-
2
-
-
23944499633
-
Horizontal gene transfer, genome innovation and evolution
-
Gogarten, J. P. & Townsend, J. P. Horizontal gene transfer, genome innovation and evolution. Nat. Rev. Microbiol. 3, 679-687 (2005)
-
(2005)
Nat. Rev. Microbiol
, vol.3
, pp. 679-687
-
-
Gogarten, J.P.1
Townsend, J.P.2
-
3
-
-
33947260230
-
Molecular mechanisms of antibacterial multidrug resistance
-
Alekshun, M. N. & Levy, S. B. Molecular mechanisms of antibacterial multidrug resistance. Cell 128, 1037-1050 (2007)
-
(2007)
Cell
, vol.128
, pp. 1037-1050
-
-
Alekshun, M.N.1
Levy, S.B.2
-
5
-
-
84923350697
-
-
CDC Centers for Disease Control and Prevention. Antibiotic resistance threats in the United States
-
CDC. Centers for Disease Control and Prevention. Antibiotic resistance threats in the United States. http://www.cdc.gov/drugresistance/threat-report-2013/ (2013)
-
, vol.2013
-
-
-
6
-
-
0017652638
-
The population biology of bacterial plasmids: A priori conditions for the existence of conjugationally transmitted factors
-
Stewart, F. M. & Levin, B. R. The population biology of bacterial plasmids: a priori conditions for the existence of conjugationally transmitted factors. Genetics 87, 209-228 (1977)
-
(1977)
Genetics
, vol.87
, pp. 209-228
-
-
Stewart, F.M.1
Levin, B.R.2
-
7
-
-
51249172032
-
The existence conditions for bacterial plasmids: Theory and reality
-
Simonsen, L. The existence conditions for bacterial plasmids: theory and reality. Microb. Ecol. 22, 187-205 (1991)
-
(1991)
Microb. Ecol
, vol.22
, pp. 187-205
-
-
Simonsen, L.1
-
8
-
-
0033899751
-
Natural selection, infectious transfer and the existence conditions for bacterial plasmids
-
Bergstrom, C. T., Lipsitch, M. & Levin, B. R. Natural selection, infectious transfer and the existence conditions for bacterial plasmids. Genetics 155, 1505-1519 (2000)
-
(2000)
Genetics
, vol.155
, pp. 1505-1519
-
-
Bergstrom, C.T.1
Lipsitch, M.2
Levin, B.R.3
-
9
-
-
35048860903
-
The persistence of parasitic plasmids
-
Lili, L. N., Britton, N. F. & Feil, E. J. The persistence of parasitic plasmids. Genetics 177, 399-405 (2007)
-
(2007)
Genetics
, vol.177
, pp. 399-405
-
-
Lili, L.N.1
Britton, N.F.2
Feil, E.J.3
-
10
-
-
84861666352
-
Plasmid-mediated horizontal gene transfer is a coevolutionary process
-
Harrison, E. & Brockhurst, M. A. Plasmid-mediated horizontal gene transfer is a coevolutionary process. Trends Microbiol. 20, 262-267 (2012)
-
(2012)
Trends Microbiol
, vol.20
, pp. 262-267
-
-
Harrison, E.1
Brockhurst, M.A.2
-
11
-
-
84880712059
-
Exploring the costs of horizontal gene transfer
-
Baltrus, D. A. Exploring the costs of horizontal gene transfer. Trends Ecol. Evol. 28, 489-495 (2013)
-
(2013)
Trends Ecol. Evol
, vol.28
, pp. 489-495
-
-
Baltrus, D.A.1
-
12
-
-
58149354386
-
Protein material costs: Single atoms can make an evolutionary difference
-
Bragg, J. G. & Wagner, A. Protein material costs: single atoms can make an evolutionary difference. Trends Genet. 25, 5-8 (2009)
-
(2009)
Trends Genet
, vol.25
, pp. 5-8
-
-
Bragg, J.G.1
Wagner, A.2
-
13
-
-
77953115788
-
Cost of unneeded proteins in e coli is reduced after several generations in exponential growth
-
Shachrai, I., Zaslaver, A., Alon, U. & Dekel, E. Cost of unneeded proteins in E. coli is reduced after several generations in exponential growth. Mol. Cell 38, 758-767 (2010)
-
(2010)
Mol. Cell
, vol.38
, pp. 758-767
-
-
Shachrai, I.1
Zaslaver, A.2
Alon, U.3
Dekel, E.4
-
14
-
-
33846511690
-
An H-NS-like stealth protein aids horizontal DNA transmission in bacteria
-
Doyle, M. et al. An H-NS-like stealth protein aids horizontal DNA transmission in bacteria. Science 315, 251-252 (2007)
-
(2007)
Science
, vol.315
, pp. 251-252
-
-
Doyle, M.1
-
15
-
-
67651227404
-
Differential regulation of horizontally acquired and core genome genes by the bacterial modulator H-NS
-
Banos, R. C. et al. Differential regulation of horizontally acquired and core genome genes by the bacterial modulator H-NS. PLoS Genet. 5, e1000513 (2009)
-
(2009)
PLoS Genet
, vol.5
, pp. e1000513
-
-
Banos, R.C.1
-
16
-
-
0024850721
-
Mechanisms that contribute to the stable segregation of plasmids
-
Nordstrom, K. & Austin, S. J. Mechanisms that contribute to the stable segregation of plasmids. Annu. Rev. Genet. 23, 37-69 (1989)
-
(1989)
Annu. Rev. Genet
, vol.23
, pp. 37-69
-
-
Nordstrom, K.1
Austin, S.J.2
-
17
-
-
0345333119
-
Unique type of plasmid maintenance function: Postsegregational killing of plasmid-free cells
-
Gerdes, K., Rasmussen, P. B. & Molin, S. Unique type of plasmid maintenance function: postsegregational killing of plasmid-free cells. Proc. Natl Acad. Sci. USA 83, 3116-3120 (1986)
-
(1986)
Proc. Natl Acad. Sci. USA
, vol.83
, pp. 3116-3120
-
-
Gerdes, K.1
Rasmussen, P.B.2
Molin, S.3
-
18
-
-
33744898365
-
-
eds Sing, C. F. & Hanis, C. L Oxford University Press
-
Levin, B. R. in Genetics of Cellular, Individual, Family, and Population Variation (eds Sing, C. F. & Hanis, C. L.) (Oxford University Press, 1993)
-
(1993)
Genetics of Cellular, Individual, Family, and Population Variation
-
-
Levin, B.R.1
-
19
-
-
34547868946
-
Modelling the spatial dynamics of plasmid transfer and persistence
-
Krone, S. M., Lu, R., Fox, R., Suzuki, H. & Top, E. M. Modelling the spatial dynamics of plasmid transfer and persistence. Microbiology 153, 2803-2816 (2007)
-
(2007)
Microbiology
, vol.153
, pp. 2803-2816
-
-
Krone, S.M.1
Lu, R.2
Fox, R.3
Suzuki, H.4
Top, E.M.5
-
20
-
-
0026513491
-
Genetic changes accompanying increased fitness in evolving populations of Escherichia coli
-
Modi, R. I., Castilla, L. H., Puskas-Rozsa, S., Helling, R. B. & Adams, J. Genetic changes accompanying increased fitness in evolving populations of Escherichia coli. Genetics 130, 241-249 (1992)
-
(1992)
Genetics
, vol.130
, pp. 241-249
-
-
Modi, R.I.1
Castilla, L.H.2
Puskas-Rozsa, S.3
Helling, R.B.4
Adams, J.5
-
21
-
-
0023694037
-
Evolution of a bacteria/plasmid association
-
Bouma, J. E. & Lenski, R. E. Evolution of a bacteria/plasmid association. Nature 335, 351-352 (1988)
-
(1988)
Nature
, vol.335
, pp. 351-352
-
-
Bouma, J.E.1
Lenski, R.E.2
-
22
-
-
78649446843
-
Shifts in the host range of a promiscuous plasmid through parallel evolution of its replication initiation protein
-
Sota, M. et al. Shifts in the host range of a promiscuous plasmid through parallel evolution of its replication initiation protein. ISME J. 4, 1568-1580 (2010)
-
(2010)
ISME J
, vol.4
, pp. 1568-1580
-
-
Sota, M.1
-
23
-
-
0347992016
-
Amelioration of the cost of conjugative plasmid carriage in Eschericha coli K12
-
Dahlberg, C. & Chao, L. Amelioration of the cost of conjugative plasmid carriage in Eschericha coli K12. Genetics 165, 1641-1649 (2003)
-
(2003)
Genetics
, vol.165
, pp. 1641-1649
-
-
Dahlberg, C.1
Chao, L.2
-
24
-
-
33847231339
-
Stability of a promiscuous plasmid in different hosts: No guarantee for a long-term relationship
-
De Gelder, L., Ponciano, J. M., Joyce, P. & Top, E. M. Stability of a promiscuous plasmid in different hosts: no guarantee for a long-term relationship. Microbiology 153, 452-463 (2007)
-
(2007)
Microbiology
, vol.153
, pp. 452-463
-
-
De Gelder, L.1
Ponciano, J.M.2
Joyce, P.3
Top, E.M.4
-
25
-
-
77957976940
-
Mobility of plasmids
-
Smillie, C., Garcillan-Barcia, M. P., Francia, M. V., Rocha, E. P. & de la Cruz, F. Mobility of plasmids. Microbiol. Mol. Biol. Rev. 74, 434-452 (2010)
-
(2010)
Microbiol. Mol. Biol. Rev
, vol.74
, pp. 434-452
-
-
Smillie, C.1
Garcillan-Barcia, M.P.2
Francia, M.V.3
Rocha, E.P.4
De La Cruz, F.5
-
26
-
-
84863856890
-
A degenerate primer MOB typing (DPMT) method to classify gamma-proteobacterial plasmids in clinical and environmental settings
-
Alvarado, A., Garcillan-Barcia, M. P. & de la Cruz, F. A degenerate primer MOB typing (DPMT) method to classify gamma-proteobacterial plasmids in clinical and environmental settings. PLoS ONE 7, e40438 (2012)
-
(2012)
PLoS ONE
, vol.7
, pp. e40438
-
-
Alvarado, A.1
Garcillan-Barcia, M.P.2
De La Cruz, F.3
-
27
-
-
84894324351
-
Positive epistasis between coinfecting plasmids promotes plasmid survival in bacterial populations
-
San Millan, A., Heilbron, K. & Maclean, R. C. Positive epistasis between coinfecting plasmids promotes plasmid survival in bacterial populations ISME J. 8, 601-612 (2013)
-
(2013)
ISME J.
, vol.8
, pp. 601-612
-
-
San Millan, A.1
Heilbron, K.2
Maclean, R.C.3
-
28
-
-
0038026189
-
Characterization of pNI10 plasmid in Pseudomonas, and the construction of an improved Escherichia and Pseudomonas shuttle vector, pNUK73
-
Itoh, N. et al. Characterization of pNI10 plasmid in Pseudomonas, and the construction of an improved Escherichia and Pseudomonas shuttle vector, pNUK73. Appl. Microbiol. Biotechnol. 61, 240-246 (2003)
-
(2003)
Appl. Microbiol. Biotechnol
, vol.61
, pp. 240-246
-
-
Itoh, N.1
-
29
-
-
0024792012
-
Stability of ColE1-like and pBR322-like plasmids in Escherichia coli
-
Ayala-Sanmartn, J. & Gomez-Eichelmann, M. C. Stability of ColE1-like and pBR322-like plasmids in Escherichia coli. Mol. Microbiol. 3, 1745-1752 (1989)
-
(1989)
Mol. Microbiol
, vol.3
, pp. 1745-1752
-
-
Ayala-Sanmartn, J.1
Gomez-Eichelmann, M.C.2
-
30
-
-
0021419102
-
Multimerization of high copy number plasmids causes instability: CoIE1 encodes a determinant essential for plasmid monomerization and stability
-
Summers, D. K. & Sherratt, D. J. Multimerization of high copy number plasmids causes instability: CoIE1 encodes a determinant essential for plasmid monomerization and stability. Cell 36, 1097-1103 (1984)
-
(1984)
Cell
, vol.36
, pp. 1097-1103
-
-
Summers, D.K.1
Sherratt, D.J.2
-
31
-
-
84885344429
-
Fixation probability of mobile genetic elements such as plasmids
-
Tazzyman, S. J. & Bonhoeffer, S. Fixation probability of mobile genetic elements such as plasmids. Theor. Popul. Biol. 90, 49-55 (2013)
-
(2013)
Theor. Popul. Biol
, vol.90
, pp. 49-55
-
-
Tazzyman, S.J.1
Bonhoeffer, S.2
-
32
-
-
77649341401
-
Modelling conjugation with stochastic differential equations
-
Philipsen, K. R., Christiansen, L. E., Hasman, H. & Madsen, H. Modelling conjugation with stochastic differential equations. J. Theor. Biol. 263, 134-142 (2010)
-
(2010)
J. Theor. Biol
, vol.263
, pp. 134-142
-
-
Philipsen, K.R.1
Christiansen, L.E.2
Hasman, H.3
Madsen, H.4
-
33
-
-
0041381036
-
A model for bacterial conjugal gene transfer on solid surfaces
-
Lagido, C., Wilson, I. J., Glover, L. A. & Prosser, J. I. A model for bacterial conjugal gene transfer on solid surfaces. FEMS Microbiol. Ecol. 44, 67-78 (2003)
-
(2003)
FEMS Microbiol. Ecol
, vol.44
, pp. 67-78
-
-
Lagido, C.1
Wilson, I.J.2
Glover, L.A.3
Prosser, J.I.4
-
34
-
-
33847188754
-
The population biology of bacterial plasmids: A hidden Markov model approach
-
Ponciano, J. M., De Gelder, L., Top, E. M. & Joyce, P. The population biology of bacterial plasmids: a hidden Markov model approach. Genetics 176, 957-968 (2007)
-
(2007)
Genetics
, vol.176
, pp. 957-968
-
-
Ponciano, J.M.1
De Gelder, L.2
Top, E.M.3
Joyce, P.4
-
35
-
-
0023445840
-
Effects of segregation and selection on instability of plasmid pACYC184 in Escherichia coli B
-
Lenski, R. E. & Bouma, J. E. Effects of segregation and selection on instability of plasmid pACYC184 in Escherichia coli B. J. Bacteriol. 169, 5314-5316 (1987)
-
(1987)
J. Bacteriol
, vol.169
, pp. 5314-5316
-
-
Lenski, R.E.1
Bouma, J.E.2
-
36
-
-
0020532809
-
Determination of plasmid copy number by fluorescence densitometry
-
Projan, S. J., Carleton, S. & Novick, R. P. Determination of plasmid copy number by fluorescence densitometry. Plasmid 9, 182-190 (1983)
-
(1983)
Plasmid
, vol.9
, pp. 182-190
-
-
Projan, S.J.1
Carleton, S.2
Novick, R.P.3
-
37
-
-
0018978451
-
The population biology of bacterial plasmids: A priori conditions for the existence of mobilizable nonconjugative factors
-
Levin, B. R. & Stewart, F. M. The population biology of bacterial plasmids: a priori conditions for the existence of mobilizable nonconjugative factors. Genetics 94, 425-443 (1980)
-
(1980)
Genetics
, vol.94
, pp. 425-443
-
-
Levin, B.R.1
Stewart, F.M.2
-
38
-
-
0025994917
-
Novel plasmid vectors for gene cloning in Pseudomonas
-
Itoh, N., Koide, Y., Fukuzawa, H., Hirose, S. & Inukai, T. Novel plasmid vectors for gene cloning in Pseudomonas. J. Biochem. 110, 614-621 (1991)
-
(1991)
J. Biochem
, vol.110
, pp. 614-621
-
-
Itoh, N.1
Koide, Y.2
Fukuzawa, H.3
Hirose, S.4
Inukai, T.5
-
39
-
-
84884263676
-
PMdT1 a small ColE1-like plasmid mobilizing a new variant of the aac 6-Ib-cr gene in Salmonella enterica serovar Typhimurium. J. Antimicrob
-
de Toro, M. et al. pMdT1, a small ColE1-like plasmid mobilizing a new variant of the aac(6)-Ib-cr gene in Salmonella enterica serovar Typhimurium. J. Antimicrob. Chemother. 68, 1277-1280 (2013)
-
(2013)
Chemother
, vol.68
, pp. 1277-1280
-
-
De Toro, M.1
-
40
-
-
62949247620
-
CMY-31 Miriagou V. and CMY-36 cephalosporinases encoded by ColE1-like plasmids
-
Zioga, A., Whichard, J. M., Kotsakis, S. D., Tzouvelekis, L. S., Tzelepi, E. & CMY-31, Miriagou V. and CMY-36 cephalosporinases encoded by ColE1-like plasmids. Antimicrob. Agents Chemother. 53, 1256-1259 (2009)
-
(2009)
Antimicrob. Agents Chemother
, vol.53
, pp. 1256-1259
-
-
Zioga, A.1
Whichard, J.M.2
Kotsakis, S.D.3
Tzouvelekis, L.S.4
Tzelepi, E.5
-
41
-
-
77649302989
-
Frequency and diversity of small cryptic plasmids in the genus Rahnella
-
Rozhon, W., Petutschnig, E., Khan, M., Summers, D. K. & Poppenberger, B. Frequency and diversity of small cryptic plasmids in the genus Rahnella. BMC Microbiol. 10, 56 (2010)
-
(2010)
BMC Microbiol
, vol.10
, pp. 56
-
-
Rozhon, W.1
Petutschnig, E.2
Khan, M.3
Summers, D.K.4
Poppenberger, B.5
-
42
-
-
79951542262
-
Retrospective evidence for a biological cost of vancomycin resistance determinants in the absence of glycopeptide selective pressures
-
Johnsen, P. J. et al. Retrospective evidence for a biological cost of vancomycin resistance determinants in the absence of glycopeptide selective pressures. J. Antimicrob. Chemother. 66, 608-610 (2011)
-
(2011)
J. Antimicrob. Chemother
, vol.66
, pp. 608-610
-
-
Johnsen, P.J.1
-
43
-
-
79960095001
-
Selection pressure required for long-term persistence of blaCMY-2-positive IncA/C plasmids
-
Subbiah, M., Top, E. M., Shah, D. H. & Call, D. R. Selection pressure required for long-term persistence of blaCMY-2-positive IncA/C plasmids. Appl. Environ. Microbiol. 77, 4486-4493 (2011)
-
(2011)
Appl. Environ. Microbiol
, vol.77
, pp. 4486-4493
-
-
Subbiah, M.1
Top, E.M.2
Shah, D.H.3
Call, D.R.4
-
44
-
-
25444496227
-
The evolution of a conjugative plasmid and its ability to increase bacterial fitness
-
Dionisio, F., Conceicao, I. C., Marques, A. C., Fernandes, L. & Gordo, I. The evolution of a conjugative plasmid and its ability to increase bacterial fitness. Biol. Lett. 1, 250-252 (2005)
-
(2005)
Biol. Lett
, vol.1
, pp. 250-252
-
-
Dionisio, F.1
Conceicao, I.C.2
Marques, A.C.3
Fernandes, L.4
Gordo, I.5
-
45
-
-
0026280941
-
Plasmid macroevolution: Selection of deletions during adaptation in a nutrient-limited environment
-
Modi, R. I., Wilke, C. M., Rosenzweig, R. F. & Adams, J. Plasmid macroevolution: selection of deletions during adaptation in a nutrient-limited environment. Genetica 84, 195-202 (1991)
-
(1991)
Genetica
, vol.84
, pp. 195-202
-
-
Modi, R.I.1
Wilke, C.M.2
Rosenzweig, R.F.3
Adams, J.4
-
46
-
-
34249822549
-
Data cloning: Easy maximum likelihood estimation for complex ecological models using Bayesian Markov chain Monte Carlo methods
-
Lele, S. R., Dennis, B. & Lutscher, F. Data cloning: easy maximum likelihood estimation for complex ecological models using Bayesian Markov chain Monte Carlo methods. Ecol. Lett. 10, 551-563 (2007)
-
(2007)
Ecol. Lett
, vol.10
, pp. 551-563
-
-
Lele, S.R.1
Dennis, B.2
Lutscher, F.3
-
47
-
-
78650349184
-
Estimability and likelihood inference for generalized linear mixed models using data cloning
-
Lele, S. R., Nadeem, K. & Schmuland, B. Estimability and likelihood inference for generalized linear mixed models using data cloning. J. Am. Stat. Assoc. 105 (2010)
-
(2010)
J. Am. Stat. Assoc
, vol.105
-
-
Lele, S.R.1
Nadeem, K.2
Schmuland, B.3
-
48
-
-
33749531431
-
Mini-Tn7 insertion in bacteria with single attTn7 sites: Example Pseudomonas aeruginosa
-
Choi, K. H. & Schweizer, H. P. mini-Tn7 insertion in bacteria with single attTn7 sites: example Pseudomonas aeruginosa. Nat. Protoc. 1, 153-161 (2006)
-
(2006)
Nat. Protoc
, vol.1
, pp. 153-161
-
-
Choi, K.H.1
Schweizer, H.P.2
-
49
-
-
34547269438
-
Clinical and laboratory standards institute performance standards for antimicrobial disk and dilution susceptibility tests for bacteria isolated from animals
-
Clinical and Laboratory Standards Institute. Performance standards for antimicrobial disk and dilution susceptibility tests for bacteria isolated from animals. Approved standards M31-A3 (CLSI, 2008)
-
(2008)
Approved Standards
, pp. M31-A3
-
-
-
50
-
-
0018800089
-
A rapid alkaline extraction procedure for screening recombinant plasmid DNA
-
Birnboim, H. C. & Doly, J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 7, 1513-1523 (1979)
-
(1979)
Nucleic Acids Res
, vol.7
, pp. 1513-1523
-
-
Birnboim, H.C.1
Doly, J.2
-
51
-
-
0038733705
-
Expression stability of six housekeeping genes: A proposal for resistance gene quantification studies of Pseudomonas aeruginosa by real-time quantitative RT-PCR
-
Savli, H. et al. Expression stability of six housekeeping genes: a proposal for resistance gene quantification studies of Pseudomonas aeruginosa by real-time quantitative RT-PCR. J. Med. Microbiol. 52, 403-408 (2003)
-
(2003)
J. Med. Microbiol
, vol.52
, pp. 403-408
-
-
Savli, H.1
-
52
-
-
80055096384
-
Fitness landscape of antibiotic tolerance in Pseudomonas aeruginosa biofilms
-
Amini, S., Hottes, A. K., Smith, L. E. & Tavazoie, S. Fitness landscape of antibiotic tolerance in Pseudomonas aeruginosa biofilms. PLoS Pathog. 7, e1002298 (2011)
-
(2011)
PLoS Pathog
, vol.7
, pp. e1002298
-
-
Amini, S.1
Hottes, A.K.2
Smith, L.E.3
Tavazoie, S.4
-
53
-
-
79952756140
-
The population dynamics of bacteria in physically structured habitats and the adaptive virtue of random motility
-
Wei, Y. et al. The population dynamics of bacteria in physically structured habitats and the adaptive virtue of random motility. Proc. Natl Acad. Sci. USA 108, 4047-4052 (2011)
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 4047-4052
-
-
Wei, Y.1
-
54
-
-
84856468953
-
NGS QC Toolkit: A toolkit for quality control of next generation sequencing data
-
Patel, R. K. & Jain, M. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS ONE 7, e30619 (2012)
-
(2012)
PLoS ONE
, vol.7
, pp. e30619
-
-
Patel, R.K.1
Jain, M.2
-
55
-
-
77949587649
-
Fast and accurate long-read alignment with Burrows-Wheeler transform
-
Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589-595 (2010)
-
(2010)
Bioinformatics
, vol.26
, pp. 589-595
-
-
Li, H.1
Durbin, R.2
-
56
-
-
79955483667
-
A framework for variation discovery and genotyping using next-generation DNA sequencing data
-
DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491-498 (2011)
-
(2011)
Nat. Genet
, vol.43
, pp. 491-498
-
-
Depristo, M.A.1
-
57
-
-
79960405019
-
The variant call format and VCFtools
-
Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156-2158 (2011)
-
(2011)
Bioinformatics
, vol.27
, pp. 2156-2158
-
-
Danecek, P.1
-
58
-
-
84862506964
-
A program for annotating and predicting the effects of single nucleotide polymorphisms SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; Iso-2; iso-3
-
Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6, 80-92 (2012)
-
(2012)
Fly Austin
, vol.6
, pp. 80-92
-
-
Cingolani, P.1
-
59
-
-
69549116107
-
BreakDancer: An algorithm for high-resolution mapping of genomic structural variation
-
Chen, K. et al. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat. Methods 6, 677-681 (2009)
-
(2009)
Nat. Methods
, vol.6
, pp. 677-681
-
-
Chen, K.1
-
60
-
-
70350694443
-
Pindel: A pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
-
Ye, K., Schulz, M. H., Long, Q., Apweiler, R. & Ning, Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25, 2865-2871 (2009)
-
(2009)
Bioinformatics
, vol.25
, pp. 2865-2871
-
-
Ye, K.1
Schulz, M.H.2
Long, Q.3
Apweiler, R.4
Ning, Z.5
-
61
-
-
84856561659
-
Control-FREEC: A tool for assessing copy number and allelic content using next-generation sequencing data
-
Boeva, V. et al. Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. Bioinformatics 28, 423-425 (2012)
-
(2012)
Bioinformatics
, vol.28
, pp. 423-425
-
-
Boeva, V.1
-
62
-
-
84870837088
-
The GEM mapper: Fast, accurate and versatile alignment by filtration
-
Marco-Sola, S., Sammeth, M., Guigo, R. & Ribeca, P. The GEM mapper: fast, accurate and versatile alignment by filtration. Nat. Methods 9, 1185-1188 (2012)
-
(2012)
Nat. Methods
, vol.9
, pp. 1185-1188
-
-
Marco-Sola, S.1
Sammeth, M.2
Guigo, R.3
Ribeca, P.4
-
63
-
-
84856246802
-
De novo assembly and genotyping of variants using colored de Bruijn graphs
-
Iqbal, Z., Caccamo, M., Turner, I., Flicek, P. & McVean, G. De novo assembly and genotyping of variants using colored de Bruijn graphs. Nat. Genet. 44, 226-232 (2012)
-
(2012)
Nat. Genet
, vol.44
, pp. 226-232
-
-
Iqbal, Z.1
Caccamo, M.2
Turner, I.3
Flicek, P.4
McVean, G.5
-
64
-
-
70350641005
-
Genome evolution and adaptation in a long-term experiment with Escherichia coli
-
Barrick, J. E. et al. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461, 1243-1247 (2009)
-
(2009)
Nature
, vol.461
, pp. 1243-1247
-
-
Barrick, J.E.1
-
65
-
-
43149115851
-
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
-
Zerbino, D. R. & 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.R.1
Birney, E.2
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