-
1
-
-
85011620410
-
Somatic clonal evolution: a selection-centric perspective
-
COI: 1:CAS:528:DC%2BC2sXit1Skurw%3D
-
Scott, J. & Marusyk, A. Somatic clonal evolution: a selection-centric perspective. Biochim. Biophys. Acta Rev. Cancer 1867, 139–150 (2017)
-
(2017)
Biochim. Biophys. Acta Rev. Cancer
, vol.1867
, pp. 139-150
-
-
Scott, J.1
Marusyk, A.2
-
2
-
-
77957980707
-
Origins and evolution of antibiotic resistance
-
COI: 1:CAS:528:DC%2BC3cXhsVSqurnO
-
Davies, J. & Davies, D. Origins and evolution of antibiotic resistance. Microbiol. Mol. Biol. Rev. 74, 417–433 (2010)
-
(2010)
Microbiol. Mol. Biol. Rev.
, vol.74
, pp. 417-433
-
-
Davies, J.1
Davies, D.2
-
3
-
-
84856013431
-
Clonal evolution in cancer
-
COI: 1:CAS:528:DC%2BC38Xps1CrtA%3D%3D
-
Greaves, M. & Maley, C. C. Clonal evolution in cancer. Nature 481, 306–313 (2012)
-
(2012)
Nature
, vol.481
, pp. 306-313
-
-
Greaves, M.1
Maley, C.C.2
-
4
-
-
1442355578
-
HIV drug resistance
-
COI: 1:CAS:528:DC%2BD2cXhvFGjs7c%3D
-
Clavel, F. & Hance, A. J. HIV drug resistance. N. Engl. J. Med. 350, 1023–1035 (2004)
-
(2004)
N. Engl. J. Med.
, vol.350
, pp. 1023-1035
-
-
Clavel, F.1
Hance, A.J.2
-
5
-
-
0000262081
-
The evolution of insecticide resistance: have the insects won?
-
COI: 1:STN:280:DC%2BC3M7gvFClsQ%3D%3D
-
Mallet, J. The evolution of insecticide resistance: have the insects won? Trends Ecol. Evol. 4, 336–340 (1989)
-
(1989)
Trends Ecol. Evol.
, vol.4
, pp. 336-340
-
-
Mallet, J.1
-
6
-
-
54149088214
-
Epistasis—the essential role of gene interactions in the structure and evolution of genetic systems
-
COI: 1:CAS:528:DC%2BD1cXht1Ggu77J
-
Phillips, P. C. Epistasis—the essential role of gene interactions in the structure and evolution of genetic systems. Nat. Rev. Genet. 9, 855 (2008)
-
(2008)
Nat. Rev. Genet.
, vol.9
, pp. 855
-
-
Phillips, P.C.1
-
7
-
-
33645666942
-
Darwinian evolution can follow only very few mutational paths to fitter proteins
-
COI: 1:CAS:528:DC%2BD28XjtFalsLs%3D
-
Weinreich, D. M., Delaney, N. F., DePristo, M. A. & Hartl, D. L. Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312, 111–114 (2006)
-
(2006)
Science
, vol.312
, pp. 111-114
-
-
Weinreich, D.M.1
Delaney, N.F.2
DePristo, M.A.3
Hartl, D.L.4
-
8
-
-
33846551980
-
Empirical fitness landscapes reveal accessible evolutionary paths
-
COI: 1:CAS:528:DC%2BD2sXos12ntA%3D%3D
-
Poelwijk, F. J., Kiviet, D. J., Weinreich, D. M. & Tans, S. J. Empirical fitness landscapes reveal accessible evolutionary paths. Nature 445, 383 (2007)
-
(2007)
Nature
, vol.445
, pp. 383
-
-
Poelwijk, F.J.1
Kiviet, D.J.2
Weinreich, D.M.3
Tans, S.J.4
-
9
-
-
79960624826
-
Hidden randomness between fitness landscapes limits reverse evolution
-
Tan, L., Serene, S., Chao, H. X. & Gore, J. Hidden randomness between fitness landscapes limits reverse evolution. Phys. Rev. Lett. 106, 198102 (2011)
-
(2011)
Phys. Rev. Lett.
, vol.106
, pp. 198102
-
-
Tan, L.1
Serene, S.2
Chao, H.X.3
Gore, J.4
-
10
-
-
84884680278
-
Use of collateral sensitivity networks to design drug cycling protocols that avoid resistance development
-
Imamovic, L. & Sommer, M. O. Use of collateral sensitivity networks to design drug cycling protocols that avoid resistance development. Sci. Transl. Med. 5, 204ra132–204ra132 (2013)
-
(2013)
Sci. Transl. Med.
, vol.5
, pp. 204ra132
-
-
Imamovic, L.1
Sommer, M.O.2
-
11
-
-
84925934394
-
Alternating antibiotic treatments constrain evolutionary paths to multidrug resistance
-
COI: 1:CAS:528:DC%2BC2cXhsFyhtbbL
-
Kim, S., Lieberman, T. D. & Kishony, R. Alternating antibiotic treatments constrain evolutionary paths to multidrug resistance. Proc. Natl Acad. Sci. USA 111, 14494–14499 (2014)
-
(2014)
Proc. Natl Acad. Sci. USA
, vol.111
, pp. 14494-14499
-
-
Kim, S.1
Lieberman, T.D.2
Kishony, R.3
-
12
-
-
84943537607
-
Steering evolution with sequential therapy to prevent the emergence of bacterial antibiotic resistance
-
Nichol, D. et al. Steering evolution with sequential therapy to prevent the emergence of bacterial antibiotic resistance. PLoS Comput. Biol. 11, e1004493 (2015)
-
(2015)
PLoS Comput. Biol.
, vol.11
-
-
Nichol, D.1
-
13
-
-
84929493835
-
Using a sequential regimen to eliminate bacteria at sublethal antibiotic dosages
-
Fuentes-Hernandez, A. et al. Using a sequential regimen to eliminate bacteria at sublethal antibiotic dosages. PLoS Biol. 13, e1002104 (2015)
-
(2015)
PLoS Biol.
, vol.13
-
-
Fuentes-Hernandez, A.1
-
14
-
-
84555171441
-
Evolutionary paths to antibiotic resistance under dynamically sustained drug selection
-
COI: 1:CAS:528:DC%2BC3MXhs1eisbbN
-
Toprak, E. et al. Evolutionary paths to antibiotic resistance under dynamically sustained drug selection. Nat. Genet. 44, 101 (2012)
-
(2012)
Nat. Genet.
, vol.44
, pp. 101
-
-
Toprak, E.1
-
15
-
-
84889590334
-
Bacterial evolution of antibiotic hypersensitivity
-
Lázár, V. et al. Bacterial evolution of antibiotic hypersensitivity. Mol. Syst. Biol. 9, 700 (2013)
-
(2013)
Mol. Syst. Biol.
, vol.9
, pp. 700
-
-
Lázár, V.1
-
16
-
-
84910654894
-
Prediction of resistance development against drug combinations by collateral responses to component drugs
-
Munck, C., Gumpert, H. K., Wallin, A. I. N., Wang, H. H. & Sommer, M. O. Prediction of resistance development against drug combinations by collateral responses to component drugs. Sci. Transl. Med. 6, 262ra156–262ra156 (2014)
-
(2014)
Sci. Transl. Med.
, vol.6
, pp. 262ra156
-
-
Munck, C.1
Gumpert, H.K.2
Wallin, A.I.N.3
Wang, H.H.4
Sommer, M.O.5
-
17
-
-
84922718635
-
Prediction of antibiotic resistance by gene expression profiles
-
COI: 1:CAS:528:DC%2BC2MXjvFWqsbk%3D
-
Suzuki, S., Horinouchi, T. & Furusawa, C. Prediction of antibiotic resistance by gene expression profiles. Nat. Commun. 5, 5792 (2014)
-
(2014)
Nat. Commun.
, vol.5
-
-
Suzuki, S.1
Horinouchi, T.2
Furusawa, C.3
-
18
-
-
84928794246
-
Collateral resistance and sensitivity modulate evolution of high-level resistance to drug combination treatment in staphylococcus aureus
-
COI: 1:CAS:528:DC%2BC28XhtlWnu7zN
-
Rodriguez de Evgrafov, M., Gumpert, H., Munck, C., Thomsen, T. T. & Sommer, M. O. Collateral resistance and sensitivity modulate evolution of high-level resistance to drug combination treatment in staphylococcus aureus. Mol. Biol. Evol. 32, 1175–1185 (2015)
-
(2015)
Mol. Biol. Evol.
, vol.32
, pp. 1175-1185
-
-
Rodriguez de Evgrafov, M.1
Gumpert, H.2
Munck, C.3
Thomsen, T.T.4
Sommer, M.O.5
-
19
-
-
84975717783
-
Exploiting temporal collateral sensitivity in tumor clonal evolution
-
COI: 1:CAS:528:DC%2BC28XjsVanu7Y%3D
-
Zhao, B. et al. Exploiting temporal collateral sensitivity in tumor clonal evolution. Cell 165, 234–246 (2016)
-
(2016)
Cell
, vol.165
, pp. 234-246
-
-
Zhao, B.1
-
20
-
-
85018251806
-
Collateral sensitivity networks reveal evolutionary instability and novel treatment strategies in ALK mutated non-small cell lung cancer
-
Dhawan, A. et al. Collateral sensitivity networks reveal evolutionary instability and novel treatment strategies in ALK mutated non-small cell lung cancer. Sci. Rep. 7, 1232 (2017)
-
(2017)
Sci. Rep.
, vol.7
-
-
Dhawan, A.1
-
21
-
-
84877100240
-
Analysis of mechanisms of acquired resistance to EGFR TKI therapy in 155 patients with EGFR-mutant lung cancers
-
COI: 1:CAS:528:DC%2BC3sXlvFyjtrw%3D
-
Yu, H. et al. Analysis of mechanisms of acquired resistance to EGFR TKI therapy in 155 patients with EGFR-mutant lung cancers. Clin. Cancer Res. 19, 2240–2247 (2013)
-
(2013)
Clin. Cancer Res.
, vol.19
, pp. 2240-2247
-
-
Yu, H.1
-
22
-
-
84923611351
-
Molecular mechanisms of antibiotic resistance
-
COI: 1:CAS:528:DC%2BC2cXitVSitbzP
-
Blair, J. M., Webber, M. A., Baylay, A. J., Ogbolu, D. O. & Piddock, L. J. Molecular mechanisms of antibiotic resistance. Nat. Rev. Microbiol. 13, 42 (2015)
-
(2015)
Nat. Rev. Microbiol.
, vol.13
, pp. 42
-
-
Blair, J.M.1
Webber, M.A.2
Baylay, A.J.3
Ogbolu, D.O.4
Piddock, L.J.5
-
23
-
-
85047793125
-
-
Preprint
-
Jiao, Y. J., Baym, M., Veres, A. & Kishony, R. Population diversity jeopardizes the efficacy of antibiotic cycling. Preprint available at https://www.biorxiv.org/content/early/2016/10/20/082107 (2016)
-
(2016)
Population Diversity Jeopardizes the Efficacy of Antibiotic Cycling
-
-
Jiao, Y.J.1
Baym, M.2
Veres, A.3
Kishony, R.4
-
24
-
-
85037593154
-
Alternative evolutionary paths to bacterial antibiotic resistance cause distinct collateral effects
-
COI: 1:CAS:528:DC%2BC1cXhvFarurfJ
-
Barbosa, C. et al. Alternative evolutionary paths to bacterial antibiotic resistance cause distinct collateral effects. Mol. Biol. Evol. 34, 2229–2244 (2017)
-
(2017)
Mol. Biol. Evol.
, vol.34
, pp. 2229-2244
-
-
Barbosa, C.1
-
25
-
-
84906751681
-
Strength of selection pressure is an important parameter contributing to the complexity of antibiotic resistance evolution
-
COI: 1:CAS:528:DC%2BC28Xht1CitLvO
-
Oz, T. et al. Strength of selection pressure is an important parameter contributing to the complexity of antibiotic resistance evolution. Mol. Biol. Evol. 31, 2387–2401 (2014)
-
(2014)
Mol. Biol. Evol.
, vol.31
, pp. 2387-2401
-
-
Oz, T.1
-
26
-
-
0000907353
-
The roles of mutation, inbreeding, crossbreeding and selection in evolution
-
Wright, S. The roles of mutation, inbreeding, crossbreeding and selection in evolution. In Proceedings of the Sixth International Congress on Genetics, vol. 1, 356–366 (1932)
-
(1932)
Proceedings of the Sixth International Congress on Genetics
, vol.1
, pp. 356-366
-
-
Wright, S.1
-
27
-
-
84902775598
-
Empirical fitness landscapes and the predictability of evolution
-
De Visser, J. A. G. & Krug, J. Empirical fitness landscapes and the predictability of evolution. Nat. Rev. Genet. 15, 480 (2014)
-
(2014)
Nat. Rev. Genet.
, vol.15
, pp. 480
-
-
De Visser, J.A.G.1
Krug, J.2
-
28
-
-
84931274969
-
Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes
-
COI: 1:CAS:528:DC%2BC2MXhtF2it7fK
-
Palmer, A. C. et al. Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes. Nat. Commun. 6, 7385 (2015)
-
(2015)
Nat. Commun.
, vol.6
-
-
Palmer, A.C.1
-
29
-
-
84929094800
-
Rational design of antibiotic treatment plans: a treatment strategy for managing evolution and reversing resistance
-
Mira, P. M. et al. Rational design of antibiotic treatment plans: a treatment strategy for managing evolution and reversing resistance. PLoS One 10, e0122283 (2015)
-
(2015)
PLoS One
, vol.10
-
-
Mira, P.M.1
-
30
-
-
0037025378
-
EnvZ–OmpR interaction and osmoregulation in Escherichia coli
-
COI: 1:CAS:528:DC%2BD38XltlOhsr8%3D
-
Cai, S. J. & Inouye, M. EnvZ–OmpR interaction and osmoregulation in Escherichia coli. J. Biol. Chem. 277, 24155–24161 (2002)
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 24155-24161
-
-
Cai, S.J.1
Inouye, M.2
-
31
-
-
0020444488
-
Role of porin proteins ompf and ompc in the permeation of beta-lactams
-
COI: 1:CAS:528:DyaL3sXjtFahsA%3D%3D
-
Jaffe, A., Chabbert, Y. A. & Semonin, O. Role of porin proteins ompf and ompc in the permeation of beta-lactams. Antimicrob. Agents Chemother. 22, 942–948 (1982)
-
(1982)
Antimicrob. Agents Chemother.
, vol.22
, pp. 942-948
-
-
Jaffe, A.1
Chabbert, Y.A.2
Semonin, O.3
-
32
-
-
84861144335
-
Loss of outer membrane protein c in escherichia coli contributes both to antibiotic resistance and escaping antibody-dependent bactericidal activity
-
COI: 1:CAS:528:DC%2BC38XmsVKmsLg%3D
-
Liu, Y.-F. et al. Loss of outer membrane protein c in escherichia coli contributes both to antibiotic resistance and escaping antibody-dependent bactericidal activity. Infect. Immun. 80, 1815–1822 (2012)
-
(2012)
Infect. Immun.
, vol.80
, pp. 1815-1822
-
-
Liu, Y.F.1
-
33
-
-
84965014204
-
Combinations of mutations in envz, ftsi, mrda, acrb and acrr can cause high-level carbapenem resistance in escherichia coli
-
Adler, M., Anjum, M., Andersson, D. I. & Sandegren, L. Combinations of mutations in envz, ftsi, mrda, acrb and acrr can cause high-level carbapenem resistance in escherichia coli. J. Antimicrob. Chemother. 71, 1188–1198 (2016)
-
(2016)
J. Antimicrob. Chemother.
, vol.71
, pp. 1188-1198
-
-
Adler, M.1
Anjum, M.2
Andersson, D.I.3
Sandegren, L.4
-
34
-
-
21244473267
-
Maintaining a healthy SPANC balance through regulatory and mutational adaptation
-
COI: 1:CAS:528:DC%2BD2MXmtVemsb4%3D
-
Ferenci, T. Maintaining a healthy SPANC balance through regulatory and mutational adaptation. Mol. Microbiol. 57, 1–8 (2005)
-
(2005)
Mol. Microbiol.
, vol.57
, pp. 1-8
-
-
Ferenci, T.1
-
35
-
-
66349121917
-
Adaptive therapy
-
COI: 1:CAS:528:DC%2BD1MXmsFGksrk%3D
-
Gatenby, R. A., Silva, A. S., Gillies, R. J. & Frieden, B. R. Adaptive therapy. Cancer Res. 69, 4894–4903 (2009)
-
(2009)
Cancer Res.
, vol.69
, pp. 4894-4903
-
-
Gatenby, R.A.1
Silva, A.S.2
Gillies, R.J.3
Frieden, B.R.4
-
36
-
-
84959450201
-
Exploiting evolutionary principles to prolong tumor control in preclinical models of breast cancer
-
Enriquez-Navas, P. M. et al. Exploiting evolutionary principles to prolong tumor control in preclinical models of breast cancer. Sci. Transl. Med. 8, 327ra24–327ra24 (2016)
-
(2016)
Sci. Transl. Med.
, vol.8
, pp. 327ra24
-
-
Enriquez-Navas, P.M.1
-
37
-
-
85046548646
-
Optimal therapy scheduling based on a pair of collaterally sensitive drugs
-
Yoon, N., Vander Velde, R., Marusyk, A., Scott, G.S. Optimal therapy scheduling based on a pair of collaterally sensitive drugs. Bull. Math. Biol. 80, 1776-1809 (2018)
-
(2018)
Bull. Math. Biol.
, vol.80
, pp. 1776-1809
-
-
Yoon, N.1
Vander Velde, R.2
Marusyk, A.3
Scott, G.S.4
-
38
-
-
85045535425
-
It's too soon to pull the plug on antibiotic cycling
-
P
-
Nichol, D., Bonomo, R.A., Scott, J.G. It's too soon to pull the plug on antibiotic cycling. Lancet. Infect. Dis. 18, P493 (2018)
-
(2018)
Lancet. Infect. Dis.
, vol.18
, pp. 493
-
-
Nichol, D.1
Bonomo, R.A.2
Scott, J.G.3
-
39
-
-
84875138391
-
Building a morbidostat: an automated continuous-culture device for studying bacterial drug resistance under dynamically sustained drug inhibition
-
Toprak, E. et al. Building a morbidostat: an automated continuous-culture device for studying bacterial drug resistance under dynamically sustained drug inhibition. Nat. Protoc. 8, 555 (2013)
-
(2013)
Nat. Protoc.
, vol.8
, pp. 555
-
-
Toprak, E.1
-
40
-
-
51649093471
-
Understanding the limits to generalizability of experimental evolutionary models
-
COI: 1:CAS:528:DC%2BD1cXhtV2qtLrE
-
Forde, S. E. et al. Understanding the limits to generalizability of experimental evolutionary models. Nature 455, 220 (2008)
-
(2008)
Nature
, vol.455
, pp. 220
-
-
Forde, S.E.1
-
41
-
-
79955423458
-
A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase
-
COI: 1:CAS:528:DC%2BC3MXjvVOhsLk%3D
-
Hinkley, T. et al. A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase. Nat. Genet. 43, 487 (2011)
-
(2011)
Nat. Genet.
, vol.43
, pp. 487
-
-
Hinkley, T.1
-
42
-
-
84859257158
-
Exploring the complexity of the HIV-1 fitness landscape
-
COI: 1:CAS:528:DC%2BC38XktF2htbo%3D
-
Kouyos, R. D. et al. Exploring the complexity of the HIV-1 fitness landscape. PLoS Genet. 8, e1002551 (2012)
-
(2012)
PLoS Genet.
, vol.8
-
-
Kouyos, R.D.1
-
43
-
-
0033984076
-
High-level expression of chromosomally encoded SHV-1 β-lactamase and an outer membrane protein change confer resistance to ceftazidime and piperacillin-tazobactam in a clinical isolate of Klebsiella pneumoniae
-
COI: 1:CAS:528:DC%2BD3cXmvFGgtA%3D%3D
-
Rice, L. B. et al. High-level expression of chromosomally encoded SHV-1 β-lactamase and an outer membrane protein change confer resistance to ceftazidime and piperacillin-tazobactam in a clinical isolate of Klebsiella pneumoniae. Antimicrob. Agents Chemother. 44, 362–367 (2000)
-
(2000)
Antimicrob. Agents Chemother.
, vol.44
, pp. 362-367
-
-
Rice, L.B.1
-
44
-
-
85060306797
-
-
Clinical & Laboratory Standards Institute, P., Wayne. Performance standards for antimicrobial susceptibility testing: 22nd informational supplement. CLSI document M100-S22. (2012)
-
-
-
-
45
-
-
43149115851
-
Velvet: algorithms for de novo short read assembly using de bruijn graphs
-
COI: 1:CAS:528:DC%2BD1cXlslChsLg%3D
-
Zerbino, D. & Birney, E. Velvet: algorithms for de novo short read assembly using de bruijn graphs. Genome Res. 18, 821–829 (2008)
-
(2008)
Genome Res.
, vol.18
, pp. 821-829
-
-
Zerbino, D.1
Birney, E.2
-
46
-
-
77956295988
-
The genome analysis toolkit: a mapreduce framework for analyzing next-generation dna sequencing data
-
COI: 1:CAS:528:DC%2BC3cXhtFeru7jM
-
McKenna, A. et al. The genome analysis toolkit: a mapreduce framework for analyzing next-generation dna sequencing data. Genome Res. 20, 1297–1303 (2010)
-
(2010)
Genome Res.
, vol.20
, pp. 1297-1303
-
-
McKenna, A.1
-
47
-
-
33644873699
-
Isfinder: the reference centre for bacterial insertion sequences
-
COI: 1:CAS:528:DC%2BD28XisFOhug%3D%3D
-
Siguier, P., Pérochon, J., Lestrade, L., Mahillon, J. & Chandler, M. Isfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res. 34, D32–D36 (2006)
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. D32-D36
-
-
Siguier, P.1
Pérochon, J.2
Lestrade, L.3
Mahillon, J.4
Chandler, M.5
-
48
-
-
85045997584
-
Quantitative assessment of insertion sequence impact on bacterial genome architecture
-
PID: 28348858
-
Adams, M. D., Bishop, B. & Wright, M. S. Quantitative assessment of insertion sequence impact on bacterial genome architecture. Microb. Genom. 2, e000062 (2016)
-
(2016)
Microb. Genom.
, vol.2
-
-
Adams, M.D.1
Bishop, B.2
Wright, M.S.3
|