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Items: 1 to 50 of 129

1.

Estimating Vaccine-Driven Selection in Seasonal Influenza.

Wen FT, Bell SM, Bedford T, Cobey S.

Viruses. 2018 Sep 18;10(9). pii: E509. doi: 10.3390/v10090509.

2.

Real-time analysis and visualization of pathogen sequence data.

Neher RA, Bedford T.

J Clin Microbiol. 2018 Aug 22. pii: JCM.00480-18. doi: 10.1128/JCM.00480-18. [Epub ahead of print] Review.

PMID:
30135232
3.

Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants.

Lee JM, Huddleston J, Doud MB, Hooper KA, Wu NC, Bedford T, Bloom JD.

Proc Natl Acad Sci U S A. 2018 Aug 28;115(35):E8276-E8285. doi: 10.1073/pnas.1806133115. Epub 2018 Aug 13.

4.

Sequential Refined Partitioning for Probabilistic Dependence Assessment.

Werner C, Bedford T, Quigley J.

Risk Anal. 2018 Aug 8. doi: 10.1111/risa.13162. [Epub ahead of print]

PMID:
30089193
5.

Urinary Bladder Matrix Reinforcement for Laparoscopic Hiatal Hernia Repair.

Zografakis J, Johnston G, Haas J, Berbiglia L, Bedford T, Spear J, Dan A, Pozsgay M.

JSLS. 2018 Apr-Jun;22(2). pii: e2017.00060. doi: 10.4293/JSLS.2017.00060.

6.

Nextstrain: real-time tracking of pathogen evolution.

Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C, Sagulenko P, Bedford T, Neher RA.

Bioinformatics. 2018 May 22. doi: 10.1093/bioinformatics/bty407. [Epub ahead of print]

PMID:
29790939
7.

A marker of biological ageing predicts adult risk preference in European starlings, Sturnus vulgaris.

Andrews C, Nettle D, Reichert S, Bedford T, Monaghan P, Bateson M.

Behav Ecol. 2018 May-Jun;29(3):589-597. doi: 10.1093/beheco/ary009. Epub 2018 Feb 24.

8.

Correction: MERS-CoV spillover at the camel-human interface.

Dudas G, Carvalho LM, Rambaut A, Bedford T.

Elife. 2018 Apr 19;7. pii: e37324. doi: 10.7554/eLife.37324. No abstract available.

9.

Within-Host Evolution of Human Influenza Virus.

Xue KS, Moncla LH, Bedford T, Bloom JD.

Trends Microbiol. 2018 Sep;26(9):781-793. doi: 10.1016/j.tim.2018.02.007. Epub 2018 Mar 10. Review.

PMID:
29534854
10.

MERS-CoV spillover at the camel-human interface.

Dudas G, Carvalho LM, Rambaut A, Bedford T.

Elife. 2018 Jan 16;7. pii: e31257. doi: 10.7554/eLife.31257. Erratum in: Elife. 2018 Apr 19;7:.

11.

Genome-wide evolutionary dynamics of influenza B viruses on a global scale.

Langat P, Raghwani J, Dudas G, Bowden TA, Edwards S, Gall A, Bedford T, Rambaut A, Daniels RS, Russell CA, Pybus OG, McCauley J, Kellam P, Watson SJ.

PLoS Pathog. 2017 Dec 28;13(12):e1006749. doi: 10.1371/journal.ppat.1006749. eCollection 2017 Dec.

12.

Massive Iatrogenic Outbreak of Human Immunodeficiency Virus Type 1 in Rural Cambodia, 2014-2015.

Rouet F, Nouhin J, Zheng DP, Roche B, Black A, Prak S, Leoz M, Gaudy-Graffin C, Ferradini L, Mom C, Mam S, Gautier C, Lesage G, Ken S, Phon K, Kerleguer A, Yang C, Killam W, Fujita M, Mean C, Fontenille D, Barin F, Plantier JC, Bedford T, Ramos A, Saphonn V.

Clin Infect Dis. 2018 May 17;66(11):1733-1741. doi: 10.1093/cid/cix1071.

13.

Lorenzo-Redondo et al. reply.

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

Nature. 2017 Nov 22;551(7681):E10. doi: 10.1038/nature24635. No abstract available.

PMID:
29168807
14.

Predictive Modeling of Influenza Shows the Promise of Applied Evolutionary Biology.

Morris DH, Gostic KM, Pompei S, Bedford T, Łuksza M, Neher RA, Grenfell BT, Lässig M, McCauley JW.

Trends Microbiol. 2018 Feb;26(2):102-118. doi: 10.1016/j.tim.2017.09.004. Epub 2017 Oct 30. Review.

PMID:
29097090
15.

A marker of biological age explains individual variation in the strength of the adult stress response.

Andrews C, Nettle D, Larriva M, Gillespie R, Reichert S, Brilot BO, Bedford T, Monaghan P, Spencer KA, Bateson M.

R Soc Open Sci. 2017 Sep 27;4(9):171208. doi: 10.1098/rsos.171208. eCollection 2017 Sep.

16.

Modern-day SIV viral diversity generated by extensive recombination and cross-species transmission.

Bell SM, Bedford T.

PLoS Pathog. 2017 Jul 3;13(7):e1006466. doi: 10.1371/journal.ppat.1006466. eCollection 2017 Jul.

17.

Effects of early life adversity and sex on dominance in European starlings.

Bedford T, Oliver CJ, Andrews C, Bateson M, Nettle D.

Anim Behav. 2017 Jun;128:51-60. doi: 10.1016/j.anbehav.2017.03.026.

18.

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples.

Quick J, Grubaugh ND, Pullan ST, Claro IM, Smith AD, Gangavarapu K, Oliveira G, Robles-Sikisaka R, Rogers TF, Beutler NA, Burton DR, Lewis-Ximenez LL, de Jesus JG, Giovanetti M, Hill SC, Black A, Bedford T, Carroll MW, Nunes M, Alcantara LC Jr, Sabino EC, Baylis SA, Faria NR, Loose M, Simpson JT, Pybus OG, Andersen KG, Loman NJ.

Nat Protoc. 2017 Jun;12(6):1261-1276. doi: 10.1038/nprot.2017.066. Epub 2017 May 24.

19.

Establishment and cryptic transmission of Zika virus in Brazil and the Americas.

Faria NR, Quick J, Claro IM, Thézé J, de Jesus JG, Giovanetti M, Kraemer MUG, Hill SC, Black A, da Costa AC, Franco LC, Silva SP, Wu CH, Raghwani J, Cauchemez S, du Plessis L, Verotti MP, de Oliveira WK, Carmo EH, Coelho GE, Santelli ACFS, Vinhal LC, Henriques CM, Simpson JT, Loose M, Andersen KG, Grubaugh ND, Somasekar S, Chiu CY, Muñoz-Medina JE, Gonzalez-Bonilla CR, Arias CF, Lewis-Ximenez LL, Baylis SA, Chieppe AO, Aguiar SF, Fernandes CA, Lemos PS, Nascimento BLS, Monteiro HAO, Siqueira IC, de Queiroz MG, de Souza TR, Bezerra JF, Lemos MR, Pereira GF, Loudal D, Moura LC, Dhalia R, França RF, Magalhães T, Marques ET Jr, Jaenisch T, Wallau GL, de Lima MC, Nascimento V, de Cerqueira EM, de Lima MM, Mascarenhas DL, Neto JPM, Levin AS, Tozetto-Mendoza TR, Fonseca SN, Mendes-Correa MC, Milagres FP, Segurado A, Holmes EC, Rambaut A, Bedford T, Nunes MRT, Sabino EC, Alcantara LCJ, Loman NJ, Pybus OG.

Nature. 2017 Jun 15;546(7658):406-410. doi: 10.1038/nature22401. Epub 2017 May 24.

20.

Genomic epidemiology reveals multiple introductions of Zika virus into the United States.

Grubaugh ND, Ladner JT, Kraemer MUG, Dudas G, Tan AL, Gangavarapu K, Wiley MR, White S, Thézé J, Magnani DM, Prieto K, Reyes D, Bingham AM, Paul LM, Robles-Sikisaka R, Oliveira G, Pronty D, Barcellona CM, Metsky HC, Baniecki ML, Barnes KG, Chak B, Freije CA, Gladden-Young A, Gnirke A, Luo C, MacInnis B, Matranga CB, Park DJ, Qu J, Schaffner SF, Tomkins-Tinch C, West KL, Winnicki SM, Wohl S, Yozwiak NL, Quick J, Fauver JR, Khan K, Brent SE, Reiner RC Jr, Lichtenberger PN, Ricciardi MJ, Bailey VK, Watkins DI, Cone MR, Kopp EW 4th, Hogan KN, Cannons AC, Jean R, Monaghan AJ, Garry RF, Loman NJ, Faria NR, Porcelli MC, Vasquez C, Nagle ER, Cummings DAT, Stanek D, Rambaut A, Sanchez-Lockhart M, Sabeti PC, Gillis LD, Michael SF, Bedford T, Pybus OG, Isern S, Palacios G, Andersen KG.

Nature. 2017 Jun 15;546(7658):401-405. doi: 10.1038/nature22400. Epub 2017 May 24.

21.

Virus genomes reveal factors that spread and sustained the Ebola epidemic.

Dudas G, Carvalho LM, Bedford T, Tatem AJ, Baele G, Faria NR, Park DJ, Ladner JT, Arias A, Asogun D, Bielejec F, Caddy SL, Cotten M, D'Ambrozio J, Dellicour S, Di Caro A, Diclaro JW, Duraffour S, Elmore MJ, Fakoli LS, Faye O, Gilbert ML, Gevao SM, Gire S, Gladden-Young A, Gnirke A, Goba A, Grant DS, Haagmans BL, Hiscox JA, Jah U, Kugelman JR, Liu D, Lu J, Malboeuf CM, Mate S, Matthews DA, Matranga CB, Meredith LW, Qu J, Quick J, Pas SD, Phan MVT, Pollakis G, Reusken CB, Sanchez-Lockhart M, Schaffner SF, Schieffelin JS, Sealfon RS, Simon-Loriere E, Smits SL, Stoecker K, Thorne L, Tobin EA, Vandi MA, Watson SJ, West K, Whitmer S, Wiley MR, Winnicki SM, Wohl S, Wölfel R, Yozwiak NL, Andersen KG, Blyden SO, Bolay F, Carroll MW, Dahn B, Diallo B, Formenty P, Fraser C, Gao GF, Garry RF, Goodfellow I, Günther S, Happi CT, Holmes EC, Kargbo B, Keïta S, Kellam P, Koopmans MPG, Kuhn JH, Loman NJ, Magassouba N, Naidoo D, Nichol ST, Nyenswah T, Palacios G, Pybus OG, Sabeti PC, Sall A, Ströher U, Wurie I, Suchard MA, Lemey P, Rambaut A.

Nature. 2017 Apr 20;544(7650):309-315. doi: 10.1038/nature22040. Epub 2017 Apr 12.

22.

Bayesian nonparametric clustering in phylogenetics: modeling antigenic evolution in influenza.

Cybis GB, Sinsheimer JS, Bedford T, Rambaut A, Lemey P, Suchard MA.

Stat Med. 2018 Jan 30;37(2):195-206. doi: 10.1002/sim.7196. Epub 2017 Jan 18.

23.

Early-life adversity accelerates cellular ageing and affects adult inflammation: Experimental evidence from the European starling.

Nettle D, Andrews C, Reichert S, Bedford T, Kolenda C, Parker C, Martin-Ruiz C, Monaghan P, Bateson M.

Sci Rep. 2017 Jan 17;7:40794. doi: 10.1038/srep40794.

24.

Geography and host species shape the evolutionary dynamics of U genogroup infectious hematopoietic necrosis virus.

Black A, Breyta R, Bedford T, Kurath G.

Virus Evol. 2016 Dec 26;2(2):vew034. doi: 10.1093/ve/vew034. eCollection 2016 Jul.

25.

Brood size moderates associations between relative size, telomere length, and immune development in European starling nestlings.

Nettle D, Andrews C, Reichert S, Bedford T, Gott A, Parker C, Kolenda C, Martin-Ruiz C, Monaghan P, Bateson M.

Ecol Evol. 2016 Oct 17;6(22):8138-8148. eCollection 2016 Nov.

26.

Viral factors in influenza pandemic risk assessment.

Lipsitch M, Barclay W, Raman R, Russell CJ, Belser JA, Cobey S, Kasson PM, Lloyd-Smith JO, Maurer-Stroh S, Riley S, Beauchemin CA, Bedford T, Friedrich TC, Handel A, Herfst S, Murcia PR, Roche B, Wilke CO, Russell CA.

Elife. 2016 Nov 11;5. pii: e18491. doi: 10.7554/eLife.18491.

27.

Did a Single Amino Acid Change Make Ebola Virus More Virulent?

Bedford T, Malik HS.

Cell. 2016 Nov 3;167(4):892-894. doi: 10.1016/j.cell.2016.10.032.

28.

Explaining the geographical origins of seasonal influenza A (H3N2).

Wen F, Bedford T, Cobey S.

Proc Biol Sci. 2016 Sep 14;283(1838). pii: 20161312. doi: 10.1098/rspb.2016.1312.

29.

Identification of Low- and High-Impact Hemagglutinin Amino Acid Substitutions That Drive Antigenic Drift of Influenza A(H1N1) Viruses.

Harvey WT, Benton DJ, Gregory V, Hall JP, Daniels RS, Bedford T, Haydon DT, Hay AJ, McCauley JW, Reeve R.

PLoS Pathog. 2016 Apr 8;12(4):e1005526. doi: 10.1371/journal.ppat.1005526. eCollection 2016 Apr.

30.

ASSESSING PHENOTYPIC CORRELATION THROUGH THE MULTIVARIATE PHYLOGENETIC LATENT LIABILITY MODEL.

Cybis GB, Sinsheimer JS, Bedford T, Mather AE, Lemey P, Suchard MA.

Ann Appl Stat. 2015 Jun;9(2):969-991.

31.

Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses.

Neher RA, Bedford T, Daniels RS, Russell CA, Shraiman BI.

Proc Natl Acad Sci U S A. 2016 Mar 22;113(12):E1701-9. doi: 10.1073/pnas.1525578113. Epub 2016 Mar 7.

32.

Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference.

Karcher MD, Palacios JA, Bedford T, Suchard MA, Minin VN.

PLoS Comput Biol. 2016 Mar 3;12(3):e1004789. doi: 10.1371/journal.pcbi.1004789. eCollection 2016 Mar.

33.

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

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

Nature. 2016 Feb 4;530(7588):51-56. doi: 10.1038/nature16933. Epub 2016 Jan 27.

34.

Time dependence of evolutionary metrics during the 2009 pandemic influenza virus outbreak.

Meyer AG, Spielman SJ, Bedford T, Wilke CO.

Virus Evol. 2015 Jan;1(1). pii: vev006. Epub 2015 Jan 1.

35.

Early life adversity increases foraging and information gathering in European starlings, Sturnus vulgaris.

Andrews C, Viviani J, Egan E, Bedford T, Brilot B, Nettle D, Bateson M.

Anim Behav. 2015 Nov;109:123-132.

36.

Genetic Diversity and Protective Efficacy of the RTS,S/AS01 Malaria Vaccine.

Neafsey DE, Juraska M, Bedford T, Benkeser D, Valim C, Griggs A, Lievens M, Abdulla S, Adjei S, Agbenyega T, Agnandji ST, Aide P, Anderson S, Ansong D, Aponte JJ, Asante KP, Bejon P, Birkett AJ, Bruls M, Connolly KM, D'Alessandro U, Dobaño C, Gesase S, Greenwood B, Grimsby J, Tinto H, Hamel MJ, Hoffman I, Kamthunzi P, Kariuki S, Kremsner PG, Leach A, Lell B, Lennon NJ, Lusingu J, Marsh K, Martinson F, Molel JT, Moss EL, Njuguna P, Ockenhouse CF, Ogutu BR, Otieno W, Otieno L, Otieno K, Owusu-Agyei S, Park DJ, Pellé K, Robbins D, Russ C, Ryan EM, Sacarlal J, Sogoloff B, Sorgho H, Tanner M, Theander T, Valea I, Volkman SK, Yu Q, Lapierre D, Birren BW, Gilbert PB, Wirth DF.

N Engl J Med. 2015 Nov 19;373(21):2025-2037. doi: 10.1056/NEJMoa1505819. Epub 2015 Oct 21.

37.

Developmental and familial predictors of adult cognitive traits in the European starling.

Nettle D, Andrews CP, Monaghan P, Brilot BO, Bedford T, Gillespie R, Bateson M.

Anim Behav. 2015 Sep;107:239-248.

38.

Approximate Uncertainty Modeling in Risk Analysis with Vine Copulas.

Bedford T, Daneshkhah A, Wilson KJ.

Risk Anal. 2016 Apr;36(4):792-815. doi: 10.1111/risa.12471. Epub 2015 Sep 2.

39.

Positive Selection in CD8+ T-Cell Epitopes of Influenza Virus Nucleoprotein Revealed by a Comparative Analysis of Human and Swine Viral Lineages.

Machkovech HM, Bedford T, Suchard MA, Bloom JD.

J Virol. 2015 Nov;89(22):11275-83. doi: 10.1128/JVI.01571-15. Epub 2015 Aug 26.

40.

Quantifying evolutionary constraints on B-cell affinity maturation.

McCoy CO, Bedford T, Minin VN, Bradley P, Robins H, Matsen FA 4th.

Philos Trans R Soc Lond B Biol Sci. 2015 Sep 5;370(1676). pii: 20140244. doi: 10.1098/rstb.2014.0244.

41.

nextflu: real-time tracking of seasonal influenza virus evolution in humans.

Neher RA, Bedford T.

Bioinformatics. 2015 Nov 1;31(21):3546-8. doi: 10.1093/bioinformatics/btv381. Epub 2015 Jun 26.

42.

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.

43.

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.

44.

Early life disadvantage strengthens flight performance trade-offs in European starlings, Sturnus vulgaris.

O'Hagan D, Andrews CP, Bedford T, Bateson M, Nettle D.

Anim Behav. 2015 Apr;102:141-148.

45.

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.

46.

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.

47.

Seasonality in the migration and establishment of H3N2 Influenza lineages with epidemic growth and decline.

Zinder D, Bedford T, Baskerville EB, Woods RJ, Roy M, Pascual M.

BMC Evol Biol. 2014 Dec 24;14:272. doi: 10.1186/s12862-014-0272-2.

48.

An experimental demonstration that early-life competitive disadvantage accelerates telomere loss.

Nettle D, Monaghan P, Gillespie R, Brilot B, Bedford T, Bateson M.

Proc Biol Sci. 2015 Jan 7;282(1798):20141610. doi: 10.1098/rspb.2014.1610.

49.

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.

50.

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.

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