-
1
-
-
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.
-
(2014)
Nat Methods
, vol.11
, Issue.8
, pp. 801-807
-
-
Fowler, D.M.1
Fields, S.2
-
2
-
-
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.
-
(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
-
3
-
-
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; 423:397-412.
-
(2012)
J Mol Biol.
, vol.423
, pp. 397-412
-
-
Traxlmayr, M.W.1
Hasenhindl, C.2
Hackl, M.3
Stadlmayr, G.4
Rybka, J.D.5
Borth, N.6
-
4
-
-
84868365613
-
The spatial architecture of protein function and adaptation
-
McLaughlin Jr RN, Poelwijk FJ, Raman A, Gosal WS, Ranganathan R. The spatial architecture of protein function and adaptation. Nature. 2012; 491(7422):138.
-
(2012)
Nature
, vol.491
, Issue.7422
, pp. 138
-
-
McLaughlin Jr, R.N.1
Poelwijk, F.J.2
Raman, A.3
Gosal, W.S.4
Ranganathan, R.5
-
5
-
-
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 USA. 2013; 110(14):1263-72.
-
(2013)
Proc Natl Acad Sci USA
, 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
-
6
-
-
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.
-
(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
-
7
-
-
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; 425:1363-77.
-
(2013)
J Mol Biol.
, vol.425
, pp. 1363-1377
-
-
Roscoe, B.P.1
Thayer, K.M.2
Zeldovich, K.B.3
Fushman, D.4
Bolon, D.N.5
-
8
-
-
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; 31(6):1581-92.
-
(2014)
Mol Biol Evol
, vol.31
, Issue.6
, pp. 1581-1592
-
-
Firnberg, E.1
Labonte, J.W.2
Gray, J.J.3
Ostermeier, M.4
-
9
-
-
84905001681
-
An experimentally determined evolutionary model dramatically improves phylogenetic fit
-
Bloom JD. An experimentally determined evolutionary model dramatically improves phylogenetic fit. Mol Biol Evol. 2014; 30:1956-78. http://mbe.oxfordjournals.org/content/31/8/1956 .
-
(2014)
Mol Biol Evol
, vol.30
, pp. 1956-1978
-
-
Bloom, J.D.1
-
10
-
-
84906217475
-
Comprehensive mutational scanning of a kinase in vivo reveals context-dependent fitness landscapes
-
Melnikov A, Rogov P, Wang L, Gnirke A, Mikkelsen TS. Comprehensive mutational scanning of a kinase in vivo reveals context-dependent fitness landscapes. Nucleic Acids Res. 2014; 42:112.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. 112
-
-
Melnikov, A.1
Rogov, P.2
Wang, L.3
Gnirke, A.4
Mikkelsen, T.S.5
-
11
-
-
84905197658
-
The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin
-
Thyagarajan B, Bloom JD. The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin. eLife. 2014; 3:03300. http://elifesciences.org/content/3/e03300 .
-
(2014)
eLife
, vol.3
, pp. 03300
-
-
Thyagarajan, B.1
Bloom, J.D.2
-
12
-
-
84900431101
-
High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution
-
Wu NC, Young AP, Al-Mawsawi LQ, Olson CA, Feng J, Qi H, et al. High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution. Sci Rep. 2014; 4:4942.
-
(2014)
Sci Rep
, vol.4
, pp. 4942
-
-
Wu, N.C.1
Young, A.P.2
Al-Mawsawi, L.Q.3
Olson, C.A.4
Feng, J.5
Qi, H.6
-
13
-
-
84910670272
-
High-throughput identification of loss-of-function mutations for anti-interferon activity in the influenza A virus NS segment
-
10157-64
-
Wu NC, Young AP, Al-Mawsawi LQ, Olson CA, Feng J, Qi H, et al. High-throughput identification of loss-of-function mutations for anti-interferon activity in the influenza A virus NS segment. J Virol. 2014; 88(17):10157-64.
-
(2014)
J Virol
, vol.88
, Issue.17
-
-
Wu, N.C.1
Young, A.P.2
Al-Mawsawi, L.Q.3
Olson, C.A.4
Feng, J.5
Qi, H.6
-
14
-
-
84923249936
-
A comprehensive biophysical description of pairwise epistasis throughout an entire protein domain
-
Olson CA, Wu NC, Sun R. A comprehensive biophysical description of pairwise epistasis throughout an entire protein domain. Curr Biol. 2014; 24(22):2643-51.
-
(2014)
Curr Biol
, vol.24
, Issue.22
, pp. 2643-2651
-
-
Olson, C.A.1
Wu, N.C.2
Sun, R.3
-
15
-
-
84923848137
-
Massively parallel single-amino-acid mutagenesis
-
Kitzman JO, Starita LM, Lo RS, Fields S, Shendure J. Massively parallel single-amino-acid mutagenesis. Nat Methods. 2015; 12:203-6.
-
(2015)
Nat Methods
, vol.12
, pp. 203-206
-
-
Kitzman, J.O.1
Starita, L.M.2
Lo, R.S.3
Fields, S.4
Shendure, J.5
-
16
-
-
84871288267
-
PFunkel: efficient, expansive, user-defined mutagenesis
-
Firnberg E, Ostermeier M. PFunkel: efficient, expansive, user-defined mutagenesis. PLoS One. 2012; 7:52031.
-
(2012)
PLoS One
, vol.7
, pp. 52031
-
-
Firnberg, E.1
Ostermeier, M.2
-
17
-
-
84892698156
-
A rapid, efficient, and economical inverse polymerase chain reaction-based method for generating a site saturation mutant library
-
Jain PC, Varadarajan R. A rapid, efficient, and economical inverse polymerase chain reaction-based method for generating a site saturation mutant library. Anal Biochem. 2014; 449:90-8.
-
(2014)
Anal Biochem
, vol.449
, pp. 90-98
-
-
Jain, P.C.1
Varadarajan, R.2
-
18
-
-
84907257107
-
Saturation editing of genomic regions by multiplex homology-directed repair
-
Findlay GM, Boyle EA, Hause RJ, Klein JC, Shendure J. Saturation editing of genomic regions by multiplex homology-directed repair. Nat. 2014; 513(7516):120-3.
-
(2014)
Nat
, vol.513
, Issue.7516
, pp. 120-123
-
-
Findlay, G.M.1
Boyle, E.A.2
Hause, R.J.3
Klein, J.C.4
Shendure, J.5
-
19
-
-
83355174920
-
Enrich: software for analysis of protein function by enrichment and depletion of variants
-
Fowler DM, Araya CL, Gerard W, Fields S. Enrich: software for analysis of protein function by enrichment and depletion of variants. Bioinformatics. 2011; 27(24):3430-1.
-
(2011)
Bioinformatics
, vol.27
, Issue.24
, pp. 3430-3431
-
-
Fowler, D.M.1
Araya, C.L.2
Gerard, W.3
Fields, S.4
-
20
-
-
84895727363
-
A bayesian mcmc approach to assess the complete distribution of fitness effects of new mutations: uncovering the potential for adaptive walks in challenging environments
-
Bank C, Hietpas RT, Wong A, Bolon DN, Jensen JD. A bayesian mcmc approach to assess the complete distribution of fitness effects of new mutations: uncovering the potential for adaptive walks in challenging environments. Genet. 2014; 196(3):841-52.
-
(2014)
Genet
, vol.196
, Issue.3
, pp. 841-852
-
-
Bank, C.1
Hietpas, R.T.2
Wong, A.3
Bolon, D.N.4
Jensen, J.D.5
-
21
-
-
84867644046
-
A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function
-
16858-63
-
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. 2012; 109(42):16858-63.
-
(2012)
Proc Natl Acad Sci
, vol.109
, Issue.42
-
-
Araya, C.L.1
Fowler, D.M.2
Chen, W.3
Muniez, I.4
Kelly, J.W.5
Fields, S.6
-
22
-
-
84922384542
-
A systematic survey of an intragenic epistatic landscape
-
Bank C, Hietpas RT, Jensen JD, Bolon DN. A systematic survey of an intragenic epistatic landscape. Mol Biol Evol. 2015; 32(1):229-38.
-
(2015)
Mol Biol Evol
, vol.32
, Issue.1
, pp. 229-238
-
-
Bank, C.1
Hietpas, R.T.2
Jensen, J.D.3
Bolon, D.N.4
-
23
-
-
77449144323
-
Parallel, tag-directed assembly of locally derived short sequence reads
-
Hiatt JB, Patwardhan RP, Turner EH, Lee C, Shendure J. Parallel, tag-directed assembly of locally derived short sequence reads. Nat Methods. 2010; 7(2):119-22.
-
(2010)
Nat Methods
, vol.7
, Issue.2
, pp. 119-122
-
-
Hiatt, J.B.1
Patwardhan, R.P.2
Turner, E.H.3
Lee, C.4
Shendure, J.5
-
24
-
-
84901292975
-
HIV-1 quasispecies delineation by tag linkage deep sequencing
-
Wu NC, De La Cruz J, Al-Mawsawi LQ, Olson CA, Qi H, Luan HH, et al. HIV-1 quasispecies delineation by tag linkage deep sequencing. PloS one. 2014; 9(5):97505.
-
(2014)
PloS one
, vol.9
, Issue.5
, pp. 97505
-
-
Wu, N.C.1
De La Cruz, J.2
Al-Mawsawi, L.Q.3
Olson, C.A.4
Qi, H.5
Luan, H.H.6
-
25
-
-
84923357744
-
An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs
-
Bloom JD. An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs. Mol Biol Evol. 2014; 31:2753-769. http://mbe.oxfordjournals.org/content/31/10/2753 .
-
(2014)
Mol Biol Evol
, vol.31
, pp. 2753-2769
-
-
Bloom, J.D.1
-
26
-
-
25444482352
-
The exchangeability of amino acids in proteins
-
Yampolsky LY, Stoltzfus A. The exchangeability of amino acids in proteins. Genet. 2005; 170(4):1459-72.
-
(2005)
Genet
, vol.170
, Issue.4
, pp. 1459-1472
-
-
Yampolsky, L.Y.1
Stoltzfus, A.2
-
27
-
-
69249205499
-
Climbing mount probable: mutation as a cause of nonrandomness in evolution
-
Stoltzfus A, Yampolsky LY. Climbing mount probable: mutation as a cause of nonrandomness in evolution. J Hered. 2009; 100(5):637-47.
-
(2009)
J Hered
, vol.100
, Issue.5
, pp. 637-647
-
-
Stoltzfus, A.1
Yampolsky, L.Y.2
-
28
-
-
0000629281
-
Mathematical contributions to the theory of evolution. On a form of spurious correlation which may arise when indices are used in the measurement of organs
-
Pearson K. Mathematical contributions to the theory of evolution. On a form of spurious correlation which may arise when indices are used in the measurement of organs. Proc Royal Society London. 1896; 60(359-367):489-98.
-
(1896)
Proc Royal Society London
, vol.60
, Issue.359-367
, pp. 489-498
-
-
Pearson, K.1
-
29
-
-
0004770050
-
On the constants of index-distributions as deduced from the like constants for the components of the ratio, with special reference to the opsonic index
-
Pearson K. On the constants of index-distributions as deduced from the like constants for the components of the ratio, with special reference to the opsonic index. Biometrika. 1910; 7(4):531-41. doi:10.1093/biomet/7.4.531.
-
(1910)
Biometrika
, vol.7
, Issue.4
, pp. 531-541
-
-
Pearson, K.1
-
31
-
-
0034175543
-
Mean and variance of ratio estimators used in fluorescence ratio imaging
-
Van Kempen G, Van Vliet L. Mean and variance of ratio estimators used in fluorescence ratio imaging. Cytometry. 2000; 39(4):300-5.
-
(2000)
Cytometry
, vol.39
, Issue.4
, pp. 300-305
-
-
Van Kempen, G.1
Van Vliet, L.2
-
32
-
-
84930212284
-
PyStan: the Python interface to Stan, Version 2.5.0.
-
Stan Development Team. PyStan: the Python interface to Stan, Version 2.5.0. 2014. http://mc-stan.org/pystan.html .
-
(2014)
-
-
-
33
-
-
84972492387
-
Inference from iterative simulation using multiple sequences
-
Gelman A, Rubin DB. Inference from iterative simulation using multiple sequences. Stat Sci. 1992; 7:457-72.
-
(1992)
Stat Sci
, vol.7
, pp. 457-472
-
-
Gelman, A.1
Rubin, D.B.2
-
34
-
-
2142738304
-
Weblogo: a sequence logo generator
-
Crooks GE, Hon G, Chandonia JM, Brenner SE. Weblogo: a sequence logo generator. Genome Res. 2004; 14(6):1188-90. doi:10.1101/gr.849004.
-
(2004)
Genome Res
, vol.14
, Issue.6
, pp. 1188-1190
-
-
Crooks, G.E.1
Hon, G.2
Chandonia, J.M.3
Brenner, S.E.4
-
35
-
-
84921873998
-
Points of significance: replication
-
Blainey P, Krzywinski M, Altman N. Points of significance: replication. Nat Methods. 2014; 11(9):879-80.
-
(2014)
Nat Methods
, vol.11
, Issue.9
, pp. 879-880
-
-
Blainey, P.1
Krzywinski, M.2
Altman, N.3
-
36
-
-
0021968408
-
Genetic analysis of staphylococcal nuclease: identification of three intragenic "global" suppressors of nuclease-minus mutations
-
Shortle D, Lin B. Genetic analysis of staphylococcal nuclease: identification of three intragenic "global" suppressors of nuclease-minus mutations. Genet. 1985; 110:539-55.
-
(1985)
Genet
, vol.110
, pp. 539-555
-
-
Shortle, D.1
Lin, B.2
-
38
-
-
0030737949
-
Generation of large libraries of random mutants in Bacillus subtilis by PCR-based plasmid multimerization
-
Shafikhani S, Siegel RA, Ferrari E, Schellenberger V. Generation of large libraries of random mutants in Bacillus subtilis by PCR-based plasmid multimerization. Biotechniques. 1997; 23:304-10.
-
(1997)
Biotechniques
, vol.23
, pp. 304-310
-
-
Shafikhani, S.1
Siegel, R.A.2
Ferrari, E.3
Schellenberger, V.4
-
39
-
-
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 USA. 2004; 101:9205-210.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 9205-9210
-
-
Guo, H.H.1
Choe, J.2
Loeb, L.A.3
-
40
-
-
14144251690
-
Thermodynamic prediction of protein neutrality
-
Bloom JD, Silberg JJ, Wilke CO, Drummond DA, Adami C, Arnold FH. Thermodynamic prediction of protein neutrality. Proc Natl Acad Sci USA. 2005; 102:606-11.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 606-611
-
-
Bloom, J.D.1
Silberg, J.J.2
Wilke, C.O.3
Drummond, D.A.4
Adami, C.5
Arnold, F.H.6
|