-
1
-
-
84860771820
-
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing
-
Bankevich A., Nurk S., Antipov D., Gurevich A.A., Dvorkin M., Kulikov A.S., Lesin V.M., Nikolenko S.I., Pham S., Prjibelski A.D., Pyshkin A.V., Sirotkin A.V., Vyahhi N., Tesler G., Alekseyev M.A., Pevzner P.A. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 2012, 19:455-477.
-
(2012)
J. Comput. Biol.
, vol.19
, pp. 455-477
-
-
Bankevich, A.1
Nurk, S.2
Antipov, D.3
Gurevich, A.A.4
Dvorkin, M.5
Kulikov, A.S.6
Lesin, V.M.7
Nikolenko, S.I.8
Pham, S.9
Prjibelski, A.D.10
Pyshkin, A.V.11
Sirotkin, A.V.12
Vyahhi, N.13
Tesler, G.14
Alekseyev, M.A.15
Pevzner, P.A.16
-
2
-
-
84864490075
-
Phase variable genes of Campylobacter jejuni exhibit high mutation rates and specific mutational patterns but mutability is not the major determinant of population structure during host colonization
-
Bayliss C.D., Bidmos F.A., Anjum A., Manchev V.T., Richards R.L., Grossier J.P., Wooldridge K.G., Ketley J.M., Barrow P.A., Jones M.A., Tretyakov M.V. Phase variable genes of Campylobacter jejuni exhibit high mutation rates and specific mutational patterns but mutability is not the major determinant of population structure during host colonization. Nucleic Acids Res. 2012, 40:5876-5889.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 5876-5889
-
-
Bayliss, C.D.1
Bidmos, F.A.2
Anjum, A.3
Manchev, V.T.4
Richards, R.L.5
Grossier, J.P.6
Wooldridge, K.G.7
Ketley, J.M.8
Barrow, P.A.9
Jones, M.A.10
Tretyakov, M.V.11
-
3
-
-
84859055752
-
Using sequence data to identify alternative routes and risk of infection: a case-study of Campylobacter in Scotland
-
(12 2012)
-
Bessell P.R., Rotariu O., Innocent G.T., Smith-Palmer A., Strachan N.J.C., Forbes K.J., Cowden J.M., Reid S.W.J., Matthews L. Using sequence data to identify alternative routes and risk of infection: a case-study of Campylobacter in Scotland. BMC Infect. Dis. 2012, 12(80). (12 2012). 10.1186/1471-2334-12-80.
-
(2012)
BMC Infect. Dis.
, vol.12
, Issue.80
-
-
Bessell, P.R.1
Rotariu, O.2
Innocent, G.T.3
Smith-Palmer, A.4
Strachan, N.J.C.5
Forbes, K.J.6
Cowden, J.M.7
Reid, S.W.J.8
Matthews, L.9
-
4
-
-
84880621689
-
Real-time genomic epidemiological evaluation of human Campylobacter isolates by use of whole-genome multilocus sequence typing
-
Cody A.J., McCarthy N.D., Van Rensburg M.J., Isinkaye T., Bentley S.D., Parkhill J., Dingle K.E., Bowler I.C.J.W., Jolley K.A., Maiden M.C.J. Real-time genomic epidemiological evaluation of human Campylobacter isolates by use of whole-genome multilocus sequence typing. J. Clin. Microbiol. 2013, 51:2526-2534.
-
(2013)
J. Clin. Microbiol.
, vol.51
, pp. 2526-2534
-
-
Cody, A.J.1
McCarthy, N.D.2
Van Rensburg, M.J.3
Isinkaye, T.4
Bentley, S.D.5
Parkhill, J.6
Dingle, K.E.7
Bowler, I.C.J.W.8
Jolley, K.A.9
Maiden, M.C.J.10
-
5
-
-
84868311394
-
Campylobacter sequence typing databases: applications and future prospects
-
Colles F.M., Maiden M.C. Campylobacter sequence typing databases: applications and future prospects. Microbiology 2012, 158:2695-2709.
-
(2012)
Microbiology
, vol.158
, pp. 2695-2709
-
-
Colles, F.M.1
Maiden, M.C.2
-
6
-
-
84873250396
-
Multilocus sequence types of environmental Campylobacter jejuni isolates and their similarities to those of human, poultry and bovine C. jejuni isolates
-
de Haan C.P.A., Lampen K., Corander J., Hänninen M.L. Multilocus sequence types of environmental Campylobacter jejuni isolates and their similarities to those of human, poultry and bovine C. jejuni isolates. Zoonoses Public Health 2013, 60:125-133.
-
(2013)
Zoonoses Public Health
, vol.60
, pp. 125-133
-
-
de Haan, C.P.A.1
Lampen, K.2
Corander, J.3
Hänninen, M.L.4
-
7
-
-
84910129699
-
How molecular typing has changed our understanding on sources and transmission routes of campylobacteriosis in Finland
-
S.K. Sheppard (Ed.)
-
de Haan C.P.A., Kivistö R.I., Rautelin H., Hänninen M. How molecular typing has changed our understanding on sources and transmission routes of campylobacteriosis in Finland. Campylobacter Ecology and Evolution 2014, 241-252. S.K. Sheppard (Ed.).
-
(2014)
Campylobacter Ecology and Evolution
, pp. 241-252
-
-
de Haan, C.P.A.1
Kivistö, R.I.2
Rautelin, H.3
Hänninen, M.4
-
8
-
-
85077735046
-
Analysis of the baseline survey on the prevalence of Campylobacter in broiler batches and of Campylobacter and Salmonella on broiler carcasses in the EU, 2008, part A: Campylobacter and Salmonella prevalence estimates
-
(100 )
-
EFSA Analysis of the baseline survey on the prevalence of Campylobacter in broiler batches and of Campylobacter and Salmonella on broiler carcasses in the EU, 2008, part A: Campylobacter and Salmonella prevalence estimates. EFSA J. 2010, 8:1503. (100 pp.). 10.2903/j.efsa.2010.1503.
-
(2010)
EFSA J.
, vol.8
, pp. 1503
-
-
-
9
-
-
85021233476
-
The European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2012. European Food Safety Authority (EFSA), Parma, Italy, European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
-
(312)
-
EFSA The European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2012. European Food Safety Authority (EFSA), Parma, Italy, European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden. EFSA J. 2014, 12:3547. (312 pp.). 10.2903/j.efsa.2014.3547.
-
(2014)
EFSA J.
, vol.12
, pp. 3547
-
-
-
10
-
-
85056214520
-
Scientific opinion on Campylobacter in broiler meat production: control opinions and performance objectives and/or targets at different stages of the food chain
-
(141)
-
EFSA Panel of Biological Hazards (BIOHAZ) Scientific opinion on Campylobacter in broiler meat production: control opinions and performance objectives and/or targets at different stages of the food chain. EFSA J. 2011, 9:2105. (141 pp.). 10.2903/j.efsa.2011.2105.
-
(2011)
EFSA J.
, vol.9
, pp. 2105
-
-
-
11
-
-
84961693351
-
Campylobacter jejuni/coli/lari- bakteerien osoittaminen siipikarjan umpisuolinäytteistä
-
Finnish Food Safety Authority Evira Campylobacter jejuni/coli/lari- bakteerien osoittaminen siipikarjan umpisuolinäytteistä. Evira (3512/5) 2012.
-
(2012)
Evira (3512/5)
-
-
-
12
-
-
79957791009
-
Reduction of Campylobacter jejuni counts on chicken meat treated with different seasonings
-
Gonzalez M., Hänninen M. Reduction of Campylobacter jejuni counts on chicken meat treated with different seasonings. Food Control 2011, 22:1785-1789.
-
(2011)
Food Control
, vol.22
, pp. 1785-1789
-
-
Gonzalez, M.1
Hänninen, M.2
-
13
-
-
68549094451
-
Chickens and cattle as sources of sporadic domestically acquired Campylobacter jejuni infections in Finland
-
Hakkinen M., Nakari U.M., Siitonen A. Chickens and cattle as sources of sporadic domestically acquired Campylobacter jejuni infections in Finland. Appl. Environ. Microbiol. 2009, 75:5244-5249.
-
(2009)
Appl. Environ. Microbiol.
, vol.75
, pp. 5244-5249
-
-
Hakkinen, M.1
Nakari, U.M.2
Siitonen, A.3
-
14
-
-
84856882264
-
Poultry as a host for the zoonotic pathogen Campylobacter jejuni
-
Hermans D., Pasmans F., Messens W., Martel A., Van Immerseel F., Rasschaert G., Heyndrickx M., Van Deun K., Haesebrouck F. Poultry as a host for the zoonotic pathogen Campylobacter jejuni. Vector Borne Zoonotic Dis. 2012, 12:89-98.
-
(2012)
Vector Borne Zoonotic Dis.
, vol.12
, pp. 89-98
-
-
Hermans, D.1
Pasmans, F.2
Messens, W.3
Martel, A.4
Van Immerseel, F.5
Rasschaert, G.6
Heyndrickx, M.7
Van Deun, K.8
Haesebrouck, F.9
-
15
-
-
0347761194
-
Campylobacter spp., Giardia spp., Cryptosporidium spp., noroviruses, and indicator organisms in surface water in Southwestern Finland, 2000-2001
-
Hörman A., Rimhanen-Finne R., Maunula L., von Bonsdorff C.H., Torvela N., Heikinheimo A., Hänninen M.L. Campylobacter spp., Giardia spp., Cryptosporidium spp., noroviruses, and indicator organisms in surface water in Southwestern Finland, 2000-2001. Appl. Environ. Microbiol. 2004, 70:87-95.
-
(2004)
Appl. Environ. Microbiol.
, vol.70
, pp. 87-95
-
-
Hörman, A.1
Rimhanen-Finne, R.2
Maunula, L.3
von Bonsdorff, C.H.4
Torvela, N.5
Heikinheimo, A.6
Hänninen, M.L.7
-
16
-
-
30744470609
-
Application of phylogenetic networks in evolutionary studies
-
Huson D.H., Bryant D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 2006, 23:254-267.
-
(2006)
Mol. Biol. Evol.
, vol.23
, pp. 254-267
-
-
Huson, D.H.1
Bryant, D.2
-
17
-
-
78650827616
-
BIGSdb: scalable analysis of bacterial genome variation at the population level
-
Jolley K.A., Maiden M.C. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinforma. 2010, 11:595. 10.1186/1471-2105-11-595.
-
(2010)
BMC Bioinforma.
, vol.11
, pp. 595
-
-
Jolley, K.A.1
Maiden, M.C.2
-
18
-
-
10744229601
-
Temporal and geographical distribution and overlap of Penner heat-stable serotypes and pulsed-field gel electrophoresis genotypes of Campylobacter jejuni isolates collected from humans and chickens in Finland during a seasonal peak
-
Kärenlampi R., Rautelin H., Hakkinen M., Hänninen M.L. Temporal and geographical distribution and overlap of Penner heat-stable serotypes and pulsed-field gel electrophoresis genotypes of Campylobacter jejuni isolates collected from humans and chickens in Finland during a seasonal peak. J. Clin. Microbiol. 2003, 41:4870-4872.
-
(2003)
J. Clin. Microbiol.
, vol.41
, pp. 4870-4872
-
-
Kärenlampi, R.1
Rautelin, H.2
Hakkinen, M.3
Hänninen, M.L.4
-
19
-
-
84910152219
-
Multilocus sequence typing (MLST) and whole-genome MLST of Campylobacter jejuni isolates from human infections in three districts during a seasonal peak in Finland
-
Kovanen S.M., Kivistö R.I., Rossi M., Schott T., Kärkkäinen U.M., Tuuminen T., Uksila J., Rautelin H., Hänninen M.L. Multilocus sequence typing (MLST) and whole-genome MLST of Campylobacter jejuni isolates from human infections in three districts during a seasonal peak in Finland. J. Clin. Microbiol. 2014, 52:4147-4154.
-
(2014)
J. Clin. Microbiol.
, vol.52
, pp. 4147-4154
-
-
Kovanen, S.M.1
Kivistö, R.I.2
Rossi, M.3
Schott, T.4
Kärkkäinen, U.M.5
Tuuminen, T.6
Uksila, J.7
Rautelin, H.8
Hänninen, M.L.9
-
20
-
-
84891280084
-
Campylobacteriosis in urban versus rural areas: a case-case study integrated with molecular typing to validate risk factors and to attribute sources of infection
-
Levesque S., Fournier E., Carrier N., Frost E., Arbeit R.D., Michaud S. Campylobacteriosis in urban versus rural areas: a case-case study integrated with molecular typing to validate risk factors and to attribute sources of infection. PLoS One 2013, 8(12). 10.1371/journal.pone.0083731.
-
(2013)
PLoS One
, vol.8
, Issue.12
-
-
Levesque, S.1
Fournier, E.2
Carrier, N.3
Frost, E.4
Arbeit, R.D.5
Michaud, S.6
-
21
-
-
84923674055
-
Predominant Campylobacter jejuni sequence types persist in Finnish chicken production
-
Llarena A.K., Huneau A., Hakkinen M., Hänninen M.L. Predominant Campylobacter jejuni sequence types persist in Finnish chicken production. PLoS One 2015, 10(2). 10.1371/journal.pone.0116585.
-
(2015)
PLoS One
, vol.10
, Issue.2
-
-
Llarena, A.K.1
Huneau, A.2
Hakkinen, M.3
Hänninen, M.L.4
-
22
-
-
84961740961
-
Maa ja Metsätalousministeriön asetus broilereiden kampylobakteerivalvonnasta. 10/EEO/2007
-
Maa- ja Metsätalousministeriö Maa ja Metsätalousministeriön asetus broilereiden kampylobakteerivalvonnasta. 10/EEO/2007 2007.
-
(2007)
-
-
-
23
-
-
84864571431
-
Risk factors for campylobacteriosis of chicken, ruminant, and environmental origin: a combined case-control and source attribution analysis
-
Mughini Gras L., Smid J.H., Wagenaar J.A., de Boer A.G., Havelaar A.H., Friesema I.H., French N.P., Busani L., van Pelt W. Risk factors for campylobacteriosis of chicken, ruminant, and environmental origin: a combined case-control and source attribution analysis. PLoS One 2012, 7(8). 10.1371/journal.pone.0042599.
-
(2012)
PLoS One
, vol.7
, Issue.8
-
-
Mughini Gras, L.1
Smid, J.H.2
Wagenaar, J.A.3
de Boer, A.G.4
Havelaar, A.H.5
Friesema, I.H.6
French, N.P.7
Busani, L.8
van Pelt, W.9
-
24
-
-
84876332673
-
Genetic heterogeneity of Campylobacter jejuni NCTC 11168 upon human infection
-
Revez J., Schott T., Llarena A.K., Rossi M., Hänninen M.L. Genetic heterogeneity of Campylobacter jejuni NCTC 11168 upon human infection. Infect. Genet. Evol. 2013, 16:305-309.
-
(2013)
Infect. Genet. Evol.
, vol.16
, pp. 305-309
-
-
Revez, J.1
Schott, T.2
Llarena, A.K.3
Rossi, M.4
Hänninen, M.L.5
-
25
-
-
84905263677
-
Genomic variation between milkborne outbreak-associated Campylobacter jejuni isolates
-
Revez J., Zhang J., Schott T., Kivistö R., Rossi M., Hänninen M.L. Genomic variation between milkborne outbreak-associated Campylobacter jejuni isolates. J. Clin. Microbiol. 2014, 52:2782-2786.
-
(2014)
J. Clin. Microbiol.
, vol.52
, pp. 2782-2786
-
-
Revez, J.1
Zhang, J.2
Schott, T.3
Kivistö, R.4
Rossi, M.5
Hänninen, M.L.6
-
26
-
-
3543002236
-
Swimming and Campylobacter infections
-
Schönberg-Norio D., Takkinen J., Hänninen M.L., Katila M.L., Kaukoranta S.S., Mattila L., Rautelin H. Swimming and Campylobacter infections. Emerg. Infect. Dis. 2004, 10:1474-1477.
-
(2004)
Emerg. Infect. Dis.
, vol.10
, pp. 1474-1477
-
-
Schönberg-Norio, D.1
Takkinen, J.2
Hänninen, M.L.3
Katila, M.L.4
Kaukoranta, S.S.5
Mattila, L.6
Rautelin, H.7
-
27
-
-
68749116461
-
Campylobacter genotypes from food animals, environmental sources and clinical disease in Scotland 2005/6
-
Sheppard S.K., Dallas J.F., MacRae M., McCarthy N.D., Sproston E.L., Gormley F.J., Strachan N.J.C., Ogden I.D., Maiden M.C.J., Forbes K.J. Campylobacter genotypes from food animals, environmental sources and clinical disease in Scotland 2005/6. Int. J. Food Microbiol. 2009, 134:96-103.
-
(2009)
Int. J. Food Microbiol.
, vol.134
, pp. 96-103
-
-
Sheppard, S.K.1
Dallas, J.F.2
MacRae, M.3
McCarthy, N.D.4
Sproston, E.L.5
Gormley, F.J.6
Strachan, N.J.C.7
Ogden, I.D.8
Maiden, M.C.J.9
Forbes, K.J.10
-
28
-
-
84863322057
-
A gene-by-gene approach to bacterial population genomics: whole genome MLST of Campylobacter
-
Sheppard S.K., Jolley K.A., Maiden M.C.J. A gene-by-gene approach to bacterial population genomics: whole genome MLST of Campylobacter. Gene 2012, 3:261-277.
-
(2012)
Gene
, vol.3
, pp. 261-277
-
-
Sheppard, S.K.1
Jolley, K.A.2
Maiden, M.C.J.3
-
29
-
-
0017688031
-
Campylobacter enteritis: a "new" disease
-
Skirrow M.B. Campylobacter enteritis: a "new" disease. Br. Med. J. 1977, 2:9-11.
-
(1977)
Br. Med. J.
, vol.2
, pp. 9-11
-
-
Skirrow, M.B.1
-
30
-
-
84876934616
-
Identifying the seasonal origins of human campylobacteriosis
-
Strachan N.J., Rotariu O., Smith-Palmer A., Cowden J., Sheppard S.K., O'Brien S.J., Maiden M.C., Macrae M., Bessell P.R., Matthews L., Reid S.W., Innocent G.T., Ogden I.D., Forbes K.J. Identifying the seasonal origins of human campylobacteriosis. Epidemiol. Infect. 2013, 141:1267-1275.
-
(2013)
Epidemiol. Infect.
, vol.141
, pp. 1267-1275
-
-
Strachan, N.J.1
Rotariu, O.2
Smith-Palmer, A.3
Cowden, J.4
Sheppard, S.K.5
O'Brien, S.J.6
Maiden, M.C.7
Macrae, M.8
Bessell, P.R.9
Matthews, L.10
Reid, S.W.11
Innocent, G.T.12
Ogden, I.D.13
Forbes, K.J.14
-
31
-
-
0346100590
-
Domestically acquired Campylobacter infections in Finland
-
Vierikko A., Hänninen M.L., Siitonen A., Ruutu P., Rautelin H. Domestically acquired Campylobacter infections in Finland. Emerg. Infect. Dis. 2004, 10:127-130.
-
(2004)
Emerg. Infect. Dis.
, vol.10
, pp. 127-130
-
-
Vierikko, A.1
Hänninen, M.L.2
Siitonen, A.3
Ruutu, P.4
Rautelin, H.5
-
32
-
-
52949148195
-
Tracing the source of campylobacteriosis
-
Wilson D.J., Gabriel E., Leatherbarrow A.J.H., Cheesbrough J., Gee S., Bolton E., Fox A., Fearnhead P., Hart C.A., Diggle P.J. Tracing the source of campylobacteriosis. PLoS Genet. 2008, 4(9). 10.1371/journal.pgen.1000203.
-
(2008)
PLoS Genet.
, vol.4
, Issue.9
-
-
Wilson, D.J.1
Gabriel, E.2
Leatherbarrow, A.J.H.3
Cheesbrough, J.4
Gee, S.5
Bolton, E.6
Fox, A.7
Fearnhead, P.8
Hart, C.A.9
Diggle, P.J.10
-
33
-
-
84928036627
-
Refinement of whole-genome multilocus sequence typing analysis by addressing gene paralogy
-
Zhang J., Halkilahti J., Hänninen M.L., Rossi M. Refinement of whole-genome multilocus sequence typing analysis by addressing gene paralogy. J. Clin. Microbiol. 2015, 53:1765-1767.
-
(2015)
J. Clin. Microbiol.
, vol.53
, pp. 1765-1767
-
-
Zhang, J.1
Halkilahti, J.2
Hänninen, M.L.3
Rossi, M.4
|