-
1
-
-
0014935646
-
Natural selection and the concept of a protein space
-
.;:
-
Smith JM, Natural selection and the concept of a protein space. Nature. 1970;255:563–564. doi: 10.1038/225563a0
-
(1970)
Nature
, vol.255
, pp. 563-564
-
-
Smith, J.M.1
-
2
-
-
0014421064
-
Evolutionary rate at the molecular level
-
5637732, ..;():
-
Kimura M, et al. Evolutionary rate at the molecular level. Nature. 1968;217(5129):624–626. doi: 10.1038/217624a05637732
-
(1968)
Nature
, vol.217
, Issue.5129
, pp. 624-626
-
-
Kimura, M.1
-
3
-
-
0014680905
-
Non-Darwinian evolution
-
.;()
-
King J, Jukes T, Non-Darwinian evolution. Science (New York, NY). 1969;164(881):788. doi: 10.1126/science.164.3881.788
-
(1969)
Science (New York, NY)
, vol.164
, Issue.881
, pp. 788
-
-
King, J.1
Jukes, T.2
-
5
-
-
0022423920
-
Theory for the folding and stability of globular proteins
-
3986190, .;():
-
Dill KA, Theory for the folding and stability of globular proteins. Biochemistry. 1985;24(6):1501–1509. doi: 10.1021/bi00327a0323986190
-
(1985)
Biochemistry
, vol.24
, Issue.6
, pp. 1501-1509
-
-
Dill, K.A.1
-
6
-
-
0024750637
-
A lattice statistical mechanics model of the conformational and sequence spaces of proteins
-
.;():
-
Lau KF, Dill KA, A lattice statistical mechanics model of the conformational and sequence spaces of proteins. Macromolecules. 1989;22(10):3986–3997. doi: 10.1021/ma00200a030
-
(1989)
Macromolecules
, vol.22
, Issue.10
, pp. 3986-3997
-
-
Lau, K.F.1
Dill, K.A.2
-
7
-
-
0028196714
-
From sequences to shapes and back: A case study in RNA secondary structures
-
.;():
-
Schuster P, Fontana W, Stadler PF, Hofacker IL, From sequences to shapes and back: A case study in RNA secondary structures. Proceedings: Biological Sciences. 1994;255(1344):279–284.
-
(1994)
Proceedings: Biological Sciences
, vol.255
, Issue.1344
, pp. 279-284
-
-
Schuster, P.1
Fontana, W.2
Stadler, P.F.3
Hofacker, I.L.4
-
8
-
-
34249772381
-
Fast folding and comparison of RNA secondary structures
-
.;():
-
Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, Schuster P, Fast folding and comparison of RNA secondary structures. Monatshefte für Chemie/Chemical Monthly. 1994;125(2):167–188. doi: 10.1007/BF00818163
-
(1994)
Monatshefte für Chemie/Chemical Monthly
, vol.125
, Issue.2
, pp. 167-188
-
-
Hofacker, I.L.1
Fontana, W.2
Stadler, P.F.3
Bonhoeffer, L.S.4
Tacker, M.5
Schuster, P.6
-
9
-
-
2442626706
-
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
-
15123812, .;():
-
Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH, Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proceedings of the National Academy of Sciences of the United States of America. 2004;101(19):7287–7292. doi: 10.1073/pnas.040179910115123812
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.19
, pp. 7287-7292
-
-
Mathews, D.H.1
Disney, M.D.2
Childs, J.L.3
Schroeder, S.J.4
Zuker, M.5
Turner, D.H.6
-
10
-
-
77949447172
-
RNAstructure: software for RNA secondary structure prediction and analysis
-
20230624, .;()
-
Reuter JS, Mathews DH, RNAstructure: software for RNA secondary structure prediction and analysis. BMC bioinformatics. 2010;11(1):129. doi: 10.1186/1471-2105-11-12920230624
-
(2010)
BMC bioinformatics
, vol.11
, Issue.1
, pp. 129
-
-
Reuter, J.S.1
Mathews, D.H.2
-
11
-
-
0036903361
-
Modelling ‘evo-devo’ with RNA
-
12447981, .;():
-
Fontana W, Modelling ‘evo-devo’ with RNA. BioEssays. 2002;24(12):1164–1177. doi: 10.1002/bies.1019012447981
-
(2002)
BioEssays
, vol.24
, Issue.12
, pp. 1164-1177
-
-
Fontana, W.1
-
12
-
-
48249115639
-
The ascent of the abundant: how mutational networks constrain evolution
-
18636097, .;()
-
Cowperthwaite MC, Economo EP, Harcombe WR, Miller EL, Meyers LA, The ascent of the abundant: how mutational networks constrain evolution. PLoS computational biology. 2008;4(7):e1000110. doi: 10.1371/journal.pcbi.100011018636097
-
(2008)
PLoS computational biology
, vol.4
, Issue.7
, pp. 1000110
-
-
Cowperthwaite, M.C.1
Economo, E.P.2
Harcombe, W.R.3
Miller, E.L.4
Meyers, L.A.5
-
13
-
-
80054765283
-
Topological structure of the space of phenotypes: the case of RNA neutral networks
-
22028856, .;()
-
Aguirre J, Buldú JM, Stich M, Manrubia SC, Topological structure of the space of phenotypes: the case of RNA neutral networks. PloS one. 2011;6(10):e26324. doi: 10.1371/journal.pone.002632422028856
-
(2011)
PloS one
, vol.6
, Issue.10
, pp. 26324
-
-
Aguirre, J.1
Buldú, J.M.2
Stich, M.3
Manrubia, S.C.4
-
14
-
-
84895529107
-
The Arrival of the Frequent: How Bias in Genotype-Phenotype Maps Can Steer Populations to Local Optima
-
24505262, .;()
-
Schaper S, Louis AA, The Arrival of the Frequent: How Bias in Genotype-Phenotype Maps Can Steer Populations to Local Optima. PloS one. 2014;9(2):e86635. doi: 10.1371/journal.pone.008663524505262
-
(2014)
PloS one
, vol.9
, Issue.2
, pp. 86635
-
-
Schaper, S.1
Louis, A.A.2
-
17
-
-
33847268619
-
Robustness can evolve gradually in complex regulatory gene networks with varying topology
-
17274682, .;()
-
Ciliberti S, Martin OC, Wagner A, Robustness can evolve gradually in complex regulatory gene networks with varying topology. PLoS computational biology. 2007;3(2):e15. doi: 10.1371/journal.pcbi.003001517274682
-
(2007)
PLoS computational biology
, vol.3
, Issue.2
, pp. 15
-
-
Ciliberti, S.1
Martin, O.C.2
Wagner, A.3
-
18
-
-
79952666135
-
Evolvability and robustness in a complex signalling circuit
-
Raman K, Wagner A, Evolvability and robustness in a complex signalling circuit. Mol BioSyst. 2011;. doi: 10.1039/c0mb00165a
-
(2011)
Mol BioSyst
-
-
Raman, K.1
Wagner, A.2
-
19
-
-
77952295145
-
Genotype networks in metabolic reaction spaces
-
20302636, .;()
-
Samal A, Rodrigues JFM, Jost J, Martin OC, Wagner A, Genotype networks in metabolic reaction spaces. BMC systems biology. 2010;4(1):30. doi: 10.1186/1752-0509-4-3020302636
-
(2010)
BMC systems biology
, vol.4
, Issue.1
, pp. 30
-
-
Samal, A.1
Rodrigues, J.F.M.2
Jost, J.3
Martin, O.C.4
Wagner, A.5
-
20
-
-
84901436725
-
A tractable genotype–phenotype map modelling the self-assembly of protein quaternary structure
-
.;()
-
Greenbury SF, Johnston IG, Louis AA, Ahnert SE, A tractable genotype–phenotype map modelling the self-assembly of protein quaternary structure. Journal of The Royal Society Interface. 2014;11(95):20140249. doi: 10.1098/rsif.2014.0249
-
(2014)
Journal of The Royal Society Interface
, vol.11
, Issue.95
, pp. 20140249
-
-
Greenbury, S.F.1
Johnston, I.G.2
Louis, A.A.3
Ahnert, S.E.4
-
21
-
-
0015722319
-
Slightly deleterious mutant substitutions in evolution
-
4585855, .;():
-
Ohta T, Slightly deleterious mutant substitutions in evolution. Nature. 1973;246(5428):96–98. doi: 10.1038/246096a04585855
-
(1973)
Nature
, vol.246
, Issue.5428
, pp. 96-98
-
-
Ohta, T.1
-
22
-
-
36348992094
-
Robustness and evolvability: a paradox resolved
-
17971325, .;()
-
Wagner A, Robustness and evolvability: a paradox resolved. Proceedings of the Royal Society B. 2008;275(1630):91. doi: 10.1098/rspb.2007.113717971325
-
(2008)
Proceedings of the Royal Society B
, vol.275
, Issue.1630
, pp. 91
-
-
Wagner, A.1
-
23
-
-
0000907353
-
The roles of mutation, inbreeding, crossbreeding and selection in evolution
-
.;1:
-
Wright SG, The roles of mutation, inbreeding, crossbreeding and selection in evolution. Proc 6th Int Cong Genet. 1932;1:356–366.
-
(1932)
Proc 6th Int Cong Genet
, pp. 356-366
-
-
Wright, S.G.1
-
24
-
-
0034698298
-
One sequence, two ribozymes: implications for the emergence of new ribozyme folds
-
10903205, .;():
-
Schultes EA, Bartel DP, One sequence, two ribozymes: implications for the emergence of new ribozyme folds. Science. 2000;289(5478):448–452. doi: 10.1126/science.289.5478.44810903205
-
(2000)
Science
, vol.289
, Issue.5478
, pp. 448-452
-
-
Schultes, E.A.1
Bartel, D.P.2
-
25
-
-
79957944389
-
Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme
-
21637259, .;():
-
Hayden EJ, Ferrada E, Wagner A, Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme. Nature. 2011;474(7349):92–95. doi: 10.1038/nature1008321637259
-
(2011)
Nature
, vol.474
, Issue.7349
, pp. 92-95
-
-
Hayden, E.J.1
Ferrada, E.2
Wagner, A.3
-
26
-
-
84894229927
-
The Robustness and Evolvability of Transcription Factor Binding Sites
-
24558158, .;():
-
Payne JL, Wagner A, The Robustness and Evolvability of Transcription Factor Binding Sites. Science. 2014;343(6173):875–877. doi: 10.1126/science.124904624558158
-
(2014)
Science
, vol.343
, Issue.6173
, pp. 875-877
-
-
Payne, J.L.1
Wagner, A.2
-
27
-
-
84859919548
-
A comparison of genotype-phenotype maps for RNA and proteins
-
22768948, .;():
-
Ferrada E, Wagner A, A comparison of genotype-phenotype maps for RNA and proteins. Biophysical journal. 2012;102(8):1916–1925. doi: 10.1016/j.bpj.2012.01.04722768948
-
(2012)
Biophysical journal
, vol.102
, Issue.8
, pp. 1916-1925
-
-
Ferrada, E.1
Wagner, A.2
-
28
-
-
80052796317
-
The molecular origins of evolutionary innovations
-
21872964, .;():
-
Wagner A, The molecular origins of evolutionary innovations. Trends in Genetics. 2011;27(10):397–410. doi: 10.1016/j.tig.2011.06.00221872964
-
(2011)
Trends in Genetics
, vol.27
, Issue.10
, pp. 397-410
-
-
Wagner, A.1
-
29
-
-
77956118094
-
Self-assembly, modularity, and physical complexity
-
.;()
-
Ahnert S, Johnston I, Fink T, Doye J, Louis A, Self-assembly, modularity, and physical complexity. Physical Review E. 2010;82(2):026117. doi: 10.1103/PhysRevE.82.026117
-
(2010)
Physical Review E
, vol.82
, Issue.2
, pp. 026117
-
-
Ahnert, S.1
Johnston, I.2
Fink, T.3
Doye, J.4
Louis, A.5
-
30
-
-
79961067755
-
Evolutionary Dynamics in a Simple Model of Self-Assembly
-
.;
-
Johnston IG, Ahnert SA, Doye JPK, Louis AA, Evolutionary Dynamics in a Simple Model of Self-Assembly. Physical Review E. 2011;83:066105. doi: 10.1103/PhysRevE.83.066105
-
(2011)
Physical Review E
, vol.83
, pp. 066105
-
-
Johnston, I.G.1
Ahnert, S.A.2
Doye, J.P.K.3
Louis, A.A.4
-
31
-
-
0036345270
-
Enumerating designing sequences in the HP model
-
23345753, .;():
-
Irbäck A, Troein C, Enumerating designing sequences in the HP model. Journal of Biological Physics. 2002;28(1):1–15. doi: 10.1023/A:101622501065923345753
-
(2002)
Journal of Biological Physics
, vol.28
, Issue.1
, pp. 1-15
-
-
Irbäck, A.1
Troein, C.2
-
32
-
-
0029772552
-
Emergence of preferred structures in a simple model of protein folding
-
8662562, .;()
-
Li H, Helling R, Tang C, Wingreen N, Emergence of preferred structures in a simple model of protein folding. Science. 1996;273(5275):666. doi: 10.1126/science.273.5275.6668662562
-
(1996)
Science
, vol.273
, Issue.5275
, pp. 666
-
-
Li, H.1
Helling, R.2
Tang, C.3
Wingreen, N.4
-
33
-
-
84962107711
-
The structure of the genotype-phenotype map strongly constrains the evolution of non-coding RNA
-
Dingle K, Schaper S, Louis AA, The structure of the genotype-phenotype map strongly constrains the evolution of non-coding RNA. arxiv. 2015;.
-
(2015)
arxiv
-
-
Dingle, K.1
Schaper, S.2
Louis, A.A.3
-
34
-
-
84888621950
-
Exact enumeration of Hamiltonian walks on the 4× 4× 4 cube and applications to protein folding
-
.;()
-
Schram RD, Schiessel H, Exact enumeration of Hamiltonian walks on the 4× 4× 4 cube and applications to protein folding. Journal of Physics A: Mathematical and Theoretical. 2013;46(48):485001. doi: 10.1088/1751-8113/46/48/485001
-
(2013)
Journal of Physics A: Mathematical and Theoretical
, vol.46
, Issue.48
, pp. 485001
-
-
Schram, R.D.1
Schiessel, H.2
-
35
-
-
0031105866
-
Generic properties of combinatory maps: neutral networks of RNA secondary structures
-
9116604, .;():
-
Reidys C, Stadler PF, Schuster P, Generic properties of combinatory maps: neutral networks of RNA secondary structures. Bulletin of mathematical biology. 1997;59(2):339–397. doi: 10.1007/BF024620079116604
-
(1997)
Bulletin of mathematical biology
, vol.59
, Issue.2
, pp. 339-397
-
-
Reidys, C.1
Stadler, P.F.2
Schuster, P.3
-
37
-
-
79952192799
-
Mathematical modeling of evolution. Solved and open problems
-
20809365, .;():
-
Schuster P, Mathematical modeling of evolution. Solved and open problems. Theory in Biosciences. 2011;130(1):71–89. http://dx.doi.org/10.1007/s12064-010-0110-z. doi: 10.1007/s12064-010-0110-z20809365
-
(2011)
Theory in Biosciences
, vol.130
, Issue.1
, pp. 71-89
-
-
Schuster, P.1
-
39
-
-
34547642136
-
Population size effects in evolutionary dynamics on neutral networks and toy landscapes
-
.;()
-
Sumedha Martin OC, Peliti L, Population size effects in evolutionary dynamics on neutral networks and toy landscapes. J Stat Mech: Theory and Experiment. 2007;2007(05):P05011. doi: 10.1088/1742-5468/2007/05/P05011
-
(2007)
J Stat Mech: Theory and Experiment
, vol.2007
, Issue.5
, pp. 05011
-
-
Sumedha1
Martin, O.C.2
Peliti, L.3
-
41
-
-
60749114979
-
Neutral network sizes of biological RNA molecules can be computed and are not atypically small
-
18973652, .;()
-
Jorg T, Martin OC, Wagner A, Neutral network sizes of biological RNA molecules can be computed and are not atypically small. BMC bioinformatics. 2008;9(1):464. doi: 10.1186/1471-2105-9-46418973652
-
(2008)
BMC bioinformatics
, vol.9
, Issue.1
, pp. 464
-
-
Jorg, T.1
Martin, O.C.2
Wagner, A.3
-
43
-
-
69449106377
-
Robustness: mechanisms and consequences
-
19717203, .;():
-
Masel J, Siegal ML, Robustness: mechanisms and consequences. Trends in Genetics. 2009;25(9):395–403. doi: 10.1016/j.tig.2009.07.00519717203
-
(2009)
Trends in Genetics
, vol.25
, Issue.9
, pp. 395-403
-
-
Masel, J.1
Siegal, M.L.2
-
44
-
-
75149186552
-
Mutational robustness can facilitate adaptation
-
20090752, .;():
-
Draghi JA, Parsons TL, Wagner GP, Plotkin JB, Mutational robustness can facilitate adaptation. Nature. 2010;463(7279):353–355. doi: 10.1038/nature0869420090752
-
(2010)
Nature
, vol.463
, Issue.7279
, pp. 353-355
-
-
Draghi, J.A.1
Parsons, T.L.2
Wagner, G.P.3
Plotkin, J.B.4
-
45
-
-
0035913336
-
Digital organisms: survival of the flattest
-
.;:
-
Wilke CO, Wang J, Ofria C, Lenski RE, Adami C, Digital organisms: survival of the flattest. Nature. 2001;412:331–333.
-
(2001)
Nature
, vol.412
, pp. 331-333
-
-
Wilke, C.O.1
Wang, J.2
Ofria, C.3
Lenski, R.E.4
Adami, C.5
-
46
-
-
41949103740
-
The structure of protein evolution and the evolution of protein structure
-
18328690, .;():
-
Goldstein RA, The structure of protein evolution and the evolution of protein structure. Current opinion in structural biology. 2008;18(2):170–177. doi: 10.1016/j.sbi.2008.01.00618328690
-
(2008)
Current opinion in structural biology
, vol.18
, Issue.2
, pp. 170-177
-
-
Goldstein, R.A.1
-
47
-
-
0025316459
-
The geometry of evolution
-
2224072, .;():
-
Conrad M, The geometry of evolution. BioSystems. 1990;24(1):61–81. doi: 10.1016/0303-2647(90)90030-52224072
-
(1990)
BioSystems
, vol.24
, Issue.1
, pp. 61-81
-
-
Conrad, M.1
-
48
-
-
0029661332
-
Perspective: complex adaptations and the evolution of evolvability
-
.;p
-
Wagner GP, Altenberg L, Perspective: complex adaptations and the evolution of evolvability. Evolution. 1996;p. 967–976. doi: 10.2307/2410639
-
(1996)
Evolution
, pp. 967-976
-
-
Wagner, G.P.1
Altenberg, L.2
-
49
-
-
0032555135
-
Evolvability
-
9671692, .;():
-
Kirschner M, Gerhart J, Evolvability. Proc Natl Acad Sci USA. 1998July;95(15):8420–8427. doi: 10.1073/pnas.95.15.84209671692
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, Issue.15
, pp. 8420-8427
-
-
Kirschner, M.1
Gerhart, J.2
-
50
-
-
0000656226
-
The Evolution of Evolvability
-
.;p
-
Dawkins R, The Evolution of Evolvability. Artificial Life. 1989;p. 201–220.
-
(1989)
Artificial Life
, pp. 201-220
-
-
Dawkins, R.1
-
51
-
-
37249030834
-
Is evolvability evolvable?
-
18059367, .;():
-
Pigliucci M, Is evolvability evolvable?Nature Reviews Genetics. 2008;9(1):75–82. doi: 10.1038/nrg227818059367
-
(2008)
Nature Reviews Genetics
, vol.9
, Issue.1
, pp. 75-82
-
-
Pigliucci, M.1
-
52
-
-
0030030533
-
Smoothness within ruggedness: The role of neutrality in adaptation
-
8552647, .;()
-
Huynen MA, Stadler PF, Fontana W, Smoothness within ruggedness: The role of neutrality in adaptation. Proc Nat Acad Sci USA. 1996;93(1):397. doi: 10.1073/pnas.93.1.3978552647
-
(1996)
Proc Nat Acad Sci USA
, vol.93
, Issue.1
, pp. 397
-
-
Huynen, M.A.1
Stadler, P.F.2
Fontana, W.3
|