-
Notifications
You must be signed in to change notification settings - Fork 3
/
Copy pathwhitepaper.bib
112 lines (97 loc) · 5.94 KB
/
whitepaper.bib
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
%% This BibTeX bibliography file was created using BibDesk.
%% http://bibdesk.sourceforge.net/
%% Created for Trevor Bedford at 2018-04-18 14:29:46 -0700
%% Saved with string encoding Unicode (UTF-8)
@article{sagulenko2018treetime,
Author = {Sagulenko, Pavel and Puller, Vadim and Neher, Richard A},
Date-Added = {2018-04-18 21:00:09 +0000},
Date-Modified = {2018-04-18 21:00:18 +0000},
Journal = {Virus Evol},
Number = {1},
Pages = {vex042},
Title = {TreeTime: Maximum-likelihood phylodynamic analysis},
Volume = {4},
Year = {2018}}
@article{neher2015nextflu,
Author = {Neher, Richard A and Bedford, Trevor},
Date-Added = {2015-08-17 22:33:51 +0000},
Date-Modified = {2017-08-11 19:07:31 +0000},
Journal = {Bioinformatics},
Pages = {3546--3548},
Title = {nextflu: real-time tracking of seasonal influenza virus evolution in humans},
Volume = {31},
Year = {2015}}
@article{quick2016real,
Author = {Quick, Joshua and Loman, Nicholas J and Duraffour, Sophie and Simpson, Jared T and Severi, Ettore and Cowley, Lauren and Bore, Joseph Akoi and Koundouno, Raymond and Dudas, Gytis and Mikhail, Amy and others},
Date-Modified = {2018-04-18 21:04:45 +0000},
Journal = {Nature},
Number = {7589},
Pages = {228--232},
Title = {Real-time, portable genome sequencing for {Ebola} surveillance},
Volume = {530},
Year = {2016}}
@article{pybus2013evolutionary,
Author = {Pybus, OG and Fraser, C and Rambaut, A},
Date-Modified = {2018-04-18 21:03:23 +0000},
Journal = {Phil Trans R Soc B},
Number = {1614},
Pages = {20120193--20120193},
Title = {Evolutionary epidemiology: preparing for an age of genomic plenty},
Volume = {368},
Year = {2013}}
@article{croucher2015application,
Author = {Croucher, Nicholas J and Didelot, Xavier},
Date-Modified = {2017-09-06 19:20:17 +0000},
Journal = {Curr. Opin. Microbiol.},
Pages = {62--67},
Title = {The application of genomics to tracing bacterial pathogen transmission},
Volume = {23},
Year = {2015}}
@article{devries2017three,
Author = {de Vries, Robert P and Peng, Wenjie and Grant, Oliver C and Thompson, Andrew J and Zhu, Xueyong and Bouwman, Kim M and de la Pena, Alba T Torrents and van Breemen, Marielle J and Wickramasinghe, Iresha N Ambepitiya and de Haan, Cornelis AM and others},
Date-Modified = {2018-04-18 21:29:46 +0000},
Journal = {PLoS Pathog},
Number = {6},
Pages = {e1006390--16},
Title = {Three mutations switch {H7N9} influenza to human-type receptor specificity},
Volume = {13},
Year = {2017}}
@article{tang2017global,
Author = {Tang, Julian W and Lam, Tommy T and Zaraket, Hassan and Lipkin, W Ian and Drews, Steven J and Hatchette, Todd F and Heraud, Jean-Michel and Koopmans, Marion P and Abraham, Ashta Mary and Baraket, Amal and others},
Date-Modified = {2018-04-18 21:06:41 +0000},
Journal = {Lancet Infect. Dis.},
Pages = {1--7},
Title = {Global epidemiology of non-influenza {RNA} respiratory viruses: data gaps and a growing need for surveillance},
Volume = {17},
Year = {2017}}
@article{faria2017epidemic,
Abstract = {Zika virus (ZIKV) transmission in the Americas was first confirmed in May 2015 in Northeast Brazil1. Brazil has the highest number of reported ZIKV cases worldwide (\>200,000 by 24 Dec 2016) as well as the greatest number of cases associated with microcephaly and other birth defects (2,366 confirmed cases by 31 Dec 2016). Following the initial detection of ZIKV in Brazil, 47 countries and territories in the Americas have reported local ZIKV transmission, with 24 of these reporting ZIKV-associated severe disease. Yet the origin and epidemic history of ZIKV in Brazil and the Americas remain poorly understood, despite the value of such information for interpreting past and future trends in reported microcephaly. To address this we generated 54 complete or partial ZIKV genomes, mostly from Brazil, and report data generated by the ZiBRA project - a mobile genomics lab that travelled across Northeast (NE) Brazil in 2016. One sequence represents the earliest confirmed ZIKV infection in Brazil. Joint analyses of viral genomes with ecological and epidemiological data estimate that ZIKV epidemic was present in NE Brazil by March 2014 and likely disseminated from there, both nationally and internationally, before the first detection of ZIKV in the Americas. Estimated dates of the international spread of ZIKV from Brazil indicate the duration of pre-detection cryptic transmission in recipient regions. NE Brazil{\textquoteright}s role in the establishment of ZIKV in the Americas is further supported by geographic analysis of ZIKV transmission potential and by estimates of the virus{\textquoteright} basic reproduction number.},
Author = {Faria, Nuno R and Quick, Josh and Claro, IM and Theze, Julien and de Jesus, Jacqueline G and Giovanetti, Marta and Kraemer, Moritz UG and Hill, Sarah C and Black, Allison and da Costa, Antonio C and others},
Date-Modified = {2018-04-18 21:03:54 +0000},
Journal = {Nature},
Pages = {406--410},
Title = {Epidemic establishment and cryptic transmission of {Zika} virus in {Brazil} and the {Americas}},
Volume = {546},
Year = {2017},
Bdsk-Url-1 = {http://www.biorxiv.org/content/early/2017/03/27/105171},
Bdsk-Url-2 = {http://dx.doi.org/10.1101/105171}}
@article{li2014epidemiology,
Author = {Li, Qun and Zhou, Lei and Zhou, Minghao and Chen, Zhiping and Li, Furong and Wu, Huanyu and Xiang, Nijuan and Chen, Enfu and Tang, Fenyang and Wang, Dayan and others},
Date-Modified = {2018-04-18 21:24:48 +0000},
Journal = {N. Engl. J. Med.},
Number = {6},
Pages = {520--532},
Title = {Epidemiology of human infections with avian influenza {A(H7N9)} virus in {China}},
Volume = {370},
Year = {2014},
Bdsk-Url-1 = {http://dx.doi.org/10.1056/NEJMoa1304617}}
@article{volz2013viral,
Author = {Volz, E. M. and Koelle, K. and Bedford, T.},
Date-Modified = {2018-04-18 21:02:31 +0000},
Journal = {PLoS Comput Biol},
Number = {3},
Pages = {e1002947},
Title = {Viral phylodynamics},
Volume = {9},
Year = {2013},
Bdsk-Url-1 = {https://doi.org/10.1371/journal.pcbi.1002947}}