-
1
-
-
0035969492
-
Index case of fatal inhalational anthrax due to bioterrorism in the United States
-
Bush LM, Abrams BH, Beall A, Johnson CC. Index case of fatal inhalational anthrax due to bioterrorism in the United States. N Engl J Med 2001, 345:1607-1610.
-
(2001)
N Engl J Med
, vol.345
, pp. 1607-1610
-
-
Bush, L.M.1
Abrams, B.H.2
Beall, A.3
Johnson, C.C.4
-
2
-
-
0036775353
-
First case of bioterrorism-related inhalational anthrax in the United States, Palm Beach County, Florida, 2001
-
Traeger MS, Wiersma ST, Rosenstein NE, Malecki JM, Shepard CW, Raghunathan PL, Pillai SP, Popovic T, Quinn CP, Meyer RF, Zaki SR, Kumar S, Bruce SM, Sejvar JJ, Dull PM, Tierney BC, Jones JD, Perkins BA, Team FI. First case of bioterrorism-related inhalational anthrax in the United States, Palm Beach County, Florida, 2001. Emerg Infect Dis 2002, 8:1029-1034.
-
(2002)
Emerg Infect Dis
, vol.8
, pp. 1029-1034
-
-
Traeger, M.S.1
Wiersma, S.T.2
Rosenstein, N.E.3
Malecki, J.M.4
Shepard, C.W.5
Raghunathan, P.L.6
Pillai, S.P.7
Popovic, T.8
Quinn, C.P.9
Meyer, R.F.10
Zaki, S.R.11
Kumar, S.12
Bruce, S.M.13
Sejvar, J.J.14
Dull, P.M.15
Tierney, B.C.16
Jones, J.D.17
Perkins, B.A.18
Team, F.I.19
-
3
-
-
0035202697
-
Anthrax Bioterrorism Investigation Team: Bioterrorism-related inhalational anthrax: the first 10 cases reported in the United States
-
Jernigan JA, Stephens DS, Ashford DA, Omenaca C, Topiel MS, Galbraith M, Tapper M, Fisk TL, Zaki S, Popovic T, Meyer RF, Quinn CP, Harper SA, Fridkin SK, Sejvar JJ, Shepard CW, McConnell M, Guarner J, Shieh WJ, Malecki JM, Gerberding JL, Hughes JM, Perkins BA. Anthrax Bioterrorism Investigation Team: Bioterrorism-related inhalational anthrax: the first 10 cases reported in the United States. Emerg Infect Dis 2001, 7:933-944.
-
(2001)
Emerg Infect Dis
, vol.7
, pp. 933-944
-
-
Jernigan, J.A.1
Stephens, D.S.2
Ashford, D.A.3
Omenaca, C.4
Topiel, M.S.5
Galbraith, M.6
Tapper, M.7
Fisk, T.L.8
Zaki, S.9
Popovic, T.10
Meyer, R.F.11
Quinn, C.P.12
Harper, S.A.13
Fridkin, S.K.14
Sejvar, J.J.15
Shepard, C.W.16
McConnell, M.17
Guarner, J.18
Shieh, W.J.19
Malecki, J.M.20
Gerberding, J.L.21
Hughes, J.M.22
Perkins, B.A.23
more..
-
4
-
-
0036774151
-
Opening a bacillus anthracis-containing envelope, Capitol Hill, Washington, D.C.: the public health response
-
Hsu VP, Lukacs SL, Handzel T, Hayslett J, Harper S, Hales T, Semenova VA, Romero-Steiner S, Elie C, Quinn CP, Khabbaz R, Khan AS, Martin G, Eisold J, Schuchat A, Hajjeh RA. Opening a bacillus anthracis-containing envelope, Capitol Hill, Washington, D.C.: the public health response. Emerg Infect Dis 2002, 8:1039-1043.
-
(2002)
Emerg Infect Dis
, vol.8
, pp. 1039-1043
-
-
Hsu, V.P.1
Lukacs, S.L.2
Handzel, T.3
Hayslett, J.4
Harper, S.5
Hales, T.6
Semenova, V.A.7
Romero-Steiner, S.8
Elie, C.9
Quinn, C.P.10
Khabbaz, R.11
Khan, A.S.12
Martin, G.13
Eisold, J.14
Schuchat, A.15
Hajjeh, R.A.16
-
6
-
-
2142705302
-
Microbial forensics: building a national capacity to investigate bioterrorism
-
Murch RS. Microbial forensics: building a national capacity to investigate bioterrorism. Biosecur Bioterror 2003, 1:117-122.
-
(2003)
Biosecur Bioterror
, vol.1
, pp. 117-122
-
-
Murch, R.S.1
-
7
-
-
0141868978
-
Public health
-
Budowle B, Schutzer SE, Einseln A, Kelley LC, Walsh AC, Smith JA, Marrone BL, Robertson J, Campos J. Public health. Building microbial forensics as a response to bioterrorism. Science 2003, 301:1852-1853.
-
(2003)
Building microbial forensics as a response to bioterrorism. Science
, vol.301
, pp. 1852-1853
-
-
Budowle, B.1
Schutzer, S.E.2
Einseln, A.3
Kelley, L.C.4
Walsh, A.C.5
Smith, J.A.6
Marrone, B.L.7
Robertson, J.8
Campos, J.9
-
8
-
-
33744527832
-
Microbial forensics: application to bioterrorism preparedness and response
-
Morse SA, Budowle B. Microbial forensics: application to bioterrorism preparedness and response. Infect Dis Clin North Am 2006, 20:455-473.
-
(2006)
Infect Dis Clin North Am
, vol.20
, pp. 455-473
-
-
Morse, S.A.1
Budowle, B.2
-
9
-
-
0036314263
-
Bioterrorism preparedness. II: the community and emergency medical services systems
-
Flowers LK, Mothershead JL, Blackwell TH. Bioterrorism preparedness. II: the community and emergency medical services systems. Emerg Med Clin North Am 2002, 20:457-476.
-
(2002)
Emerg Med Clin North Am
, vol.20
, pp. 457-476
-
-
Flowers, L.K.1
Mothershead, J.L.2
Blackwell, T.H.3
-
10
-
-
0344526684
-
Detecting biothreat agents: the Laboratory Response Network
-
Morse SA, Kellogg RB, Perry S, Meyer RF, Bray D, Nichelson D, Miller JM. Detecting biothreat agents: the Laboratory Response Network. ASM News 2003, 69:433-437.
-
(2003)
ASM News
, vol.69
, pp. 433-437
-
-
Morse, S.A.1
Kellogg, R.B.2
Perry, S.3
Meyer, R.F.4
Bray, D.5
Nichelson, D.6
Miller, J.M.7
-
11
-
-
84882874868
-
The need for forensic tools in a balanced national agricultural security program
-
Springer Science + Business Media B.V, Gullino M, Fletcher J, Gamliel A, Stacks J
-
Fletcher J. The need for forensic tools in a balanced national agricultural security program. Crop Biosecurity: Assuring Our Global Food Supply 2008, 93-101. Springer Science + Business Media B.V, Gullino M, Fletcher J, Gamliel A, Stacks J.
-
(2008)
Crop Biosecurity: Assuring Our Global Food Supply
, pp. 93-101
-
-
Fletcher, J.1
-
12
-
-
84882915942
-
Forensic plant pathology
-
Elsevier Inc, Budowle B, Schutzer SE, Breeze RG, Keim PS, Morse SA
-
Fletcher J, Barnaby N, Burans J, Melcher U, Ochoa Corona F. Forensic plant pathology. Microbial Forensics 2010, 89-105. Elsevier Inc, Budowle B, Schutzer SE, Breeze RG, Keim PS, Morse SA.
-
(2010)
Microbial Forensics
, pp. 89-105
-
-
Fletcher, J.1
Barnaby, N.2
Burans, J.3
Melcher, U.4
Ochoa Corona, F.5
-
13
-
-
33745121579
-
Plant pathogen forensics: capabilities, needs, and recommendations
-
Fletcher J, Bender C, Budowle B, Cobb WT, Gold SE, Ishimaru CA, Luster D, Melcher U, Murch R, Scherm H, Seem RC, Sherwood JL, Sobral BW, Tolin SA. Plant pathogen forensics: capabilities, needs, and recommendations. Microbiol Mol Biol Rev 2006, 70:450-471.
-
(2006)
Microbiol Mol Biol Rev
, vol.70
, pp. 450-471
-
-
Fletcher, J.1
Bender, C.2
Budowle, B.3
Cobb, W.T.4
Gold, S.E.5
Ishimaru, C.A.6
Luster, D.7
Melcher, U.8
Murch, R.9
Scherm, H.10
Seem, R.C.11
Sherwood, J.L.12
Sobral, B.W.13
Tolin, S.A.14
-
14
-
-
52649154721
-
Admissibility standards for scientific evidence
-
Academic Press, Budowle B, Schutzer SE, Breeze RG
-
Harmon R. Admissibility standards for scientific evidence. Microbial Forensics 2005, 382-392. Academic Press, Budowle B, Schutzer SE, Breeze RG.
-
(2005)
Microbial Forensics
, pp. 382-392
-
-
Harmon, R.1
-
15
-
-
0029653518
-
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
-
Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM, McKenney K, Sutton G, FitzHugh W, Fields C, Gocayne JD, Scott J, Shirley R, Liu LI, Glodek A, Kelley JM, Weidman JF, Phillips CA, Spriggs T, Hedblom E, Cotton MD, Utterback TR, Hanna MC, Nguyen DT, Saudek DM, Brandon RC, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 1995, 269:496-512.
-
(1995)
Science
, vol.269
, pp. 496-512
-
-
Fleischmann, R.D.1
Adams, M.D.2
White, O.3
Clayton, R.A.4
Kirkness, E.F.5
Kerlavage, A.R.6
Bult, C.J.7
Tomb, J.F.8
Dougherty, B.A.9
Merrick, J.M.10
McKenney, K.11
Sutton, G.12
FitzHugh, W.13
Fields, C.14
Gocayne, J.D.15
Scott, J.16
Shirley, R.17
Liu, L.I.18
Glodek, A.19
Kelley, J.M.20
Weidman, J.F.21
Phillips, C.A.22
Spriggs, T.23
Hedblom, E.24
Cotton, M.D.25
Utterback, T.R.26
Hanna, M.C.27
Nguyen, D.T.28
Saudek, D.M.29
Brandon, R.C.30
more..
-
16
-
-
0028829125
-
The minimal gene complement of Mycoplasma genitalium
-
Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, Bult CJ, Kerlavage AR, Sutton G, Kelley JM, Fritchman RD, Weidman JF, Small KV, Sandusky M, Fuhrmann J, Nguyen D, Utterback TR, Saudek DM, Phillips CA, Merrick JM, Tomb JF, Dougherty BA, Bott KF, Hu PC, Lucier TS, Peterson SN, Smith HO, Hutchison CA, Venter JC. The minimal gene complement of Mycoplasma genitalium. Science 1995, 270:397-403.
-
(1995)
Science
, vol.270
, pp. 397-403
-
-
Fraser, C.M.1
Gocayne, J.D.2
White, O.3
Adams, M.D.4
Clayton, R.A.5
Fleischmann, R.D.6
Bult, C.J.7
Kerlavage, A.R.8
Sutton, G.9
Kelley, J.M.10
Fritchman, R.D.11
Weidman, J.F.12
Small, K.V.13
Sandusky, M.14
Fuhrmann, J.15
Nguyen, D.16
Utterback, T.R.17
Saudek, D.M.18
Phillips, C.A.19
Merrick, J.M.20
Tomb, J.F.21
Dougherty, B.A.22
Bott, K.F.23
Hu, P.C.24
Lucier, T.S.25
Peterson, S.N.26
Smith, H.O.27
Hutchison, C.A.28
Venter, J.C.29
more..
-
17
-
-
0035895505
-
The sequence of the human genome
-
Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N. The sequence of the human genome. Science 2001, 291:1304-1351.
-
(2001)
Science
, vol.291
, pp. 1304-1351
-
-
Venter, J.C.1
Adams, M.D.2
Myers, E.W.3
Li, P.W.4
Mural, R.J.5
Sutton, G.G.6
Smith, H.O.7
Yandell, M.8
Evans, C.A.9
Holt, R.A.10
Gocayne, J.D.11
Amanatides, P.12
Ballew, R.M.13
Huson, D.H.14
Wortman, J.R.15
Zhang, Q.16
Kodira, C.D.17
Zheng, X.H.18
Chen, L.19
Skupski, M.20
Subramanian, G.21
Thomas, P.D.22
Zhang, J.23
Gabor Miklos, G.L.24
Nelson, C.25
Broder, S.26
Clark, A.G.27
Nadeau, J.28
McKusick, V.A.29
Zinder, N.30
more..
-
18
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, et al. Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921.
-
(2001)
Nature
, vol.409
, pp. 860-921
-
-
Lander, E.S.1
Linton, L.M.2
Birren, B.3
Nusbaum, C.4
Zody, M.C.5
Baldwin, J.6
Devon, K.7
Dewar, K.8
Doyle, M.9
FitzHugh, W.10
Funke, R.11
Gage, D.12
Harris, K.13
Heaford, A.14
Howland, J.15
Kann, L.16
Lehoczky, J.17
LeVine, R.18
McEwan, P.19
McKernan, K.20
Meldrim, J.21
Mesirov, J.P.22
Miranda, C.23
Morris, W.24
Naylor, J.25
Raymond, C.26
Rosetti, M.27
Santos, R.28
Sheridan, A.29
Sougnez, C.30
more..
-
19
-
-
42249087308
-
The complete genome of an individual by massively parallel DNA sequencing
-
Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, Gomes X, Tartaro K, Niazi F, Turcotte CL, Irzyk GP, Lupski JR, Chinault C, Song XZ, Liu Y, Yuan Y, Nazareth L, Qin X, Muzny DM, Margulies M, Weinstock GM, Gibbs RA, Rothberg JM. The complete genome of an individual by massively parallel DNA sequencing. Nature 2008, 452:872-876.
-
(2008)
Nature
, vol.452
, pp. 872-876
-
-
Wheeler, D.A.1
Srinivasan, M.2
Egholm, M.3
Shen, Y.4
Chen, L.5
McGuire, A.6
He, W.7
Chen, Y.J.8
Makhijani, V.9
Roth, G.T.10
Gomes, X.11
Tartaro, K.12
Niazi, F.13
Turcotte, C.L.14
Irzyk, G.P.15
Lupski, J.R.16
Chinault, C.17
Song, X.Z.18
Liu, Y.19
Yuan, Y.20
Nazareth, L.21
Qin, X.22
Muzny, D.M.23
Margulies, M.24
Weinstock, G.M.25
Gibbs, R.A.26
Rothberg, J.M.27
more..
-
20
-
-
82355173436
-
Genome sequence analyses of two isolates from the recent Escherichia coli outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic Escherichia coli (EAHEC)
-
Brzuszkiewicz E, Thürmer A, Schuldes J, Leimbach A, Liesegang H, Meyer FD, Boelter J, Petersen H, Gottschalk G, Daniel R. Genome sequence analyses of two isolates from the recent Escherichia coli outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic Escherichia coli (EAHEC). Arch Microbiol 2011, 193:883-891.
-
(2011)
Arch Microbiol
, vol.193
, pp. 883-891
-
-
Brzuszkiewicz, E.1
Thürmer, A.2
Schuldes, J.3
Leimbach, A.4
Liesegang, H.5
Meyer, F.D.6
Boelter, J.7
Petersen, H.8
Gottschalk, G.9
Daniel, R.10
-
21
-
-
78650854393
-
The origin of the Haitian cholera outbreak strain
-
Chin CS, Sorenson J, Harris JB, Robins WP, Charles RC, Jean-Charles RR, Bullard J, Webster DR, Kasarskis A, Peluso P, Paxinos EE, Yamaichi Y, Calderwood SB, Mekalanos JJ, Schadt EE, Waldor MK. The origin of the Haitian cholera outbreak strain. N Engl J Med 2011, 364:33-42.
-
(2011)
N Engl J Med
, vol.364
, pp. 33-42
-
-
Chin, C.S.1
Sorenson, J.2
Harris, J.B.3
Robins, W.P.4
Charles, R.C.5
Jean-Charles, R.R.6
Bullard, J.7
Webster, D.R.8
Kasarskis, A.9
Peluso, P.10
Paxinos, E.E.11
Yamaichi, Y.12
Calderwood, S.B.13
Mekalanos, J.J.14
Schadt, E.E.15
Waldor, M.K.16
-
22
-
-
79953868820
-
Accurate, rapid and high-throughput detection of strain-specific polymorphisms in Bacillus anthracis and Yersinia pestis by next-generation sequencing
-
Cummings CA, Bormann Chung CA, Fang R, Barker M, Brzoska P, Williamson PC, Beaudry J, Matthews M, Schupp J, Wagner DM, Birdsell D, Vogler AJ, Furtado MR, Keim P, Budowle B. Accurate, rapid and high-throughput detection of strain-specific polymorphisms in Bacillus anthracis and Yersinia pestis by next-generation sequencing. Investig Genet 2010, 1:5.
-
(2010)
Investig Genet
, vol.1
, pp. 5
-
-
Cummings, C.A.1
Bormann Chung, C.A.2
Fang, R.3
Barker, M.4
Brzoska, P.5
Williamson, P.C.6
Beaudry, J.7
Matthews, M.8
Schupp, J.9
Wagner, D.M.10
Birdsell, D.11
Vogler, A.J.12
Furtado, M.R.13
Keim, P.14
Budowle, B.15
-
23
-
-
84857411659
-
Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011
-
Grad YH, Lipsitch M, Feldgarden M, Arachchi HM, Cerqueira GC, Fitzgerald M, Godfrey P, Haas BJ, Murphy CI, Russ C, Sykes S, Walker BJ, Wortman JR, Young S, Zeng Q, Abouelleil A, Bochicchio J, Chauvin S, Desmet T, Gujja S, McCowan C, Montmayeur A, Steelman S, Frimodt-Møller J, Petersen AM, Struve C, Krogfelt KA, Bingen E, Weill FX, Lander ES, et al. Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011. Proc Natl Acad Sci U S A 2012, 109:3065-3070.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 3065-3070
-
-
Grad, Y.H.1
Lipsitch, M.2
Feldgarden, M.3
Arachchi, H.M.4
Cerqueira, G.C.5
Fitzgerald, M.6
Godfrey, P.7
Haas, B.J.8
Murphy, C.I.9
Russ, C.10
Sykes, S.11
Walker, B.J.12
Wortman, J.R.13
Young, S.14
Zeng, Q.15
Abouelleil, A.16
Bochicchio, J.17
Chauvin, S.18
Desmet, T.19
Gujja, S.20
McCowan, C.21
Montmayeur, A.22
Steelman, S.23
Frimodt-Møller, J.24
Petersen, A.M.25
Struve, C.26
Krogfelt, K.A.27
Bingen, E.28
Weill, F.X.29
Lander, E.S.30
more..
-
24
-
-
33947221422
-
Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes
-
Eisen JA. Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biol 2007, 5:e82.
-
(2007)
PLoS Biol
, vol.5
-
-
Eisen, J.A.1
-
25
-
-
84863888444
-
Genomic diversity of 2010 Haitian cholera outbreak strains
-
Hasan NA, Choi SY, Eppinger M, Clark PW, Chen A, Alam M, Haley BJ, Taviani E, Hine E, Su Q, Tallon LJ, Prosper JB, Furth K, Hoq MM, Li H, Fraser-Liggett CM, Cravioto A, Huq A, Ravel J, Cebula TA, Colwell RR. Genomic diversity of 2010 Haitian cholera outbreak strains. Proc Natl Acad Sci U S A 2012, 109:E2010-E2017.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
-
-
Hasan, N.A.1
Choi, S.Y.2
Eppinger, M.3
Clark, P.W.4
Chen, A.5
Alam, M.6
Haley, B.J.7
Taviani, E.8
Hine, E.9
Su, Q.10
Tallon, L.J.11
Prosper, J.B.12
Furth, K.13
Hoq, M.M.14
Li, H.15
Fraser-Liggett, C.M.16
Cravioto, A.17
Huq, A.18
Ravel, J.19
Cebula, T.A.20
Colwell, R.R.21
more..
-
26
-
-
80052597651
-
Population genetics of Vibrio cholerae from Nepal in 2010: evidence on the origin of the Haitian outbreak
-
e00157-11
-
Hendriksen RS, Price LB, Schupp JM, Gillece JD, Kaas RS, Engelthaler DM, Bortolaia V, Pearson T, Waters AE, Upadhyay BP, Shrestha SD, Adhikari S, Shakya G, Keim PS, Aarestrup FM. Population genetics of Vibrio cholerae from Nepal in 2010: evidence on the origin of the Haitian outbreak. MBio 2011, 2:e00157-11.
-
(2011)
MBio
, vol.2
-
-
Hendriksen, R.S.1
Price, L.B.2
Schupp, J.M.3
Gillece, J.D.4
Kaas, R.S.5
Engelthaler, D.M.6
Bortolaia, V.7
Pearson, T.8
Waters, A.E.9
Upadhyay, B.P.10
Shrestha, S.D.11
Adhikari, S.12
Shakya, G.13
Keim, P.S.14
Aarestrup, F.M.15
-
27
-
-
48349124258
-
High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi
-
Holt KE, Parkhill J, Mazzoni CJ, Roumagnac P, Weill FX, Goodhead I, Rance R, Baker S, Maskell DJ, Wain J, Dolecek C, Achtman M, Dougan G. High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet 2008, 40:987-993.
-
(2008)
Nat Genet
, vol.40
, pp. 987-993
-
-
Holt, K.E.1
Parkhill, J.2
Mazzoni, C.J.3
Roumagnac, P.4
Weill, F.X.5
Goodhead, I.6
Rance, R.7
Baker, S.8
Maskell, D.J.9
Wain, J.10
Dolecek, C.11
Achtman, M.12
Dougan, G.13
-
28
-
-
80355129294
-
Rapid typing of Coxiella burnetii
-
Hornstra HM, Priestley RA, Georgia SM, Kachur S, Birdsell DN, Hilsabeck R, Gates LT, Samuel JE, Heinzen RA, Kersh GJ, Keim P, Massung RF, Pearson T. Rapid typing of Coxiella burnetii. PLoS One 2011, 6:e26201.
-
(2011)
PLoS One
, vol.6
-
-
Hornstra, H.M.1
Priestley, R.A.2
Georgia, S.M.3
Kachur, S.4
Birdsell, D.N.5
Hilsabeck, R.6
Gates, L.T.7
Samuel, J.E.8
Heinzen, R.A.9
Kersh, G.J.10
Keim, P.11
Massung, R.F.12
Pearson, T.13
-
29
-
-
81755177765
-
Evolution of multidrug resistance during Staphylococcus aureus infection involves mutation of the essential two component regulator WalKR
-
Howden BP, McEvoy CR, Allen DL, Chua K, Gao W, Harrison PF, Bell J, Coombs G, Bennett-Wood V, Porter JL, Robins-Browne R, Davies JK, Seemann T, Stinear TP. Evolution of multidrug resistance during Staphylococcus aureus infection involves mutation of the essential two component regulator WalKR. PLoS Pathog 2011, 7:e1002359.
-
(2011)
PLoS Pathog
, vol.7
-
-
Howden, B.P.1
McEvoy, C.R.2
Allen, D.L.3
Chua, K.4
Gao, W.5
Harrison, P.F.6
Bell, J.7
Coombs, G.8
Bennett-Wood, V.9
Porter, J.L.10
Robins-Browne, R.11
Davies, J.K.12
Seemann, T.13
Stinear, T.P.14
-
30
-
-
84866148001
-
Routine use of microbial whole genome sequencing in diagnostic and public health microbiology
-
Köser CU, Ellington MJ, Cartwright EJ, Gillespie SH, Brown NM, Farrington M, Holden MT, Dougan G, Bentley SD, Parkhill J, Peacock SJ. Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog 2012, 8:e1002824.
-
(2012)
PLoS Pathog
, vol.8
-
-
Köser, C.U.1
Ellington, M.J.2
Cartwright, E.J.3
Gillespie, S.H.4
Brown, N.M.5
Farrington, M.6
Holden, M.T.7
Dougan, G.8
Bentley, S.D.9
Parkhill, J.10
Peacock, S.J.11
-
31
-
-
63249121217
-
Application of " next-generation" sequencing technologies to microbial genetics
-
MacLean D, Jones JD, Studholme DJ. Application of " next-generation" sequencing technologies to microbial genetics. Nat Rev Microbiol 2009, 7:287-296.
-
(2009)
Nat Rev Microbiol
, vol.7
, pp. 287-296
-
-
MacLean, D.1
Jones, J.D.2
Studholme, D.J.3
-
32
-
-
79960609901
-
Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology
-
Mellmann A, Harmsen D, Cummings CA, Zentz EB, Leopold SR, Rico A, Prior K, Szczepanowski R, Ji Y, Zhang W, McLaughlin SF, Henkhaus JK, Leopold B, Bielaszewska M, Prager R, Brzoska PM, Moore RL, Guenther S, Rothberg JM, Karch H. Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology. PLoS One 2011, 6:e22751.
-
(2011)
PLoS One
, vol.6
-
-
Mellmann, A.1
Harmsen, D.2
Cummings, C.A.3
Zentz, E.B.4
Leopold, S.R.5
Rico, A.6
Prior, K.7
Szczepanowski, R.8
Ji, Y.9
Zhang, W.10
McLaughlin, S.F.11
Henkhaus, J.K.12
Leopold, B.13
Bielaszewska, M.14
Prager, R.15
Brzoska, P.M.16
Moore, R.L.17
Guenther, S.18
Rothberg, J.M.19
Karch, H.20
more..
-
33
-
-
80052150179
-
Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany
-
Rasko DA, Webster DR, Sahl JW, Bashir A, Boisen N, Scheutz F, Paxinos EE, Sebra R, Chin CS, Iliopoulos D, Klammer A, Peluso P, Lee L, Kislyuk AO, Bullard J, Kasarskis A, Wang S, Eid J, Rank D, Redman JC, Steyert SR, Frimodt-Møller J, Struve C, Petersen AM, Krogfelt KA, Nataro JP, Schadt EE, Waldor MK. Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med 2011, 365:709-717.
-
(2011)
N Engl J Med
, vol.365
, pp. 709-717
-
-
Rasko, D.A.1
Webster, D.R.2
Sahl, J.W.3
Bashir, A.4
Boisen, N.5
Scheutz, F.6
Paxinos, E.E.7
Sebra, R.8
Chin, C.S.9
Iliopoulos, D.10
Klammer, A.11
Peluso, P.12
Lee, L.13
Kislyuk, A.O.14
Bullard, J.15
Kasarskis, A.16
Wang, S.17
Eid, J.18
Rank, D.19
Redman, J.C.20
Steyert, S.R.21
Frimodt-Møller, J.22
Struve, C.23
Petersen, A.M.24
Krogfelt, K.A.25
Nataro, J.P.26
Schadt, E.E.27
Waldor, M.K.28
more..
-
34
-
-
80052173621
-
Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4
-
Rohde H, Qin J, Cui Y, Li D, Loman NJ, Hentschke M, Chen W, Pu F, Peng Y, Li J, Xi F, Li S, Li Y, Zhang Z, Yang X, Zhao M, Wang P, Guan Y, Cen Z, Zhao X, Christner M, Kobbe R, Loos S, Oh J, Yang L, Danchin A, Gao GF, Song Y, Li Y, Yang H, et al. Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N Engl J Med 2011, 365:718-724.
-
(2011)
N Engl J Med
, vol.365
, pp. 718-724
-
-
Rohde, H.1
Qin, J.2
Cui, Y.3
Li, D.4
Loman, N.J.5
Hentschke, M.6
Chen, W.7
Pu, F.8
Peng, Y.9
Li, J.10
Xi, F.11
Li, S.12
Li, Y.13
Zhang, Z.14
Yang, X.15
Zhao, M.16
Wang, P.17
Guan, Y.18
Cen, Z.19
Zhao, X.20
Christner, M.21
Kobbe, R.22
Loos, S.23
Oh, J.24
Yang, L.25
Danchin, A.26
Gao, G.F.27
Song, Y.28
Li, Y.29
Yang, H.30
more..
-
35
-
-
79951995822
-
Whole-genome sequencing and social-network analysis of a tuberculosis outbreak
-
Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ, Shah L, Brodkin E, Rempel S, Moore R, Zhao Y, Holt R, Varhol R, Birol I, Lem M, Sharma MK, Elwood K, Jones SJ, Brinkman FS, Brunham RC, Tang P. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med 2011, 364:730-739.
-
(2011)
N Engl J Med
, vol.364
, pp. 730-739
-
-
Gardy, J.L.1
Johnston, J.C.2
Ho Sui, S.J.3
Cook, V.J.4
Shah, L.5
Brodkin, E.6
Rempel, S.7
Moore, R.8
Zhao, Y.9
Holt, R.10
Varhol, R.11
Birol, I.12
Lem, M.13
Sharma, M.K.14
Elwood, K.15
Jones, S.J.16
Brinkman, F.S.17
Brunham, R.C.18
Tang, P.19
-
36
-
-
75649084906
-
Evolution of MRSA during hospital transmission and intercontinental spread
-
Harris SR, Feil EJ, Holden MT, Quail MA, Nickerson EK, Chantratita N, Gardete S, Tavares A, Day N, Lindsay JA, Edgeworth JD, de Lencastre H, Parkhill J, Peacock SJ, Bentley SD. Evolution of MRSA during hospital transmission and intercontinental spread. Science 2010, 327:469-474.
-
(2010)
Science
, vol.327
, pp. 469-474
-
-
Harris, S.R.1
Feil, E.J.2
Holden, M.T.3
Quail, M.A.4
Nickerson, E.K.5
Chantratita, N.6
Gardete, S.7
Tavares, A.8
Day, N.9
Lindsay, J.A.10
Edgeworth, J.D.11
de Lencastre, H.12
Parkhill, J.13
Peacock, S.J.14
Bentley, S.D.15
-
37
-
-
84872515273
-
Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study
-
Harris SR, Cartwright EJ, Török ME, Holden MT, Brown NM, Ogilvy-Stuart AL, Ellington MJ, Quail MA, Bentley SD, Parkhill J, Peacock SJ. Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. Lancet Infect Dis 2013, 13:130-136.
-
(2013)
Lancet Infect Dis
, vol.13
, pp. 130-136
-
-
Harris, S.R.1
Cartwright, E.J.2
Török, M.E.3
Holden, M.T.4
Brown, N.M.5
Ogilvy-Stuart, A.L.6
Ellington, M.J.7
Quail, M.A.8
Bentley, S.D.9
Parkhill, J.10
Peacock, S.J.11
-
38
-
-
84874469388
-
Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study
-
Roetzer A, Diel R, Kohl TA, Rückert C, Nübel U, Blom J, Wirth T, Jaenicke S, Schuback S, Rüsch-Gerdes S, Supply P, Kalinowski J, Niemann S. Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study. PLoS Med 2013, 10:e1001387.
-
(2013)
PLoS Med
, vol.10
-
-
Roetzer, A.1
Diel, R.2
Kohl, T.A.3
Rückert, C.4
Nübel, U.5
Blom, J.6
Wirth, T.7
Jaenicke, S.8
Schuback, S.9
Rüsch-Gerdes, S.10
Supply, P.11
Kalinowski, J.12
Niemann, S.13
-
39
-
-
84872513471
-
Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study
-
Walker TM, Ip CL, Harrell RH, Evans JT, Kapatai G, Dedicoat MJ, Eyre DW, Wilson DJ, Hawkey PM, Crook DW, Parkhill J, Harris D, Walker AS, Bowden R, Monk P, Smith EG, Peto TE. Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect Dis 2013, 13:137-146.
-
(2013)
Lancet Infect Dis
, vol.13
, pp. 137-146
-
-
Walker, T.M.1
Ip, C.L.2
Harrell, R.H.3
Evans, J.T.4
Kapatai, G.5
Dedicoat, M.J.6
Eyre, D.W.7
Wilson, D.J.8
Hawkey, P.M.9
Crook, D.W.10
Parkhill, J.11
Harris, D.12
Walker, A.S.13
Bowden, R.14
Monk, P.15
Smith, E.G.16
Peto, T.E.17
-
40
-
-
84875921666
-
A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4
-
Loman NJ, Constantinidou C, Christner M, Rohde H, Chan JZ, Quick J, Weir JC, Quince C, Smith GP, Betley JR, Aepfelbacher M, Pallen MJ. A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4. JAMA 2013, 309:1502-1510.
-
(2013)
JAMA
, vol.309
, pp. 1502-1510
-
-
Loman, N.J.1
Constantinidou, C.2
Christner, M.3
Rohde, H.4
Chan, J.Z.5
Quick, J.6
Weir, J.C.7
Quince, C.8
Smith, G.P.9
Betley, J.R.10
Aepfelbacher, M.11
Pallen, M.J.12
-
41
-
-
84882798441
-
E-probe Diagnostic Nucleic acid Analysis (EDNA): a theoretical approach for handling of next generation sequencing data for diagnostics
-
Stobbe AH, Daniels J, Espindola AS, Verma R, Melcher U, Ochoa-Corona F, Garzon C, Fletcher J, Schneider W. E-probe Diagnostic Nucleic acid Analysis (EDNA): a theoretical approach for handling of next generation sequencing data for diagnostics. J Microbiol Methods 2013, 94:356-366.
-
(2013)
J Microbiol Methods
, vol.94
, pp. 356-366
-
-
Stobbe, A.H.1
Daniels, J.2
Espindola, A.S.3
Verma, R.4
Melcher, U.5
Ochoa-Corona, F.6
Garzon, C.7
Fletcher, J.8
Schneider, W.9
-
42
-
-
84905830420
-
Screening metagenomic data for viruses using the e-probe diagnostic nucleic acid assay (EDNA)
-
in press
-
Stobbe AH, Schneider W, Hoyt P, Melcher U. Screening metagenomic data for viruses using the e-probe diagnostic nucleic acid assay (EDNA). Phytopathology in press.
-
Phytopathology
-
-
Stobbe, A.H.1
Schneider, W.2
Hoyt, P.3
Melcher, U.4
-
44
-
-
84905830422
-
-
Amsterdam: Academic Press, 2
-
Budowle B, Schutzer SE, Breeze RG, Keim PS, Morse SA. (Eds): Microbial Forensics 2011, Amsterdam: Academic Press, 2.
-
(2011)
(Eds): Microbial Forensics
-
-
Budowle, B.1
Schutzer, S.E.2
Breeze, R.G.3
Keim, P.S.4
Morse, S.A.5
-
45
-
-
84905822388
-
The microbial forensics pathway for use of massively-parallel sequencing technologies
-
Washington DC: The National Academies Press
-
Budowle B, Schmedes S, Murch RS. The microbial forensics pathway for use of massively-parallel sequencing technologies. The Science and Applications of Microbial Genomics 2013, 117-133. Washington DC: The National Academies Press.
-
(2013)
The Science and Applications of Microbial Genomics
, pp. 117-133
-
-
Budowle, B.1
Schmedes, S.2
Murch, R.S.3
-
48
-
-
12944293179
-
-
Brenner S, Williams SR, Vermaas EH, Storck T, Moon K, McCollum C, Mao JI, Luo S, Kirchner JJ, Eletr S, DuBridge RB, Burcham T, Albrecht G. In vitro cloning of complex mixtures of DNA on microbeads: physical separation of differentially expressed cDNAs Proc Natl Acad Sci U S A 2000, 97:1665-1670.
-
(2000)
In vitro cloning of complex mixtures of DNA on microbeads: physical separation of differentially expressed cDNAs Proc Natl Acad Sci U S A
, vol.97
, pp. 1665-1670
-
-
Brenner, S.1
Williams, S.R.2
Vermaas, E.H.3
Storck, T.4
Moon, K.5
McCollum, C.6
Mao, J.I.7
Luo, S.8
Kirchner, J.J.9
Eletr, S.10
DuBridge, R.B.11
Burcham, T.12
Albrecht, G.13
-
49
-
-
24044455869
-
Genome sequencing in microfabricated high-density picolitre reactors
-
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437:376-380.
-
(2005)
Nature
, vol.437
, pp. 376-380
-
-
Margulies, M.1
Egholm, M.2
Altman, W.E.3
Attiya, S.4
Bader, J.S.5
Bemben, L.A.6
Berka, J.7
Braverman, M.S.8
Chen, Y.J.9
Chen, Z.10
Dewell, S.B.11
Du, L.12
Fierro, J.M.13
Gomes, X.V.14
Godwin, B.C.15
He, W.16
Helgesen, S.17
Ho, C.H.18
Irzyk, G.P.19
Jando, S.C.20
Alenquer, M.L.21
Jarvie, T.P.22
Jirage, K.B.23
Kim, J.B.24
Knight, J.R.25
Lanza, J.R.26
Leamon, J.H.27
Lefkowitz, S.M.28
Lei, M.29
Li, J.30
more..
-
50
-
-
84870495569
-
Progress in ion torrent semiconductor chip based sequencing
-
Merriman B, Rothberg JM. Progress in ion torrent semiconductor chip based sequencing. Electrophoresis 2012, 33:3397-3417.
-
(2012)
Electrophoresis
, vol.33
, pp. 3397-3417
-
-
Merriman, B.1
Rothberg, J.M.2
-
51
-
-
72849144434
-
Sequencing technologies - the next generation
-
Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010, 11:31-46.
-
(2010)
Nat Rev Genet
, vol.11
, pp. 31-46
-
-
Metzker, M.L.1
-
52
-
-
57049122389
-
A large genome center's improvements to the Illumina sequencing system
-
Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R, Swerdlow H, Turner DJ. A large genome center's improvements to the Illumina sequencing system. Nat Methods 2008, 5:1005-1010.
-
(2008)
Nat Methods
, vol.5
, pp. 1005-1010
-
-
Quail, M.A.1
Kozarewa, I.2
Smith, F.3
Scally, A.4
Stephens, P.J.5
Durbin, R.6
Swerdlow, H.7
Turner, D.J.8
-
53
-
-
53649106195
-
Next-generation DNA sequencing
-
Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol 2008, 26:1135-1145.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 1135-1145
-
-
Shendure, J.1
Ji, H.2
-
55
-
-
77952967431
-
Direct detection of DNA methylation during single-molecule, real-time sequencing
-
Flusberg BA, Webster DR, Lee JH, Travers KJ, Olivares EC, Clark TA, Korlach J, Turner SW. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Methods 2010, 7:461-465.
-
(2010)
Nat Methods
, vol.7
, pp. 461-465
-
-
Flusberg, B.A.1
Webster, D.R.2
Lee, J.H.3
Travers, K.J.4
Olivares, E.C.5
Clark, T.A.6
Korlach, J.7
Turner, S.W.8
-
56
-
-
84859643160
-
Oxford Nanopore announcement sets sequencing sector abuzz
-
Eisenstein M. Oxford Nanopore announcement sets sequencing sector abuzz. Nat Biotechnol 2012, 30:295-296.
-
(2012)
Nat Biotechnol
, vol.30
, pp. 295-296
-
-
Eisenstein, M.1
-
57
-
-
84865231395
-
Transforming clinical microbiology with bacterial genome sequencing
-
Didelot X, Bowden R, Wilson DJ, Peto TE, Crook DW. Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet 2012, 13:601-612.
-
(2012)
Nat Rev Genet
, vol.13
, pp. 601-612
-
-
Didelot, X.1
Bowden, R.2
Wilson, D.J.3
Peto, T.E.4
Crook, D.W.5
-
58
-
-
52649166352
-
Criteria for validation of methods in microbial forensics
-
Budowle B, Schutzer SE, Morse SA, Martinez KF, Chakraborty R, Marrone BL, Messenger SL, Murch RS, Jackson PJ, Williamson P, Harmon R, Velsko SP. Criteria for validation of methods in microbial forensics. Appl Environ Microbiol 2008, 74:5599-5607.
-
(2008)
Appl Environ Microbiol
, vol.74
, pp. 5599-5607
-
-
Budowle, B.1
Schutzer, S.E.2
Morse, S.A.3
Martinez, K.F.4
Chakraborty, R.5
Marrone, B.L.6
Messenger, S.L.7
Murch, R.S.8
Jackson, P.J.9
Williamson, P.10
Harmon, R.11
Velsko, S.P.12
-
59
-
-
84883897500
-
Working Group of the American College of Medical Genetics and Genomics Laboratory Quality Assurance Committee: ACMG clinical laboratory standards for next-generation sequencing
-
Rehm HL, Bale SJ, Bayrak-Toydemir P, Berg JS, Brown KK, Deignan JL, Friez MJ, Funke BH, Hegde MR, Lyon E. Working Group of the American College of Medical Genetics and Genomics Laboratory Quality Assurance Committee: ACMG clinical laboratory standards for next-generation sequencing. Genet Med 2013, 15:733-747.
-
(2013)
Genet Med
, vol.15
, pp. 733-747
-
-
Rehm, H.L.1
Bale, S.J.2
Bayrak-Toydemir, P.3
Berg, J.S.4
Brown, K.K.5
Deignan, J.L.6
Friez, M.J.7
Funke, B.H.8
Hegde, M.R.9
Lyon, E.10
-
60
-
-
84869429716
-
Assuring the quality of next-generation sequencing in clinical laboratory practice
-
Gargis AS, Kalman L, Berry MW, Bick DP, Dimmock DP, Hambuch T, Lu F, Lyon E, Voelkerding KV, Zehnbauer BA, Agarwala R, Bennett SF, Chen B, Chin EL, Compton JG, Das S, Farkas DH, Ferber MJ, Funke BH, Furtado MR, Ganova-Raeva LM, Geigenmüller U, Gunselman SJ, Hegde MR, Johnson PL, Kasarskis A, Kulkarni S, Lenk T, Liu CS, Manion M, et al. Assuring the quality of next-generation sequencing in clinical laboratory practice. Nat Biotechnol 2012, 30:1033-1036.
-
(2012)
Nat Biotechnol
, vol.30
, pp. 1033-1036
-
-
Gargis, A.S.1
Kalman, L.2
Berry, M.W.3
Bick, D.P.4
Dimmock, D.P.5
Hambuch, T.6
Lu, F.7
Lyon, E.8
Voelkerding, K.V.9
Zehnbauer, B.A.10
Agarwala, R.11
Bennett, S.F.12
Chen, B.13
Chin, E.L.14
Compton, J.G.15
Das, S.16
Farkas, D.H.17
Ferber, M.J.18
Funke, B.H.19
Furtado, M.R.20
Ganova-Raeva, L.M.21
Geigenmüller, U.22
Gunselman, S.J.23
Hegde, M.R.24
Johnson, P.L.25
Kasarskis, A.26
Kulkarni, S.27
Lenk, T.28
Liu, C.S.29
Manion, M.30
more..
-
61
-
-
84856035237
-
Biochemical and Molecular Genetic Resource Committee of the College of American Pathologists: Design and analytical validation of clinical DNA sequencing assays
-
Pont-Kingdon G, Gedge F, Wooderchak-Donahue W, Schrijver I, Weck KE, Kant JA, Oglesbee D, Bayrak-Toydemir P, Lyon E. Biochemical and Molecular Genetic Resource Committee of the College of American Pathologists: Design and analytical validation of clinical DNA sequencing assays. Arch Pathol Lab Med 2012, 136:41-46.
-
(2012)
Arch Pathol Lab Med
, vol.136
, pp. 41-46
-
-
Pont-Kingdon, G.1
Gedge, F.2
Wooderchak-Donahue, W.3
Schrijver, I.4
Weck, K.E.5
Kant, J.A.6
Oglesbee, D.7
Bayrak-Toydemir, P.8
Lyon, E.9
-
62
-
-
85014940645
-
Validation guidelines for DNA analysis methods
-
Available at: , SWGDAM
-
SWGDAM Validation guidelines for DNA analysis methods. 2012, Available at: http://swgdam.org/SWGDAM_Validation_Guidelines_APPROVED_Dec_2012.pdf, SWGDAM.
-
(2012)
-
-
-
63
-
-
77955067191
-
Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags
-
Wu GD, Lewis JD, Hoffmann C, Chen YY, Knight R, Bittinger K, Hwang J, Chen J, Berkowsky R, Nessel L, Li H, Bushman FD. Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol 2010, 10:206.
-
(2010)
BMC Microbiol
, vol.10
, pp. 206
-
-
Wu, G.D.1
Lewis, J.D.2
Hoffmann, C.3
Chen, Y.Y.4
Knight, R.5
Bittinger, K.6
Hwang, J.7
Chen, J.8
Berkowsky, R.9
Nessel, L.10
Li, H.11
Bushman, F.D.12
-
64
-
-
83755185513
-
Experimental and analytical tools for studying the human microbiome
-
Kuczynski J, Lauber CL, Walters WA, Parfrey LW, Clemente JC, Gevers D, Knight R. Experimental and analytical tools for studying the human microbiome. Nat Rev Genet 2012, 13:47-58.
-
(2012)
Nat Rev Genet
, vol.13
, pp. 47-58
-
-
Kuczynski, J.1
Lauber, C.L.2
Walters, W.A.3
Parfrey, L.W.4
Clemente, J.C.5
Gevers, D.6
Knight, R.7
-
65
-
-
19144366982
-
The metagenomics of soil
-
Daniel R. The metagenomics of soil. Nat Rev Microbiol 2005, 3:470-478.
-
(2005)
Nat Rev Microbiol
, vol.3
, pp. 470-478
-
-
Daniel, R.1
-
66
-
-
19144362371
-
Microbial community genomics in the ocean
-
DeLong EF. Microbial community genomics in the ocean. Nat Rev Microbiol 2005, 3:459-469.
-
(2005)
Nat Rev Microbiol
, vol.3
, pp. 459-469
-
-
DeLong, E.F.1
-
67
-
-
33947238287
-
The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific
-
Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, Thorpe J, Freeman J, Andrews-Pfannkoch C, Venter JE, Li K, Kravitz S, Heidelberg JF, Utterback T, Rogers YH, Falcón LI, Souza V, Bonilla-Rosso G, Eguiarte LE, Karl DM, Sathyendranath S, et al. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 2007, 5:e77.
-
(2007)
PLoS Biol
, vol.5
-
-
Rusch, D.B.1
Halpern, A.L.2
Sutton, G.3
Heidelberg, K.B.4
Williamson, S.5
Yooseph, S.6
Wu, D.7
Eisen, J.A.8
Hoffman, J.M.9
Remington, K.10
Beeson, K.11
Tran, B.12
Smith, H.13
Baden-Tillson, H.14
Stewart, C.15
Thorpe, J.16
Freeman, J.17
Andrews-Pfannkoch, C.18
Venter, J.E.19
Li, K.20
Kravitz, S.21
Heidelberg, J.F.22
Utterback, T.23
Rogers, Y.H.24
Falcón, L.I.25
Souza, V.26
Bonilla-Rosso, G.27
Eguiarte, L.E.28
Karl, D.M.29
Sathyendranath, S.30
more..
-
68
-
-
84863988682
-
Architectural design influences the diversity and structure of the built environment microbiome
-
Kembel SW, Jones E, Kline J, Northcutt D, Stenson J, Womack AM, Bohannan BJ, Brown GZ, Green JL. Architectural design influences the diversity and structure of the built environment microbiome. ISME J 2012, 6:1469-1479.
-
(2012)
ISME J
, vol.6
, pp. 1469-1479
-
-
Kembel, S.W.1
Jones, E.2
Kline, J.3
Northcutt, D.4
Stenson, J.5
Womack, A.M.6
Bohannan, B.J.7
Brown, G.Z.8
Green, J.L.9
-
69
-
-
84862276328
-
Structure, function and diversity of the healthy human microbiome
-
Human Microbiome Project Consortium
-
Human Microbiome Project Consortium Structure, function and diversity of the healthy human microbiome. Nature 2012, 486:207-214. Human Microbiome Project Consortium.
-
(2012)
Nature
, vol.486
, pp. 207-214
-
-
-
70
-
-
84862286169
-
A framework for human microbiome research
-
Human Microbiome Project Consortium
-
Human Microbiome Project Consortium A framework for human microbiome research. Nature 2012, 486:215-221. Human Microbiome Project Consortium.
-
(2012)
Nature
, vol.486
, pp. 215-221
-
-
-
71
-
-
84862989346
-
Metagenomics - a guide from sampling to data analysis
-
Thomas T, Gilbert J, Meyer F. Metagenomics - a guide from sampling to data analysis. Microb Inform Exp 2012, 2:3.
-
(2012)
Microb Inform Exp
, vol.2
, pp. 3
-
-
Thomas, T.1
Gilbert, J.2
Meyer, F.3
-
72
-
-
0034020175
-
Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis
-
Keim P, Price LB, Klevytska AM, Smith KL, Schupp JM, Okinaka R, Jackson PJ, Hugh-Jones ME. Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis. J Bacteriol 2000, 182:2928-2936.
-
(2000)
J Bacteriol
, vol.182
, pp. 2928-2936
-
-
Keim, P.1
Price, L.B.2
Klevytska, A.M.3
Smith, K.L.4
Schupp, J.M.5
Okinaka, R.6
Jackson, P.J.7
Hugh-Jones, M.E.8
-
73
-
-
0036774995
-
Molecular subtyping of Bacillus anthracis and the 2001 bioterrorism-associated anthrax outbreak, United States
-
Hoffmaster AR, Fitzgerald CC, Ribot E, Mayer LW, Popovic T. Molecular subtyping of Bacillus anthracis and the 2001 bioterrorism-associated anthrax outbreak, United States. Emerg Infect Dis 2002, 8:1111-1116.
-
(2002)
Emerg Infect Dis
, vol.8
, pp. 1111-1116
-
-
Hoffmaster, A.R.1
Fitzgerald, C.C.2
Ribot, E.3
Mayer, L.W.4
Popovic, T.5
-
74
-
-
77954678952
-
Use of forensic methods under exigent circumstances without full validation
-
Schutzer SE, Keim P, Czerwinski K, Budowle B. Use of forensic methods under exigent circumstances without full validation. Sci Transl Med 2009, 1:8cm7.
-
(2009)
Sci Transl Med
, vol.1
, pp. 7-8
-
-
Schutzer, S.E.1
Keim, P.2
Czerwinski, K.3
Budowle, B.4
-
75
-
-
33750045187
-
Quality sample collection, handling, and preservation for an effective microbial forensics program
-
Budowle B, Schutzer SE, Burans JP, Beecher DJ, Cebula TA, Chakraborty R, Cobb WT, Fletcher J, Hale ML, Harris RB, Heitkamp MA, Keller FP, Kuske C, Leclerc JE, Marrone BL, McKenna TS, Morse SA, Rodriguez LL, Valentine NB, Yadev J. Quality sample collection, handling, and preservation for an effective microbial forensics program. Appl Environ Microbiol 2006, 72:6431-6438.
-
(2006)
Appl Environ Microbiol
, vol.72
, pp. 6431-6438
-
-
Budowle, B.1
Schutzer, S.E.2
Burans, J.P.3
Beecher, D.J.4
Cebula, T.A.5
Chakraborty, R.6
Cobb, W.T.7
Fletcher, J.8
Hale, M.L.9
Harris, R.B.10
Heitkamp, M.A.11
Keller, F.P.12
Kuske, C.13
Leclerc, J.E.14
Marrone, B.L.15
McKenna, T.S.16
Morse, S.A.17
Rodriguez, L.L.18
Valentine, N.B.19
Yadev, J.20
more..
-
76
-
-
84905830413
-
-
Practice Guidelines for Targeted Next Generation Sequencing Analysis and Interpretation. Clinical Molecular GeneticsSociety: Taylor GR, Available at:
-
Ellard S, Charlton R, Lindsay H, Camm N, Watson C, Abb S. Mattocks C 2012, Practice Guidelines for Targeted Next Generation Sequencing Analysis and Interpretation. Clinical Molecular GeneticsSociety: Taylor GR, Available at: http://cmgsweb.shared.hosting.zen.co.uk/BPGs/BPG%20for%20targeted%20next%20generation%20sequencing%20final.pdf.
-
(2012)
Mattocks C
-
-
Ellard, S.1
Charlton, R.2
Lindsay, H.3
Camm, N.4
Watson, C.5
Abb, S.6
-
77
-
-
84905830414
-
PCR-free sample preparation kits for whole genome DNA sequencing
-
Available at:
-
Illumina PCR-free sample preparation kits for whole genome DNA sequencing. 2013, Available at: http://www.illumina.com/products/truseq-dna-pcr-free-sample-prep-kits.ilmn, Illumina.
-
(2013)
-
-
-
78
-
-
84905830415
-
HaloPlex target enrichment system-ILM
-
Available at: Agilent
-
Agilent HaloPlex target enrichment system-ILM. 2013, Available at: http://www.chem.agilent.com/Library/usermanuals/Public/G9900-90001.pdf, Agilent.
-
(2013)
-
-
-
79
-
-
84905830411
-
Nextera XT DNA sample preparation kit
-
Available at: , Illumina
-
Illumina Nextera XT DNA sample preparation kit. 2013, Available at: http://www.illumina.com/products/nextera_xt_dna_sample_prep_kit.ilmn, Illumina.
-
(2013)
-
-
-
80
-
-
64749109065
-
Laboratory procedures to generate viral metagenomes
-
Thurber RV, Haynes M, Breitbart M, Wegley L, Rohwer F. Laboratory procedures to generate viral metagenomes. Nat Protoc 2009, 4:470-483.
-
(2009)
Nat Protoc
, vol.4
, pp. 470-483
-
-
Thurber, R.V.1
Haynes, M.2
Breitbart, M.3
Wegley, L.4
Rohwer, F.5
-
81
-
-
84886624088
-
A method for selectively enriching microbial DNA from contaminating vertebrate host DNA
-
Feehery G, Yigit E, Oyola S, Langhorst B, Schmidt V, Stewart FJ, Dimalanta ET, Amaral-Zettler LA, Davis T, Quail MA, Pradhan S. A method for selectively enriching microbial DNA from contaminating vertebrate host DNA. PLoS One 2013, 8:e76096.
-
(2013)
PLoS One
, vol.8
-
-
Feehery, G.1
Yigit, E.2
Oyola, S.3
Langhorst, B.4
Schmidt, V.5
Stewart, F.J.6
Dimalanta, E.T.7
Amaral-Zettler, L.A.8
Davis, T.9
Quail, M.A.10
Pradhan, S.11
-
82
-
-
0026736251
-
Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer
-
Telenius H, Carter NP, Bebb CE, Nordenskjöld M, Ponder BA, Tunnacliffe A. Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. Genomics 1992, 13:718-725.
-
(1992)
Genomics
, vol.13
, pp. 718-725
-
-
Telenius, H.1
Carter, N.P.2
Bebb, C.E.3
Nordenskjöld, M.4
Ponder, B.A.5
Tunnacliffe, A.6
-
83
-
-
0029966845
-
Whole genome amplification using a degenerate oligonucleotide primer allows hundreds of genotypes to be performed on less than one nanogram of genomic DNA
-
Cheung VG, Nelson SF. Whole genome amplification using a degenerate oligonucleotide primer allows hundreds of genotypes to be performed on less than one nanogram of genomic DNA. Proc Natl Acad Sci U S A 1996, 93:14676-14679.
-
(1996)
Proc Natl Acad Sci U S A
, vol.93
, pp. 14676-14679
-
-
Cheung, V.G.1
Nelson, S.F.2
-
84
-
-
18344396798
-
Comprehensive human genome amplification using multiple displacement amplification
-
Dean FB, Hosono S, Fang L, Wu X, Faruqi AF, Bray-Ward P, Sun Z, Zong Q, Du Y, Du J, Driscoll M, Song W, Kingsmore SF, Egholm M, Lasken RS. Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci U S A 2002, 99:5261-5266.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 5261-5266
-
-
Dean, F.B.1
Hosono, S.2
Fang, L.3
Wu, X.4
Faruqi, A.F.5
Bray-Ward, P.6
Sun, Z.7
Zong, Q.8
Du, Y.9
Du, J.10
Driscoll, M.11
Song, W.12
Kingsmore, S.F.13
Egholm, M.14
Lasken, R.S.15
-
85
-
-
79961051856
-
Next-generation sequencing library preparation: simultaneous fragmentation and tagging using in vitro transposition
-
Available at:
-
Syed F, Gruenwald H, Caruccio N. Next-generation sequencing library preparation: simultaneous fragmentation and tagging using in vitro transposition. Nat Methods 2009, Available at: http://www.nature.com/nmeth/journal/v6/n11/full/nmeth.f.272.html.
-
(2009)
Nat Methods
-
-
Syed, F.1
Gruenwald, H.2
Caruccio, N.3
-
86
-
-
84856305295
-
Generating barcoded libraries for multiplex high-throughput sequencing
-
Knapp M, Stiller M, Meyer M. Generating barcoded libraries for multiplex high-throughput sequencing. Methods Mol Biol 2012, 840:155-170.
-
(2012)
Methods Mol Biol
, vol.840
, pp. 155-170
-
-
Knapp, M.1
Stiller, M.2
Meyer, M.3
-
87
-
-
40149103278
-
Error-correcting barcoded primers allow hundreds of samples to be pyrosequenced in multiplex
-
Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R. Error-correcting barcoded primers allow hundreds of samples to be pyrosequenced in multiplex. Nat Methods 2012, 5:235-237.
-
(2012)
Nat Methods
, vol.5
, pp. 235-237
-
-
Hamady, M.1
Walker, J.J.2
Harris, J.K.3
Gold, N.J.4
Knight, R.5
-
88
-
-
84863981120
-
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
-
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 2012, 6:1621-1624.
-
(2012)
ISME J
, vol.6
, pp. 1621-1624
-
-
Caporaso, J.G.1
Lauber, C.L.2
Walters, W.A.3
Berg-Lyons, D.4
Huntley, J.5
Fierer, N.6
Owens, S.M.7
Betley, J.8
Fraser, L.9
Bauer, M.10
Gormley, N.11
Gilbert, J.A.12
Smith, G.13
Knight, R.14
-
89
-
-
84862182131
-
Next-generation sequencing technologies and applications for human genetic history and forensics
-
Berglund EC, Kiialainen A, Syvänen AC. Next-generation sequencing technologies and applications for human genetic history and forensics. Investig Genet 2011, 2:23.
-
(2011)
Investig Genet
, vol.2
, pp. 23
-
-
Berglund, E.C.1
Kiialainen, A.2
Syvänen, A.C.3
-
90
-
-
84877266636
-
Updating benchtop sequencing performance comparison
-
Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U, Kalinowski J, Mellmann A, Goesmann A, von Haeseler A, Stoye J, Harmsen D. Updating benchtop sequencing performance comparison. Nat Biotechnol 2013, 31:294-296.
-
(2013)
Nat Biotechnol
, vol.31
, pp. 294-296
-
-
Jünemann, S.1
Sedlazeck, F.J.2
Prior, K.3
Albersmeier, A.4
John, U.5
Kalinowski, J.6
Mellmann, A.7
Goesmann, A.8
von Haeseler, A.9
Stoye, J.10
Harmsen, D.11
-
91
-
-
84865179264
-
High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity
-
Loman NJ, Constantinidou C, Chan JZ, Halachev M, Sergeant M, Penn CW, Robinson ER, Pallen MJ. High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nat Rev Microbiol 2012, 10:599-606.
-
(2012)
Nat Rev Microbiol
, vol.10
, pp. 599-606
-
-
Loman, N.J.1
Constantinidou, C.2
Chan, J.Z.3
Halachev, M.4
Sergeant, M.5
Penn, C.W.6
Robinson, E.R.7
Pallen, M.J.8
-
92
-
-
84865591846
-
A tale of three next generation sequencing platforms: comparison of Ion Torrent
-
Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y. A tale of three next generation sequencing platforms: comparison of Ion Torrent. Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 2012, 13:341.
-
(2012)
Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics
, vol.13
, pp. 341
-
-
Quail, M.A.1
Smith, M.2
Coupland, P.3
Otto, T.D.4
Harris, S.R.5
Connor, T.R.6
Bertoni, A.7
Swerdlow, H.P.8
Gu, Y.9
-
93
-
-
84855566198
-
Performance comparison of whole-genome sequencing platforms
-
Lam H, Clark M, Chen R, Natsoulis G, O'Huallachain M, Dewey FE, Habegger L, Ashley EA, Gerstein MB, Butte AJ, Ji HP, Snyder M. Performance comparison of whole-genome sequencing platforms. Nat Biotechnol 2011, 30:78-82.
-
(2011)
Nat Biotechnol
, vol.30
, pp. 78-82
-
-
Lam, H.1
Clark, M.2
Chen, R.3
Natsoulis, G.4
O'Huallachain, M.5
Dewey, F.E.6
Habegger, L.7
Ashley, E.A.8
Gerstein, M.B.9
Butte, A.J.10
Ji, H.P.11
Snyder, M.12
-
94
-
-
65449144325
-
Evaluation of next generation sequencing platforms for population targeted sequencing studies
-
Harismendy O, Ng P, Strausberg R, Wang X, Stockwell T, Beeson KY, Schork NJ, Murray SS, Topol EJ, Levy S, Frazer KA. Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol 2009, 10:R32.
-
(2009)
Genome Biol
, vol.10
-
-
Harismendy, O.1
Ng, P.2
Strausberg, R.3
Wang, X.4
Stockwell, T.5
Beeson, K.Y.6
Schork, N.J.7
Murray, S.S.8
Topol, E.J.9
Levy, S.10
Frazer, K.A.11
-
95
-
-
0031978181
-
Base-calling of automated sequencer traces using phred
-
Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998, 8:186-194.
-
(1998)
II. Error probabilities. Genome Res
, vol.8
, pp. 186-194
-
-
Ewing, B.1
Green, P.2
-
96
-
-
84905830412
-
Microbial community profiling of human saliva using shotgun metagenomic sequencing
-
in press
-
Hasan NA, Young BA, Minard-Smith EM, McMillan NJ, Isom R, Abdullah AS, Bornman DM, Faith SA, Choi SY, Longmire G, Dickens ML, Cebula TA, Colwell RR. Microbial community profiling of human saliva using shotgun metagenomic sequencing. PLoS One in press.
-
PLoS One
-
-
Hasan, N.A.1
Young, B.A.2
Minard-Smith, E.M.3
McMillan, N.J.4
Isom, R.5
Abdullah, A.S.6
Bornman, D.M.7
Faith, S.A.8
Choi, S.Y.9
Longmire, G.10
Dickens, M.L.11
Cebula, T.A.12
Colwell, R.R.13
-
97
-
-
84883468661
-
Scalable metagenomic taxonomy classification using a reference genome database
-
Ames SK, Hysom DA, Gardner SN, Lloyd GS, Gokhale MB, Allen JE. Scalable metagenomic taxonomy classification using a reference genome database. Bioinformatics 2013, 29:2253-2260.
-
(2013)
Bioinformatics
, vol.29
, pp. 2253-2260
-
-
Ames, S.K.1
Hysom, D.A.2
Gardner, S.N.3
Lloyd, G.S.4
Gokhale, M.B.5
Allen, J.E.6
-
99
-
-
84899090573
-
Kraken: ultrafast metagenomic sequence classification using exact alignments
-
Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol 2014, 15:R46.
-
(2014)
Genome Biol
, vol.15
-
-
Wood, D.E.1
Salzberg, S.L.2
-
100
-
-
15644363954
-
Molecular evolution and diversity in Bacillus anthracis as detected by amplified fragment length polymorphism markers
-
Keim P, Kalif A, Schupp J, Hill K, Travis SE, Richmond K, Adair DM, Hugh-Jones M, Kuske CR, Jackson P. Molecular evolution and diversity in Bacillus anthracis as detected by amplified fragment length polymorphism markers. J Bacteriol 1997, 179:818-824.
-
(1997)
J Bacteriol
, vol.179
, pp. 818-824
-
-
Keim, P.1
Kalif, A.2
Schupp, J.3
Hill, K.4
Travis, S.E.5
Richmond, K.6
Adair, D.M.7
Hugh-Jones, M.8
Kuske, C.R.9
Jackson, P.10
-
101
-
-
84882729023
-
Harnessing virtual machines to simplify next-generation DNA sequencing analysis
-
Nocq J, Celton M, Gendron P, Lemieux S, Wilhelm BT. Harnessing virtual machines to simplify next-generation DNA sequencing analysis. Bioinformatics 2013, 29:2075-2083.
-
(2013)
Bioinformatics
, vol.29
, pp. 2075-2083
-
-
Nocq, J.1
Celton, M.2
Gendron, P.3
Lemieux, S.4
Wilhelm, B.T.5
-
102
-
-
0003726721
-
IEEE Standard 610.12 Glossary of software engineering terminology
-
Available at: , Board IS
-
Board IS IEEE Standard 610.12 Glossary of software engineering terminology. 1990, Available at: http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?reload=true&punumber=2238, Board IS.
-
(1990)
-
-
-
103
-
-
0038703389
-
-
Available at:
-
Crumpler S, Cheng J, Tillman DB, Benesch B, Sawyer D, Murray J, Press H, Snipes C, Godziemski A, Bergeson D, Loreng J. General principles of software validation; Final guidance for industry and FDA staff 2002, Available at: http://www.fda.gov/medicaldevices/deviceregulationandguidance/guidancedocuments/ucm085281.htm.
-
(2002)
General principles of software validation; Final guidance for industry and FDA staff
-
-
Crumpler, S.1
Cheng, J.2
Tillman, D.B.3
Benesch, B.4
Sawyer, D.5
Murray, J.6
Press, H.7
Snipes, C.8
Godziemski, A.9
Bergeson, D.10
Loreng, J.11
-
104
-
-
79952580139
-
Compression of DNA sequence reads in FASTQ format
-
Deorowicz S, Grabowski S. Compression of DNA sequence reads in FASTQ format. Bioinformatics 2011, 27:860-862.
-
(2011)
Bioinformatics
, vol.27
, pp. 860-862
-
-
Deorowicz, S.1
Grabowski, S.2
-
105
-
-
84875363204
-
Compression of FASTQ and SAM format sequencing data
-
Bonfield J, Mahoney M. Compression of FASTQ and SAM format sequencing data. PLoS One 2013, 8:e59190.
-
(2013)
PLoS One
, vol.8
-
-
Bonfield, J.1
Mahoney, M.2
-
106
-
-
84886206473
-
-
Washington DC: American Academy of Microbiology, Available at:
-
Buckley M, Roberts RJ. Reconciling Microbial Systematics and Genomics 2007, Washington DC: American Academy of Microbiology, Available at: http://academy.asm.org/index.php/genetics-genomics-molecular-microbiology/454-reconciling-microbial-systematics-and-genomics.
-
(2007)
Reconciling Microbial Systematics and Genomics
-
-
Buckley, M.1
Roberts, R.J.2
-
107
-
-
84880673210
-
Molecular evolution in court analysis of a large hepatitis C virus outbreak from an evolving source
-
Gonzalez-Candelas F, Bracho M, Wrobel B, Moya A. Molecular evolution in court analysis of a large hepatitis C virus outbreak from an evolving source. BMC Biol 2013, 11:76.
-
(2013)
BMC Biol
, vol.11
, pp. 76
-
-
Gonzalez-Candelas, F.1
Bracho, M.2
Wrobel, B.3
Moya, A.4
-
108
-
-
84872152255
-
MetAMOS: a modular and open source metagenomic assemblyand analysis pipeline
-
Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M. MetAMOS: a modular and open source metagenomic assemblyand analysis pipeline. Genome Biol 2013, 14:R2.
-
(2013)
Genome Biol
, vol.14
-
-
Treangen, T.J.1
Koren, S.2
Sommer, D.D.3
Liu, B.4
Astrovskaya, I.5
Ondov, B.6
Darling, A.E.7
Phillippy, A.M.8
Pop, M.9
-
109
-
-
43149115851
-
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
-
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18:821-829.
-
(2008)
Genome Res
, vol.18
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
-
110
-
-
79955724657
-
Comparing de novo genome assembly: the long and short of it
-
Narzisi G, Mishra B. Comparing de novo genome assembly: the long and short of it. PLoS One 2011, 6:e19175.
-
(2011)
PLoS One
, vol.6
-
-
Narzisi, G.1
Mishra, B.2
-
111
-
-
43149085041
-
De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer
-
Hernandez D, François P, Farinelli L, Osterås M, Schrenzel J. De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res 2008, 18:802-809.
-
(2008)
Genome Res
, vol.18
, pp. 802-809
-
-
Hernandez, D.1
François, P.2
Farinelli, L.3
Osterås, M.4
Schrenzel, J.5
-
112
-
-
39049156065
-
Short read fragment assembly of bacterial genomes
-
Chaisson MJ, Pevzner PA. Short read fragment assembly of bacterial genomes. Genome Res 2008, 18:324-330.
-
(2008)
Genome Res
, vol.18
, pp. 324-330
-
-
Chaisson, M.J.1
Pevzner, P.A.2
-
113
-
-
84991528460
-
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
-
Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience 2013, 2:10.
-
(2013)
Gigascience
, vol.2
, pp. 10
-
-
Bradnam, K.R.1
Fass, J.N.2
Alexandrov, A.3
Baranay, P.4
Bechner, M.5
Birol, I.6
Boisvert, S.7
Chapman, J.A.8
Chapuis, G.9
Chikhi, R.10
Chitsaz, H.11
Chou, W.C.12
Corbeil, J.13
Del Fabbro, C.14
Docking, T.R.15
Durbin, R.16
Earl, D.17
Emrich, S.18
Fedotov, P.19
Fonseca, N.A.20
Ganapathy, G.21
Gibbs, R.A.22
Gnerre, S.23
Godzaridis, E.24
Goldstein, S.25
Haimel, M.26
Hall, G.27
Haussler, D.28
Hiatt, J.B.29
Ho, I.Y.30
more..
-
114
-
-
84876266928
-
QUAST: quality assessment tool for genome assemblies
-
Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013, 29:1072-1075.
-
(2013)
Bioinformatics
, vol.29
, pp. 1072-1075
-
-
Gurevich, A.1
Saveliev, V.2
Vyahhi, N.3
Tesler, G.4
-
115
-
-
84878629521
-
Benchmarking short sequence mapping tools
-
Hatem A, Bozdaǧ D, Toland AE, Çatalyürek T. Benchmarking short sequence mapping tools. BMC Bioinformatics 2013, 14:184.
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 184
-
-
Hatem, A.1
Bozdaǧ, D.2
Toland, A.E.3
Çatalyürek, T.4
-
116
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012, 9:357-359.
-
(2012)
Nat Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
117
-
-
0036606576
-
Fast algorithms for large-scale genome alignment and comparison
-
Delcher AL, Phillippy A, Carlton J, Salzberg SL. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res 2002, 30:2478-2483.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 2478-2483
-
-
Delcher, A.L.1
Phillippy, A.2
Carlton, J.3
Salzberg, S.L.4
-
118
-
-
33845957530
-
Accurate phylogenetic classification of variable-length DNA fragments
-
McHardy AC, Martín HG, Tsirigos A, Hugenholtz P, Rigoutsos I. Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods 2007, 4:63-72.
-
(2007)
Nat Methods
, vol.4
, pp. 63-72
-
-
McHardy, A.C.1
Martín, H.G.2
Tsirigos, A.3
Hugenholtz, P.4
Rigoutsos, I.5
-
119
-
-
84862697946
-
The PhyloPythiaS web server for taxonomic assignment of metagenome sequences
-
Patil KR, Roune L, McHardy AC. The PhyloPythiaS web server for taxonomic assignment of metagenome sequences. PLoS One 2012, 7:e38581.
-
(2012)
PLoS One
, vol.7
-
-
Patil, K.R.1
Roune, L.2
McHardy, A.C.3
-
120
-
-
69549135124
-
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
-
Brady A, Salzberg SL. Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat Methods 2009, 6:673-676.
-
(2009)
Nat Methods
, vol.6
, pp. 673-676
-
-
Brady, A.1
Salzberg, S.L.2
-
121
-
-
78650549608
-
NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads
-
Rosen GL, Reichenberger ER, Rosenfeld AM. NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads. Bioinformatics 2011, 27:127-129.
-
(2011)
Bioinformatics
, vol.27
, pp. 127-129
-
-
Rosen, G.L.1
Reichenberger, E.R.2
Rosenfeld, A.M.3
-
122
-
-
84865331226
-
Rapid phylogenetic and functional classification of short genomic fragments with signature peptides
-
Berendzen J, Bruno WJ, Cohn JD, Hengartner NW, Kuske R, McMahon BH, Wolinsky MA, Xie G. Rapid phylogenetic and functional classification of short genomic fragments with signature peptides. BMC Res Notes 2012, 5:460.
-
(2012)
BMC Res Notes
, vol.5
, pp. 460
-
-
Berendzen, J.1
Bruno, W.J.2
Cohn, J.D.3
Hengartner, N.W.4
Kuske, R.5
McMahon, B.H.6
Wolinsky, M.A.7
Xie, G.8
-
123
-
-
33847702910
-
MEGAN analysis of metagenomic data
-
Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome Res 2007, 17:377-386.
-
(2007)
Genome Res
, vol.17
, pp. 377-386
-
-
Huson, D.H.1
Auch, A.F.2
Qi, J.3
Schuster, S.C.4
-
124
-
-
84865161908
-
Genometa-a fast and accurate classifier for short metagenomic shotgun reads
-
Davenport CF, Neugebauer J, Beckmann N, Friedrich B, Kameri B, Kokott S, Paetow M, Siekmann B, Wieding-Drewes M, Wienhöfer M, Wolf S, Tümmler B, Ahlers V, Sprengel F. Genometa-a fast and accurate classifier for short metagenomic shotgun reads. PLoS One 2012, 7:e41224.
-
(2012)
PLoS One
, vol.7
-
-
Davenport, C.F.1
Neugebauer, J.2
Beckmann, N.3
Friedrich, B.4
Kameri, B.5
Kokott, S.6
Paetow, M.7
Siekmann, B.8
Wieding-Drewes, M.9
Wienhöfer, M.10
Wolf, S.11
Tümmler, B.12
Ahlers, V.13
Sprengel, F.14
-
125
-
-
84859358278
-
Fast and accurate taxonomic assignments of metagenomic sequences using MetaBin
-
Sharma VK, Kumar N, Prakash T, Taylor TD. Fast and accurate taxonomic assignments of metagenomic sequences using MetaBin. PLoS One 2012, 7:e34030.
-
(2012)
PLoS One
, vol.7
-
-
Sharma, V.K.1
Kumar, N.2
Prakash, T.3
Taylor, T.D.4
-
126
-
-
79960869431
-
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences
-
Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M. Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. BMC Genomics 2011, 12(Suppl 2):S4.
-
(2011)
BMC Genomics
, vol.12
, Issue.SUPPL. 2
-
-
Liu, B.1
Gibbons, T.2
Ghodsi, M.3
Treangen, T.4
Pop, M.5
-
127
-
-
84864440400
-
Metagenomic microbial community profiling using unique clade-specific marker genes
-
Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C. Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods 2012, 9:811-814.
-
(2012)
Nat Methods
, vol.9
, pp. 811-814
-
-
Segata, N.1
Waldron, L.2
Ballarini, A.3
Narasimhan, V.4
Jousson, O.5
Huttenhower, C.6
-
128
-
-
84864446502
-
High-speed microbial community profiling
-
Haft DH, Tovchigrechko A. High-speed microbial community profiling. Nat Methods 2012, 9:793-794.
-
(2012)
Nat Methods
, vol.9
, pp. 793-794
-
-
Haft, D.H.1
Tovchigrechko, A.2
-
129
-
-
42449162998
-
Phylogenetic classification of short environmental DNA fragments
-
Krause L, Diaz NN, Goesmann A, Kelley S, Nattkemper TW, Rohwer F, Edwards RA, Stoye J. Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Res 2008, 36:2230-2239.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 2230-2239
-
-
Krause, L.1
Diaz, N.N.2
Goesmann, A.3
Kelley, S.4
Nattkemper, T.W.5
Rohwer, F.6
Edwards, R.A.7
Stoye, J.8
-
130
-
-
74049132798
-
WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads
-
Gerlach W, Jünemann S, Tille F, Goesmann A, Stoye J. WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. BMC Bioinformatics 2009, 10:430.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 430
-
-
Gerlach, W.1
Jünemann, S.2
Tille, F.3
Goesmann, A.4
Stoye, J.5
-
131
-
-
84862024797
-
IMG/M: the integrated metagenome data management and comparative analysis system
-
Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Grechkin Y, Ratner A, Jacob B, Pati A, Huntemann M, Liolios K, Pagani I, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC. IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res 2012, 40:D123-D129.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Markowitz, V.M.1
Chen, I.M.2
Chu, K.3
Szeto, E.4
Palaniappan, K.5
Grechkin, Y.6
Ratner, A.7
Jacob, B.8
Pati, A.9
Huntemann, M.10
Liolios, K.11
Pagani, I.12
Anderson, I.13
Mavromatis, K.14
Ivanova, N.N.15
Kyrpides, N.C.16
-
132
-
-
53549118607
-
The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
-
Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 2008, 9:386.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 386
-
-
Meyer, F.1
Paarmann, D.2
D'Souza, M.3
Olson, R.4
Glass, E.M.5
Kubal, M.6
Paczian, T.7
Rodriguez, A.8
Stevens, R.9
Wilke, A.10
Wilkening, J.11
Edwards, R.A.12
-
133
-
-
84863049441
-
MetaCluster 4.0: a novel binning algorithm for NGS reads and huge number of species
-
Wang Y, Leung HC, Yiu SM, Chin FY. MetaCluster 4.0: a novel binning algorithm for NGS reads and huge number of species. J Comput Biol 2012, 19:241-249.
-
(2012)
J Comput Biol
, vol.19
, pp. 241-249
-
-
Wang, Y.1
Leung, H.C.2
Yiu, S.M.3
Chin, F.Y.4
-
134
-
-
84864945803
-
Rapid identification of high-confidence taxonomic assignments for metagenomic data
-
MacDonald NJ, Parks DH, Beiko RG. Rapid identification of high-confidence taxonomic assignments for metagenomic data. Nucleic Acids Res 2012, 40:e111.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
MacDonald, N.J.1
Parks, D.H.2
Beiko, R.G.3
-
135
-
-
79955611184
-
PhymmBL expanded: confidence scores, custom databases, parallelization and more
-
Brady A, Salzberg S. PhymmBL expanded: confidence scores, custom databases, parallelization and more. Nat Methods 2011, 8:367.
-
(2011)
Nat Methods
, vol.8
, pp. 367
-
-
Brady, A.1
Salzberg, S.2
-
136
-
-
84860672197
-
A comparative evaluation of sequence classification programs
-
Bazinet A, Cummings M. A comparative evaluation of sequence classification programs. BMC Bioinformatics 2012, 13:1-13.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 1-13
-
-
Bazinet, A.1
Cummings, M.2
-
137
-
-
77950904616
-
Forensic identification using skin bacterial communities
-
Fierer N, Lauber CL, Zhou N, Mcdonald D, Costello EK, Knight R. Forensic identification using skin bacterial communities. Proc Natl Acad Sci U S A 2010, 107:6477-6481.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 6477-6481
-
-
Fierer, N.1
Lauber, C.L.2
Zhou, N.3
Mcdonald, D.4
Costello, E.K.5
Knight, R.6
-
138
-
-
0000594195
-
Evolution and measurement of species diversity
-
Whittaker RH. Evolution and measurement of species diversity. Taxon 1972, 21:213-251.
-
(1972)
Taxon
, vol.21
, pp. 213-251
-
-
Whittaker, R.H.1
-
139
-
-
84890558766
-
Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions
-
Fricke WF, Rasko DA. Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions. Nat Rev Genet 2013, 15:49-55.
-
(2013)
Nat Rev Genet
, vol.15
, pp. 49-55
-
-
Fricke, W.F.1
Rasko, D.A.2
|