-
1
-
-
23944490117
-
Missense meanderings in sequence space: a biophysical view of protein evolution
-
DePristo MA, Weinreich DM, Hartl DL, Missense meanderings in sequence space: a biophysical view of protein evolution. Nat Rev Genet. 2005;6(9):678–87. 16074985
-
(2005)
Nat Rev Genet
, vol.6
, Issue.9
, pp. 678-687
-
-
DePristo, M.A.1
Weinreich, D.M.2
Hartl, D.L.3
-
2
-
-
77953718211
-
Sequence space and the ongoing expansion of the protein universe
-
Povolotskaya IS, Kondrashov FA, Sequence space and the ongoing expansion of the protein universe. Nature. 2010;465(7300):922–6. doi: 10.1038/nature09105 20485343
-
(2010)
Nature
, vol.465
, Issue.7300
, pp. 922-926
-
-
Povolotskaya, I.S.1
Kondrashov, F.A.2
-
3
-
-
25144523127
-
Loss of protein structure stability as a major causative factor in monogenic disease
-
Yue P, Li Z, Moult J, Loss of protein structure stability as a major causative factor in monogenic disease. J Mol Biol. 2005;353(2):459–73. 16169011
-
(2005)
J Mol Biol
, vol.353
, Issue.2
, pp. 459-473
-
-
Yue, P.1
Li, Z.2
Moult, J.3
-
4
-
-
77951640946
-
A method and server for predicting damaging missense mutations
-
Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, et al. A method and server for predicting damaging missense mutations. Nat Methods. 2010;7(4):248–9. doi: 10.1038/nmeth0410-248 20354512
-
(2010)
Nat Methods
, vol.7
, Issue.4
, pp. 248-249
-
-
Adzhubei, I.A.1
Schmidt, S.2
Peshkin, L.3
Ramensky, V.E.4
Gerasimova, A.5
Bork, P.6
-
5
-
-
80051968181
-
Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data
-
Cooper GM, Shendure J, Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat Rev Genet. 2011;12(9):628–40. doi: 10.1038/nrg3046 21850043
-
(2011)
Nat Rev Genet
, vol.12
, Issue.9
, pp. 628-640
-
-
Cooper, G.M.1
Shendure, J.2
-
6
-
-
84874527653
-
Prediction of deleterious nonsynonymous single-nucleotide polymorphism for human diseases
-
Wu J, Jiang R, Prediction of deleterious nonsynonymous single-nucleotide polymorphism for human diseases. ScientificWorldJournal. 2013;2013:675851. doi: 10.1155/2013/675851 23431257
-
(2013)
ScientificWorldJournal
, vol.2013
, pp. 675851
-
-
Wu, J.1
Jiang, R.2
-
7
-
-
84872474093
-
Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes
-
Studer RA, Dessailly BH, Orengo CA, Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes. Biochem J. 2013;449(3):581–94. doi: 10.1042/BJ20121221 23301657
-
(2013)
Biochem J
, vol.449
, Issue.3
, pp. 581-594
-
-
Studer, R.A.1
Dessailly, B.H.2
Orengo, C.A.3
-
8
-
-
84886247811
-
Assessment of computational methods for predicting the effects of missense mutations in human cancers
-
Gnad F, Baucom A, Mukhyala K, Manning G, Zhang Z, Assessment of computational methods for predicting the effects of missense mutations in human cancers. BMC Genomics. 2013;14 Suppl 3:S7. doi: 10.1186/1471-2164-14-S3-S7 23819521
-
(2013)
BMC Genomics
, vol.14
, pp. 7
-
-
Gnad, F.1
Baucom, A.2
Mukhyala, K.3
Manning, G.4
Zhang, Z.5
-
9
-
-
84896698938
-
PredictSNP: robust and accurate consensus classifier for prediction of disease-related mutations
-
Bendl J, Stourac J, Salanda O, Pavelka A, Wieben ED, Zendulka J, et al. PredictSNP: robust and accurate consensus classifier for prediction of disease-related mutations. PLoS Comput Biol. 2014;10(1):e1003440. doi: 10.1371/journal.pcbi.1003440 24453961
-
(2014)
PLoS Comput Biol
, vol.10
, Issue.1
-
-
Bendl, J.1
Stourac, J.2
Salanda, O.3
Pavelka, A.4
Wieben, E.D.5
Zendulka, J.6
-
10
-
-
84870900036
-
Deleterious- and disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing
-
Xue Y, Chen Y, Ayub Q, Huang N, Ball EV, Mort M, et al. Deleterious- and disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing. Am J Hum Genet. 2012;91(6):1022–32. doi: 10.1016/j.ajhg.2012.10.015 23217326
-
(2012)
Am J Hum Genet
, vol.91
, Issue.6
, pp. 1022-1032
-
-
Xue, Y.1
Chen, Y.2
Ayub, Q.3
Huang, N.4
Ball, E.V.5
Mort, M.6
-
11
-
-
80052825195
-
The functional spectrum of low-frequency coding variation
-
Marth GT, Yu F, Indap AR, Garimella K, Gravel S, Leong WF, et al. The functional spectrum of low-frequency coding variation. Genome Biol. 2011;12(9):R84. doi: 10.1186/gb-2011-12-9-r84 21917140
-
(2011)
Genome Biol
, vol.12
, Issue.9
, pp. 84
-
-
Marth, G.T.1
Yu, F.2
Indap, A.R.3
Garimella, K.4
Gravel, S.5
Leong, W.F.6
-
12
-
-
84874189972
-
Genotype to phenotype: lessons from model organisms for human genetics
-
Lehner B, Genotype to phenotype: lessons from model organisms for human genetics. Nat Rev Genet. 2013;14(3):168–78. doi: 10.1038/nrg3404 23358379
-
(2013)
Nat Rev Genet
, vol.14
, Issue.3
, pp. 168-178
-
-
Lehner, B.1
-
13
-
-
84865064881
-
Performance of computational tools in evaluating the functional impact of laboratory-induced amino acid mutations
-
Gray VE, Kukurba KR, Kumar S, Performance of computational tools in evaluating the functional impact of laboratory-induced amino acid mutations. Bioinformatics. 2012;28(16):2093–6. doi: 10.1093/bioinformatics/bts336 22685075
-
(2012)
Bioinformatics
, vol.28
, Issue.16
, pp. 2093-2096
-
-
Gray, V.E.1
Kukurba, K.R.2
Kumar, S.3
-
14
-
-
84880956874
-
Predicting phenotypic variation from genotypes, phenotypes and a combination of the two
-
Burga A, Lehner B, Predicting phenotypic variation from genotypes, phenotypes and a combination of the two. Curr Opin Biotechnol. 2013;24(4):803–9. doi: 10.1016/j.copbio.2013.03.004 23540420
-
(2013)
Curr Opin Biotechnol
, vol.24
, Issue.4
, pp. 803-809
-
-
Burga, A.1
Lehner, B.2
-
15
-
-
85047688149
-
News from the protein mutability landscape
-
Hecht M, Bromberg Y, Rost B, News from the protein mutability landscape. J Mol Biol. 2013;425(21):3937–48. doi: 10.1016/j.jmb.2013.07.028 23896297
-
(2013)
J Mol Biol
, vol.425
, Issue.21
, pp. 3937-3948
-
-
Hecht, M.1
Bromberg, Y.2
Rost, B.3
-
16
-
-
84905217368
-
Deep mutational scanning: a new style of protein science
-
Fowler DM, Fields S, Deep mutational scanning: a new style of protein science. Nat Methods. 2014;11(8):801–7. doi: 10.1038/nmeth.3027 25075907
-
(2014)
Nat Methods
, vol.11
, Issue.8
, pp. 801-807
-
-
Fowler, D.M.1
Fields, S.2
-
17
-
-
84866073112
-
Prediction of mutational tolerance in HIV-1 protease and reverse transcriptase using flexible backbone protein design
-
Humphris-Narayanan E, Akiva E, Varela R, S OC, Kortemme T, Prediction of mutational tolerance in HIV-1 protease and reverse transcriptase using flexible backbone protein design. PLoS Comput Biol. 2012;8(8):e1002639. doi: 10.1371/journal.pcbi.1002639 22927804
-
(2012)
PLoS Comput Biol
, vol.8
, Issue.8
-
-
Humphris-Narayanan, E.1
Akiva, E.2
Varela, R.3
S, O.C.4
Kortemme, T.5
-
18
-
-
0024406911
-
3rd. Complete mutagenesis of the HIV-1 protease
-
Loeb DD, Swanstrom R, Everitt L, Manchester M, Stamper SE, Hutchison CA, 3rd. Complete mutagenesis of the HIV-1 protease. Nature. 1989;340(6232):397–400. 2666861
-
(1989)
Nature
, vol.340
, Issue.6232
, pp. 397-400
-
-
Loeb, D.D.1
Swanstrom, R.2
Everitt, L.3
Manchester, M.4
Stamper, S.E.5
Hutchison, C.A.6
-
19
-
-
0025955349
-
Systematic mutation of bacteriophage T4 lysozyme
-
Rennell D, Bouvier SE, Hardy LW, Poteete AR, Systematic mutation of bacteriophage T4 lysozyme. J Mol Biol. 1991;222(1):67–88. 1942069
-
(1991)
J Mol Biol
, vol.222
, Issue.1
, pp. 67-88
-
-
Rennell, D.1
Bouvier, S.E.2
Hardy, L.W.3
Poteete, A.R.4
-
20
-
-
2342519701
-
Genetic studies of the Lac repressor. XV: 4000 single amino acid substitutions and analysis of the resulting phenotypes on the basis of the protein structure
-
Suckow J, Markiewicz P, Kleina LG, Miller J, Kisters-Woike B, Muller-Hill B, Genetic studies of the Lac repressor. XV: 4000 single amino acid substitutions and analysis of the resulting phenotypes on the basis of the protein structure. J Mol Biol. 1996;261(4):509–23. 8794873
-
(1996)
J Mol Biol
, vol.261
, Issue.4
, pp. 509-523
-
-
Suckow, J.1
Markiewicz, P.2
Kleina, L.G.3
Miller, J.4
Kisters-Woike, B.5
Muller-Hill, B.6
-
21
-
-
0029962946
-
Amino acid sequence determinants of beta-lactamase structure and activity
-
Huang W, Petrosino J, Hirsch M, Shenkin PS, Palzkill T, Amino acid sequence determinants of beta-lactamase structure and activity. J Mol Biol. 1996;258(4):688–703. 8637002
-
(1996)
J Mol Biol
, vol.258
, Issue.4
, pp. 688-703
-
-
Huang, W.1
Petrosino, J.2
Hirsch, M.3
Shenkin, P.S.4
Palzkill, T.5
-
22
-
-
3042681604
-
Protein tolerance to random amino acid change
-
Guo HH, Choe J, Loeb LA, Protein tolerance to random amino acid change. Proc Natl Acad Sci U S A. 2004;101(25):9205–10. 15197260
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, Issue.25
, pp. 9205-9210
-
-
Guo, H.H.1
Choe, J.2
Loeb, L.A.3
-
23
-
-
77956338533
-
High-resolution mapping of protein sequence-function relationships
-
Fowler DM, Araya CL, Fleishman SJ, Kellogg EH, Stephany JJ, Baker D, et al. High-resolution mapping of protein sequence-function relationships. Nat Methods. 2010;7(9):741–6. doi: 10.1038/nmeth.1492 20711194
-
(2010)
Nat Methods
, vol.7
, Issue.9
, pp. 741-746
-
-
Fowler, D.M.1
Araya, C.L.2
Fleishman, S.J.3
Kellogg, E.H.4
Stephany, J.J.5
Baker, D.6
-
24
-
-
77956544553
-
Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing
-
Ernst A, Gfeller D, Kan Z, Seshagiri S, Kim PM, Bader GD, et al. Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing. Mol Biosyst. 2010;6(10):1782–90. doi: 10.1039/c0mb00061b 20714644
-
(2010)
Mol Biosyst
, vol.6
, Issue.10
, pp. 1782-1790
-
-
Ernst, A.1
Gfeller, D.2
Kan, Z.3
Seshagiri, S.4
Kim, P.M.5
Bader, G.D.6
-
25
-
-
79956357160
-
Experimental illumination of a fitness landscape
-
Hietpas RT, Jensen JD, Bolon DN, Experimental illumination of a fitness landscape. Proc Natl Acad Sci U S A. 2011;108(19):7896–901. doi: 10.1073/pnas.1016024108 21464309
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, Issue.19
, pp. 7896-7901
-
-
Hietpas, R.T.1
Jensen, J.D.2
Bolon, D.N.3
-
26
-
-
84868365613
-
The spatial architecture of protein function and adaptation
-
McLaughlin RN, Jr.Poelwijk FJ, Raman A, Gosal WS, Ranganathan R, The spatial architecture of protein function and adaptation. Nature. 2012;491(7422):138–42. doi: 10.1038/nature11500 23041932
-
(2012)
Nature
, vol.491
, Issue.7422
, pp. 138-142
-
-
McLaughlin, R.N.1
Poelwijk, F.J.2
Raman, A.3
Gosal, W.S.4
Ranganathan, R.5
-
27
-
-
84869080668
-
Deep Sequencing of Systematic Combinatorial Libraries Reveals beta-Lactamase Sequence Constraints at High Resolution
-
Deng Z, Huang W, Bakkalbasi E, Brown NG, Adamski CJ, Rice K, et al. Deep Sequencing of Systematic Combinatorial Libraries Reveals beta-Lactamase Sequence Constraints at High Resolution. J Mol Biol. 2012.
-
(2012)
J Mol Biol
-
-
Deng, Z.1
Huang, W.2
Bakkalbasi, E.3
Brown, N.G.4
Adamski, C.J.5
Rice, K.6
-
28
-
-
84862546176
-
Critical features for biosynthesis, stability, and functionality of a G protein-coupled receptor uncovered by all-versus-all mutations
-
Schlinkmann KM, Honegger A, Tureci E, Robison KE, Lipovsek D, Pluckthun A, Critical features for biosynthesis, stability, and functionality of a G protein-coupled receptor uncovered by all-versus-all mutations. Proc Natl Acad Sci U S A. 2012;109(25):9810–5. doi: 10.1073/pnas.1202107109 22665811
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, Issue.25
, pp. 9810-9815
-
-
Schlinkmann, K.M.1
Honegger, A.2
Tureci, E.3
Robison, K.E.4
Lipovsek, D.5
Pluckthun, A.6
-
29
-
-
84856702590
-
Protein model discrimination using mutational sensitivity derived from deep sequencing
-
Adkar BV, Tripathi A, Sahoo A, Bajaj K, Goswami D, Chakrabarti P, et al. Protein model discrimination using mutational sensitivity derived from deep sequencing. Structure. 2012;20(2):371–81. doi: 10.1016/j.str.2011.11.021 22325784
-
(2012)
Structure
, vol.20
, Issue.2
, pp. 371-381
-
-
Adkar, B.V.1
Tripathi, A.2
Sahoo, A.3
Bajaj, K.4
Goswami, D.5
Chakrabarti, P.6
-
30
-
-
84867069553
-
Construction of a stability landscape of the CH3 domain of human IgG1 by combining directed evolution with high throughput sequencing
-
Traxlmayr MW, Hasenhindl C, Hackl M, Stadlmayr G, Rybka JD, Borth N, et al. Construction of a stability landscape of the CH3 domain of human IgG1 by combining directed evolution with high throughput sequencing. J Mol Biol. 2012;423(3):397–412. doi: 10.1016/j.jmb.2012.07.017 22846908
-
(2012)
J Mol Biol
, vol.423
, Issue.3
, pp. 397-412
-
-
Traxlmayr, M.W.1
Hasenhindl, C.2
Hackl, M.3
Stadlmayr, G.4
Rybka, J.D.5
Borth, N.6
-
31
-
-
84867644046
-
A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function
-
Araya CL, Fowler DM, Chen W, Muniez I, Kelly JW, Fields S, A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function. Proc Natl Acad Sci U S A. 2012;109(42):16858–63. doi: 10.1073/pnas.1209751109 23035249
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, Issue.42
, pp. 16858-16863
-
-
Araya, C.L.1
Fowler, D.M.2
Chen, W.3
Muniez, I.4
Kelly, J.W.5
Fields, S.6
-
32
-
-
84871965903
-
Systematic identification of H274Y compensatory mutations in influenza A virus neuraminidase by high-throughput screening
-
Wu NC, Young AP, Dandekar S, Wijersuriya H, Al-Mawsawi LQ, Wu TT, et al. Systematic identification of H274Y compensatory mutations in influenza A virus neuraminidase by high-throughput screening. J Virol. 2013;87(2):1193–9. doi: 10.1128/JVI.01658-12 23152521
-
(2013)
J Virol
, vol.87
, Issue.2
, pp. 1193-1199
-
-
Wu, N.C.1
Young, A.P.2
Dandekar, S.3
Wijersuriya, H.4
Al-Mawsawi, L.Q.5
Wu, T.T.6
-
33
-
-
84886037483
-
Deep mutational scanning of an RRM domain of the Saccharomyces cerevisiae poly(A)-binding protein
-
Melamed D, Young DL, Gamble CE, Miller CR, Fields S, Deep mutational scanning of an RRM domain of the Saccharomyces cerevisiae poly(A)-binding protein. Rna. 2013;19(11):1537–51. doi: 10.1261/rna.040709.113 24064791
-
(2013)
Rna
, vol.19
, Issue.11
, pp. 1537-1551
-
-
Melamed, D.1
Young, D.L.2
Gamble, C.E.3
Miller, C.R.4
Fields, S.5
-
34
-
-
84875703570
-
Analyses of the effects of all ubiquitin point mutants on yeast growth rate
-
Roscoe BP, Thayer KM, Zeldovich KB, Fushman D, Bolon DN, Analyses of the effects of all ubiquitin point mutants on yeast growth rate. J Mol Biol. 2013;425(8):1363–77. doi: 10.1016/j.jmb.2013.01.032 23376099
-
(2013)
J Mol Biol
, vol.425
, Issue.8
, pp. 1363-1377
-
-
Roscoe, B.P.1
Thayer, K.M.2
Zeldovich, K.B.3
Fushman, D.4
Bolon, D.N.5
-
35
-
-
84875870975
-
Activity-enhancing mutations in an E3 ubiquitin ligase identified by high-throughput mutagenesis
-
Starita LM, Pruneda JN, Lo RS, Fowler DM, Kim HJ, Hiatt JB, et al. Activity-enhancing mutations in an E3 ubiquitin ligase identified by high-throughput mutagenesis. Proc Natl Acad Sci U S A. 2013;110(14):E1263–72. doi: 10.1073/pnas.1303309110 23509263
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, Issue.14
, pp. 1263-1272
-
-
Starita, L.M.1
Pruneda, J.N.2
Lo, R.S.3
Fowler, D.M.4
Kim, H.J.5
Hiatt, J.B.6
-
36
-
-
84901408859
-
A Comprehensive, High-Resolution Map of a Gene's Fitness Landscape
-
Firnberg E, Labonte JW, Gray JJ, Ostermeier M, A Comprehensive, High-Resolution Map of a Gene's Fitness Landscape. Mol Biol Evol. 2014.
-
(2014)
Mol Biol Evol
-
-
Firnberg, E.1
Labonte, J.W.2
Gray, J.J.3
Ostermeier, M.4
-
37
-
-
84889677831
-
Mutational and fitness landscapes of an RNA virus revealed through population sequencing
-
Acevedo A, Brodsky L, Andino R, Mutational and fitness landscapes of an RNA virus revealed through population sequencing. Nature. 2014;505(7485):686–90. doi: 10.1038/nature12861 24284629
-
(2014)
Nature
, vol.505
, Issue.7485
, pp. 686-690
-
-
Acevedo, A.1
Brodsky, L.2
Andino, R.3
-
38
-
-
84902324441
-
Exploring the functional residues in a flavin-binding fluorescent protein using deep mutational scanning
-
Shin H, Cho Y, Choe DH, Jeong Y, Cho S, Kim SC, et al. Exploring the functional residues in a flavin-binding fluorescent protein using deep mutational scanning. PLoS One. 2014;9(6):e97817. doi: 10.1371/journal.pone.0097817 24887409
-
(2014)
PLoS One
, vol.9
, Issue.6
-
-
Shin, H.1
Cho, Y.2
Choe, D.H.3
Jeong, Y.4
Cho, S.5
Kim, S.C.6
-
39
-
-
0036900082
-
Quantifying the slightly deleterious mutation model of molecular evolution
-
Eyre-Walker A, Keightley PD, Smith NG, Gaffney D, Quantifying the slightly deleterious mutation model of molecular evolution. Mol Biol Evol. 2002;19(12):2142–9. 12446806
-
(2002)
Mol Biol Evol
, vol.19
, Issue.12
, pp. 2142-2149
-
-
Eyre-Walker, A.1
Keightley, P.D.2
Smith, N.G.3
Gaffney, D.4
-
40
-
-
34147116715
-
Most rare missense alleles are deleterious in humans: implications for complex disease and association studies
-
Kryukov GV, Pennacchio LA, Sunyaev SR, Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. Am J Hum Genet. 2007;80(4):727–39. 17357078
-
(2007)
Am J Hum Genet
, vol.80
, Issue.4
, pp. 727-739
-
-
Kryukov, G.V.1
Pennacchio, L.A.2
Sunyaev, S.R.3
-
41
-
-
84867781208
-
Epistasis as the primary factor in molecular evolution
-
Breen MS, Kemena C, Vlasov PK, Notredame C, Kondrashov FA, Epistasis as the primary factor in molecular evolution. Nature. 2012;490(7421):535–8. doi: 10.1038/nature11510 23064225
-
(2012)
Nature
, vol.490
, Issue.7421
, pp. 535-538
-
-
Breen, M.S.1
Kemena, C.2
Vlasov, P.K.3
Notredame, C.4
Kondrashov, F.A.5
-
42
-
-
84883389319
-
Neutral and weakly nonneutral sequence variants may define individuality
-
Bromberg Y, Kahn PC, Rost B, Neutral and weakly nonneutral sequence variants may define individuality. Proc Natl Acad Sci U S A. 2013;110(35):14255–60. doi: 10.1073/pnas.1216613110 23940345
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, Issue.35
, pp. 14255-14260
-
-
Bromberg, Y.1
Kahn, P.C.2
Rost, B.3
-
44
-
-
79960601166
-
Slow protein evolutionary rates are dictated by surface-core association
-
Toth-Petroczy A, Tawfik DS, Slow protein evolutionary rates are dictated by surface-core association. Proc Natl Acad Sci U S A. 2011;108(27):11151–6. doi: 10.1073/pnas.1015994108 21690394
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, Issue.27
, pp. 11151-11156
-
-
Toth-Petroczy, A.1
Tawfik, D.S.2
-
45
-
-
78449233935
-
Pervasive cryptic epistasis in molecular evolution
-
Lunzer M, Golding GB, Dean AM, Pervasive cryptic epistasis in molecular evolution. PLoS Genet. 2010;6(10):e1001162. doi: 10.1371/journal.pgen.1001162 20975933
-
(2010)
PLoS Genet
, vol.6
, Issue.10
-
-
Lunzer, M.1
Golding, G.B.2
Dean, A.M.3
-
46
-
-
77954743785
-
Mutational effects and the evolution of new protein functions
-
Soskine M, Tawfik DS, Mutational effects and the evolution of new protein functions. Nat Rev Genet. 2010;11(8):572–82. doi: 10.1038/nrg2808 20634811
-
(2010)
Nat Rev Genet
, vol.11
, Issue.8
, pp. 572-582
-
-
Soskine, M.1
Tawfik, D.S.2
-
47
-
-
33845864966
-
Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein
-
Bershtein S, Segal M, Bekerman R, Tokuriki N, Tawfik DS, Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein. Nature. 2006;444(7121):929–32. 17122770
-
(2006)
Nature
, vol.444
, Issue.7121
, pp. 929-932
-
-
Bershtein, S.1
Segal, M.2
Bekerman, R.3
Tokuriki, N.4
Tawfik, D.S.5
-
48
-
-
84879619070
-
Latent effects of Hsp90 mutants revealed at reduced expression levels
-
Jiang L, Mishra P, Hietpas RT, Zeldovich KB, Bolon DN, Latent effects of Hsp90 mutants revealed at reduced expression levels. PLoS Genet. 2013;9(6):e1003600. doi: 10.1371/journal.pgen.1003600 23825969
-
(2013)
PLoS Genet
, vol.9
, Issue.6
-
-
Jiang, L.1
Mishra, P.2
Hietpas, R.T.3
Zeldovich, K.B.4
Bolon, D.N.5
-
49
-
-
34447546660
-
The distribution of fitness effects of new mutations
-
Eyre-Walker A, Keightley PD, The distribution of fitness effects of new mutations. Nat Rev Genet. 2007;8(8):610–8. 17637733
-
(2007)
Nat Rev Genet
, vol.8
, Issue.8
, pp. 610-618
-
-
Eyre-Walker, A.1
Keightley, P.D.2
-
50
-
-
84904381004
-
Effects of new mutations on fitness: insights from models and data
-
Bataillon T, Bailey SF, Effects of new mutations on fitness: insights from models and data. Ann N Y Acad Sci. 2014;1320(1):76–92.
-
(2014)
Ann N Y Acad Sci
, vol.1320
, Issue.1
, pp. 76-92
-
-
Bataillon, T.1
Bailey, S.F.2
-
51
-
-
84871226912
-
Evolutionary transitions to new DNA methyltransferases through target site expansion and shrinkage
-
Rockah-Shmuel L, Tawfik DS, Evolutionary transitions to new DNA methyltransferases through target site expansion and shrinkage. Nucleic Acids Res. 2012.
-
(2012)
Nucleic Acids Res
-
-
Rockah-Shmuel, L.1
Tawfik, D.S.2
-
52
-
-
84887306726
-
Correlated occurrence and bypass of frame-shifting insertion-deletions (InDels) to give functional proteins
-
Rockah-Shmuel L, Toth-Petroczy A, Sela A, Wurtzel O, Sorek R, Tawfik DS, Correlated occurrence and bypass of frame-shifting insertion-deletions (InDels) to give functional proteins. PLoS Genet. 2013;9(10):e1003882. doi: 10.1371/journal.pgen.1003882 24204297
-
(2013)
PLoS Genet
, vol.9
, Issue.10
-
-
Rockah-Shmuel, L.1
Toth-Petroczy, A.2
Sela, A.3
Wurtzel, O.4
Sorek, R.5
Tawfik, D.S.6
-
53
-
-
44349161622
-
Intense neutral drifts yield robust and evolvable consensus proteins
-
Bershtein S, Goldin K, Tawfik DS, Intense neutral drifts yield robust and evolvable consensus proteins. J Mol Biol. 2008;379(5):1029–44. doi: 10.1016/j.jmb.2008.04.024 18495157
-
(2008)
J Mol Biol
, vol.379
, Issue.5
, pp. 1029-1044
-
-
Bershtein, S.1
Goldin, K.2
Tawfik, D.S.3
-
54
-
-
0035883519
-
Behavior of restriction–modification systems as selfish mobile elements and their impact on genome evolution
-
Kobayashi I, Behavior of restriction–modification systems as selfish mobile elements and their impact on genome evolution Nucleic Acids Research. 2001;29(18):3742–56. 11557807
-
(2001)
Nucleic Acids Research
, vol.29
, Issue.18
, pp. 3742-3756
-
-
Kobayashi, I.1
-
55
-
-
43349095997
-
Real-time kinetics of restriction-modification gene expression after entry into a new host cell
-
Mruk I, Blumenthal RM, Real-time kinetics of restriction-modification gene expression after entry into a new host cell. Nucleic Acids Res. 2008;36(8):2581–93. doi: 10.1093/nar/gkn097 18334533
-
(2008)
Nucleic Acids Res
, vol.36
, Issue.8
, pp. 2581-2593
-
-
Mruk, I.1
Blumenthal, R.M.2
-
56
-
-
35148814896
-
A simple selection strategy for evolving highly efficient enzymes
-
Neuenschwander M, Butz M, Heintz C, Kast P, Hilvert D, A simple selection strategy for evolving highly efficient enzymes. Nat Biotechnol. 2007;25(10):1145–7. 17873865
-
(2007)
Nat Biotechnol
, vol.25
, Issue.10
, pp. 1145-1147
-
-
Neuenschwander, M.1
Butz, M.2
Heintz, C.3
Kast, P.4
Hilvert, D.5
-
57
-
-
0036193868
-
Predicting evolutionary potential: in vitro evolution accurately reproduces natural evolution of the tem beta-lactamase
-
Barlow M, Hall BG, Predicting evolutionary potential: in vitro evolution accurately reproduces natural evolution of the tem beta-lactamase. Genetics. 2002;160(3):823–32. 11901104
-
(2002)
Genetics
, vol.160
, Issue.3
, pp. 823-832
-
-
Barlow, M.1
Hall, B.G.2
-
58
-
-
84867339877
-
Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing
-
Lee H, Popodi E, Tang H, Foster PL, Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. Proc Natl Acad Sci U S A. 2012;109(41):E2774–83. doi: 10.1073/pnas.1210309109 22991466
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, Issue.41
, pp. 2774-2783
-
-
Lee, H.1
Popodi, E.2
Tang, H.3
Foster, P.L.4
-
59
-
-
77951600170
-
What can we learn about the distribution of fitness effects of new mutations from DNA sequence data?
-
Keightley PD, Eyre-Walker A, What can we learn about the distribution of fitness effects of new mutations from DNA sequence data? Philos Trans R Soc Lond B Biol Sci. 2010;365(1544):1187–93. doi: 10.1098/rstb.2009.0266 20308093
-
(2010)
Philos Trans R Soc Lond B Biol Sci
, vol.365
, Issue.1544
, pp. 1187-1193
-
-
Keightley, P.D.1
Eyre-Walker, A.2
-
60
-
-
80051532482
-
Inference of site frequency spectra from high-throughput sequence data: quantification of selection on nonsynonymous and synonymous sites in humans
-
Keightley PD, Halligan DL, Inference of site frequency spectra from high-throughput sequence data: quantification of selection on nonsynonymous and synonymous sites in humans. Genetics. 2011;188(4):931–40. doi: 10.1534/genetics.111.128355 21596896
-
(2011)
Genetics
, vol.188
, Issue.4
, pp. 931-940
-
-
Keightley, P.D.1
Halligan, D.L.2
-
61
-
-
79957950801
-
SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples
-
Le SQ, Durbin R, SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples. Genome Res. 2011;21(6):952–60. doi: 10.1101/gr.113084.110 20980557
-
(2011)
Genome Res
, vol.21
, Issue.6
, pp. 952-960
-
-
Le, S.Q.1
Durbin, R.2
-
62
-
-
0036295508
-
Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs
-
Wang X, Minasov G, Shoichet BK, Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs. J Mol Biol. 2002;320(1):85–95. 12079336
-
(2002)
J Mol Biol
, vol.320
, Issue.1
, pp. 85-95
-
-
Wang, X.1
Minasov, G.2
Shoichet, B.K.3
-
63
-
-
33645811495
-
Protein stability promotes evolvability
-
Bloom JD, Labthavikul ST, Otey CR, Arnold FH, Protein stability promotes evolvability. Proc Natl Acad Sci U S A. 2006;103(15):5869–74. 16581913
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, Issue.15
, pp. 5869-5874
-
-
Bloom, J.D.1
Labthavikul, S.T.2
Otey, C.R.3
Arnold, F.H.4
-
64
-
-
40149099484
-
How protein stability and new functions trade off
-
Tokuriki N, Stricher F, Serrano L, Tawfik DS, How protein stability and new functions trade off. PLoS Comput Biol. 2008;4(2):e1000002. doi: 10.1371/journal.pcbi.1000002 18463696
-
(2008)
PLoS Comput Biol
, vol.4
, Issue.2
-
-
Tokuriki, N.1
Stricher, F.2
Serrano, L.3
Tawfik, D.S.4
-
65
-
-
4143051195
-
Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior
-
Mayrose I, Graur D, Ben-Tal N, Pupko T, Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior. Mol Biol Evol. 2004;21(9):1781–91. 15201400
-
(2004)
Mol Biol Evol
, vol.21
, Issue.9
, pp. 1781-1791
-
-
Mayrose, I.1
Graur, D.2
Ben-Tal, N.3
Pupko, T.4
-
66
-
-
84880443165
-
Congruency in the prediction of pathogenic missense mutations: state-of-the-art web-based tools
-
Castellana S, Mazza T, Congruency in the prediction of pathogenic missense mutations: state-of-the-art web-based tools. Brief Bioinform. 2013;14(4):448–59. doi: 10.1093/bib/bbt013 23505257
-
(2013)
Brief Bioinform
, vol.14
, Issue.4
, pp. 448-459
-
-
Castellana, S.1
Mazza, T.2
-
67
-
-
84880787307
-
Mechanisms of protein sequence divergence and incompatibility
-
Wellner A, Raitses Gurevich M, Tawfik DS, Mechanisms of protein sequence divergence and incompatibility. PLoS Genet. 2013;9(7):e1003665. doi: 10.1371/journal.pgen.1003665 23935519
-
(2013)
PLoS Genet
, vol.9
, Issue.7
-
-
Wellner, A.1
Raitses Gurevich, M.2
Tawfik, D.S.3
-
68
-
-
84867301515
-
Predicting the functional effect of amino acid substitutions and indels
-
Choi Y, Sims GE, Murphy S, Miller JR, Chan AP, Predicting the functional effect of amino acid substitutions and indels. PLoS One. 2012;7(10):e46688. http://provean.jcvi.org doi: 10.1371/journal.pone.0046688 23056405
-
(2012)
PLoS One
, vol.7
, Issue.10
-
-
Choi, Y.1
Sims, G.E.2
Murphy, S.3
Miller, J.R.4
Chan, A.P.5
-
69
-
-
0036291145
-
Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations
-
Guerois R, Nielsen JE, Serrano L, Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol. 2002;320(2):369–87. 12079393
-
(2002)
J Mol Biol
, vol.320
, Issue.2
, pp. 369-387
-
-
Guerois, R.1
Nielsen, J.E.2
Serrano, L.3
-
70
-
-
34248674895
-
The stability effects of protein mutations appear to be universally distributed
-
Tokuriki N, Stricher F, Schymkowitz J, Serrano L, Tawfik DS, The stability effects of protein mutations appear to be universally distributed. J Mol Biol. 2007;369(5):1318–32. 17482644
-
(2007)
J Mol Biol
, vol.369
, Issue.5
, pp. 1318-1332
-
-
Tokuriki, N.1
Stricher, F.2
Schymkowitz, J.3
Serrano, L.4
Tawfik, D.S.5
-
71
-
-
79952685998
-
A geometry-based generic predictor for catalytic and allosteric sites
-
Mitternacht S, Berezovsky IN, A geometry-based generic predictor for catalytic and allosteric sites. Protein Eng Des Sel. 2011;24(4):405–9. http://allostery.bii.a-star.edu.sg/ doi: 10.1093/protein/gzq115 21159618
-
(2011)
Protein Eng Des Sel
, vol.24
, Issue.4
, pp. 405-409
-
-
Mitternacht, S.1
Berezovsky, I.N.2
-
72
-
-
84883568730
-
SPACER: Server for predicting allosteric communication and effects of regulation
-
Goncearenco A, Mitternacht S, Yong T, Eisenhaber B, Eisenhaber F, Berezovsky IN, SPACER: Server for predicting allosteric communication and effects of regulation. Nucleic Acids Res. 2013;41(Web Server issue):W266–72. doi: 10.1093/nar/gkt460 23737445
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 266-272
-
-
Goncearenco, A.1
Mitternacht, S.2
Yong, T.3
Eisenhaber, B.4
Eisenhaber, F.5
Berezovsky, I.N.6
-
73
-
-
70349901079
-
Stability effects of mutations and protein evolvability
-
Tokuriki N, Tawfik DS, Stability effects of mutations and protein evolvability. Curr Opin Struct Biol. 2009;19(5):596–604. doi: 10.1016/j.sbi.2009.08.003 19765975
-
(2009)
Curr Opin Struct Biol
, vol.19
, Issue.5
, pp. 596-604
-
-
Tokuriki, N.1
Tawfik, D.S.2
-
74
-
-
84908049845
-
Viewing Protein Fitness Landscapes Through a Next-Gen Lens
-
Boucher JI, Cote P, Flynn J, Jiang L, Laban A, Mishra P, et al. Viewing Protein Fitness Landscapes Through a Next-Gen Lens. Genetics. 2014;198(2):461–71. doi: 10.1534/genetics.114.168351 25316787
-
(2014)
Genetics
, vol.198
, Issue.2
, pp. 461-471
-
-
Boucher, J.I.1
Cote, P.2
Flynn, J.3
Jiang, L.4
Laban, A.5
Mishra, P.6
-
75
-
-
84892475033
-
Comparing protein folding in vitro and in vivo: foldability meets the fitness challenge
-
Hingorani KS, Gierasch LM, Comparing protein folding in vitro and in vivo: foldability meets the fitness challenge. Curr Opin Struct Biol. 2014;24:81–90. doi: 10.1016/j.sbi.2013.11.007 24434632
-
(2014)
Curr Opin Struct Biol
, vol.24
, pp. 81-90
-
-
Hingorani, K.S.1
Gierasch, L.M.2
-
76
-
-
79957786626
-
In vitro evolution goes deep
-
Moses AM, Davidson AR, In vitro evolution goes deep. Proc Natl Acad Sci U S A. 2011;108(20):8071–2. doi: 10.1073/pnas.1104843108 21551096
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, Issue.20
, pp. 8071-8072
-
-
Moses, A.M.1
Davidson, A.R.2
-
77
-
-
2942565781
-
The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus
-
Sanjuan R, Moya A, Elena SF, The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus. Proc Natl Acad Sci U S A. 2004;101(22):8396–401. 15159545
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, Issue.22
, pp. 8396-8401
-
-
Sanjuan, R.1
Moya, A.2
Elena, S.F.3
-
78
-
-
1542802459
-
Our load of mutations
-
Muller HJ, Our load of mutations. Am J Hum Genet. 1950;2(2):111–76. 14771033
-
(1950)
Am J Hum Genet
, vol.2
, Issue.2
, pp. 111-176
-
-
Muller, H.J.1
-
79
-
-
84891814272
-
Contribution of selection for protein folding stability in shaping the patterns of polymorphisms in coding regions
-
Serohijos AW, Shakhnovich EI, Contribution of selection for protein folding stability in shaping the patterns of polymorphisms in coding regions. Mol Biol Evol. 2014;31(1):165–76. doi: 10.1093/molbev/mst189 24124208
-
(2014)
Mol Biol Evol
, vol.31
, Issue.1
, pp. 165-176
-
-
Serohijos, A.W.1
Shakhnovich, E.I.2
-
80
-
-
0001359641
-
Molecular Evolution Over the Mutational Landscape
-
Gillespie JH, Molecular Evolution Over the Mutational Landscape. Evolution. 1984;38(5):1116–29.
-
(1984)
Evolution
, vol.38
, Issue.5
, pp. 1116-1129
-
-
Gillespie, J.H.1
-
81
-
-
52449148668
-
The role of compensatory neutral mutations in molecular evolution
-
Kimura M, The role of compensatory neutral mutations in molecular evolution. Journal of Genetics. 1985;64(1):7–19.
-
(1985)
Journal of Genetics
, vol.64
, Issue.1
, pp. 7-19
-
-
Kimura, M.1
-
82
-
-
84876581271
-
Strong mutational bias toward deletions in the Drosophila melanogaster genome is compensated by selection
-
Leushkin EV, Bazykin GA, Kondrashov AS, Strong mutational bias toward deletions in the Drosophila melanogaster genome is compensated by selection. Genome Biol Evol. 2013;5(3):514–24. doi: 10.1093/gbe/evt021 23395983
-
(2013)
Genome Biol Evol
, vol.5
, Issue.3
, pp. 514-524
-
-
Leushkin, E.V.1
Bazykin, G.A.2
Kondrashov, A.S.3
-
83
-
-
84875601072
-
Protein Insertions and Deletions Enabled by Neutral Roaming in Sequence Space
-
Toth-Petroczy A, Tawfik DS, Protein Insertions and Deletions Enabled by Neutral Roaming in Sequence Space. Mol Biol Evol. 2013.
-
(2013)
Mol Biol Evol
-
-
Toth-Petroczy, A.1
Tawfik, D.S.2
-
84
-
-
84865074474
-
Dynamic mutation-selection balance as an evolutionary attractor
-
Goyal S, Balick DJ, Jerison ER, Neher RA, Shraiman BI, Desai MM, Dynamic mutation-selection balance as an evolutionary attractor. Genetics. 2012;191(4):1309–19. doi: 10.1534/genetics.112.141291 22661327
-
(2012)
Genetics
, vol.191
, Issue.4
, pp. 1309-1319
-
-
Goyal, S.1
Balick, D.J.2
Jerison, E.R.3
Neher, R.A.4
Shraiman, B.I.5
Desai, M.M.6
-
85
-
-
77953200847
-
The use of orthologous sequences to predict the impact of amino acid substitutions on protein function
-
Marini NJ, Thomas PD, Rine J, The use of orthologous sequences to predict the impact of amino acid substitutions on protein function. PLoS Genet. 2010;6(5):e1000968. doi: 10.1371/journal.pgen.1000968 20523748
-
(2010)
PLoS Genet
, vol.6
, Issue.5
-
-
Marini, N.J.1
Thomas, P.D.2
Rine, J.3
-
86
-
-
84902383419
-
EFIN: predicting the functional impact of nonsynonymous single nucleotide polymorphisms in human genome
-
Zeng S, Yang J, Chung BH, Lau YL, Yang W, EFIN: predicting the functional impact of nonsynonymous single nucleotide polymorphisms in human genome. BMC Genomics. 2014;15:455. doi: 10.1186/1471-2164-15-455 24916671
-
(2014)
BMC Genomics
, vol.15
, pp. 455
-
-
Zeng, S.1
Yang, J.2
Chung, B.H.3
Lau, Y.L.4
Yang, W.5
-
87
-
-
84908154345
-
Biophysics of protein evolution and evolutionary protein biophysics
-
Sikosek T, Chan HS, Biophysics of protein evolution and evolutionary protein biophysics. J R Soc Interface. 2014;11(100):20140419. doi: 10.1098/rsif.2014.0419 25165599
-
(2014)
J R Soc Interface
, vol.11
, Issue.100
, pp. 20140419
-
-
Sikosek, T.1
Chan, H.S.2
-
88
-
-
8544221118
-
Network analysis of protein structures identifies functional residues
-
Amitai G, Shemesh A, Sitbon E, Shklar M, Netanely D, Venger I, et al. Network analysis of protein structures identifies functional residues. J Mol Biol. 2004;344(4):1135–46. 15544817
-
(2004)
J Mol Biol
, vol.344
, Issue.4
, pp. 1135-1146
-
-
Amitai, G.1
Shemesh, A.2
Sitbon, E.3
Shklar, M.4
Netanely, D.5
Venger, I.6
-
89
-
-
78651230959
-
Predicting disease-associated substitution of a single amino acid by analyzing residue interactions
-
Li Y, Wen Z, Xiao J, Yin H, Yu L, Yang L, et al. Predicting disease-associated substitution of a single amino acid by analyzing residue interactions. BMC Bioinformatics. 2011;12:14. doi: 10.1186/1471-2105-12-14 21223604
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 14
-
-
Li, Y.1
Wen, Z.2
Xiao, J.3
Yin, H.4
Yu, L.5
Yang, L.6
-
90
-
-
84923642418
-
Single nucleotide variations: biological impact and theoretical interpretation
-
Katsonis P, Koire A, Wilson SJ, Hsu TK, Lua RC, Wilkins AD, et al. Single nucleotide variations: biological impact and theoretical interpretation. Protein Sci. 2014;23(12):1650–66. doi: 10.1002/pro.2552 25234433
-
(2014)
Protein Sci
, vol.23
, Issue.12
, pp. 1650-1666
-
-
Katsonis, P.1
Koire, A.2
Wilson, S.J.3
Hsu, T.K.4
Lua, R.C.5
Wilkins, A.D.6
-
91
-
-
0036387236
-
Evaluation of structural and evolutionary contributions to deleterious mutation prediction
-
Saunders CT, Baker D, Evaluation of structural and evolutionary contributions to deleterious mutation prediction. J Mol Biol. 2002;322(4):891–901. 12270722
-
(2002)
J Mol Biol
, vol.322
, Issue.4
, pp. 891-901
-
-
Saunders, C.T.1
Baker, D.2
-
92
-
-
84904418029
-
PredictProtein—an open resource for online prediction of protein structural and functional features
-
Yachdav G, Kloppmann E, Kajan L, Hecht M, Goldberg T, Hamp T, et al. PredictProtein—an open resource for online prediction of protein structural and functional features. Nucleic Acids Res. 2014;42(Web Server issue):W337–43. doi: 10.1093/nar/gku366 24799431
-
(2014)
Nucleic Acids Res
, vol.42
, pp. 337-343
-
-
Yachdav, G.1
Kloppmann, E.2
Kajan, L.3
Hecht, M.4
Goldberg, T.5
Hamp, T.6
-
93
-
-
84903147593
-
SuSPect: enhanced prediction of single amino acid variant (SAV) phenotype using network features
-
Yates CM, Filippis I, Kelley LA, Sternberg MJ, SuSPect: enhanced prediction of single amino acid variant (SAV) phenotype using network features. J Mol Biol. 2014;426(14):2692–701. doi: 10.1016/j.jmb.2014.04.026 24810707
-
(2014)
J Mol Biol
, vol.426
, Issue.14
, pp. 2692-2701
-
-
Yates, C.M.1
Filippis, I.2
Kelley, L.A.3
Sternberg, M.J.4
-
94
-
-
0022872027
-
Escherichia coli K-12 restricts DNA containing 5-methylcytosine
-
Raleigh EA, Wilson G, Escherichia coli K-12 restricts DNA containing 5-methylcytosine. Proc Natl Acad Sci U S A. 1986;83(23):9070–4. 3024165
-
(1986)
Proc Natl Acad Sci U S A
, vol.83
, Issue.23
, pp. 9070-9074
-
-
Raleigh, E.A.1
Wilson, G.2
-
95
-
-
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, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25(17):3389–402. 9254694
-
(1997)
Nucleic Acids Res
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
-
96
-
-
79959842126
-
Genomic island variability facilitates Prochlorococcus-virus coexistence
-
Avrani S, Wurtzel O, Sharon I, Sorek R, Lindell D, Genomic island variability facilitates Prochlorococcus-virus coexistence. Nature. 2011;474(7353):604–8. doi: 10.1038/nature10172 21720364
-
(2011)
Nature
, vol.474
, Issue.7353
, pp. 604-608
-
-
Avrani, S.1
Wurtzel, O.2
Sharon, I.3
Sorek, R.4
Lindell, D.5
-
97
-
-
79251528560
-
Mutation detection with next-generation resequencing through a mediator genome
-
Wurtzel O, Dori-Bachash M, Pietrokovski S, Jurkevitch E, Sorek R, Mutation detection with next-generation resequencing through a mediator genome. PLoS One. 2010;5(12):e15628. doi: 10.1371/journal.pone.0015628 21209874
-
(2010)
PLoS One
, vol.5
, Issue.12
-
-
Wurtzel, O.1
Dori-Bachash, M.2
Pietrokovski, S.3
Jurkevitch, E.4
Sorek, R.5
-
98
-
-
58449126084
-
The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria
-
Moran NA, McLaughlin HJ, Sorek R, The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria. Science. 2009;323(5912):379–82. doi: 10.1126/science.1167140 19150844
-
(2009)
Science
, vol.323
, Issue.5912
, pp. 379-382
-
-
Moran, N.A.1
McLaughlin, H.J.2
Sorek, R.3
-
99
-
-
75549086595
-
REBASE—a database for DNA restriction and modification: enzymes, genes and genomes
-
Roberts RJ, Vincze T, Posfai J, Macelis D, REBASE—a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res. 2010;38(Database issue):D234–6. doi: 10.1093/nar/gkp874 19846593
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 234-236
-
-
Roberts, R.J.1
Vincze, T.2
Posfai, J.3
Macelis, D.4
-
100
-
-
3042666256
-
MUSCLE: multiple sequence alignment with high accuracy and high throughput
-
Edgar RC, MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792–7. 15034147
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.5
, pp. 1792-1797
-
-
Edgar, R.C.1
-
101
-
-
0242578620
-
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
-
Guindon S, Gascuel O, A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003;52(5):696–704. 14530136
-
(2003)
Syst Biol
, vol.52
, Issue.5
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
102
-
-
0035026704
-
Predicting deleterious amino acid substitutions
-
Ng PC, Henikoff S, Predicting deleterious amino acid substitutions. Genome Res. 2001;11(5):863–74. Available: http://sift.jcvi.org 11337480
-
(2001)
Genome Res
, vol.11
, Issue.5
, pp. 863-874
-
-
Ng, P.C.1
Henikoff, S.2
-
103
-
-
0029068629
-
The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing
-
Reinisch KM, Chen L, Verdine GL, Lipscomb WN, The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing. Cell. 1995;82(1):143–53. 7606780
-
(1995)
Cell
, vol.82
, Issue.1
, pp. 143-153
-
-
Reinisch, K.M.1
Chen, L.2
Verdine, G.L.3
Lipscomb, W.N.4
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