-
1
-
-
0015133749
-
Self-organization of matter and the evolution of biological macromolecules
-
Eigen M, (1971) Self-organization of matter and the evolution of biological macromolecules. Naturwissenschaften 58: 465-523.
-
(1971)
Naturwissenschaften
, vol.58
, pp. 465-523
-
-
Eigen, M.1
-
3
-
-
0020370504
-
Oligomerization of guanosine 5′-phosphor-2-methylimidazolide on poly(C): a polymerase model
-
Inoue T, Orgel LE, (1982) Oligomerization of guanosine 5′-phosphor-2-methylimidazolide on poly(C): a polymerase model. J Mol Biol. 162: 201-217.
-
(1982)
J Mol Biol
, vol.162
, pp. 201-217
-
-
Inoue, T.1
Orgel, L.E.2
-
4
-
-
0035906978
-
RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension
-
Johnston WK, Unrau PJ, Lawrence MS, Glasen ME, Bartel DP, (2001) RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension. Science 292: 1319-1325.
-
(2001)
Science
, vol.292
, pp. 1319-1325
-
-
Johnston, W.K.1
Unrau, P.J.2
Lawrence, M.S.3
Glasen, M.E.4
Bartel, D.P.5
-
5
-
-
4544371669
-
Determination of the core of a minimal bacterial gene set. Microbiol
-
Gil R, Silva FJ, Pereto J, Moya A, (2004) Determination of the core of a minimal bacterial gene set. Microbiol. Mol Biol Rev 68: 518-537.
-
(2004)
Mol Biol Rev
, vol.68
, pp. 518-537
-
-
Gil, R.1
Silva, F.J.2
Pereto, J.3
Moya, A.4
-
6
-
-
25144450882
-
Real ribozymes suggest a relaxed error threshold
-
Kun A, Santos M, Szathmary, E, (2005) Real ribozymes suggest a relaxed error threshold. Nature Genetics 37: 1008-1011.
-
(2005)
Nature Genetics
, vol.37
, pp. 1008-1011
-
-
Kun, A.1
Santos, M.2
Szathmary3
E4
-
7
-
-
77954503943
-
Selection via flatness as a dynamical effect in evolution models with finite population
-
Saakian DB, Hu CK, (2010) Selection via flatness as a dynamical effect in evolution models with finite population. Phys Rev E 82: 011902.
-
(2010)
Phys Rev
, vol.82
, pp. 011902
-
-
Saakian, D.B.1
Hu, C.K.2
-
8
-
-
2942565781
-
The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus
-
Sanjuan R, Moya A, Elena SF, (2004) The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus. Proc Natl Acad Sci USA 101: 8396-8401.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 8396-8401
-
-
Sanjuan, R.1
Moya, A.2
Elena, S.F.3
-
9
-
-
77954479040
-
Evolution models with lethal mutations on symmetric or random fitness landscapes
-
Kirakosyan Z, Saakian DB, Hu CK, (2010) Evolution models with lethal mutations on symmetric or random fitness landscapes. Phys Rev E 82: 011904.
-
(2010)
Phys Rev E
, vol.82
, pp. 011904
-
-
Kirakosyan, Z.1
Saakian, D.B.2
Hu, C.K.3
-
10
-
-
0028294555
-
Muller rachet under the epistatic selection
-
Kondrashov AS, (1994) Muller rachet under the epistatic selection. Genetics 136: 1469-1472.
-
(1994)
Genetics
, vol.136
, pp. 1469-1472
-
-
Kondrashov, A.S.1
-
11
-
-
33645978710
-
Examining the theory of error catastrophe
-
Summers J, Litwin M, (2006) Examining the theory of error catastrophe. J Virol 80: 20-26.
-
(2006)
J Virol
, vol.80
, pp. 20-26
-
-
Summers, J.1
Litwin, M.2
-
12
-
-
65549128054
-
Phase diagram for the Eigen quasispecies theory with the truncated fitness landscape
-
Saakian DB, Biebricher CK, Hu CK, (2009) Phase diagram for the Eigen quasispecies theory with the truncated fitness landscape. Physical Review E 79: 041905.
-
(2009)
Physical Review E
, vol.79
, pp. 041905
-
-
Saakian, D.B.1
Biebricher, C.K.2
Hu, C.K.3
-
13
-
-
0030030533
-
Smothness within ruggedness: The role of neutrality in adaptation
-
Huynen MA, Stadler PF, Fontana W, (1996) Smothness within ruggedness: The role of neutrality in adaptation. Proc Natl Acad Sci USA 93: 397-401.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 397-401
-
-
Huynen, M.A.1
Stadler, P.F.2
Fontana, W.3
-
15
-
-
0035544542
-
Selection for Fitness vs. Selection for Robustness in RNA Secondary Structure Folding
-
Wilke CO, (2001) Selection for Fitness vs. Selection for Robustness in RNA Secondary Structure Folding. Evolution 55: 2412-2420.
-
(2001)
Evolution
, vol.55
, pp. 2412-2420
-
-
Wilke, C.O.1
-
16
-
-
0038101338
-
Selective Pressures on Genomes in Molecular Evolution J
-
Ofria CO, Adami C, Collier TC, (2003) Selective Pressures on Genomes in Molecular Evolution J. Theor Biol 222: 477-483.
-
(2003)
Theor Biol
, vol.222
, pp. 477-483
-
-
Ofria, C.O.1
Adami, C.2
Collier, T.C.3
-
17
-
-
15244359731
-
Phenotypic error threshold: additivity and epistatis in RNA evolution
-
Takeuchi N, Poorthuis PH, Hogeweg P, (2005) Phenotypic error threshold: additivity and epistatis in RNA evolution. BMC Evol Biol 5: 9-17.
-
(2005)
BMC Evol Biol
, vol.5
, pp. 9-17
-
-
Takeuchi, N.1
Poorthuis, P.H.2
Hogeweg, P.3
-
18
-
-
0000307578
-
Ising quantum chain is equivalent a model of biological evolution
-
Baake E, Baake M, Wagner H, Ising quantum chain is equivalent a model of biological evolution. Phys Rev Lett 78: 559 (1997).
-
(1997)
Phys Rev Lett
, vol.78
, pp. 559
-
-
Baake, E.1
Baake, M.2
Wagner, H.3
-
19
-
-
42749105043
-
Eigen model as a quantum spin chain: exact dynamics
-
Saakian DB, Hu CK, (2004) Eigen model as a quantum spin chain: exact dynamics. Phys Rev E 69: 021913.
-
(2004)
Phys Rev E
, vol.69
, pp. 021913
-
-
Saakian, D.B.1
Hu, C.K.2
-
20
-
-
42749102280
-
Solvable biological evolution model with a parallel mutation-selection scheme
-
Saakian DB, Hu CK, (2004) Solvable biological evolution model with a parallel mutation-selection scheme. Phys Rev E 69: 046121.
-
(2004)
Phys Rev E
, vol.69
, pp. 046121
-
-
Saakian, D.B.1
Hu, C.K.2
-
21
-
-
37649032281
-
Solvable biological evolution models with general fitness functions and multiple mutations in parallel mutation-selection scheme
-
Saakian DB, Hu CK, Khachatryan H, (2004) Solvable biological evolution models with general fitness functions and multiple mutations in parallel mutation-selection scheme. Phys Rev E 70: 041908.
-
(2004)
Phys Rev E
, vol.70
, pp. 041908
-
-
Saakian, D.B.1
Hu, C.K.2
Khachatryan, H.3
-
22
-
-
33645510409
-
Exact solution of the Eigen model with general fitness functions and degradation rates
-
Saakian DB, Hu CK, (2006) Exact solution of the Eigen model with general fitness functions and degradation rates. Proc Natl Acad Sci USA 103: 4935.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 4935
-
-
Saakian, D.B.1
Hu, C.K.2
-
23
-
-
33645787418
-
Quasispecies theory for multiple-peak fitness landscapes
-
Saakian DB, Munoz E, Hu CK, Deem MW, (2006) Quasispecies theory for multiple-peak fitness landscapes. Phys Rev E 73: 041913.
-
(2006)
Phys Rev E
, vol.73
, pp. 041913
-
-
Saakian, D.B.1
Munoz, E.2
Hu, C.K.3
Deem, M.W.4
-
24
-
-
0036691639
-
Mutation-Selection Balance: Ancestry, Load, and Maximum Principle, Theor
-
Hermisson J, Redner O, Wagner H, Baake E, (2002) Mutation-Selection Balance: Ancestry, Load, and Maximum Principle, Theor. Pop Biol 62: 9-46.
-
(2002)
Pop Biol
, vol.62
, pp. 9-46
-
-
Hermisson, J.1
Redner, O.2
Wagner, H.3
Baake, E.4
-
25
-
-
34547277414
-
Evolution equation of phenotype distribution: General formulation and application to error catastrophe
-
Sato K, Kaneko K, (2007) Evolution equation of phenotype distribution: General formulation and application to error catastrophe. Phys Rev E 75: 061909.
-
(2007)
Phys Rev E
, vol.75
, pp. 061909
-
-
Sato, K.1
Kaneko, K.2
-
26
-
-
45249094249
-
Diploid Biological Evolution Models with General Smooth Fitness Landscapes
-
Saakian DB, Kirakosan Z, Hu CK, (2008) Diploid Biological Evolution Models with General Smooth Fitness Landscapes. Phys Rev E 77: 061907.
-
(2008)
Phys Rev E
, vol.77
, pp. 061907
-
-
Saakian, D.B.1
Kirakosan, Z.2
Hu, C.K.3
-
27
-
-
67349152655
-
Solution of the Crow-Kimura and Eigen models for alphabets of arbitrary size by Schwinger spin coherent states
-
Munoz E, Park JM, Deem MW, (2009) Solution of the Crow-Kimura and Eigen models for alphabets of arbitrary size by Schwinger spin coherent states. J Stat Phys 135: 429.
-
(2009)
J Stat Phys
, vol.135
, pp. 429
-
-
Munoz, E.1
Park, J.M.2
Deem, M.W.3
-
28
-
-
67649969564
-
Robustness and epistasis in mutation-selection models
-
Wolff A, Krug J, (2009) Robustness and epistasis in mutation-selection models. Phys Biol 6: 036007.
-
(2009)
Phys Biol
, vol.6
, pp. 036007
-
-
Wolff, A.1
Krug, J.2
-
30
-
-
7444221704
-
The contribution of epistasis to the architecture of fitness in an RNA virus. Proc
-
Sanjuan R, Moya A, Elena SF, (2004) The contribution of epistasis to the architecture of fitness in an RNA virus. Proc. Natl Acad Sci USA 101: 15376-15379.
-
(2004)
Natl Acad Sci USA
, vol.101
, pp. 15376-15379
-
-
Sanjuan, R.1
Moya, A.2
Elena, S.F.3
-
31
-
-
0037022396
-
Redundancy, antiredundancy, and the robustness of genomes
-
Krakauer DC, Plotkin JB, (2002) Redundancy, antiredundancy, and the robustness of genomes. Proc Natl Acad Sci U S A99: 1405-1409.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 1405-1409
-
-
Krakauer, D.C.1
Plotkin, J.B.2
-
32
-
-
0033531773
-
About a three states molecular evolution model
-
Bonnaz D, (1999) About a three states molecular evolution model. J Theor Biol 197: 415-423.
-
(1999)
J Theor Biol
, vol.197
, pp. 415-423
-
-
Bonnaz, D.1
-
33
-
-
33847251630
-
Error-threshold exists in fitness landscapes with lethal mutants
-
Takeuchi N, Hogeweg P, (2007) Error-threshold exists in fitness landscapes with lethal mutants. BMC Evol. Biol 7: 15-17.
-
(2007)
BMC Evol. Biol
, vol.7
, pp. 15-17
-
-
Takeuchi, N.1
Hogeweg, P.2
-
34
-
-
77954479040
-
Evolution models with lethal mutations on symmetric or random fitness landscapes
-
Kirakosyan Z, Saakian DB, Hu CK, (2010) Evolution models with lethal mutations on symmetric or random fitness landscapes. Phys. RevE 82: 011904.
-
(2010)
Phys. RevE
, vol.82
, pp. 011904
-
-
Kirakosyan, Z.1
Saakian, D.B.2
Hu, C.K.3
-
35
-
-
77649341255
-
Effect of lethality on the extinction and on the error threshold of quasispecies, J
-
Tejero H, Marin A, Monterof F, (2010) Effect of lethality on the extinction and on the error threshold of quasispecies, J. Theor. Biol 262: 733-741.
-
(2010)
Theor. Biol
, vol.262
, pp. 733-741
-
-
Tejero, H.1
Marin, A.2
Monterof, F.3
-
36
-
-
33847247125
-
Theory of Lethal Mutagenesis for Viruses
-
Bull JJ, Sanjuan R, Wilke CO, (2007) Theory of Lethal Mutagenesis for Viruses. J Virol 81: 2930-2939.
-
(2007)
J Virol
, vol.81
, pp. 2930-2939
-
-
Bull, J.J.1
Sanjuan, R.2
Wilke, C.O.3
-
37
-
-
58149335560
-
Lethal mutagenesis of bacteria
-
Bull JJ, Wilke CO, (2008) Lethal mutagenesis of bacteria. Genetics 180: 1061-1070.
-
(2008)
Genetics
, vol.180
, pp. 1061-1070
-
-
Bull, J.J.1
Wilke, C.O.2
-
39
-
-
0034338307
-
Heteropolymer freezing and design: Towards physical models of protein folding Rev
-
Pande VS, Grosberg AYu, Tanaka T, (2000) Heteropolymer freezing and design: Towards physical models of protein folding Rev. Mod. Phys 72: 259-314.
-
(2000)
Mod. Phys
, vol.72
, pp. 259-314
-
-
Pande, V.S.1
Grosberg, A.Y.2
Tanaka, T.3
-
40
-
-
27344449197
-
Progress in Modeling of Protein Structures and Interactions
-
Schueler-Furman O, Wang C, Bradley P, Misura K, Baker D, (2005) Progress in Modeling of Protein Structures and Interactions. Science 310: 638-642.
-
(2005)
Science
, vol.310
, pp. 638-642
-
-
Schueler-Furman, O.1
Wang, C.2
Bradley, P.3
Misura, K.4
Baker, D.5
-
41
-
-
1242269423
-
Structural motifs in ribosomal RNAs: implications for RNA design and genomics
-
Zorn J, Gan HH, Shiffeldrim NT, Schlick T, (2004) Structural motifs in ribosomal RNAs: implications for RNA design and genomics. Biopolymers 73: 340-347.
-
(2004)
Biopolymers
, vol.73
, pp. 340-347
-
-
Zorn, J.1
Gan, H.H.2
Shiffeldrim, N.T.3
Schlick, T.4
-
42
-
-
79951976845
-
Life as a cosmic imperative? Philos
-
de Duve C, (2011) Life as a cosmic imperative? Philos. Transact. Royal. Soc A 369: 620-623.
-
(2011)
Transact. Royal. Soc A
, vol.369
, pp. 620-623
-
-
de Duve, C.1
-
43
-
-
66149108671
-
Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions
-
Powner MW, Gerland B, Sutherland JD, (2009) Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature 459: 239-242.
-
(2009)
Nature
, vol.459
, pp. 239-242
-
-
Powner, M.W.1
Gerland, B.2
Sutherland, J.D.3
-
45
-
-
77952906690
-
Expanding roles for diverse physical phenomena during the origin of life
-
Budin I, Szostak JW, (2010) Expanding roles for diverse physical phenomena during the origin of life. Annu Rev Biophys 39: 245-263.
-
(2010)
Annu Rev Biophys
, vol.39
, pp. 245-263
-
-
Budin, I.1
Szostak, J.W.2
-
47
-
-
61349193830
-
Self-Sustained Replication of an RNA Enzyme
-
Lincoln TA, Joyce GF, (2009) Self-Sustained Replication of an RNA Enzyme. Science 323: 1229-1232.
-
(2009)
Science
, vol.323
, pp. 1229-1232
-
-
Lincoln, T.A.1
Joyce, G.F.2
-
48
-
-
77958590981
-
Is life impossible? Information, sex, and the origin of complex organisms
-
Peck JR, Waxman D, (2010) Is life impossible? Information, sex, and the origin of complex organisms. Evolution 64: 3300-3309.
-
(2010)
Evolution
, vol.64
, pp. 3300-3309
-
-
Peck, J.R.1
Waxman, D.2
-
49
-
-
33846610113
-
Phase Diagrams of Quasispecies Theory with Recombination and Horizontal Gene Transfer
-
Park JM, Deem MW, (2007) Phase Diagrams of Quasispecies Theory with Recombination and Horizontal Gene Transfer. Phys. Rev. Lett 98: 058101.
-
(2007)
Phys. Rev. Lett
, vol.98
, pp. 058101
-
-
Park, J.M.1
Deem, M.W.2
-
50
-
-
77953109132
-
Recombination in one and two dimensional fitness landscapes
-
Avetisyan Z, Saakian, DB, (2010) Recombination in one and two dimensional fitness landscapes. Phys. Rev E 81: 051916.
-
(2010)
Phys. Rev E.
, vol.81
, pp. 051916
-
-
Avetisyan, Z.1
Saakian, D.B.2
-
51
-
-
77952562924
-
Effect of Stalling after Mismatches on the Error Catastrophe in Nonenzymatic Nucleic Acid Replication
-
Rajamani S, Ichida JK, Antal T, Treco DA, et al. (2010) Effect of Stalling after Mismatches on the Error Catastrophe in Nonenzymatic Nucleic Acid Replication. J AM CHEM SOC 132: 5880-5885.
-
(2010)
J AM CHEM SOC
, vol.132
, pp. 5880-5885
-
-
Rajamani, S.1
Ichida, J.K.2
Antal, T.3
Treco, D.A.4
-
52
-
-
77953369330
-
Different fitnesses for in vivo and in vitro evolutions due to the finite generation-time effect
-
Saakian DB, Martirosyan AS, Hu CK, (2010) Different fitnesses for in vivo and in vitro evolutions due to the finite generation-time effect. Phys. Rev E 81: 061913.
-
(2010)
Phys. Rev E
, vol.81
, pp. 061913
-
-
Saakian, D.B.1
Martirosyan, A.S.2
Hu, C.K.3
-
53
-
-
46449105488
-
Template-directed synthesis of a genetic polymer in a model protocell
-
Mansy SS, Schrum JP, Krishnamurthy M, Tobe S, et al. (2008) Template-directed synthesis of a genetic polymer in a model protocell. Nature 454: 122-126.
-
(2008)
Nature
, vol.454
, pp. 122-126
-
-
Mansy, S.S.1
Schrum, J.P.2
Krishnamurthy, M.3
Tobe, S.4
-
55
-
-
77956414975
-
Constructing Partial Models of Cells
-
Ichihashi N, Matsuura T, Kita H, Sunami T, Suzuki H, Yomo T, (2010) Constructing Partial Models of Cells. Cold Spring Harbor Perspectives in Biology 2: a004945.
-
(2010)
Cold Spring Harbor Perspectives in Biology
, vol.2
-
-
Ichihashi, N.1
Matsuura, T.2
Kita, H.3
Sunami, T.4
Suzuki, H.5
Yomo, T.6
-
56
-
-
77952658445
-
On the Origin of Primitive Cells: From Nutrient Intake to Elongation of Encapsulated Nucleotides
-
Meierhenrich UJ, Filippi JJ, Meinert C, Vierling P, et al. (2010) On the Origin of Primitive Cells: From Nutrient Intake to Elongation of Encapsulated Nucleotides. Angewandte Chemie-International Edition 49: 3738-3750.
-
(2010)
Angewandte Chemie-International Edition
, vol.49
, pp. 3738-3750
-
-
Meierhenrich, U.J.1
Filippi, J.J.2
Meinert, C.3
Vierling, P.4
-
57
-
-
77956761906
-
Mimivirus: the emerging paradox of quasi-autonomous viruses
-
Claverie JM, Abergel C, (2010) Mimivirus: the emerging paradox of quasi-autonomous viruses. Trends in Genetics 26: 431-437.
-
(2010)
Trends in Genetics
, vol.26
, pp. 431-437
-
-
Claverie, J.M.1
Abergel, C.2
|