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Items: 1 to 20 of 170

1.

The effect of genetic structure on molecular dating and tests for temporal signal.

Murray GG, Wang F, Harrison EM, Paterson GK, Mather AE, Harris SR, Holmes MA, Rambaut A, Welch JJ.

Methods Ecol Evol. 2016 Jan;7(1):80-89. Epub 2015 Sep 22.

2.

Revealing the Micro-scale Signature of Endemic Zoonotic Disease Transmission in an African Urban Setting.

Bourhy H, Nakouné E, Hall M, Nouvellet P, Lepelletier A, Talbi C, Watier L, Holmes EC, Cauchemez S, Lemey P, Donnelly CA, Rambaut A.

PLoS Pathog. 2016 Apr 8;12(4):e1005525. doi: 10.1371/journal.ppat.1005525. eCollection 2016 Apr.

3.

Real-time, portable genome sequencing for Ebola surveillance.

Quick J, Loman NJ, Duraffour S, Simpson JT, Severi E, Cowley L, Bore JA, Koundouno R, Dudas G, Mikhail A, Ouédraogo N, Afrough B, Bah A, Baum JH, Becker-Ziaja B, Boettcher JP, Cabeza-Cabrerizo M, Camino-Sánchez Á, Carter LL, Doerrbecker J, Enkirch T, García-Dorival I, Hetzelt N, Hinzmann J, Holm T, Kafetzopoulou LE, Koropogui M, Kosgey A, Kuisma E, Logue CH, Mazzarelli A, Meisel S, Mertens M, Michel J, Ngabo D, Nitzsche K, Pallasch E, Patrono LV, Portmann J, Repits JG, Rickett NY, Sachse A, Singethan K, Vitoriano I, Yemanaberhan RL, Zekeng EG, Racine T, Bello A, Sall AA, Faye O, Faye O, Magassouba N, Williams CV, Amburgey V, Winona L, Davis E, Gerlach J, Washington F, Monteil V, Jourdain M, Bererd M, Camara A, Somlare H, Camara A, Gerard M, Bado G, Baillet B, Delaune D, Nebie KY, Diarra A, Savane Y, Pallawo RB, Gutierrez GJ, Milhano N, Roger I, Williams CJ, Yattara F, Lewandowski K, Taylor J, Rachwal P, Turner DJ, Pollakis G, Hiscox JA, Matthews DA, O'Shea MK, Johnston AM, Wilson D, Hutley E, Smit E, Di Caro A, Wölfel R, Stoecker K, Fleischmann E, Gabriel M, Weller SA, Koivogui L, Diallo B, Keïta S, Rambaut A, Formenty P, Günther S, Carroll MW.

Nature. 2016 Feb 11;530(7589):228-32. doi: 10.1038/nature16996. Epub 2016 Feb 3.

PMID:
26840485
4.

Persistent HIV-1 replication maintains the tissue reservoir during therapy.

Lorenzo-Redondo R, Fryer HR, Bedford T, Kim EY, Archer J, Kosakovsky Pond SL, Chung YS, Penugonda S, Chipman JG, Fletcher CV, Schacker TW, Malim MH, Rambaut A, Haase AT, McLean AR, Wolinsky SM.

Nature. 2016 Feb 4;530(7588):51-6. doi: 10.1038/nature16933. Epub 2016 Jan 27.

PMID:
26814962
5.

Epidemic History and Iatrogenic Transmission of Blood-borne Viruses in Mid-20th Century Kinshasa.

Hogan CA, Iles J, Frost EH, Giroux G, Cassar O, Gessain A, Dion MJ, Ilunga V, Rambaut A, Yengo-Ki-Ngimbi AÉ, Behets F, Pybus OG, Pépin J.

J Infect Dis. 2016 Jan 14. pii: jiw009. [Epub ahead of print]

PMID:
26768251
6.

Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set.

Hall M, Woolhouse M, Rambaut A.

PLoS Comput Biol. 2015 Dec 30;11(12):e1004613. doi: 10.1371/journal.pcbi.1004613. eCollection 2015 Dec.

7.

Evolution and Spread of Ebola Virus in Liberia, 2014-2015.

Ladner JT, Wiley MR, Mate S, Dudas G, Prieto K, Lovett S, Nagle ER, Beitzel B, Gilbert ML, Fakoli L, Diclaro JW 2nd, Schoepp RJ, Fair J, Kuhn JH, Hensley LE, Park DJ, Sabeti PC, Rambaut A, Sanchez-Lockhart M, Bolay FK, Kugelman JR, Palacios G.

Cell Host Microbe. 2015 Dec 9;18(6):659-69. doi: 10.1016/j.chom.2015.11.008.

PMID:
26651942
8.

Lessons from Ebola: Improving infectious disease surveillance to inform outbreak management.

Woolhouse ME, Rambaut A, Kellam P.

Sci Transl Med. 2015 Sep 30;7(307):307rv5. doi: 10.1126/scitranslmed.aab0191. Review.

PMID:
26424572
9.

The Vietnam Initiative on Zoonotic Infections (VIZIONS): A Strategic Approach to Studying Emerging Zoonotic Infectious Diseases.

Rabaa MA, Tue NT, Phuc TM, Carrique-Mas J, Saylors K, Cotten M, Bryant JE, Nghia HD, Cuong NV, Pham HA, Berto A, Phat VV, Dung TT, Bao LH, Hoa NT, Wertheim H, Nadjm B, Monagin C, van Doorn HR, Rahman M, Tra MP, Campbell JI, Boni MF, Tam PT, van der Hoek L, Simmonds P, Rambaut A, Toan TK, Van Vinh Chau N, Hien TT, Wolfe N, Farrar JJ, Thwaites G, Kellam P, Woolhouse ME, Baker S.

Ecohealth. 2015 Dec;12(4):726-35. doi: 10.1007/s10393-015-1061-0. Epub 2015 Sep 24.

10.

Relationship between haemagglutination inhibition titre and immunity to influenza in ferrets.

Wikramaratna PS, Rambaut A.

Vaccine. 2015 Oct 5;33(41):5380-5. doi: 10.1016/j.vaccine.2015.08.065. Epub 2015 Sep 3.

11.

Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone.

Park DJ, Dudas G, Wohl S, Goba A, Whitmer SL, Andersen KG, Sealfon RS, Ladner JT, Kugelman JR, Matranga CB, Winnicki SM, Qu J, Gire SK, Gladden-Young A, Jalloh S, Nosamiefan D, Yozwiak NL, Moses LM, Jiang PP, Lin AE, Schaffner SF, Bird B, Towner J, Mamoh M, Gbakie M, Kanneh L, Kargbo D, Massally JL, Kamara FK, Konuwa E, Sellu J, Jalloh AA, Mustapha I, Foday M, Yillah M, Erickson BR, Sealy T, Blau D, Paddock C, Brault A, Amman B, Basile J, Bearden S, Belser J, Bergeron E, Campbell S, Chakrabarti A, Dodd K, Flint M, Gibbons A, Goodman C, Klena J, McMullan L, Morgan L, Russell B, Salzer J, Sanchez A, Wang D, Jungreis I, Tomkins-Tinch C, Kislyuk A, Lin MF, Chapman S, MacInnis B, Matthews A, Bochicchio J, Hensley LE, Kuhn JH, Nusbaum C, Schieffelin JS, Birren BW, Forget M, Nichol ST, Palacios GF, Ndiaye D, Happi C, Gevao SM, Vandi MA, Kargbo B, Holmes EC, Bedford T, Gnirke A, Ströher U, Rambaut A, Garry RF, Sabeti PC.

Cell. 2015 Jun 18;161(7):1516-26. doi: 10.1016/j.cell.2015.06.007.

12.

Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa.

Carroll MW, Matthews DA, Hiscox JA, Elmore MJ, Pollakis G, Rambaut A, Hewson R, García-Dorival I, Bore JA, Koundouno R, Abdellati S, Afrough B, Aiyepada J, Akhilomen P, Asogun D, Atkinson B, Badusche M, Bah A, Bate S, Baumann J, Becker D, Becker-Ziaja B, Bocquin A, Borremans B, Bosworth A, Boettcher JP, Cannas A, Carletti F, Castilletti C, Clark S, Colavita F, Diederich S, Donatus A, Duraffour S, Ehichioya D, Ellerbrok H, Fernandez-Garcia MD, Fizet A, Fleischmann E, Gryseels S, Hermelink A, Hinzmann J, Hopf-Guevara U, Ighodalo Y, Jameson L, Kelterbaum A, Kis Z, Kloth S, Kohl C, Korva M, Kraus A, Kuisma E, Kurth A, Liedigk B, Logue CH, Lüdtke A, Maes P, McCowen J, Mély S, Mertens M, Meschi S, Meyer B, Michel J, Molkenthin P, Muñoz-Fontela C, Muth D, Newman EN, Ngabo D, Oestereich L, Okosun J, Olokor T, Omiunu R, Omomoh E, Pallasch E, Pályi B, Portmann J, Pottage T, Pratt C, Priesnitz S, Quartu S, Rappe J, Repits J, Richter M, Rudolf M, Sachse A, Schmidt KM, Schudt G, Strecker T, Thom R, Thomas S, Tobin E, Tolley H, Trautner J, Vermoesen T, Vitoriano I, Wagner M, Wolff S, Yue C, Capobianchi MR, Kretschmer B, Hall Y, Kenny JG, Rickett NY, Dudas G, Coltart CE, Kerber R, Steer D, Wright C, Senyah F, Keita S, Drury P, Diallo B, de Clerck H, Van Herp M, Sprecher A, Traore A, Diakite M, Konde MK, Koivogui L, Magassouba N, Avšič-Županc T, Nitsche A, Strasser M, Ippolito G, Becker S, Stoecker K, Gabriel M, Raoul H, Di Caro A, Wölfel R, Formenty P, Günther S.

Nature. 2015 Aug 6;524(7563):97-101. doi: 10.1038/nature14594. Epub 2015 Jun 17.

PMID:
26083749
13.

Global circulation patterns of seasonal influenza viruses vary with antigenic drift.

Bedford T, Riley S, Barr IG, Broor S, Chadha M, Cox NJ, Daniels RS, Gunasekaran CP, Hurt AC, Kelso A, Klimov A, Lewis NS, Li X, McCauley JW, Odagiri T, Potdar V, Rambaut A, Shu Y, Skepner E, Smith DJ, Suchard MA, Tashiro M, Wang D, Xu X, Lemey P, Russell CA.

Nature. 2015 Jul 9;523(7559):217-20. doi: 10.1038/nature14460. Epub 2015 Jun 8.

14.

Global migration of influenza A viruses in swine.

Nelson MI, Viboud C, Vincent AL, Culhane MR, Detmer SE, Wentworth DE, Rambaut A, Suchard MA, Holmes EC, Lemey P.

Nat Commun. 2015 Mar 27;6:6696. doi: 10.1038/ncomms7696.

15.

Simultaneously estimating evolutionary history and repeated traits phylogenetic signal: applications to viral and host phenotypic evolution.

Vrancken B, Lemey P, Rambaut A, Bedford T, Longdon B, Günthard HF, Suchard MA.

Methods Ecol Evol. 2015 Jan 1;6(1):67-82.

16.

An observational, laboratory-based study of outbreaks of middle East respiratory syndrome coronavirus in Jeddah and Riyadh, kingdom of Saudi Arabia, 2014.

Drosten C, Muth D, Corman VM, Hussain R, Al Masri M, HajOmar W, Landt O, Assiri A, Eckerle I, Al Shangiti A, Al-Tawfiq JA, Albarrak A, Zumla A, Rambaut A, Memish ZA.

Clin Infect Dis. 2015 Feb 1;60(3):369-77. doi: 10.1093/cid/ciu812. Epub 2014 Oct 16.

17.

Reassortment between influenza B lineages and the emergence of a coadapted PB1-PB2-HA gene complex.

Dudas G, Bedford T, Lycett S, Rambaut A.

Mol Biol Evol. 2015 Jan;32(1):162-72. doi: 10.1093/molbev/msu287. Epub 2014 Oct 15.

18.

Improving pandemic influenza risk assessment.

Russell CA, Kasson PM, Donis RO, Riley S, Dunbar J, Rambaut A, Asher J, Burke S, Davis CT, Garten RJ, Gnanakaran S, Hay SI, Herfst S, Lewis NS, Lloyd-Smith JO, Macken CA, Maurer-Stroh S, Neuhaus E, Parrish CR, Pepin KM, Shepard SS, Smith DL, Suarez DL, Trock SC, Widdowson MA, George DB, Lipsitch M, Bloom JD.

Elife. 2014 Oct 16;3:e03883. doi: 10.7554/eLife.03883.

19.

HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations.

Faria NR, Rambaut A, Suchard MA, Baele G, Bedford T, Ward MJ, Tatem AJ, Sousa JD, Arinaminpathy N, Pépin J, Posada D, Peeters M, Pybus OG, Lemey P.

Science. 2014 Oct 3;346(6205):56-61. doi: 10.1126/science.1256739. Epub 2014 Oct 2.

20.

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak.

Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, Jalloh S, Momoh M, Fullah M, Dudas G, Wohl S, Moses LM, Yozwiak NL, Winnicki S, Matranga CB, Malboeuf CM, Qu J, Gladden AD, Schaffner SF, Yang X, Jiang PP, Nekoui M, Colubri A, Coomber MR, Fonnie M, Moigboi A, Gbakie M, Kamara FK, Tucker V, Konuwa E, Saffa S, Sellu J, Jalloh AA, Kovoma A, Koninga J, Mustapha I, Kargbo K, Foday M, Yillah M, Kanneh F, Robert W, Massally JL, Chapman SB, Bochicchio J, Murphy C, Nusbaum C, Young S, Birren BW, Grant DS, Scheiffelin JS, Lander ES, Happi C, Gevao SM, Gnirke A, Rambaut A, Garry RF, Khan SH, Sabeti PC.

Science. 2014 Sep 12;345(6202):1369-72. doi: 10.1126/science.1259657. Epub 2014 Aug 28.

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