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Items: 47

1.

Plasticity of Amino Acid Residue 145 Near the Receptor Binding Site of H3 Swine Influenza A Viruses and Its Impact on Receptor Binding and Antibody Recognition.

Santos JJS, Abente EJ, Obadan AO, Thompson AJ, Ferreri L, Geiger G, Gonzalez-Reiche AS, Lewis NS, Burke DF, Rajão DS, Paulson JC, Vincent AL, Perez DR.

J Virol. 2019 Jan 4;93(2). pii: e01413-18. doi: 10.1128/JVI.01413-18. Print 2019 Jan 15.

2.

Antigenic characterization of highly pathogenic avian influenza A(H5N1) viruses with chicken and ferret antisera reveals clade-dependent variation in hemagglutination inhibition profiles.

Thi Nguyen D, Shepard SS, Burke DF, Jones J, Thor S, Nguyen LV, Nguyen TD, Balish A, Hoang DN, To TL, Iqbal M, Wentworth DE, Spackman E, van Doorn HR, Davis CT, Bryant JE.

Emerg Microbes Infect. 2018 May 31;7(1):100. doi: 10.1038/s41426-018-0100-7.

3.

Characterization of influenza A(H1N1)pdm09 viruses isolated from Nepalese and Indian outbreak patients in early 2015.

Nakamura K, Shirakura M, Fujisaki S, Kishida N, Burke DF, Smith DJ, Kuwahara T, Takashita E, Takayama I, Nakauchi M, Chadha M, Potdar V, Bhushan A, Upadhyay BP, Shakya G, Odagiri T, Kageyama T, Watanabe S.

Influenza Other Respir Viruses. 2017 Sep;11(5):399-403. doi: 10.1111/irv.12469. Epub 2017 Aug 9.

4.

Influenza Research Database: An integrated bioinformatics resource for influenza virus research.

Zhang Y, Aevermann BD, Anderson TK, Burke DF, Dauphin G, Gu Z, He S, Kumar S, Larsen CN, Lee AJ, Li X, Macken C, Mahaffey C, Pickett BE, Reardon B, Smith T, Stewart L, Suloway C, Sun G, Tong L, Vincent AL, Walters B, Zaremba S, Zhao H, Zhou L, Zmasek C, Klem EB, Scheuermann RH.

Nucleic Acids Res. 2017 Jan 4;45(D1):D466-D474. doi: 10.1093/nar/gkw857. Epub 2016 Sep 26.

5.

Selection of antigenically advanced variants of seasonal influenza viruses.

Li C, Hatta M, Burke DF, Ping J, Zhang Y, Ozawa M, Taft AS, Das SC, Hanson AP, Song J, Imai M, Wilker PR, Watanabe T, Watanabe S, Ito M, Iwatsuki-Horimoto K, Russell CA, James SL, Skepner E, Maher EA, Neumann G, Klimov AI, Kelso A, McCauley J, Wang D, Shu Y, Odagiri T, Tashiro M, Xu X, Wentworth DE, Katz JM, Cox NJ, Smith DJ, Kawaoka Y.

Nat Microbiol. 2016 May 23;1(6):16058. doi: 10.1038/nmicrobiol.2016.58.

6.

The global antigenic diversity of swine influenza A viruses.

Lewis NS, Russell CA, Langat P, Anderson TK, Berger K, Bielejec F, Burke DF, Dudas G, Fonville JM, Fouchier RA, Kellam P, Koel BF, Lemey P, Nguyen T, Nuansrichy B, Peiris JM, Saito T, Simon G, Skepner E, Takemae N; ESNIP3 consortium, Webby RJ, Van Reeth K, Brookes SM, Larsen L, Watson SJ, Brown IH, Vincent AL.

Elife. 2016 Apr 15;5:e12217. doi: 10.7554/eLife.12217.

7.

Amino Acid Substitutions That Affect Receptor Binding and Stability of the Hemagglutinin of Influenza A/H7N9 Virus.

Schrauwen EJ, Richard M, Burke DF, Rimmelzwaan GF, Herfst S, Fouchier RA.

J Virol. 2016 Jan 20;90(7):3794-9. doi: 10.1128/JVI.03052-15.

8.

Identification of amino acid substitutions supporting antigenic change of influenza A(H1N1)pdm09 viruses.

Koel BF, Mögling R, Chutinimitkul S, Fraaij PL, Burke DF, van der Vliet S, de Wit E, Bestebroer TM, Rimmelzwaan GF, Osterhaus AD, Smith DJ, Fouchier RA, de Graaf M.

J Virol. 2015 Apr;89(7):3763-75. doi: 10.1128/JVI.02962-14. Epub 2015 Jan 21.

9.

A recommended numbering scheme for influenza A HA subtypes.

Burke DF, Smith DJ.

PLoS One. 2014 Nov 12;9(11):e112302. doi: 10.1371/journal.pone.0112302. eCollection 2014.

10.

Polymorphisms at amino acid residues 141 and 154 influence conformational variation in ovine PrP.

Yang S, Thackray AM, Hopkins L, Monie TP, Burke DF, Bujdoso R.

Biomed Res Int. 2014;2014:372491. doi: 10.1155/2014/372491. Epub 2014 Jul 14.

11.

Circulating avian influenza viruses closely related to the 1918 virus have pandemic potential.

Watanabe T, Zhong G, Russell CA, Nakajima N, Hatta M, Hanson A, McBride R, Burke DF, Takahashi K, Fukuyama S, Tomita Y, Maher EA, Watanabe S, Imai M, Neumann G, Hasegawa H, Paulson JC, Smith DJ, Kawaoka Y.

Cell Host Microbe. 2014 Jun 11;15(6):692-705. doi: 10.1016/j.chom.2014.05.006.

12.

Antigenic variation of clade 2.1 H5N1 virus is determined by a few amino acid substitutions immediately adjacent to the receptor binding site.

Koel BF, van der Vliet S, Burke DF, Bestebroer TM, Bharoto EE, Yasa IW, Herliana I, Laksono BM, Xu K, Skepner E, Russell CA, Rimmelzwaan GF, Perez DR, Osterhaus AD, Smith DJ, Prajitno TY, Fouchier RA.

MBio. 2014 Jun 10;5(3):e01070-14. doi: 10.1128/mBio.01070-14. Erratum in: MBio. 2014;5(4):doi:10.1128/mBio.01645-14.

13.

Substitutions near the hemagglutinin receptor-binding site determine the antigenic evolution of influenza A H3N2 viruses in U.S. swine.

Lewis NS, Anderson TK, Kitikoon P, Skepner E, Burke DF, Vincent AL.

J Virol. 2014 May;88(9):4752-63. doi: 10.1128/JVI.03805-13. Epub 2014 Feb 12.

14.

Substitutions near the receptor binding site determine major antigenic change during influenza virus evolution.

Koel BF, Burke DF, Bestebroer TM, van der Vliet S, Zondag GC, Vervaet G, Skepner E, Lewis NS, Spronken MI, Russell CA, Eropkin MY, Hurt AC, Barr IG, de Jong JC, Rimmelzwaan GF, Osterhaus AD, Fouchier RA, Smith DJ.

Science. 2013 Nov 22;342(6161):976-9. doi: 10.1126/science.1244730.

15.

Quantifying the fitness advantage of polymerase substitutions in Influenza A/H7N9 viruses during adaptation to humans.

Fonville JM, Burke DF, Lewis NS, Katzelnick LC, Russell CA.

PLoS One. 2013 Sep 27;8(9):e76047. doi: 10.1371/journal.pone.0076047. eCollection 2013.

16.

Limited airborne transmission of H7N9 influenza A virus between ferrets.

Richard M, Schrauwen EJ, de Graaf M, Bestebroer TM, Spronken MI, van Boheemen S, de Meulder D, Lexmond P, Linster M, Herfst S, Smith DJ, van den Brand JM, Burke DF, Kuiken T, Rimmelzwaan GF, Osterhaus AD, Fouchier RA.

Nature. 2013 Sep 26;501(7468):560-3. doi: 10.1038/nature12476. Epub 2013 Aug 7.

17.

The potential for respiratory droplet-transmissible A/H5N1 influenza virus to evolve in a mammalian host.

Russell CA, Fonville JM, Brown AE, Burke DF, Smith DL, James SL, Herfst S, van Boheemen S, Linster M, Schrauwen EJ, Katzelnick L, Mosterín A, Kuiken T, Maher E, Neumann G, Osterhaus AD, Kawaoka Y, Fouchier RA, Smith DJ.

Science. 2012 Jun 22;336(6088):1541-7. doi: 10.1126/science.1222526.

18.

Airborne transmission of influenza A/H5N1 virus between ferrets.

Herfst S, Schrauwen EJ, Linster M, Chutinimitkul S, de Wit E, Munster VJ, Sorrell EM, Bestebroer TM, Burke DF, Smith DJ, Rimmelzwaan GF, Osterhaus AD, Fouchier RA.

Science. 2012 Jun 22;336(6088):1534-41. doi: 10.1126/science.1213362.

19.

A review of influenza haemagglutinin receptor binding as it relates to pandemic properties.

Wilks S, de Graaf M, Smith DJ, Burke DF.

Vaccine. 2012 Jun 19;30(29):4369-76. doi: 10.1016/j.vaccine.2012.02.076. Review.

20.

Discordant antigenic drift of neuraminidase and hemagglutinin in H1N1 and H3N2 influenza viruses.

Sandbulte MR, Westgeest KB, Gao J, Xu X, Klimov AI, Russell CA, Burke DF, Smith DJ, Fouchier RA, Eichelberger MC.

Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):20748-53. doi: 10.1073/pnas.1113801108. Epub 2011 Dec 5.

21.

Antigenic and genetic evolution of equine influenza A (H3N8) virus from 1968 to 2007.

Lewis NS, Daly JM, Russell CA, Horton DL, Skepner E, Bryant NA, Burke DF, Rash AS, Wood JL, Chambers TM, Fouchier RA, Mumford JA, Elton DM, Smith DJ.

J Virol. 2011 Dec;85(23):12742-9. doi: 10.1128/JVI.05319-11. Epub 2011 Sep 21.

22.

Virulence-associated substitution D222G in the hemagglutinin of 2009 pandemic influenza A(H1N1) virus affects receptor binding.

Chutinimitkul S, Herfst S, Steel J, Lowen AC, Ye J, van Riel D, Schrauwen EJ, Bestebroer TM, Koel B, Burke DF, Sutherland-Cash KH, Whittleston CS, Russell CA, Wales DJ, Smith DJ, Jonges M, Meijer A, Koopmans M, Rimmelzwaan GF, Kuiken T, Osterhaus AD, García-Sastre A, Perez DR, Fouchier RA.

J Virol. 2010 Nov;84(22):11802-13. doi: 10.1128/JVI.01136-10. Epub 2010 Sep 15.

23.

Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans.

Garten RJ, Davis CT, Russell CA, Shu B, Lindstrom S, Balish A, Sessions WM, Xu X, Skepner E, Deyde V, Okomo-Adhiambo M, Gubareva L, Barnes J, Smith CB, Emery SL, Hillman MJ, Rivailler P, Smagala J, de Graaf M, Burke DF, Fouchier RA, Pappas C, Alpuche-Aranda CM, López-Gatell H, Olivera H, López I, Myers CA, Faix D, Blair PJ, Yu C, Keene KM, Dotson PD Jr, Boxrud D, Sambol AR, Abid SH, St George K, Bannerman T, Moore AL, Stringer DJ, Blevins P, Demmler-Harrison GJ, Ginsberg M, Kriner P, Waterman S, Smole S, Guevara HF, Belongia EA, Clark PA, Beatrice ST, Donis R, Katz J, Finelli L, Bridges CB, Shaw M, Jernigan DB, Uyeki TM, Smith DJ, Klimov AI, Cox NJ.

Science. 2009 Jul 10;325(5937):197-201. doi: 10.1126/science.1176225. Epub 2009 May 22.

24.

Comparative modelling by restraint-based conformational sampling.

Furnham N, de Bakker PI, Gore S, Burke DF, Blundell TL.

BMC Struct Biol. 2008 Jan 31;8:7. doi: 10.1186/1472-6807-8-7.

25.

A structural bioinformatics approach to the analysis of nonsynonymous single nucleotide polymorphisms (nsSNPs) and their relation to disease.

Worth CL, Bickerton GR, Schreyer A, Forman JR, Cheng TM, Lee S, Gong S, Burke DF, Blundell TL.

J Bioinform Comput Biol. 2007 Dec;5(6):1297-318.

PMID:
18172930
26.

Structure of a glycosylphosphatidylinositol-anchored domain from a trypanosome variant surface glycoprotein.

Jones NG, Nietlispach D, Sharma R, Burke DF, Eyres I, Mues M, Mott HR, Carrington M.

J Biol Chem. 2008 Feb 8;283(6):3584-93. Epub 2007 Nov 14.

27.

The stability and aggregation of ovine prion protein associated with classical and atypical scrapie correlates with the ease of unwinding of helix-2.

Fitzmaurice TJ, Burke DF, Hopkins L, Yang S, Yu S, Sy MS, Thackray AM, Bujdoso R.

Biochem J. 2008 Jan 15;409(2):367-75.

PMID:
17931166
28.

Genome bioinformatic analysis of nonsynonymous SNPs.

Burke DF, Worth CL, Priego EM, Cheng T, Smink LJ, Todd JA, Blundell TL.

BMC Bioinformatics. 2007 Aug 20;8:301.

29.

Andante: reducing side-chain rotamer search space during comparative modeling using environment-specific substitution probabilities.

Smith RE, Lovell SC, Burke DF, Montalvao RW, Blundell TL.

Bioinformatics. 2007 May 1;23(9):1099-105. Epub 2007 Mar 6.

PMID:
17341496
30.
31.

PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes.

Gore SP, Burke DF, Blundell TL.

Bioinformatics. 2005 Aug 1;21(15):3316-7. Epub 2005 Jun 2.

PMID:
15932902
32.

A novel type of deubiquitinating enzyme.

Evans PC, Smith TS, Lai MJ, Williams MG, Burke DF, Heyninck K, Kreike MM, Beyaert R, Blundell TL, Kilshaw PJ.

J Biol Chem. 2003 Jun 20;278(25):23180-6. Epub 2003 Apr 7.

34.

Sequence-structure homology recognition by iterative alignment refinement and comparative modeling.

Williams MG, Shirai H, Shi J, Nagendra HG, Mueller J, Mizuguchi K, Miguel RN, Lovell SC, Innis CA, Deane CM, Chen L, Campillo N, Burke DF, Blundell TL, de Bakker PI.

Proteins. 2001;Suppl 5:92-7.

PMID:
11835486
35.

HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families.

de Bakker PI, Bateman A, Burke DF, Miguel RN, Mizuguchi K, Shi J, Shirai H, Blundell TL.

Bioinformatics. 2001 Aug;17(8):748-9.

PMID:
11524380
36.

Improved protein loop prediction from sequence alone.

Burke DF, Deane CM.

Protein Eng. 2001 Jul;14(7):473-8.

PMID:
11522920
37.
38.

Protein-protein interactions in receptor activation and intracellular signalling.

Blundell TL, Burke DF, Chirgadze D, Dhanaraj V, Hyvönen M, Innis CA, Parisini E, Pellegrini L, Sayed M, Sibanda BL.

Biol Chem. 2000 Sep-Oct;381(9-10):955-9. Review.

PMID:
11076027
39.

Crystal structure of fibroblast growth factor receptor ectodomain bound to ligand and heparin.

Pellegrini L, Burke DF, von Delft F, Mulloy B, Blundell TL.

Nature. 2000 Oct 26;407(6807):1029-34.

PMID:
11069186
40.
41.

An iterative structure-assisted approach to sequence alignment and comparative modeling.

Burke DF, Deane CM, Nagarajaram HA, Campillo N, Martin-Martinez M, Mendes J, Molina F, Perry J, Reddy BV, Soares CM, Steward RE, Williams M, Carrondo MA, Blundell TL, Mizuguchi K.

Proteins. 1999;Suppl 3:55-60.

PMID:
10526352
42.

Protein three-dimensional structural databases: domains, structurally aligned homologues and superfamilies.

Sowdhamini R, Burke DF, Deane C, Huang JF, Mizuguchi K, Nagarajaram HA, Overington JP, Srinivasan N, Steward RE, Blundell TL.

Acta Crystallogr D Biol Crystallogr. 1998 Nov 1;54(Pt 6 Pt 1):1168-77.

PMID:
10089493
43.

The role of heparin in the complex formation between fibroblast growth factor 2 and its high affinity receptor: comparative modelling and biochemical studies.

Pellegrini L, Commander P, Mulloy B, Martin-Martinez M, Blundell TL, Burke DF.

Biochem Soc Trans. 1998 Aug;26(3):545-9. No abstract available.

PMID:
9765911
44.

CAMPASS: a database of structurally aligned protein superfamilies.

Sowdhamini R, Burke DF, Huang JF, Mizuguchi K, Nagarajaram HA, Srinivasan N, Steward RE, Blundell TL.

Structure. 1998 Sep 15;6(9):1087-94. Review. No abstract available.

46.

Naloxone: a word of caution.

Burke DF, Dunwoody CJ.

Orthop Nurs. 1990 Jul-Aug;9(4):44-6.

PMID:
2168031
47.

Cerebrovascular and cerebrometabolic effects of intracarotid infused platelet-activating factor in rats.

Kochanek PM, Nemoto EM, Melick JA, Evans RW, Burke DF.

J Cereb Blood Flow Metab. 1988 Aug;8(4):546-51.

PMID:
3392115

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