-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathreferences.bib
444 lines (400 loc) · 11.6 KB
/
references.bib
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
%% Created using Papers on Fri, 22 Apr 2011.
%% http://mekentosj.com/papers/
@article{Saakian:2009p711,
author = {Saakian, David B and Biebricher, Christof K},
title = {{The intermediate evolution phase in case of truncated selection}},
journal = {arXiv},
year = {2009},
volume = {q-bio.PE},
month = {jan}
}
@article{Ndifon:2009p712,
author = {Ndifon, Wilfred and Plotkin, Joshua B and Dushoff, Jonathan},
title = {{On the accessibility of adaptive phenotypes of a bacterial metabolic network}},
journal = {arXiv},
year = {2009},
volume = {q-bio.PE},
month = {jan}
}
@article{Saakian:2009p713,
author = {Saakian, David B and Fontanari, Jose F},
title = {{The optimization and shock waves in evolution dynamics}},
journal = {arXiv},
year = {2009},
volume = {q-bio.PE},
month = {jan}
}
@article{Cady:2009p718,
author = {Cady, Field and Qian, Hong},
title = {{Open-system thermodynamic analysis of DNA polymerase fidelity}},
journal = {Physical biology},
year = {2009},
volume = {6},
number = {3},
pages = {36011},
month = {jan},
note = {Reference for error rate as a function of shape}
}
@article{Griep:2006p719,
author = {Griep, M and Whitney, S and Nelson, M and Viljoen, H},
title = {{DNA polymerase chain reaction: A model of error frequencies and extension rates}},
journal = {AIChE journal},
year = {2006},
volume = {52},
number = {1}
}
@article{Sigel:1983p720,
author = {Sigel, H and Hofstetter, F},
title = {{Metal-ion-promoted dephosphorylation of the 5'-triphosphates of uridine and thymidine, and a comparison with the reactivity in the corresponding cytidine and adenosine nucleotide systems}},
journal = {European journal of biochemistry / FEBS},
year = {1983},
volume = {132},
number = {3},
pages = {569--577},
month = {may}
}
@article{Petruska:1988p721,
author = {Petruska, J and Goodman, M F and Boosalis, M S and Sowers, L C and Cheong, C and Tinoco, I},
title = {{Comparison between DNA melting thermodynamics and DNA polymerase fidelity}},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {1988},
volume = {85},
number = {17},
pages = {6252--6256},
month = {sep},
note = {Reference for base-pair mismatch ∆∆G}
}
@article{Goodman:1998p723,
author = {Goodman, M F and Fygenson, K D},
title = {{DNA polymerase fidelity: from genetics toward a biochemical understanding}},
journal = {Genetics},
year = {1998},
volume = {148},
number = {4},
pages = {1475--1482},
month = {apr}
}
@article{Taniguchi:1975p725,
author = {Taniguchi, K and Post, R L},
title = {{Synthesis of adenosine triphosphate and exchange between inorganic phosphate and adenosine triphosphate in sodium and potassium ion transport adenosine triphosphatase}},
journal = {The Journal of biological chemistry},
year = {1975},
volume = {250},
number = {8},
pages = {3010--3018},
month = {apr}
}
@article{HernandezLemus:2009p727,
author = {Hernandez-Lemus, Enrique},
title = {{Non-equilibrium thermodynamics of gene expression and transcriptional regulation}},
journal = {arXiv},
year = {2009},
volume = {q-bio.GN},
month = {jan}
}
@article{Bagshaw:1973p728,
author = {Bagshaw, C R and Trentham, D R},
title = {{The reversibility of adenosine triphosphate cleavage by myosin}},
journal = {The Biochemical journal},
year = {1973},
volume = {133},
number = {2},
pages = {323--328},
month = {jun},
note = {Reference for the ∆G of NTP hydrolysis}
}
@article{ANowak:2006p857,
author = {Nowak, Martin A},
title = {{Evolutionary dynamics: exploring the equations of life}},
year = {2006},
pages = {363},
month = {jan}
}
@article{Levene:1934p869,
author = {Levene, PA and Stiller, ET},
title = {{The Synthesis of Ribose-5-phosphoric Acid}},
journal = {Journal of Biological Chemistry},
year = {1934},
volume = {104},
number = {2},
pages = {299--306}
}
@article{Chen:2010p1784,
author = {Chen, Peiqiu and Shakhnovich, Eugene I},
title = {{Thermal Adaptation of Viruses and Bacteria}},
journal = {Biophysical Journal},
year = {2010},
volume = {98},
number = {7},
pages = {1109--1118},
month = {apr}
}
@article{Annila:2008p872,
author = {Annila, A and Annila, E},
title = {{Why did life emerge?}},
journal = {International Journal of Astrobiology},
year = {2008},
volume = {7},
number = {3-4},
pages = {293--300},
note = {Paper of interest}
}
@article{ZannisHadjopoulos:1999p1929,
author = {Zannis-Hadjopoulos, M and Price, G B},
title = {{Eukaryotic DNA replication}},
journal = {Journal of cellular biochemistry},
year = {1999},
volume = {Suppl 32-33},
pages = {1--14},
month = {jan}
}
@article{Brannstrom:2010p1930,
author = {Br{\"a}nnstr{\"o}m, {\~A}ke and Gross, Thilo and Blasius, Bernd and Dieckmann, Ulf},
title = {{Consequences of fluctuating group size for the evolution of cooperation}},
journal = {arXiv},
year = {2010},
volume = {q-bio.PE},
month = {oct}
}
@article{Lane:2010p1931,
author = {Lane, Nick and Martin, William},
title = {{The energetics of genome complexity}},
journal = {Nature},
year = {2010},
volume = {467},
number = {7318},
pages = {929--934},
month = {oct}
}
@article{Case:2010p1932,
author = {Case, Sara O and Durney, Clinton H and Pleimling, Michel and Zia, R K P},
title = {{Cyclic competition of four species: mean field theory and stochastic evolution}},
journal = {arXiv},
year = {2010},
volume = {q-bio.PE},
month = {nov}
}
@article{Wilf:2010p1933,
author = {Wilf, Herbert S and Ewens, Warren J},
title = {{There's plenty of time for evolution}},
journal = {arXiv},
year = {2010},
volume = {math.PR},
month = {oct}
}
@article{Thieffry:1998p913,
author = {Thieffry, D and Sarkar, S},
title = {{Forty years under the central dogma}},
journal = {Trends in biochemical sciences},
year = {1998},
volume = {23},
number = {8},
pages = {312--316},
month = {aug}
}
@article{Asbury:2010p1935,
author = {Asbury, Dee A and Angilletta, Michael J},
title = {{Thermodynamic effects on the evolution of performance curves}},
journal = {The American Naturalist},
year = {2010},
volume = {176},
number = {2},
pages = {E40--9},
month = {aug}
}
@article{Darwin:1883p935,
author = {Darwin, C},
title = {{On the origin of species: by means of natural selection, or, the preservation {\ldots}}},
journal = {books.google.com},
year = {1883},
month = {jan}
}
@article{Castro:2009p953,
author = {Castro, Christian and Smidansky, Eric D and Arnold, Jamie J and Maksimchuk, Kenneth R and Moustafa, Ibrahim and Uchida, Akira and G{\"o}tte, Matthias and Konigsberg, William and Cameron, Craig E},
title = {{Nucleic acid polymerases use a general acid for nucleotidyl transfer}},
journal = {Nature structural {\&} molecular biology},
year = {2009},
volume = {16},
number = {2},
pages = {212--218},
month = {feb},
note = {Reference for polymerase active site}
}
@article{Templeton:1980p954,
author = {Templeton, A R},
title = {{The theory of speciation via the founder principle}},
journal = {Genetics},
year = {1980},
volume = {94},
number = {4},
pages = {1011--1038},
month = {apr}
}
@article{Follmann:2004p955,
author = {Follmann, Hartmut},
title = {{Deoxyribonucleotides: the unusual chemistry and biochemistry of DNA precursors}},
journal = {Chemical Society reviews},
year = {2004},
volume = {33},
number = {4},
pages = {225--233},
month = {may}
}
@article{Chen:2010p1940,
author = {Chen, Peiqiu and Shakhnovich, Eugene I},
title = {{Thermal adaptation of viruses and bacteria}},
journal = {Biophysical Journal},
year = {2010},
volume = {98},
number = {7},
pages = {1109--1118},
month = {apr}
}
@article{Mora:2010p1938,
author = {Mora, Thierry and Bialek, William},
title = {{Are biological systems poised at criticality?}},
journal = {arXiv},
year = {2010},
volume = {q-bio.QM},
month = {dec}
}
@article{Goldenfeld:2010p1939,
author = {Goldenfeld, Nigel and Woese, Carl},
title = {{Life is physics: evolution as a collective phenomenon far from equilibrium}},
journal = {arXiv},
year = {2010},
volume = {q-bio.PE},
month = {nov}
}
@article{Ihaka:1996p1018,
author = {Ihaka, R and Gentleman, R},
title = {{R: A language for data analysis and graphics}},
journal = {Journal of computational and graphical statistics},
year = {1996},
month = {jan}
}
@article{Sasaki:2003p958,
author = {Sasaki, Akira and Nowak, Martin A},
title = {{Mutation landscapes}},
journal = {Journal of theoretical biology},
year = {2003},
volume = {224},
number = {2},
pages = {241--247},
month = {sep},
note = {Reference for conclusions...}
}
@article{Chia:2010p1934,
author = {Chia, Nicholas and Goldenfeld, Nigel},
title = {{Statistical Mechanics of Horizontal Gene Transfer in Evolutionary Ecology}},
journal = {arXiv},
year = {2010},
volume = {q-bio.PE},
month = {dec}
}
@article{Guiol:2009p1937,
author = {Guiol, Herve and Machado, Fabio P and Schinazi, Rinaldo B},
title = {{A stochastic model of evolution}},
journal = {arXiv},
year = {2009},
volume = {math.PR},
month = {sep}
}
@article{Leipe:1999p1040,
author = {Leipe, D D and Aravind, L and Koonin, E V},
title = {{Did DNA replication evolve twice independently?}},
journal = {Nucleic acids research},
year = {1999},
volume = {27},
number = {17},
pages = {3389--3401},
month = {sep}
}
@article{Bianconi:2010p1936,
author = {Bianconi, Ginestra and Rahmede, Christoph},
title = {{Quantum mechanical formalism for biological evolution}},
journal = {arXiv},
year = {2010},
volume = {cond-mat.stat-mech},
month = {nov}
}
@article{Smith:2011wi,
author = {Smith, Reginald D},
title = {{Information Theory and Population Genetics}},
journal = {arXiv.org},
year = {2011},
volume = {q-bio.PE},
month = {mar}
}
@article{Ferenci:1999p703,
author = {Ferenci, T},
title = {{'Growth of bacterial cultures' 50 years on: towards an uncertainty principle instead of constants in bacterial growth kinetics}},
journal = {Research in microbiology},
year = {1999},
volume = {150},
number = {7},
pages = {431--438},
month = {sep},
note = {Reference for bacterial culture growth}
}
@article{Kanayama:2008p704,
author = {Kanayama, Naoki and Takarada, Tohru and Shibata, Hideaki and Kimura, Ayumi and Maeda, Mizuo},
title = {{Evaluation of single-base substitution rate in DNA by affinity capillary electrophoresis}},
journal = {Analytica chimica acta},
year = {2008},
volume = {619},
number = {1},
pages = {101--109},
month = {jun}
}
@article{Zendlova:2009p705,
author = {Zendlov{\'a}, Lucie and {\v R}eha, David and Hocek, Michal and Hobza, Pavel},
title = {{Theoretical Study of the Stability of the DNA Duplexes Modified by a Series of Hydrophobic Base Analogues}},
journal = {Chemistry - A European Journal},
year = {2009},
volume = {15},
number = {31},
pages = {7601--7610},
month = {aug}
}
@article{Barton:2009p706,
author = {Barton, N H and Coe, J B},
title = {{On the application of statistical physics to evolutionary biology}},
journal = {Journal of theoretical biology},
year = {2009},
volume = {259},
number = {2},
pages = {317--324},
month = {jul},
note = {Paper of interest}
}
@article{Nagata:2009p707,
author = {Nagata, Maria Portia B and Yamashita, Kenichi and Miyazaki, Masaya and Nakamura, Hiroyuki and Maeda, Hideaki},
title = {{Enhanced thermal stability and mismatch discrimination of mutation-carrying DNA duplexes and their kinetic and thermodynamic properties in microchannel laminar flow}},
journal = {Analytical Biochemistry},
year = {2009},
volume = {390},
number = {1},
pages = {38--45},
month = {jul}
}
@article{Wirtz:2002p708,
author = {Wirtz, Kai W},
title = {{A generic model for changes in microbial kinetic coefficients}},
journal = {Journal of biotechnology},
year = {2002},
volume = {97},
number = {2},
pages = {147--162},
month = {aug}
}
@article{Quance:2009p710,
author = {Quance, Michael A and Travisano, Michael},
title = {{Effects of temperature on the fitness cost of resistance to bacteriophage T4 in Escherichia coli}},
journal = {Evolution; international journal of organic evolution},
year = {2009},
volume = {63},
number = {6},
pages = {1406--1416},
month = {jun}
}