
Reorganizing the protein space at the Universal Protein Resource (UniProt)
-
UniProt C. 2012. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 40(Database issue):D71-5.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.DATABASE ISSUE
, pp. D71-D75
-
-
UniProt, C.1
-
38
-
-
77953507107
-
Mitochondrial DNA mutations in disease and aging
-
Wallace DC. 2010. Mitochondrial DNA mutations in disease and aging. Environ Mol Mutagen 51:440-50.
-
(2010)
Environ Mol Mutagen
, vol.51
, pp. 440-450
-
-
Wallace, D.C.1
-
39
-
-
77953602809
-
Testing computational prediction of missense mutation phenotypes: functional characterization of 204 mutations of human cystathionine beta synthase
-
Wei Q, Wang L, Wang Q, Kruger WD, Dunbrack RL, Jr. 2010. Testing computational prediction of missense mutation phenotypes: functional characterization of 204 mutations of human cystathionine beta synthase. Proteins 78:2058-74.
-
(2010)
Proteins
, vol.78
, pp. 2058-2074
-
-
Wei, Q.1
Wang, L.2
Wang, Q.3
Kruger, W.D.4
Dunbrack, R.L.5
|