-
1
-
-
77958545304
-
Finding new genes for non-syndromic hearing loss through an in silico prioritization study
-
Accetturo, M., T. M. Creanza, C. Santoro, G. Tria, A. Giordano, S. Battagliero, A. Vaccina et al. 2010. Finding new genes for non-syndromic hearing loss through an in silico prioritization study. PLoS ONE 5:e12742.
-
(2010)
PLoS ONE
, vol.5
-
-
Accetturo, M.1
Creanza, T.M.2
Santoro, C.3
Tria, G.4
Giordano, A.5
Battagliero, S.6
Vaccina, A.7
-
2
-
-
77951640946
-
A method and server for predicting damaging missense mutations
-
Adzhubei, I. A., S. Schmidt, L. Peshkin, V. E. Ramensky, A. Gerasimova, P. Bork, A. S. Kondrashov et al. 2010. A method and server for predicting damaging missense mutations. Nature Methods 7:248-249.
-
(2010)
Nature 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
-
3
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25:3389-3402.
-
(1997)
Nucleic Acids Research
, 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
-
4
-
-
34547793042
-
Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites
-
Anisimova, M., and Z. H. Yang 2007. Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites. Molecular Biology and Evolution 24:1219-1228.
-
(2007)
Molecular Biology and Evolution
, vol.24
, pp. 1219-1228
-
-
Anisimova, M.1
Yang, Z.H.2
-
5
-
-
45549107624
-
UniPrime: a workflow-based platform for improved universal primer design
-
Bekaert, M., and E. C. Teeling 2008. UniPrime: a workflow-based platform for improved universal primer design. Nucleic Acids Research 36:e56.
-
(2008)
Nucleic Acids Research
, vol.36
-
-
Bekaert, M.1
Teeling, E.C.2
-
6
-
-
13944260197
-
Myosin-XVa is required for tip localization of whirlin and differential elongation of hair-cell stereocilia
-
Belyantseva, I. A., E. T. Boger, S. Naz, G. I. Frolenkov, J. R. Sellers, Z. M. Ahmed, A. J. Griffith et al. 2005. Myosin-XVa is required for tip localization of whirlin and differential elongation of hair-cell stereocilia. Nature Cell Biology 7:148-156.
-
(2005)
Nature Cell Biology
, vol.7
, pp. 148-156
-
-
Belyantseva, I.A.1
Boger, E.T.2
Naz, S.3
Frolenkov, G.I.4
Sellers, J.R.5
Ahmed, Z.M.6
Griffith, A.J.7
-
8
-
-
40849106619
-
Quiet as a mouse: dissecting the molecular and genetic basis of hearing
-
Brown, S. D. M., R. E. Hardisty-Hughes, and P. Mburu 2008. Quiet as a mouse: dissecting the molecular and genetic basis of hearing. Nature Reviews Genetics 9:277-290.
-
(2008)
Nature Reviews Genetics
, vol.9
, pp. 277-290
-
-
Brown, S.D.M.1
Hardisty-Hughes, R.E.2
Mburu, P.3
-
9
-
-
33644660937
-
Natural selection and mammalian BRCA1 sequences: elucidating functionally important sites relevant to breast cancer susceptibility in humans
-
Burk-Herrick, A., M. Scally, H. Amrine-Madsen, M. J. Stanhope, and M. S. Springer 2006. Natural selection and mammalian BRCA1 sequences: elucidating functionally important sites relevant to breast cancer susceptibility in humans. Mammalian Genome 17:257-270.
-
(2006)
Mammalian Genome
, vol.17
, pp. 257-270
-
-
Burk-Herrick, A.1
Scally, M.2
Amrine-Madsen, H.3
Stanhope, M.J.4
Springer, M.S.5
-
10
-
-
80051968181
-
Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data
-
Cooper, G. M., and J. Shendure 2011. Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nature Reviews Genetics 12:628-640.
-
(2011)
Nature Reviews Genetics
, vol.12
, pp. 628-640
-
-
Cooper, G.M.1
Shendure, J.2
-
11
-
-
84859934504
-
Parallel signatures of sequence evolution among hearing genes in echolocating mammals: an emerging model of genetic convergence
-
Davies, K. T., J. A. Cotton, J. D. Kirwan, E. C. Teeling, and S. J. Rossiter 2011. Parallel signatures of sequence evolution among hearing genes in echolocating mammals: an emerging model of genetic convergence. Heredity (Edinb) 108:480-489.
-
(2011)
Heredity (Edinb)
, vol.108
, pp. 480-489
-
-
Davies, K.T.1
Cotton, J.A.2
Kirwan, J.D.3
Teeling, E.C.4
Rossiter, S.J.5
-
12
-
-
13544251711
-
Myosin XVa and whirlin, two deafness gene products required for hair bundle growth, are located at the stereocilia tips and interact directly
-
Delprat, B., V. Michel, R. Goodyear, Y. Yamasaki, N. Michalski, A. El-Amraoui, I. Perfettini et al. 2005. Myosin XVa and whirlin, two deafness gene products required for hair bundle growth, are located at the stereocilia tips and interact directly. Human Molecular Genetics 14:401-410.
-
(2005)
Human Molecular Genetics
, vol.14
, pp. 401-410
-
-
Delprat, B.1
Michel, V.2
Goodyear, R.3
Yamasaki, Y.4
Michalski, N.5
El-Amraoui, A.6
Perfettini, I.7
-
13
-
-
77957911916
-
Hearing impairment: a panoply of genes and functions
-
Dror, A. A., and K. B. Avraham 2010. Hearing impairment: a panoply of genes and functions. Neuron 68:293-308.
-
(2010)
Neuron
, vol.68
, pp. 293-308
-
-
Dror, A.A.1
Avraham, K.B.2
-
14
-
-
84864616473
-
Human genomic disease variants: a neutral evolutionary explanation
-
Dudley, J. T., Y. Kim, L. Liu, G. J. Markov, K. Gerold, R. Chen, A. J. Butte et al. 2012. Human genomic disease variants: a neutral evolutionary explanation. Genome Research 22:1383-1394.
-
(2012)
Genome Research
, vol.22
, pp. 1383-1394
-
-
Dudley, J.T.1
Kim, Y.2
Liu, L.3
Markov, G.J.4
Gerold, K.5
Chen, R.6
Butte, A.J.7
-
16
-
-
71049176982
-
Genome 10K: a proposal to obtain whole-genome sequence for 10 000 vertebrate species
-
Genome 10K Community of Scientists
-
Genome 10K Community of Scientists 2009. Genome 10K: a proposal to obtain whole-genome sequence for 10 000 vertebrate species. Journal of Heredity 100:659-674.
-
(2009)
Journal of Heredity
, vol.100
, pp. 659-674
-
-
-
18
-
-
58149185123
-
Ensembl 2009
-
Hubbard, T. J. P., B. L. Aken, S. Ayling, B. Ballester, K. Beal, E. Bragin, S. Brent et al. 2009. Ensembl 2009. Nucleic Acids Research 37:D690-D697.
-
(2009)
Nucleic Acids Research
, vol.37
-
-
Hubbard, T.J.P.1
Aken, B.L.2
Ayling, S.3
Ballester, B.4
Beal, K.5
Bragin, E.6
Brent, S.7
-
19
-
-
45949109669
-
MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences
-
Kumar, S., M. Nei, J. Dudley, and K. Tamura 2008. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics 9:299-306.
-
(2008)
Briefings in Bioinformatics
, vol.9
, pp. 299-306
-
-
Kumar, S.1
Nei, M.2
Dudley, J.3
Tamura, K.4
-
20
-
-
68149165614
-
Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm
-
Kumar, P., S. Henikoff, and P. C. Ng 2009. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nature Protocols 4:1073-1082.
-
(2009)
Nature Protocols
, vol.4
, pp. 1073-1082
-
-
Kumar, P.1
Henikoff, S.2
Ng, P.C.3
-
21
-
-
84856088973
-
Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations
-
Kumar, S., J. T. Dudley, A. Filipski, and L. Liu 2011. Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations. Trends in Genetics 27:377-386.
-
(2011)
Trends in Genetics
, vol.27
, pp. 377-386
-
-
Kumar, S.1
Dudley, J.T.2
Filipski, A.3
Liu, L.4
-
22
-
-
84866111524
-
Evolutionary diagnosis method for variants in personal exomes
-
Kumar, S., M. Sanderford, V. E. Gray, J. P. Ye, and L. Liu 2012. Evolutionary diagnosis method for variants in personal exomes. Nature Methods 9:855-856.
-
(2012)
Nature Methods
, vol.9
, pp. 855-856
-
-
Kumar, S.1
Sanderford, M.2
Gray, V.E.3
Ye, J.P.4
Liu, L.5
-
23
-
-
36448991500
-
Clustal W and Clustal X version 2.0
-
Larkin, M. A., G. Blackshields, N. P. Brown, R. Chenna, P. A. McGettigan, H. McWilliam, F. Valentin et al. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948.
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
Blackshields, G.2
Brown, N.P.3
Chenna, R.4
McGettigan, P.A.5
McWilliam, H.6
Valentin, F.7
-
24
-
-
80055117714
-
Hereditary hearing loss: from human mutation to mechanism
-
Lenz, D. R., and K. B. Avraham 2011. Hereditary hearing loss: from human mutation to mechanism. Hearing Research 281:3-10.
-
(2011)
Hearing Research
, vol.281
, pp. 3-10
-
-
Lenz, D.R.1
Avraham, K.B.2
-
25
-
-
52949138684
-
The hearing gene Prestin reunites echolocating bats
-
Li, G., J. Wang, S. J. Rossiter, G. Jones, J. A. Cotton, and S. Zhang 2008. The hearing gene Prestin reunites echolocating bats. Proceedings of the National Academy of Sciences of the United States of America 105:13959-13964.
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, pp. 13959-13964
-
-
Li, G.1
Wang, J.2
Rossiter, S.J.3
Jones, G.4
Cotton, J.A.5
Zhang, S.6
-
26
-
-
74549195621
-
The hearing gene Prestin unites echolocating bats and whales
-
Li, Y., Z. Liu, P. Shi, and J. Zhang . 2010. The hearing gene Prestin unites echolocating bats and whales. Current Biology 20:R55-R56.
-
(2010)
Current Biology
, vol.20
-
-
Li, Y.1
Liu, Z.2
Shi, P.3
Zhang, J.4
-
27
-
-
74549224446
-
Convergent sequence evolution between echolocating bats and dolphins
-
Liu, Y., J. A. Cotton, B. Shen, X. Han, S. J. Rossiter, and S. Zhang . 2010a. Convergent sequence evolution between echolocating bats and dolphins. Current Biology 20:R53-R54.
-
(2010)
Current Biology
, vol.20
-
-
Liu, Y.1
Cotton, J.A.2
Shen, B.3
Han, X.4
Rossiter, S.J.5
Zhang, S.6
-
28
-
-
78049285239
-
Cetaceans on a molecular fast track to ultrasonic hearing
-
Liu, Y., S. J. Rossiter, X. Han, J. A. Cotton, and S. Zhang . 2010b. Cetaceans on a molecular fast track to ultrasonic hearing. Current Biology 20:1834-1839.
-
(2010)
Current Biology
, vol.20
, pp. 1834-1839
-
-
Liu, Y.1
Rossiter, S.J.2
Han, X.3
Cotton, J.A.4
Zhang, S.5
-
29
-
-
80055044024
-
Parallel evolution of KCNQ4 in echolocating bats
-
Liu, Z., S. Li, W. Wang, D. Xu, R. W. Murphy, and P. Shi 2011. Parallel evolution of KCNQ4 in echolocating bats. PLoS ONE 6:e26618.
-
(2011)
PLoS ONE
, vol.6
-
-
Liu, Z.1
Li, S.2
Wang, W.3
Xu, D.4
Murphy, R.W.5
Shi, P.6
-
30
-
-
84862865765
-
The voltage-gated potassium channel subfamily KQT member 4 (KCNQ4) displays parallel evolution in echolocating bats
-
Liu, Y., N. Han, L. F. Franchini, H. Xu, F. Pisciottano, A. B. Elgoyhen, K. E. Rajan et al. 2012. The voltage-gated potassium channel subfamily KQT member 4 (KCNQ4) displays parallel evolution in echolocating bats. Molecular Biology and Evolution 29:1441-1450.
-
(2012)
Molecular Biology and Evolution
, vol.29
, pp. 1441-1450
-
-
Liu, Y.1
Han, N.2
Franchini, L.F.3
Xu, H.4
Pisciottano, F.5
Elgoyhen, A.B.6
Rajan, K.E.7
-
31
-
-
0003903482
-
-
2nd ed. Oxford: Oxford University Press, England, UK.
-
MacDonald, D. 2009. The Encyclopedia of Mammals, 2nd ed. Oxford: Oxford University Press, England, UK.
-
(2009)
The Encyclopedia of Mammals
-
-
MacDonald, D.1
-
32
-
-
79960976768
-
UniProt Knowledgebase: a hub of integrated protein data
-
bar009
-
Magrane, M., and U. Consortium 2011. UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford) 2011:bar009.
-
(2011)
Database (Oxford)
, vol.2011
-
-
Magrane, M.1
Consortium, U.2
-
33
-
-
80055070300
-
Impacts of the cretaceous terrestrial revolution and KPg extinction on mammal diversification
-
Meredith, R. W., J. E. Janecka, J. Gatesy, O. A. Ryder, C. A. Fisher, E. C. Teeling, A. Goodbla et al. 2011. Impacts of the cretaceous terrestrial revolution and KPg extinction on mammal diversification. Science 334:521-524.
-
(2011)
Science
, vol.334
, pp. 521-524
-
-
Meredith, R.W.1
Janecka, J.E.2
Gatesy, J.3
Ryder, O.A.4
Fisher, C.A.5
Teeling, E.C.6
Goodbla, A.7
-
34
-
-
84864605220
-
Detecting individual sites subject to episodic diversifying selection
-
Murrell, B., J. O. Wertheim, S. Moola, T. Weighill, K. Scheffler, and S.L.K. Pond 2012. Detecting individual sites subject to episodic diversifying selection. PLoS Genetics 8:e1002764.
-
(2012)
PLoS Genetics
, vol.8
-
-
Murrell, B.1
Wertheim, J.O.2
Moola, S.3
Weighill, T.4
Scheffler, K.5
Pond, S.L.K.6
-
35
-
-
34948880109
-
Mutational spectrum of MYO15A: the large N-terminal extension of myosin XVA is required for hearing
-
Nal, N., Z. M. Ahmed, E. Erkal, O. M. Alper, G. Luleci, O. Dinc, A. M. Waryah et al. 2007. Mutational spectrum of MYO15A: the large N-terminal extension of myosin XVA is required for hearing. Human Mutation 28:1014-1019.
-
(2007)
Human Mutation
, vol.28
, pp. 1014-1019
-
-
Nal, N.1
Ahmed, Z.M.2
Erkal, E.3
Alper, O.M.4
Luleci, G.5
Dinc, O.6
Waryah, A.M.7
-
37
-
-
80053189298
-
Predicting the functional impact of protein mutations: application to cancer genomics
-
Reva, B., Y. Antipin, and C. Sander 2011. Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Research 39:e118.
-
(2011)
Nucleic Acids Research
, vol.39
-
-
Reva, B.1
Antipin, Y.2
Sander, C.3
-
38
-
-
0033990048
-
Primer3 on the WWW for general users and for biologist programmers
-
Rozen, S., and H. Skaletsky 2000. Primer3 on the WWW for general users and for biologist programmers. Methods in Molecular Biology 132:365-386.
-
(2000)
Methods in Molecular Biology
, vol.132
, pp. 365-386
-
-
Rozen, S.1
Skaletsky, H.2
-
39
-
-
84864063616
-
Parallel evolution of auditory genes for echolocation in bats and toothed whales
-
Shen, Y. Y., L. Liang, G. S. Li, R. W. Murphy, and Y. P. Zhang 2012. Parallel evolution of auditory genes for echolocation in bats and toothed whales. PLoS Genetics 8:e1002788.
-
(2012)
PLoS Genetics
, vol.8
-
-
Shen, Y.Y.1
Liang, L.2
Li, G.S.3
Murphy, R.W.4
Zhang, Y.P.5
-
40
-
-
0033951215
-
Targeted disruption of otog results in deafness and severe imbalance
-
Simmler, M. C., M. Cohen-Salmon, A. El-Amraoui, L. Guillaud, J. C. Benichou, C. Petit, and J. J. Panthier 2000. Targeted disruption of otog results in deafness and severe imbalance. Nature Genetics 24:139-143.
-
(2000)
Nature Genetics
, vol.24
, pp. 139-143
-
-
Simmler, M.C.1
Cohen-Salmon, M.2
El-Amraoui, A.3
Guillaud, L.4
Benichou, J.C.5
Petit, C.6
Panthier, J.J.7
-
41
-
-
33750403801
-
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
Stamatakis, A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
-
(2006)
Bioinformatics
, vol.22
, pp. 2688-2690
-
-
Stamatakis, A.1
-
42
-
-
50249100595
-
A rapid bootstrap algorithm for the RAxML Web servers
-
Stamatakis, A., P. Hoover, and J. Rougemont 2008. A rapid bootstrap algorithm for the RAxML Web servers. Systematic Biology 57:758-771.
-
(2008)
Systematic Biology
, vol.57
, pp. 758-771
-
-
Stamatakis, A.1
Hoover, P.2
Rougemont, J.3
-
43
-
-
0033983669
-
A take on the tectorial membrane
-
Steel, K. P. 2000. A take on the tectorial membrane. Nature Genetics 24:104.
-
(2000)
Nature Genetics
, vol.24
, pp. 104
-
-
Steel, K.P.1
-
45
-
-
12844251802
-
A molecular phylogeny for bats illuminates biogeography and the fossil record
-
Teeling, E. C., M. S. Springer, O. Madsen, P. Bates, S. J. O'Brien, and W. J. Murphy 2005. A molecular phylogeny for bats illuminates biogeography and the fossil record. Science 307:580-584.
-
(2005)
Science
, vol.307
, pp. 580-584
-
-
Teeling, E.C.1
Springer, M.S.2
Madsen, O.3
Bates, P.4
O'Brien, S.J.5
Murphy, W.J.6
-
46
-
-
67649388061
-
Hear, hear: the convergent evolution of echolocation in bats?
-
Teeling, E. C. 2009. Hear, hear: the convergent evolution of echolocation in bats? Trends in Ecology s; Evolution 24:351-354.
-
(2009)
Trends in Ecology & Evolution
, vol.24
, pp. 351-354
-
-
Teeling, E.C.1
-
47
-
-
84866080200
-
Phylogenies, fossils and functional genes: The evolution of echolocation in bats
-
G. F. Gunnell, and N. B. Simmons, eds. -, Cambridge University Press, Cambridge.
-
Teeling, E. C., S. Dool, and M. S. Springer . 2012. Phylogenies, fossils and functional genes: The evolution of echolocation in bats. In G. F. Gunnell, and N. B. Simmons, eds. Evolutionary History of Bats: Fossils, Molecules, and Morphology, pp. 1-21, Cambridge University Press, Cambridge.
-
(2012)
Evolutionary History of Bats: Fossils, Molecules, and Morphology
, pp. 1-21
-
-
Teeling, E.C.1
Dool, S.2
Springer, M.S.3
-
48
-
-
77954161995
-
Genetics and pathological mechanisms of Usher syndrome
-
Yan, D., and X. Z. Liu 2010. Genetics and pathological mechanisms of Usher syndrome. Journal of Human Genetics 55:327-335.
-
(2010)
Journal of Human Genetics
, vol.55
, pp. 327-335
-
-
Yan, D.1
Liu, X.Z.2
-
49
-
-
0031897964
-
Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution
-
Yang, Z. H. 1998. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Molecular Biology and Evolution 15:568-573.
-
(1998)
Molecular Biology and Evolution
, vol.15
, pp. 568-573
-
-
Yang, Z.H.1
-
50
-
-
34547803197
-
PAML 4: phylogenetic analysis by maximum likelihood
-
Yang, Z. H. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution 24:1586-1591.
-
(2007)
Molecular Biology and Evolution
, vol.24
, pp. 1586-1591
-
-
Yang, Z.H.1
-
51
-
-
16344378246
-
Bayes empirical Bayes inference of amino acid sites under positive selection
-
Yang, Z. H., W. S. W. Wong, and R. Nielsen 2005. Bayes empirical Bayes inference of amino acid sites under positive selection. Molecular Biology and Evolution 22:1107-1118.
-
(2005)
Molecular Biology and Evolution
, vol.22
, pp. 1107-1118
-
-
Yang, Z.H.1
Wong, W.S.W.2
Nielsen, R.3
-
52
-
-
27844439855
-
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
-
Zhang, J. Z., R. Nielsen, and Z. H. Yang 2005. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Molecular Biology and Evolution 22:2472-2479.
-
(2005)
Molecular Biology and Evolution
, vol.22
, pp. 2472-2479
-
-
Zhang, J.Z.1
Nielsen, R.2
Yang, Z.H.3
|