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Items: 36

1.

A scale-free analysis of the HIV-1 genome demonstrates multiple conserved regions of structural and functional importance.

Skittrall JP, Ingemarsdotter CK, Gog JR, Lever AML.

PLoS Comput Biol. 2019 Sep 23;15(9):e1007345. doi: 10.1371/journal.pcbi.1007345. eCollection 2019 Sep.

2.

Geographic transmission hubs of the 2009 influenza pandemic in the United States.

Kissler SM, Gog JR, Viboud C, Charu V, Bjørnstad ON, Simonsen L, Grenfell BT.

Epidemics. 2019 Mar;26:86-94. doi: 10.1016/j.epidem.2018.10.002. Epub 2018 Oct 10.

3.

Urbanization and humidity shape the intensity of influenza epidemics in U.S. cities.

Dalziel BD, Kissler S, Gog JR, Viboud C, Bjørnstad ON, Metcalf CJE, Grenfell BT.

Science. 2018 Oct 5;362(6410):75-79. doi: 10.1126/science.aat6030.

4.

A new method for detecting signal regions in ordered sequences of real numbers, and application to viral genomic data.

Gog JR, Lever AML, Skittrall JP.

PLoS One. 2018 Apr 13;13(4):e0195763. doi: 10.1371/journal.pone.0195763. eCollection 2018.

5.

Infectious Disease Surveillance in the Big Data Era: Towards Faster and Locally Relevant Systems.

Simonsen L, Gog JR, Olson D, Viboud C.

J Infect Dis. 2016 Dec 1;214(suppl_4):S380-S385. doi: 10.1093/infdis/jiw376. Review.

6.

Eight challenges in phylodynamic inference.

Frost SD, Pybus OG, Gog JR, Viboud C, Bonhoeffer S, Bedford T.

Epidemics. 2015 Mar;10:88-92. doi: 10.1016/j.epidem.2014.09.001. Epub 2014 Sep 16.

7.

Seven challenges in modeling pathogen dynamics within-host and across scales.

Gog JR, Pellis L, Wood JL, McLean AR, Arinaminpathy N, Lloyd-Smith JO.

Epidemics. 2015 Mar;10:45-8. doi: 10.1016/j.epidem.2014.09.009. Epub 2014 Sep 30.

8.

Five challenges in modelling interacting strain dynamics.

Wikramaratna PS, Kucharski A, Gupta S, Andreasen V, McLean AR, Gog JR.

Epidemics. 2015 Mar;10:31-4. doi: 10.1016/j.epidem.2014.07.005. Epub 2014 Oct 7.

9.

Capturing the dynamics of pathogens with many strains.

Kucharski AJ, Andreasen V, Gog JR.

J Math Biol. 2016 Jan;72(1-2):1-24. doi: 10.1007/s00285-015-0873-4. Epub 2015 Mar 24. Review.

10.

Spatial Transmission of 2009 Pandemic Influenza in the US.

Gog JR, Ballesteros S, Viboud C, Simonsen L, Bjornstad ON, Shaman J, Chao DL, Khan F, Grenfell BT.

PLoS Comput Biol. 2014 Jun 12;10(6):e1003635. doi: 10.1371/journal.pcbi.1003635. eCollection 2014 Jun.

11.

Identification of a novel splice variant form of the influenza A virus M2 ion channel with an antigenically distinct ectodomain.

Wise HM, Hutchinson EC, Jagger BW, Stuart AD, Kang ZH, Robb N, Schwartzman LM, Kash JC, Fodor E, Firth AE, Gog JR, Taubenberger JK, Digard P.

PLoS Pathog. 2012;8(11):e1002998. doi: 10.1371/journal.ppat.1002998. Epub 2012 Nov 1.

12.

The role of social contacts and original antigenic sin in shaping the age pattern of immunity to seasonal influenza.

Kucharski AJ, Gog JR.

PLoS Comput Biol. 2012;8(10):e1002741. doi: 10.1371/journal.pcbi.1002741. Epub 2012 Oct 25.

13.

Quantifying transmission of highly pathogenic and low pathogenicity H7N1 avian influenza in turkeys.

Saenz RA, Essen SC, Brookes SM, Iqbal M, Wood JL, Grenfell BT, McCauley JW, Brown IH, Gog JR.

PLoS One. 2012;7(9):e45059. doi: 10.1371/journal.pone.0045059. Epub 2012 Sep 18.

14.

Dynamics of Salmonella infection of macrophages at the single cell level.

Gog JR, Murcia A, Osterman N, Restif O, McKinley TJ, Sheppard M, Achouri S, Wei B, Mastroeni P, Wood JL, Maskell DJ, Cicuta P, Bryant CE.

J R Soc Interface. 2012 Oct 7;9(75):2696-707. doi: 10.1098/rsif.2012.0163. Epub 2012 May 2.

15.

Age profile of immunity to influenza: effect of original antigenic sin.

Kucharski AJ, Gog JR.

Theor Popul Biol. 2012 Mar;81(2):102-12. doi: 10.1016/j.tpb.2011.12.006. Epub 2011 Dec 22.

PMID:
22209755
16.

Influenza emergence in the face of evolutionary constraints.

Kucharski A, Gog JR.

Proc Biol Sci. 2012 Feb 22;279(1729):645-52. doi: 10.1098/rspb.2011.1168. Epub 2011 Jul 20.

17.

Overlapping signals for translational regulation and packaging of influenza A virus segment 2.

Wise HM, Barbezange C, Jagger BW, Dalton RM, Gog JR, Curran MD, Taubenberger JK, Anderson EC, Digard P.

Nucleic Acids Res. 2011 Sep 1;39(17):7775-90. doi: 10.1093/nar/gkr487. Epub 2011 Jun 21.

18.

Transmission and dose-response experiments for social animals: a reappraisal of the colonization biology of Campylobacter jejuni in chickens.

Conlan AJ, Line JE, Hiett K, Coward C, Van Diemen PM, Stevens MP, Jones MA, Gog JR, Maskell DJ.

J R Soc Interface. 2011 Dec 7;8(65):1720-35. doi: 10.1098/rsif.2011.0125. Epub 2011 May 18.

19.

A Bayesian approach to analyse genetic variation within RNA viral populations.

McKinley TJ, Murcia PR, Gog JR, Varela M, Wood JL.

PLoS Comput Biol. 2011 Mar;7(3):e1002027. doi: 10.1371/journal.pcbi.1002027. Epub 2011 Mar 31.

20.

Measuring social networks in British primary schools through scientific engagement.

Conlan AJ, Eames KT, Gage JA, von Kirchbach JC, Ross JV, Saenz RA, Gog JR.

Proc Biol Sci. 2011 May 22;278(1711):1467-75. doi: 10.1098/rspb.2010.1807. Epub 2010 Nov 3.

21.

Genomic analysis of codon, sequence and structural conservation with selective biochemical-structure mapping reveals highly conserved and dynamic structures in rotavirus RNAs with potential cis-acting functions.

Li W, Manktelow E, von Kirchbach JC, Gog JR, Desselberger U, Lever AM.

Nucleic Acids Res. 2010 Nov;38(21):7718-35. doi: 10.1093/nar/gkq663. Epub 2010 Jul 29.

22.

Dynamics of influenza virus infection and pathology.

Saenz RA, Quinlivan M, Elton D, Macrae S, Blunden AS, Mumford JA, Daly JM, Digard P, Cullinane A, Grenfell BT, McCauley JW, Wood JL, Gog JR.

J Virol. 2010 Apr;84(8):3974-83. doi: 10.1128/JVI.02078-09. Epub 2010 Feb 3.

23.

Genome packaging in influenza A virus.

Hutchinson EC, von Kirchbach JC, Gog JR, Digard P.

J Gen Virol. 2010 Feb;91(Pt 2):313-28. doi: 10.1099/vir.0.017608-0. Epub 2009 Dec 2. Review.

PMID:
19955561
24.

Mutational analysis of cis-acting RNA signals in segment 7 of influenza A virus.

Hutchinson EC, Curran MD, Read EK, Gog JR, Digard P.

J Virol. 2008 Dec;82(23):11869-79. doi: 10.1128/JVI.01634-08. Epub 2008 Sep 24.

25.

The impact of evolutionary constraints on influenza dynamics.

Gog JR.

Vaccine. 2008 Jul 18;26 Suppl 3:C15-24. Review.

PMID:
18773528
26.

Competing isogenic Campylobacter strains exhibit variable population structures in vivo.

Coward C, van Diemen PM, Conlan AJ, Gog JR, Stevens MP, Jones MA, Maskell DJ.

Appl Environ Microbiol. 2008 Jun;74(12):3857-67. doi: 10.1128/AEM.02835-07. Epub 2008 Apr 18.

27.

Campylobacter jejuni colonization and transmission in broiler chickens: a modelling perspective.

Conlan AJ, Coward C, Grant AJ, Maskell DJ, Gog JR.

J R Soc Interface. 2007 Oct 22;4(16):819-29. Review.

28.

Codon conservation in the influenza A virus genome defines RNA packaging signals.

Gog JR, Afonso Edos S, Dalton RM, Leclercq I, Tiley L, Elton D, von Kirchbach JC, Naffakh N, Escriou N, Digard P.

Nucleic Acids Res. 2007;35(6):1897-907. Epub 2007 Mar 1.

29.

Modelling dynamics of the type I interferon response to in vitro viral infection.

Howat TJ, Barreca C, O'Hare P, Gog JR, Grenfell BT.

J R Soc Interface. 2006 Oct 22;3(10):699-709.

30.

Epidemic dynamics and antigenic evolution in a single season of influenza A.

Boni MF, Gog JR, Andreasen V, Feldman MW.

Proc Biol Sci. 2006 Jun 7;273(1592):1307-16.

31.

Influenza drift and epidemic size: the race between generating and escaping immunity.

Boni MF, Gog JR, Andreasen V, Christiansen FB.

Theor Popul Biol. 2004 Mar;65(2):179-91.

PMID:
14766191
32.

Unifying the epidemiological and evolutionary dynamics of pathogens.

Grenfell BT, Pybus OG, Gog JR, Wood JL, Daly JM, Mumford JA, Holmes EC.

Science. 2004 Jan 16;303(5656):327-32. Review.

PMID:
14726583
33.

Population dynamics of rapid fixation in cytotoxic T lymphocyte escape mutants of influenza A.

Gog JR, Rimmelzwaan GF, Osterhaus AD, Grenfell BT.

Proc Natl Acad Sci U S A. 2003 Sep 16;100(19):11143-7. Epub 2003 Sep 3.

34.

Dynamics and selection of many-strain pathogens.

Gog JR, Grenfell BT.

Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):17209-14. Epub 2002 Dec 12.

35.

The onset of oscillatory dynamics in models of multiple disease strains.

Dawes JH, Gog JR.

J Math Biol. 2002 Dec;45(6):471-510.

PMID:
12439588
36.

A status-based approach to multiple strain dynamics.

Gog JR, Swinton J.

J Math Biol. 2002 Feb;44(2):169-84.

PMID:
11942531

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