-
1
-
-
84873809749
-
Integrating genome-based informatics to modernize global disease monitoring, information sharing, and response
-
Aarestrup, F. M., Brown, E. W., Detter, C., Gerner-Smidt, P., Gilmour, M. W., Harmsen, D., et al. (2012). Integrating genome-based informatics to modernize global disease monitoring, information sharing, and response. Emerg. Infect. Dis. 18:e1. doi: 10.3201/eid/1811.120453.
-
(2012)
Emerg. Infect. Dis
, vol.18
-
-
Aarestrup, F.M.1
Brown, E.W.2
Detter, C.3
Gerner-Smidt, P.4
Gilmour, M.W.5
Harmsen, D.6
-
2
-
-
84930660464
-
MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning
-
Afiahayati, R., Sato, K., Sakakibara, Y., Robertson, D. L., Prosperi, M., Afiahayati, K., et al. (2015). MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning. DNA Res. 22, 69-77. doi: 10.1093/dnares/dsu041.
-
(2015)
DNA Res
, vol.22
, pp. 69-77
-
-
Afiahayati, R.1
Sato, K.2
Sakakibara, Y.3
Robertson, D.L.4
Prosperi, M.5
Afiahayati, K.6
-
3
-
-
84925104897
-
Geospatial resolution of human and bacterial diversity with city-scale metagenomics
-
Afshinnekoo, E., Meydan, C., Chowdhury, S., Jaroudi, D., Boyer, C., Bernstein, N., et al. (2015). Geospatial resolution of human and bacterial diversity with city-scale metagenomics. Cell Syst. 1, 72-87. doi: 10.1016/j.cels.2015.01.001.
-
(2015)
Cell Syst
, vol.1
, pp. 72-87
-
-
Afshinnekoo, E.1
Meydan, C.2
Chowdhury, S.3
Jaroudi, D.4
Boyer, C.5
Bernstein, N.6
-
4
-
-
84904734421
-
Global prevalence of norovirus in cases of gastroenteritis: a systematic review and meta-analysis
-
Ahmed, S. M., Hall, A. J., Robinson, A. E., Verhoef, L., Premkumar, P., Parashar, U. D., et al. (2014). Global prevalence of norovirus in cases of gastroenteritis: a systematic review and meta-analysis. Lancet. Infect. Dis. 14, 725-730. doi: 10.1016/S1473-3099(14)70767-4.
-
(2014)
Lancet. Infect. Dis
, vol.14
, pp. 725-730
-
-
Ahmed, S.M.1
Hall, A.J.2
Robinson, A.E.3
Verhoef, L.4
Premkumar, P.5
Parashar, U.D.6
-
5
-
-
84879605153
-
Viral metagenomics: a tool for virus discovery and diversity in aquaculture
-
Alavandi, S. V., and Poornima, M. (2012). Viral metagenomics: a tool for virus discovery and diversity in aquaculture. Indian J. Virol. 23, 88-98. doi: 10.1007/s13337-012-0075-2.
-
(2012)
Indian J. Virol
, vol.23
, pp. 88-98
-
-
Alavandi, S.V.1
Poornima, M.2
-
6
-
-
34248192946
-
Detection by PCR of eight groups of enteric pathogens in 4,627 faecal samples: re-examination of the English case-control infectious intestinal disease study (1993-1996)
-
Amar, C. F. L., East, C. L., Gray, J., Iturriza-Gomara, M., Maclure, E. A., and McLauchlin, J. (2007). Detection by PCR of eight groups of enteric pathogens in 4,627 faecal samples: re-examination of the English case-control infectious intestinal disease study (1993-1996). Eur. J. Clin. Microbiol. Infect. Dis. 26, 311-323. doi: 10.1007/s10096-007-0290-8.
-
(2007)
Eur. J. Clin. Microbiol. Infect. Dis
, vol.26
, pp. 311-323
-
-
Amar, C.F.L.1
East, C.L.2
Gray, J.3
Iturriza-Gomara, M.4
Maclure, E.A.5
McLauchlin, J.6
-
7
-
-
85084326675
-
Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases
-
Arias, A., Watson, S. J., Asogun, D., Tobin, E. A., Lu, J., Phan, M. V. T., et al. (2016). Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases. Virus Evol. 2:vew016. doi: 10.1093/ve/vew016.
-
(2016)
Virus Evol
, vol.2
-
-
Arias, A.1
Watson, S.J.2
Asogun, D.3
Tobin, E.A.4
Lu, J.5
Phan, M.V.T.6
-
8
-
-
84908213690
-
Metagenomic approaches for direct and cell culture evaluation of the virological quality of wastewater
-
Aw, T. G., Howe, A., and Rose, J. B. (2014). Metagenomic approaches for direct and cell culture evaluation of the virological quality of wastewater. J. Virol. Methods 210, 15-21. doi: 10.1016/j.jviromet.2014.09.017.
-
(2014)
J. Virol. Methods
, vol.210
, pp. 15-21
-
-
Aw, T.G.1
Howe, A.2
Rose, J.B.3
-
9
-
-
84865198421
-
Unrecognized norovirus infections in health care institutions and their clinical impact
-
Beersma, M. F. C., Sukhrie, F. H. A., Bogerman, J., Verhoef, L., Melo, M. M., Vonk, A. G., et al. (2012). Unrecognized norovirus infections in health care institutions and their clinical impact. J. Clin. Microbiol. 50, 3040-3045. doi: 10.1128/JCM.00908-12.
-
(2012)
J. Clin. Microbiol
, vol.50
, pp. 3040-3045
-
-
Beersma, M.F.C.1
Sukhrie, F.H.A.2
Bogerman, J.3
Verhoef, L.4
Melo, M.M.5
Vonk, A.G.6
-
10
-
-
84874795336
-
Shellfish-borne viral outbreaks: a systematic review
-
Bellou, M., Kokkinos, P., and Vantarakis, A. (2013). Shellfish-borne viral outbreaks: a systematic review. Food Environ. Virol. 5, 13-23. doi: 10.1007/s12560-012-9097-6.
-
(2013)
Food Environ. Virol
, vol.5
, pp. 13-23
-
-
Bellou, M.1
Kokkinos, P.2
Vantarakis, A.3
-
11
-
-
84874796519
-
Norovirus and other human enteric viruses in moroccan shellfish
-
Benabbes, L., Ollivier, J., Schaeffer, J., Parnaudeau, S., Rhaissi, H., Nourlil, J., et al. (2013). Norovirus and other human enteric viruses in moroccan shellfish. Food Environ. Virol. 5, 35-40. doi: 10.1007/s12560-012-9095-8.
-
(2013)
Food Environ. Virol
, vol.5
, pp. 35-40
-
-
Benabbes, L.1
Ollivier, J.2
Schaeffer, J.3
Parnaudeau, S.4
Rhaissi, H.5
Nourlil, J.6
-
12
-
-
84947753062
-
Multiplex molecular panels for diagnosis of gastrointestinal infection: performance, result interpretation, and cost-effectiveness
-
Binnicker, M. J. (2015). Multiplex molecular panels for diagnosis of gastrointestinal infection: performance, result interpretation, and cost-effectiveness. J. Clin. Microbiol. 53, 3723-3728. doi: 10.1128/JCM.02103-15.
-
(2015)
J. Clin. Microbiol
, vol.53
, pp. 3723-3728
-
-
Binnicker, M.J.1
-
13
-
-
84871396799
-
Ray meta: scalable de novo metagenome assembly and profiling
-
Boisvert, S., Raymond, F., Godzaridis,é, Laviolette, F., Corbeil, J., Wold, B., et al. (2012). Ray meta: scalable de novo metagenome assembly and profiling. Genome Biol. 13:R122. doi: 10.1186/gb-2012-13-12-r122.
-
(2012)
Genome Biol
, vol.13
, pp. R122
-
-
Boisvert, S.1
Raymond, F.2
Godzaridis, É.3
Laviolette, F.4
Corbeil, J.5
Wold, B.6
-
14
-
-
84946601295
-
Virome capture sequencing enables sensitive viral diagnosis and comprehensive virome analysis
-
Briese, T., Kapoor, A., Mishra, N., Jain, K., Kumar, A., Jabado, O. J., et al. (2015). Virome capture sequencing enables sensitive viral diagnosis and comprehensive virome analysis. MBio 6:e1491-15. doi: 10.1128/mBio.01491-15.
-
(2015)
MBio
, vol.6
-
-
Briese, T.1
Kapoor, A.2
Mishra, N.3
Jain, K.4
Kumar, A.5
Jabado, O.J.6
-
15
-
-
84960539011
-
Key role of sequencing to trace hepatitis a viruses circulating in Italy during a large multi-country European foodborne outbreak in 2013
-
Bruni, R., Taffon, S., Equestre, M., Chionne, P., Madonna, E., Rizzo, C., et al. (2016). Key role of sequencing to trace hepatitis a viruses circulating in Italy during a large multi-country European foodborne outbreak in 2013. PLoS ONE 11:e0149642. doi: 10.1371/journal.pone.0149642.
-
(2016)
PLoS ONE
, vol.11
-
-
Bruni, R.1
Taffon, S.2
Equestre, M.3
Chionne, P.4
Madonna, E.5
Rizzo, C.6
-
16
-
-
84925021592
-
Fast and sensitive protein alignment using DIAMOND
-
Buchfink, B., Xie, C., and Huson, D. H. (2014). Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59-60. doi: 10.1038/nmeth.3176.
-
(2014)
Nat. Methods
, vol.12
, pp. 59-60
-
-
Buchfink, B.1
Xie, C.2
Huson, D.H.3
-
17
-
-
84929676980
-
The virome in host health and disease
-
Cadwell, K. (2015). The virome in host health and disease. Immunity 42, 805-813. doi: 10.1016/j.immuni.2015.05.003.
-
(2015)
Immunity
, vol.42
, pp. 805-813
-
-
Cadwell, K.1
-
18
-
-
80455127052
-
Raw sewage harbors diverse viral populations
-
Cantalupo, P. G., Calgua, B., Zhao, G., Hundesa, A., Wier, A. D., Katz, J. P., et al. (2011). Raw sewage harbors diverse viral populations. MBio 2:e180-11. doi: 10.1128/mBio.00180-11.
-
(2011)
MBio
, vol.2
-
-
Cantalupo, P.G.1
Calgua, B.2
Zhao, G.3
Hundesa, A.4
Wier, A.D.5
Katz, J.P.6
-
19
-
-
77956332518
-
Pepper mild mottle virus, a plant virus associated with specific immune responses, fever, abdominal pains, and pruritus in humans
-
Colson, P., Richet, H., Desnues, C., Balique, F., Moal, V., Grob, J.-J., et al. (2010). Pepper mild mottle virus, a plant virus associated with specific immune responses, fever, abdominal pains, and pruritus in humans. PLoS ONE 5:e10041. doi: 10.1371/journal.pone.0010041.
-
(2010)
PLoS ONE
, vol.5
-
-
Colson, P.1
Richet, H.2
Desnues, C.3
Balique, F.4
Moal, V.5
Grob, J.-J.6
-
20
-
-
84946919159
-
Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis
-
Conceição-Neto, N., Zeller, M., Lefrère, H., De Bruyn, P., Beller, L., Deboutte, W., et al. (2015). Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis. Sci. Rep. 5:16532. doi: 10.1038/srep16532.
-
(2015)
Sci. Rep
, vol.5
, pp. 16532
-
-
Conceição-Neto, N.1
Zeller, M.2
Lefrère, H.3
De Bruyn, P.4
Beller, L.5
Deboutte, W.6
-
21
-
-
4444338122
-
Survival of human enteric viruses in the environment and food
-
Cook, N., and Rze, A. (2004). Survival of human enteric viruses in the environment and food. FEMS Microbiol. Rev. 28, 441-453. doi: 10.1016/j.femsre.2004.02.001.
-
(2004)
FEMS Microbiol. Rev
, vol.28
, pp. 441-453
-
-
Cook, N.1
Rze, A.2
-
22
-
-
84898893459
-
Full genome virus detection in fecal samples using sensitive nucleic acid preparation, deep sequencing, and a novel iterative sequence classification algorithm
-
Cotten, M., Oude Munnink, B., Canuti, M., Deijs, M., Watson, S. J., Kellam, P., et al. (2014). Full genome virus detection in fecal samples using sensitive nucleic acid preparation, deep sequencing, and a novel iterative sequence classification algorithm. PLoS ONE 9:e93269. doi: 10.1371/journal.pone.0093269.
-
(2014)
PLoS ONE
, vol.9
-
-
Cotten, M.1
Oude Munnink, B.2
Canuti, M.3
Deijs, M.4
Watson, S.J.5
Kellam, P.6
-
23
-
-
79958061875
-
Nucleic acid amplification-based methods for detection of enteric viruses: definition of controls and interpretation of results
-
D'Agostino, M. D., Cook, N., Rodriguez-Lazaro, D., and Rutjes, S. (2011). Nucleic acid amplification-based methods for detection of enteric viruses: definition of controls and interpretation of results. Food Environ. Virol. 3, 55-60.
-
(2011)
Food Environ. Virol
, vol.3
, pp. 55-60
-
-
D'Agostino, M.D.1
Cook, N.2
Rodriguez-Lazaro, D.3
Rutjes, S.4
-
24
-
-
84969791255
-
Human norovirus transmission and evolution in a changing world
-
de Graaf, M., van Beek, J., and Koopmans, M. P. (2016). Human norovirus transmission and evolution in a changing world. Nat. Rev. Microbiol. 14, 421-433. doi: 10.1038/nrmicro.2016.48.
-
(2016)
Nat. Rev. Microbiol
, vol.14
, pp. 421-433
-
-
de Graaf, M.1
van Beek, J.2
Koopmans, M.P.3
-
25
-
-
0035694161
-
A comparison of gastroenteritis in a general practice-based study and a community-based study
-
de Wit, M. A., Kortbeek, L. M., Koopmans, M. P., de Jager, C. J., Wannet, W. J., Bartelds, A. I., et al. (2001). A comparison of gastroenteritis in a general practice-based study and a community-based study. Epidemiol. Infect. 127, 389-397.
-
(2001)
Epidemiol. Infect
, vol.127
, pp. 389-397
-
-
de Wit, M.A.1
Kortbeek, L.M.2
Koopmans, M.P.3
de Jager, C.J.4
Wannet, W.J.5
Bartelds, A.I.6
-
26
-
-
84959932823
-
Genomic epidemiology: whole-genome-sequencing-powered surveillance and outbreak investigation of foodborne bacterial pathogens
-
Deng, X., den Bakker, H. C., and Hendriksen, R. S. (2016). Genomic epidemiology: whole-genome-sequencing-powered surveillance and outbreak investigation of foodborne bacterial pathogens. Annu. Rev. Food Sci. Technol. 7, 353-374. doi: 10.1146/annurev-food-041715-033259.
-
(2016)
Annu. Rev. Food Sci. Technol
, vol.7
, pp. 353-374
-
-
Deng, X.1
den Bakker, H.C.2
Hendriksen, R.S.3
-
27
-
-
84908280770
-
Detection of hepatitis E virus in pork liver sausages
-
Di Bartolo, I., Angeloni, G., Ponterio, E., Ostanello, F., and Ruggeri, F. M. (2015). Detection of hepatitis E virus in pork liver sausages. Int. J. Food Microbiol. 193, 29-33. doi: 10.1016/j.ijfoodmicro.2014.10.005.
-
(2015)
Int. J. Food Microbiol
, vol.193
, pp. 29-33
-
-
Di Bartolo, I.1
Angeloni, G.2
Ponterio, E.3
Ostanello, F.4
Ruggeri, F.M.5
-
28
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar, R. C. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460-2461. doi: 10.1093/bioinformatics/btq461.
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
29
-
-
85031992458
-
Manual for reporting on food-borne outbreaks in accordance with directive 2003/99/EC for information deriving from the year 2015
-
ESFA (2016). Manual for reporting on food-borne outbreaks in accordance with directive 2003/99/EC for information deriving from the year 2015. EFSA Support Publ. 13:989E. doi: 10.2903/SP.EFSA.2016.EN-989.
-
(2016)
EFSA Support Publ
, vol.13
, pp. 989E
-
-
-
30
-
-
85014962870
-
An update on the risk of transmission of Ebola virus (EBOV) via the food chain
-
European Food Safety Authority (2014). An update on the risk of transmission of Ebola virus (EBOV) via the food chain. EFSA J. 12:3884. doi: 10.2903/j.efsa.2014.3884.
-
(2014)
EFSA J
, vol.12
, pp. 3884
-
-
-
31
-
-
84945284538
-
The European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2011 has been published
-
Eurosurveillance editorial team (2015). The European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2011 has been published. Euro Surveill. 18:20449. doi: 10.2903/j.efsa.2015.3991.
-
(2015)
Euro Surveill
, vol.18
, pp. 20449
-
-
-
32
-
-
84969961419
-
Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling
-
Flygare, S., Simmon, K., Miller, C., Qiao, Y., Kennedy, B., Di Sera, T., et al. (2016). Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling. Genome Biol. 17:111. doi: 10.1186/s13059-016-0969-1.
-
(2016)
Genome Biol
, vol.17
, pp. 111
-
-
Flygare, S.1
Simmon, K.2
Miller, C.3
Qiao, Y.4
Kennedy, B.5
Di Sera, T.6
-
33
-
-
84893206783
-
Comparison of three next-generation sequencing platforms for metagenomic sequencing and identification of pathogens in blood
-
Frey, K. G., Herrera-Galeano, J., Redden, C. L., Luu, T. V., Servetas, S. L., Mateczun, A. J., et al. (2014). Comparison of three next-generation sequencing platforms for metagenomic sequencing and identification of pathogens in blood. BMC Genomics 15:96. doi: 10.1186/1471-2164-15-96.
-
(2014)
BMC Genomics
, vol.15
, pp. 96
-
-
Frey, K.G.1
Herrera-Galeano, J.2
Redden, C.L.3
Luu, T.V.4
Servetas, S.L.5
Mateczun, A.J.6
-
34
-
-
85014480787
-
MERS-CoV at the animal-human interface: inputs on exposure pathways from an expert-opinion elicitation
-
Funk, A. L., Goutard, F. L., Miguel, E., Bourgarel, M., Chevalier, V., Faye, B., et al. (2016). MERS-CoV at the animal-human interface: inputs on exposure pathways from an expert-opinion elicitation. Front. Vet. Sci. 3:88. doi: 10.3389/fvets.2016.00088.
-
(2016)
Front. Vet. Sci
, vol.3
, pp. 88
-
-
Funk, A.L.1
Goutard, F.L.2
Miguel, E.3
Bourgarel, M.4
Chevalier, V.5
Faye, B.6
-
35
-
-
84964052754
-
Environmental surveillance of viruses by tangential flow filtration and metagenomic reconstruction
-
Furtak, V., Roivainen, M., Mirochnichenko, O., Zagorodnyaya, T., Laassri, M., Zaidi, S. Z., et al. (2016). Environmental surveillance of viruses by tangential flow filtration and metagenomic reconstruction. Euro Surveill. 21:30193. doi: 10.2807/1560-7917.ES.2016.21.15.30193.
-
(2016)
Euro Surveill
, vol.21
, pp. 30193
-
-
Furtak, V.1
Roivainen, M.2
Mirochnichenko, O.3
Zagorodnyaya, T.4
Laassri, M.5
Zaidi, S.Z.6
-
36
-
-
84907193791
-
Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak
-
Gire, S. K., Goba, A., Andersen, K. G., Sealfon, R. S. G., Park, D. J., Kanneh, L., et al. (2014). Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science 345, 1369-1372. doi: 10.1126/science.1259657.
-
(2014)
Science
, vol.345
, pp. 1369-1372
-
-
Gire, S.K.1
Goba, A.2
Andersen, K.G.3
Sealfon, R.S.G.4
Park, D.J.5
Kanneh, L.6
-
37
-
-
84908592665
-
Three simultaneous, food-borne, multi-country outbreaks of hepatitis A virus infection reported in EPIS-FWD in 2013, What does it mean for the European Union?
-
Gossner, C., Gossner, C., and Severi, E. (2014). Three simultaneous, food-borne, multi-country outbreaks of hepatitis A virus infection reported in EPIS-FWD in 2013: What does it mean for the European Union? Euro Surveill. 19:20941. doi: 10.2807/1560-7917.ES2014.19.43.20941.
-
(2014)
Euro Surveill
, vol.19
, pp. 20941
-
-
Gossner, C.1
Gossner, C.2
Severi, E.3
-
38
-
-
84942518081
-
Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
-
Greninger, A. L., Naccache, S. N., Federman, S., Yu, G., Mbala, P., Bres, V., et al. (2015). Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome Med. 7:99. doi: 10.1186/s13073-015-0220-9.
-
(2015)
Genome Med
, vol.7
, pp. 99
-
-
Greninger, A.L.1
Naccache, S.N.2
Federman, S.3
Yu, G.4
Mbala, P.5
Bres, V.6
-
39
-
-
85008413051
-
Rapid metagenomic next-generation sequencing during an investigation of hospital-acquired human parainfluenza virus 3 infections
-
Greninger, A. L., Zerr, D. M., Qin, X., Adler, A. L., Sampoleo, R., Kuypers, J. M., et al. (2016). Rapid metagenomic next-generation sequencing during an investigation of hospital-acquired human parainfluenza virus 3 infections. J. Clin. Microbiol. 55, 177-182. doi: 10.1128/JCM.01881-16.
-
(2016)
J. Clin. Microbiol
, vol.55
, pp. 177-182
-
-
Greninger, A.L.1
Zerr, D.M.2
Qin, X.3
Adler, A.L.4
Sampoleo, R.5
Kuypers, J.M.6
-
40
-
-
84938749252
-
Here, there, and everywhere: from PCRs to next-generation sequencing technologies and sequence databases, DNA contaminants creep in from the most unlikely places
-
Gruber, K. (2015). Here, there, and everywhere: from PCRs to next-generation sequencing technologies and sequence databases, DNA contaminants creep in from the most unlikely places. EMBO Rep. 16, 898-901. doi: 10.15252/embr.201540822.
-
(2015)
EMBO Rep
, vol.16
, pp. 898-901
-
-
Gruber, K.1
-
41
-
-
84962245304
-
High proportion of asymptomatic infections in an outbreak of hepatitis E associated with a spit-roasted piglet, France, 2013
-
Guillois, Y., Abravanel, F., Miura, T., Pavio, N., Vaillant, V., Lhomme, S., et al. (2016). High proportion of asymptomatic infections in an outbreak of hepatitis E associated with a spit-roasted piglet, France, 2013. Clin. Infect. Dis. 62, 351-357. doi: 10.1093/cid/civ862.
-
(2016)
Clin. Infect. Dis
, vol.62
, pp. 351-357
-
-
Guillois, Y.1
Abravanel, F.2
Miura, T.3
Pavio, N.4
Vaillant, V.5
Lhomme, S.6
-
42
-
-
34948819795
-
The Attribution of human infections with antimicrobial resistant Salmonella bacteria in Denmark to sources of animal origin
-
Hald, T., Lo Fo Wong, D. M. A., and Aarestrup, F. M. (2007). The Attribution of human infections with antimicrobial resistant Salmonella bacteria in Denmark to sources of animal origin. Foodborne Pathog. Dis. 4, 313-326. doi: 10.1089/fpd.2007.0002.
-
(2007)
Foodborne Pathog. Dis
, vol.4
, pp. 313-326
-
-
Hald, T.1
Lo Fo Wong, D.M.A.2
Aarestrup, F.M.3
-
43
-
-
81555197043
-
Methods to detect infectious human enteric viruses in environmental water samples
-
Hamza, I. A., Jurzik, L., überla, K., and Wilhelm, M. (2011). Methods to detect infectious human enteric viruses in environmental water samples. Int. J. Hyg. Environ. Health 214, 424-436. doi: 10.1016/j.ijheh.2011.07.014.
-
(2011)
Int. J. Hyg. Environ. Health
, vol.214
, pp. 424-436
-
-
Hamza, I.A.1
Jurzik, L.2
Überla, K.3
Wilhelm, M.4
-
44
-
-
10344227692
-
Metagenomics: application of genomics to uncultured microorganisms
-
Handelsman, J. (2004). Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 68, 669-685. doi: 10.1128/MMBR.68.4.669-685.2004.
-
(2004)
Microbiol. Mol. Biol. Rev
, vol.68
, pp. 669-685
-
-
Handelsman, J.1
-
45
-
-
84953218815
-
World health organization global estimates and regional comparisons of the burden of foodborne disease in 2010
-
Havelaar, A. H., Kirk, M. D., Torgerson, P. R., Gibb, H. J., Hald, T., Lake, R. J., et al. (2015). World health organization global estimates and regional comparisons of the burden of foodborne disease in 2010. PLoS Med. 12:e1001923. doi: 10.1371/journal.pmed.1001923.
-
(2015)
PLoS Med
, vol.12
-
-
Havelaar, A.H.1
Kirk, M.D.2
Torgerson, P.R.3
Gibb, H.J.4
Hald, T.5
Lake, R.J.6
-
46
-
-
84873470214
-
Global mapping of infectious disease
-
Hay, S. I., Battle, K. E., Pigott, D. M., Smith, D. L., Moyes, C. L., Bhatt, S., et al. (2013). Global mapping of infectious disease. Philos. Trans. R. Soc. Lond. B Biol. Sci. 368:20120250. doi: 10.1098/rstb.2012.0250.
-
(2013)
Philos. Trans. R. Soc. Lond. B Biol. Sci
, vol.368
-
-
Hay, S.I.1
Battle, K.E.2
Pigott, D.M.3
Smith, D.L.4
Moyes, C.L.5
Bhatt, S.6
-
47
-
-
84914124936
-
Detection of pathogenic viruses in sewage provided early warnings of hepatitis A virus and norovirus outbreaks
-
Hellmér, M., Paxéus, N., Magnius, L., Enache, L., Arnholm, B., Johansson, A., et al. (2014). Detection of pathogenic viruses in sewage provided early warnings of hepatitis A virus and norovirus outbreaks. Appl. Environ. Microbiol. 80, 6771-6781. doi: 10.1128/AEM.01981-14.
-
(2014)
Appl. Environ. Microbiol
, vol.80
, pp. 6771-6781
-
-
Hellmér, M.1
Paxéus, N.2
Magnius, L.3
Enache, L.4
Arnholm, B.5
Johansson, A.6
-
48
-
-
84883147815
-
Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes
-
Hingamp, P., Grimsley, N., Acinas, S. G., Clerissi, C., Subirana, L., Poulain, J., et al. (2013). Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes. ISME J. 7, 1678-1695. doi: 10.1038/ismej.2013.59.
-
(2013)
ISME J
, vol.7
, pp. 1678-1695
-
-
Hingamp, P.1
Grimsley, N.2
Acinas, S.G.3
Clerissi, C.4
Subirana, L.5
Poulain, J.6
-
49
-
-
84955114356
-
Nanopore sequencing as a rapidly deployable ebola outbreak tool
-
Hoenen, T., Groseth, A., Rosenke, K., Fischer, R. J., Hoenen, A., Judson, S. D., et al. (2016). Nanopore sequencing as a rapidly deployable ebola outbreak tool. Emerg. Infect. Dis. 22, 331-334. doi: 10.3201/eid2202.151796.
-
(2016)
Emerg. Infect. Dis
, vol.22
, pp. 331-334
-
-
Hoenen, T.1
Groseth, A.2
Rosenke, K.3
Fischer, R.J.4
Hoenen, A.5
Judson, S.D.6
-
50
-
-
84978431877
-
The microbiota in adaptive immune homeostasis and disease
-
Honda, K., and Littman, D. R. (2016). The microbiota in adaptive immune homeostasis and disease. Nature 535, 75-84. doi: 10.1038/nature18848.
-
(2016)
Nature
, vol.535
, pp. 75-84
-
-
Honda, K.1
Littman, D.R.2
-
51
-
-
84911808345
-
Detection and genetic characterization of human enteric viruses in oyster-associated gastroenteritis outbreaks between 2001 and 2012 in Osaka City, Japan
-
Iritani, N., Kaida, A., Abe, N., Kubo, H., Sekiguchi, J.-I., Yamamoto, S. P., et al. (2014). Detection and genetic characterization of human enteric viruses in oyster-associated gastroenteritis outbreaks between 2001 and 2012 in Osaka City, Japan. J. Med. Virol. 86, 2019-2025. doi: 10.1002/jmv.23883.
-
(2014)
J. Med. Virol
, vol.86
, pp. 2019-2025
-
-
Iritani, N.1
Kaida, A.2
Abe, N.3
Kubo, H.4
Sekiguchi, J.-I.5
Yamamoto, S.P.6
-
52
-
-
84961225996
-
Nipah virus transmission from bats to humans associated with drinking traditional liquor made from date palm sap, Bangladesh, 2011-2014
-
Islam, M. S., Sazzad, H. M. S., Satter, S. M., Sultana, S., Hossain, M. J., Hasan, M., et al. (2016). Nipah virus transmission from bats to humans associated with drinking traditional liquor made from date palm sap, Bangladesh, 2011-2014. Emerg. Infect. Dis. 22, 664-670. doi: 10.3201/eid2204.151747.
-
(2016)
Emerg. Infect. Dis
, vol.22
, pp. 664-670
-
-
Islam, M.S.1
Sazzad, H.M.S.2
Satter, S.M.3
Sultana, S.4
Hossain, M.J.5
Hasan, M.6
-
53
-
-
84864476580
-
Hepatitis E virus strains in rabbits and evidence of a closely related strain in humans, France
-
Izopet, J., Dubois, M., Bertagnoli, S., Lhomme, S., Marchandeau, S., Boucher, S., et al. (2012). Hepatitis E virus strains in rabbits and evidence of a closely related strain in humans, France. Emerg. Infect. Dis. 18, 1274-1281. doi: 10.3201/eid1808.120057.
-
(2012)
Emerg. Infect. Dis
, vol.18
, pp. 1274-1281
-
-
Izopet, J.1
Dubois, M.2
Bertagnoli, S.3
Lhomme, S.4
Marchandeau, S.5
Boucher, S.6
-
54
-
-
70350714426
-
The bushmeat trade: increased opportunities for transmission of zoonotic disease
-
Karesh, W. B., and Noble, E. (2009). The bushmeat trade: increased opportunities for transmission of zoonotic disease. Mt. Sinai J. Med. 76, 429-434. doi: 10.1002/msj.20139.
-
(2009)
Mt. Sinai J. Med
, vol.76
, pp. 429-434
-
-
Karesh, W.B.1
Noble, E.2
-
55
-
-
84957616021
-
Temporal dynamics of norovirus determined through monitoring of municipal wastewater by pyrosequencing and virological surveillance of gastroenteritis cases
-
Kazama, S., Masago, Y., Tohma, K., Souma, N., Imagawa, T., Suzuki, A., et al. (2016). Temporal dynamics of norovirus determined through monitoring of municipal wastewater by pyrosequencing and virological surveillance of gastroenteritis cases. Water Res. 92, 244-253. doi: 10.1016/j.watres.2015.10.024.
-
(2016)
Water Res
, vol.92
, pp. 244-253
-
-
Kazama, S.1
Masago, Y.2
Tohma, K.3
Souma, N.4
Imagawa, T.5
Suzuki, A.6
-
56
-
-
84904781805
-
Surveillance of hepatitis A virus in urban sewages and comparison with cases notified in the course of an outbreak, Italy 2013
-
La Rosa, G., Libera, S. D., Iaconelli, M., Ciccaglione, A. R., Bruni, R., Taffon, S., et al. (2014). Surveillance of hepatitis A virus in urban sewages and comparison with cases notified in the course of an outbreak, Italy 2013. BMC Infect. Dis. 14:419. doi: 10.1186/1471-2334-14-419.
-
(2014)
BMC Infect. Dis
, vol.14
, pp. 419
-
-
La Rosa, G.1
Libera, S.D.2
Iaconelli, M.3
Ciccaglione, A.R.4
Bruni, R.5
Taffon, S.6
-
57
-
-
74949121487
-
Transmission routes and risk factors for autochthonous hepatitis E virus infection in Europe: a systematic review
-
Lewis, H. C., Wichmann, O., and Duizer, E. (2010). Transmission routes and risk factors for autochthonous hepatitis E virus infection in Europe: a systematic review. Epidemiol. Infect. 138, 145-166. doi: 10.1017/S0950268809990847.
-
(2010)
Epidemiol. Infect
, vol.138
, pp. 145-166
-
-
Lewis, H.C.1
Wichmann, O.2
Duizer, E.3
-
58
-
-
84908564504
-
Diverse and widespread contamination evident in the unmapped depths of high throughput sequencing data
-
Lusk, R. W. (2014). Diverse and widespread contamination evident in the unmapped depths of high throughput sequencing data. PLoS ONE 9:e110808. doi: 10.1371/journal.pone.0110808.
-
(2014)
PLoS ONE
, vol.9
-
-
Lusk, R.W.1
-
59
-
-
84953302957
-
A review of the role of food and the food system in the transmission and spread of Ebolavirus
-
Mann, E., Streng, S., Bergeron, J., Kircher, A., Morvan, J., Deubel, V., et al. (2015). A review of the role of food and the food system in the transmission and spread of Ebolavirus. PLoS Negl. Trop. Dis. 9:e0004160. doi: 10.1371/journal.pntd.0004160.
-
(2015)
PLoS Negl. Trop. Dis
, vol.9
-
-
Mann, E.1
Streng, S.2
Bergeron, J.3
Kircher, A.4
Morvan, J.5
Deubel, V.6
-
60
-
-
84908129920
-
Emerging infectious diseases and pandemic potential: status quo and reducing risk of global spread
-
McCloskey, B., Dar, O., Zumla, A., and Heymann, D. L. (2014). Emerging infectious diseases and pandemic potential: status quo and reducing risk of global spread. Lancet Infect. Dis. 14, 1001-1010. doi: 10.1016/S1473-3099(14)70846-1.
-
(2014)
Lancet Infect. Dis
, vol.14
, pp. 1001-1010
-
-
McCloskey, B.1
Dar, O.2
Zumla, A.3
Heymann, D.L.4
-
61
-
-
84963963850
-
Fast and sensitive taxonomic classification for metagenomics with Kaiju
-
Menzel, P., Ng, K. L., Krogh, A., Riesenfeld, C., Schloss, P., Handelsman, J., et al. (2016). Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat. Commun. 7:11257. doi: 10.1038/ncomms11257.
-
(2016)
Nat. Commun
, vol.7
, pp. 11257
-
-
Menzel, P.1
Ng, K.L.2
Krogh, A.3
Riesenfeld, C.4
Schloss, P.5
Handelsman, J.6
-
62
-
-
84901743676
-
Emerging pathogens and vehicles of food-and water-borne disease outbreaks in Korea, 2007-2012
-
Moon, S., Sohn, I.-W., Hong, Y., Lee, H., Park, J.-H., Kwon, G.-Y., et al. (2014). Emerging pathogens and vehicles of food-and water-borne disease outbreaks in Korea, 2007-2012. Osong Public Health Res. Perspect. 5, 34-39. doi: 10.1016/j.phrp.2013.12.004.
-
(2014)
Osong Public Health Res. Perspect
, vol.5
, pp. 34-39
-
-
Moon, S.1
Sohn, I.-W.2
Hong, Y.3
Lee, H.4
Park, J.-H.5
Kwon, G.-Y.6
-
63
-
-
77952671243
-
Food-borne diseases-the challenges of 20 years ago still persist while new ones continue to emerge
-
Newell, D. G., Koopmans, M., Verhoef, L., Duizer, E., Aidara-Kane, A., Sprong, H., et al. (2010). Food-borne diseases-the challenges of 20 years ago still persist while new ones continue to emerge. Int. J. Food Microbiol. 139(Suppl.), S3-S15. doi: 10.1016/j.ijfoodmicro.2010.01.021.
-
(2010)
Int. J. Food Microbiol
, vol.139
, pp. S3-S15
-
-
Newell, D.G.1
Koopmans, M.2
Verhoef, L.3
Duizer, E.4
Aidara-Kane, A.5
Sprong, H.6
-
64
-
-
84869128210
-
High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage
-
Ng, T. F. F., Marine, R., Wang, C., Simmonds, P., Kapusinszky, B., Bodhidatta, L., et al. (2012). High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage. J. Virol. 86, 12161-12175. doi: 10.1128/JVI.00869-12.
-
(2012)
J. Virol
, vol.86
, pp. 12161-12175
-
-
Ng, T.F.F.1
Marine, R.2
Wang, C.3
Simmonds, P.4
Kapusinszky, B.5
Bodhidatta, L.6
-
65
-
-
84994014825
-
-
arXiv:1604.03071
-
Nurk, S., Meleshko, D., Korobeynikov, A., and Pevzner, P. A. (2016). metaSPAdes: a new versatile de novo metagenomics assembler. arXiv:1604.03071.
-
(2016)
metaSPAdes: a new versatile de novo metagenomics assembler
-
-
Nurk, S.1
Meleshko, D.2
Korobeynikov, A.3
Pevzner, P.A.4
-
66
-
-
80053366291
-
Interactive metagenomic visualization in a Web browser
-
Ondov, B. D., Bergman, N. H., and Phillippy, A. M. (2011). Interactive metagenomic visualization in a Web browser. BMC Bioinformatics 12:385. doi: 10.1186/1471-2105-12-385.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 385
-
-
Ondov, B.D.1
Bergman, N.H.2
Phillippy, A.M.3
-
67
-
-
84857358267
-
Global epidemiology of hepatitis B virus infection: new estimates of age-specific HBsAg seroprevalence and endemicity
-
Ott, J. J., Stevens, G. A., Groeger, J., and Wiersma, S. T. (2012). Global epidemiology of hepatitis B virus infection: new estimates of age-specific HBsAg seroprevalence and endemicity. Vaccine 30, 2212-2219. doi: 10.1016/j.vaccine.2011.12.116.
-
(2012)
Vaccine
, vol.30
, pp. 2212-2219
-
-
Ott, J.J.1
Stevens, G.A.2
Groeger, J.3
Wiersma, S.T.4
-
68
-
-
84892564875
-
Autologous antibody capture to enrich immunogenic viruses for viral discovery
-
Oude Munnink, B. B., Jazaeri Farsani, S. M., Deijs, M., Jonkers, J., Verhoeven, J. T. P., Ieven, M., et al. (2013). Autologous antibody capture to enrich immunogenic viruses for viral discovery. PLoS ONE 8:e78454. doi: 10.1371/journal.pone.0078454.
-
(2013)
PLoS ONE
, vol.8
-
-
Oude Munnink, B.B.1
Jazaeri Farsani, S.M.2
Deijs, M.3
Jonkers, J.4
Verhoeven, J.T.P.5
Ieven, M.6
-
69
-
-
84946771697
-
Epidemiologic Association between FUT2 secretor status and severe rotavirus gastroenteritis in children in the United States
-
Payne, D. C., Currier, R. L., Staat, M. A., Sahni, L. C., Selvarangan, R., Halasa, N. B., et al. (2015). Epidemiologic Association between FUT2 secretor status and severe rotavirus gastroenteritis in children in the United States. JAMA Pediatr. 169, 1040-1045. doi: 10.1001/jamapediatrics.2015.2002.
-
(2015)
JAMA Pediatr
, vol.169
, pp. 1040-1045
-
-
Payne, D.C.1
Currier, R.L.2
Staat, M.A.3
Sahni, L.C.4
Selvarangan, R.5
Halasa, N.B.6
-
70
-
-
84861760530
-
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
-
Peng, Y., Leung, H. C. M., Yiu, S. M., and Chin, F. Y. L. (2012). IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28, 1420-1428. doi: 10.1093/bioinformatics/bts174.
-
(2012)
Bioinformatics
, vol.28
, pp. 1420-1428
-
-
Peng, Y.1
Leung, H.C.M.2
Yiu, S.M.3
Chin, F.Y.L.4
-
71
-
-
84896478889
-
Underdiagnosis of foodborne hepatitis A, the Netherlands, 2008-2010
-
Petrignani, M., Verhoef, L., Vennema, H., van Hunen, R., Baas, D., van Steenbergen, J. E., et al. (2014). Underdiagnosis of foodborne hepatitis A, the Netherlands, 2008-2010. Emerg. Infect. Dis. 20, 596-602. doi: 10.3201/eid2004.130753.
-
(2014)
Emerg. Infect. Dis
, vol.20
, pp. 596-602
-
-
Petrignani, M.1
Verhoef, L.2
Vennema, H.3
van Hunen, R.4
Baas, D.5
van Steenbergen, J.E.6
-
72
-
-
67650742212
-
Attributing the human disease burden of foodborne infections to specific sources
-
Pires, S. M., Evers, E. G., van Pelt, W., Ayers, T., Scallan, E., Angulo, F. J., et al. (2009). Attributing the human disease burden of foodborne infections to specific sources. Foodborne Pathog. Dis. 6, 417-424. doi: 10.1089/fpd.2008.0208.
-
(2009)
Foodborne Pathog. Dis
, vol.6
, pp. 417-424
-
-
Pires, S.M.1
Evers, E.G.2
van Pelt, W.3
Ayers, T.4
Scallan, E.5
Angulo, F.J.6
-
73
-
-
84865591846
-
A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers
-
Quail, M., Smith, M. E., Coupland, P., Otto, T. D., Harris, S. R., Connor, T. R., et al. (2012). A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers. BMC Genomics 13:341. doi: 10.1186/1471-2164-13-341.
-
(2012)
BMC Genomics
, vol.13
, pp. 341
-
-
Quail, M.1
Smith, M.E.2
Coupland, P.3
Otto, T.D.4
Harris, S.R.5
Connor, T.R.6
-
74
-
-
84934284959
-
Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella
-
Quick, J., Ashton, P., Calus, S., Chatt, C., Gossain, S., Hawker, J., et al. (2015). Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biol. 16:114. doi: 10.1186/s13059-015-0677-2.
-
(2015)
Genome Biol
, vol.16
, pp. 114
-
-
Quick, J.1
Ashton, P.2
Calus, S.3
Chatt, C.4
Gossain, S.5
Hawker, J.6
-
75
-
-
84958068536
-
Real-time, portable genome sequencing for Ebola surveillance
-
Quick, J., Loman, N. J., Duraffour, S., Simpson, J. T., Severi, E., Cowley, L., et al. (2016). Real-time, portable genome sequencing for Ebola surveillance. Nature 530, 228-232. doi: 10.1038/nature16996.
-
(2016)
Nature
, vol.530
, pp. 228-232
-
-
Quick, J.1
Loman, N.J.2
Duraffour, S.3
Simpson, J.T.4
Severi, E.5
Cowley, L.6
-
76
-
-
84855419491
-
Date palm sap linked to nipah virus outbreak in Bangladesh, 2008
-
Rahman, M. A., Hossain, M. J., Sultana, S., Homaira, N., Khan, S. U., Rahman, M., et al. (2012). Date palm sap linked to nipah virus outbreak in Bangladesh, 2008. Vector Borne Zoonotic Dis. 12, 65-72. doi: 10.1089/vbz.2011.0656.
-
(2012)
Vector Borne Zoonotic Dis
, vol.12
, pp. 65-72
-
-
Rahman, M.A.1
Hossain, M.J.2
Sultana, S.3
Homaira, N.4
Khan, S.U.5
Rahman, M.6
-
77
-
-
84865169911
-
Going viral: next-generation sequencing applied to phage populations in the human gut
-
Reyes, A., Semenkovich, N. P., Whiteson, K., Rohwer, F., and Gordon, J. I. (2012). Going viral: next-generation sequencing applied to phage populations in the human gut. Nat. Rev. Microbiol. 10, 607-617. doi: 10.1038/nrmicro2853.
-
(2012)
Nat. Rev. Microbiol
, vol.10
, pp. 607-617
-
-
Reyes, A.1
Semenkovich, N.P.2
Whiteson, K.3
Rohwer, F.4
Gordon, J.I.5
-
78
-
-
84893944995
-
Adenovirus and norovirus contaminants in commercially distributed shellfish
-
Rodriguez-Manzano, J., Hundesa, A., Calgua, B., Carratala, A., Maluquer de Motes, C., Rusiñol, M., et al. (2014). Adenovirus and norovirus contaminants in commercially distributed shellfish. Food Environ. Virol. 6, 31-41. doi: 10.1007/s12560-013-9133-1.
-
(2014)
Food Environ. Virol
, vol.6
, pp. 31-41
-
-
Rodriguez-Manzano, J.1
Hundesa, A.2
Calgua, B.3
Carratala, A.4
Maluquer de Motes, C.5
Rusiñol, M.6
-
79
-
-
84983606013
-
Coinfections of Zika and Chikungunya viruses in Bahia, Brazil, identified by metagenomic next-generation sequencing
-
Sardi, S. I., Somasekar, S., Naccache, S. N., Bandeira, A. C., Tauro, L. B., Campos, G. S., et al. (2016). Coinfections of Zika and Chikungunya viruses in Bahia, Brazil, identified by metagenomic next-generation sequencing. J. Clin. Microbiol. 54, 2348-2353. doi: 10.1128/JCM.00877-16.
-
(2016)
J. Clin. Microbiol
, vol.54
, pp. 2348-2353
-
-
Sardi, S.I.1
Somasekar, S.2
Naccache, S.N.3
Bandeira, A.C.4
Tauro, L.B.5
Campos, G.S.6
-
80
-
-
79952390994
-
Fast identification and removal of sequence contamination from genomic and metagenomic datasets
-
Schmieder, R., and Edwards, R. (2011). Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS ONE 6:e17288. doi: 10.1371/journal.pone.0017288.
-
(2011)
PLoS ONE
, vol.6
-
-
Schmieder, R.1
Edwards, R.2
-
81
-
-
0032976116
-
Investigation of under-ascertainment in epidemiological studies based in general practice
-
Sethi, D., Wheeler, J., Rodrigues, L. C., Fox, S., and Roderick, P. (1999). Investigation of under-ascertainment in epidemiological studies based in general practice. Int. J. Epidemiol. 28, 106-112.
-
(1999)
Int. J. Epidemiol
, vol.28
, pp. 106-112
-
-
Sethi, D.1
Wheeler, J.2
Rodrigues, L.C.3
Fox, S.4
Roderick, P.5
-
82
-
-
84938153335
-
Large and prolonged food-borne multistate hepatitis A outbreak in Europe associated with consumption offrozen berries, 2013 to 2014
-
Severi, E., Verhoef, L., Thornton, L., Guzman-Herrador, B. R., Faber, M., Sundqvist, L., et al. (2015). Large and prolonged food-borne multistate hepatitis A outbreak in Europe associated with consumption offrozen berries, 2013 to 2014. Euro Surveill. 20:21192. doi: 10.2807/1560-7917.ES2015.20.29.21192.
-
(2015)
Euro Surveill
, vol.20
, pp. 21192
-
-
Severi, E.1
Verhoef, L.2
Thornton, L.3
Guzman-Herrador, B.R.4
Faber, M.5
Sundqvist, L.6
-
83
-
-
84946825915
-
Recovering full-length viral genomes from metagenomes
-
Smits, S. L., Bodewes, R., Ruiz-González, A., Baumgärtner, W., Koopmans, M. P., Osterhaus, A. D. M. E., et al. (2015). Recovering full-length viral genomes from metagenomes. Front. Microbiol. 6:1069. doi: 10.3389/fmicb.2015.01069.
-
(2015)
Front. Microbiol
, vol.6
, pp. 1069
-
-
Smits, S.L.1
Bodewes, R.2
Ruiz-González, A.3
Baumgärtner, W.4
Koopmans, M.P.5
Osterhaus, A.D.M.E.6
-
84
-
-
85006201981
-
Recommendations on e-infrastructures for next-generation sequencing
-
Spjuth, O., Bongcam-Rudloff, E., Dahlberg, J., Dahlö, M., Kallio, A., Pireddu, L., et al. (2016). Recommendations on e-infrastructures for next-generation sequencing. Gigascience 5:26. doi: 10.1186/s13742-016-0132-7.
-
(2016)
Gigascience
, vol.5
, pp. 26
-
-
Spjuth, O.1
Bongcam-Rudloff, E.2
Dahlberg, J.3
Dahlö, M.4
Kallio, A.5
Pireddu, L.6
-
85
-
-
83555177370
-
Longitudinal study of infectious intestinal disease in the UK (IID2 study): incidence in the community and presenting to general practice
-
Tam, C. C., Rodrigues, L. C., Viviani, L., Dodds, J. P., Evans, M. R., Hunter, P. R., et al. (2012). Longitudinal study of infectious intestinal disease in the UK (IID2 study): incidence in the community and presenting to general practice. Gut 61, 69-77. doi: 10.1136/gut.2011.238386.
-
(2012)
Gut
, vol.61
, pp. 69-77
-
-
Tam, C.C.1
Rodrigues, L.C.2
Viviani, L.3
Dodds, J.P.4
Evans, M.R.5
Hunter, P.R.6
-
86
-
-
84948706161
-
Environmental surveillance of genogroup i and ii noroviruses in Shandong Province, China in 2013
-
Tao, Z., Xu, M., Lin, X., Wang, H., Song, L., Wang, S., et al. (2015). Environmental surveillance of genogroup i and ii noroviruses in Shandong Province, China in 2013. Sci. Rep. 5:17444. doi: 10.1038/srep17444.
-
(2015)
Sci. Rep
, vol.5
, pp. 17444
-
-
Tao, Z.1
Xu, M.2
Lin, X.3
Wang, H.4
Song, L.5
Wang, S.6
-
87
-
-
84938099162
-
Food-borne diseases associated with frozen berries consumption: a historical perspective, European Union, 1983 to 2013
-
Tavoschi, L., Severi, E., Niskanen, T., Boelaert, F., Rizzi, V., Liebana, E., et al. (2015). Food-borne diseases associated with frozen berries consumption: a historical perspective, European Union, 1983 to 2013. Euro Surveill. 20:21193. doi: 10.2807/1560-7917.ES2015.20.29.21193.
-
(2015)
Euro Surveill
, vol.20
, pp. 21193
-
-
Tavoschi, L.1
Severi, E.2
Niskanen, T.3
Boelaert, F.4
Rizzi, V.5
Liebana, E.6
-
88
-
-
0042671196
-
Zoonotic transmission of hepatitis E virus from deer to human beings
-
Tei, S., Kitajima, N., Takahashi, K., and Mishiro, S. (2003). Zoonotic transmission of hepatitis E virus from deer to human beings. Lancet 362, 371-373. doi: 10.1016/S0140-6736(03)14025-1.
-
(2003)
Lancet
, vol.362
, pp. 371-373
-
-
Tei, S.1
Kitajima, N.2
Takahashi, K.3
Mishiro, S.4
-
89
-
-
84992077438
-
Prevalence of hepatitis E virus antibodies in workers occupationally exposed to swine in Portugal
-
Teixeira, J., Mesquita, J. R., Pereira, S. S., Oliveira, R. M. S., Abreu-Silva, J., Rodrigues, A., et al. (2016). Prevalence of hepatitis E virus antibodies in workers occupationally exposed to swine in Portugal. Med. Microbiol. Immunol. 206, 77-81. doi: 10.1007/s00430-016-0484-8.
-
(2016)
Med. Microbiol. Immunol
, vol.206
, pp. 77-81
-
-
Teixeira, J.1
Mesquita, J.R.2
Pereira, S.S.3
Oliveira, R.M.S.4
Abreu-Silva, J.5
Rodrigues, A.6
-
90
-
-
84975677663
-
Screening for viral pathogens in african simian bushmeat seized at a French airport
-
[Epub ahead of print]
-
Temmam, S., Davoust, B., Chaber, A.-L., Lignereux, Y., Michelle, C., Monteil-Bouchard, S., et al. (2016). Screening for viral pathogens in african simian bushmeat seized at a French airport. Transb. Emerg. Dis. doi: 10.1111/tbed.12481 [Epub ahead of print].
-
(2016)
Transb. Emerg. Dis
-
-
Temmam, S.1
Davoust, B.2
Chaber, A.-L.3
Lignereux, Y.4
Michelle, C.5
Monteil-Bouchard, S.6
-
91
-
-
84872152255
-
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline
-
Treangen, T. J., Koren, S., Sommer, D. D., Liu, B., Astrovskaya, I., Ondov, B., et al. (2013). MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome Biol. 14:R2. doi: 10.1186/gb-2013-14-1-r2.
-
(2013)
Genome Biol
, vol.14
, pp. R2
-
-
Treangen, T.J.1
Koren, S.2
Sommer, D.D.3
Liu, B.4
Astrovskaya, I.5
Ondov, B.6
-
92
-
-
84892457697
-
Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut
-
Vázquez-Castellanos, J. F., García-López, R., Pérez-Brocal, V., Pignatelli, M., Moya, A., Handelsman, J., et al. (2014). Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut. BMC Genomics 15:37. doi: 10.1186/1471-2164-15-37.
-
(2014)
BMC Genomics
, vol.15
, pp. 37
-
-
Vázquez-Castellanos, J.F.1
García-López, R.2
Pérez-Brocal, V.3
Pignatelli, M.4
Moya, A.5
Handelsman, J.6
-
93
-
-
84924985007
-
Norovirus genotype profiles associated with foodborne transmission, 1999-2012
-
Verhoef, L., Hewitt, J., Barclay, L., Ahmed, S. M., Lake, R., Hall, A. J., et al. (2015). Norovirus genotype profiles associated with foodborne transmission, 1999-2012. Emerg. Infect. Dis. 21, 592-599. doi: 10.3201/eid2104.141073.
-
(2015)
Emerg. Infect. Dis
, vol.21
, pp. 592-599
-
-
Verhoef, L.1
Hewitt, J.2
Barclay, L.3
Ahmed, S.M.4
Lake, R.5
Hall, A.J.6
-
94
-
-
79952347025
-
An integrated approach to identifying international foodborne norovirus outbreaks
-
Verhoef, L., Kouyos, R. D., Vennema, H., Kroneman, A., Siebenga, J., van Pelt, W., et al. (2011). An integrated approach to identifying international foodborne norovirus outbreaks. Emerg. Infect. Dis. 17, 412-418. doi: 10.3201/eid1703.100979.
-
(2011)
Emerg. Infect. Dis
, vol.17
, pp. 412-418
-
-
Verhoef, L.1
Kouyos, R.D.2
Vennema, H.3
Kroneman, A.4
Siebenga, J.5
van Pelt, W.6
-
95
-
-
84949423657
-
The impact of calicivirus mixed infection in an oyster-associated outbreak during a food festival
-
Wang, Y., Zhang, J., and Shen, Z. (2015). The impact of calicivirus mixed infection in an oyster-associated outbreak during a food festival. J. Clin. Virol. 73, 55-63. doi: 10.1016/j.jcv.2015.10.004.
-
(2015)
J. Clin. Virol
, vol.73
, pp. 55-63
-
-
Wang, Y.1
Zhang, J.2
Shen, Z.3
-
96
-
-
33644828207
-
Bushmeat hunting, deforestation, and prediction of zoonotic disease
-
Wolfe, N. D., Daszak, P., Kilpatrick, A. M., and Burke, D. S. (2005). Bushmeat hunting, deforestation, and prediction of zoonotic disease. Emerg. Infect. Dis. 11, 1822-1827. doi: 10.3201/eid1112.040789.
-
(2005)
Emerg. Infect. Dis
, vol.11
, pp. 1822-1827
-
-
Wolfe, N.D.1
Daszak, P.2
Kilpatrick, A.M.3
Burke, D.S.4
-
97
-
-
84899090573
-
Kraken: ultrafast metagenomic sequence classification using exact alignments
-
Wood, D. E., Salzberg, S. L., Venter, C., Remington, K., Heidelberg, J., Halpern, A., et al. (2014). Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 15:R46. doi: 10.1186/gb-2014-15-3-r46.
-
(2014)
Genome Biol
, vol.15
, pp. R46
-
-
Wood, D.E.1
Salzberg, S.L.2
Venter, C.3
Remington, K.4
Heidelberg, J.5
Halpern, A.6
-
98
-
-
84862141704
-
Human gut microbiome viewed across age and geography
-
Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., et al. (2012). Human gut microbiome viewed across age and geography. Nature 486, 222-227. doi: 10.1038/nature11053.
-
(2012)
Nature
, vol.486
, pp. 222-227
-
-
Yatsunenko, T.1
Rey, F.E.2
Manary, M.J.3
Trehan, I.4
Dominguez-Bello, M.G.5
Contreras, M.6
-
99
-
-
31144459030
-
RNA viral community in human feces: prevalence of plant pathogenic viruses
-
Zhang, T., Breitbart, M., Lee, W. H., Run, J.-Q., Wei, C. L., Soh, S. W. L., et al. (2006). RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol. 4:e3. doi: 10.1371/journal.pbio.0040003.
-
(2006)
PLoS Biol
, vol.4
-
-
Zhang, T.1
Breitbart, M.2
Lee, W.H.3
Run, J.-Q.4
Wei, C.L.5
Soh, S.W.L.6
|