Trevor B. Bedford, Ph.D. - Publications

Affiliations: 
Harvard University, Cambridge, MA, United States 
Area:
evolutionary biology, molecular genetics

35 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Harvey WT, Benton DJ, Gregory V, Hall JP, Daniels RS, Bedford T, Haydon DT, Hay AJ, McCauley JW, Reeve R. Identification of Low- and High-Impact Hemagglutinin Amino Acid Substitutions That Drive Antigenic Drift of Influenza A(H1N1) Viruses. Plos Pathogens. 12: e1005526. PMID 27057693 DOI: 10.1371/Journal.Ppat.1005526  0.8
2016 Neher RA, Bedford T, Daniels RS, Russell CA, Shraiman BI. Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses. Proceedings of the National Academy of Sciences of the United States of America. PMID 26951657 DOI: 10.1073/Pnas.1525578113  0.8
2016 Karcher MD, Palacios JA, Bedford T, Suchard MA, Minin VN. Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference. Plos Computational Biology. 12: e1004789. PMID 26938243 DOI: 10.1371/Journal.Pcbi.1004789  0.8
2016 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, et al. Persistent HIV-1 replication maintains the tissue reservoir during therapy. Nature. PMID 26814962 DOI: 10.1038/Nature16933  0.8
2015 Cybis GB, Sinsheimer JS, Bedford T, Mather AE, Lemey P, Suchard MA. ASSESSING PHENOTYPIC CORRELATION THROUGH THE MULTIVARIATE PHYLOGENETIC LATENT LIABILITY MODEL. The Annals of Applied Statistics. 9: 969-991. PMID 27053974 DOI: 10.1214/15-Aoas821  0.8
2015 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, et al. Genetic Diversity and Protective Efficacy of the RTS,S/AS01 Malaria Vaccine. The New England Journal of Medicine. PMID 26488565 DOI: 10.1056/Nejmoa1505819  0.4
2015 Machkovech HM, Bedford T, Suchard MA, Bloom JD. Positive Selection in CD8+ T-Cell Epitopes of Influenza Virus Nucleoprotein Revealed by a Comparative Analysis of Human and Swine Viral Lineages. Journal of Virology. 89: 11275-83. PMID 26311880 DOI: 10.1128/Jvi.01571-15  0.8
2015 McCoy CO, Bedford T, Minin VN, Bradley P, Robins H, Matsen FA. Quantifying evolutionary constraints on B-cell affinity maturation. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370. PMID 26194758 DOI: 10.1098/Rstb.2014.0244  0.8
2015 Neher RA, Bedford T. nextflu: real-time tracking of seasonal influenza virus evolution in humans. Bioinformatics (Oxford, England). PMID 26115986 DOI: 10.1093/Bioinformatics/Btv381  0.8
2015 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, ... ... Bedford T, et al. Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone. Cell. 161: 1516-26. PMID 26091036 DOI: 10.1016/J.Cell.2015.06.007  0.8
2015 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, et al. Global circulation patterns of seasonal influenza viruses vary with antigenic drift. Nature. 523: 217-20. PMID 26053121 DOI: 10.1038/Nature14460  0.8
2015 Frost SD, Pybus OG, Gog JR, Viboud C, Bonhoeffer S, Bedford T. Eight challenges in phylodynamic inference. Epidemics. 10: 88-92. PMID 25843391 DOI: 10.1016/J.Epidem.2014.09.001  0.8
2015 Vrancken B, Lemey P, Rambaut A, Bedford T, Longdon B, Günthard HF, Suchard MA. Simultaneously estimating evolutionary history and repeated traits phylogenetic signal: Applications to viral and host phenotypic evolution Methods in Ecology and Evolution. 6: 67-82. DOI: 10.1111/2041-210X.12293  0.8
2015 Dudas G, Bedford T, Lycett S, Rambaut A. Reassortment between Influenza B Lineages and the Emergence of a Coadapted PB1-PB2-HA Gene Complex Molecular Biology and Evolution. 32: 162-172. DOI: 10.1093/molbev/msu287  0.8
2014 Zinder D, Bedford T, Baskerville EB, Woods RJ, Roy M, Pascual M. Seasonality in the migration and establishment of H3N2 Influenza lineages with epidemic growth and decline. Bmc Evolutionary Biology. 14: 272. PMID 25539729 DOI: 10.1186/S12862-014-0272-2  0.8
2014 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. HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations. Science (New York, N.Y.). 346: 56-61. PMID 25278604 DOI: 10.1126/Science.1256739  0.8
2014 Roche B, Drake JM, Brown J, Stallknecht DE, Bedford T, Rohani P. Adaptive evolution and environmental durability jointly structure phylodynamic patterns in avian influenza viruses. Plos Biology. 12: e1001931. PMID 25116957 DOI: 10.1371/Journal.Pbio.1001931  0.8
2014 Lemey P, Rambaut A, Bedford T, Faria N, Bielejec F, Baele G, Russell CA, Smith DJ, Pybus OG, Brockmann D, Suchard MA. Unifying viral genetics and human transportation data to predict the global transmission dynamics of human influenza H3N2. Plos Pathogens. 10: e1003932. PMID 24586153 DOI: 10.1371/Journal.Ppat.1003932  0.8
2014 Bedford T, Suchard MA, Lemey P, Dudas G, Gregory V, Hay AJ, McCauley JW, Russell CA, Smith DJ, Rambaut A. Integrating influenza antigenic dynamics with molecular evolution. Elife. 3: e01914. PMID 24497547 DOI: 10.7554/Elife.01914  0.8
2014 Landis MJ, Bedford T. Phylowood: interactive web-based animations of biogeographic and phylogeographic histories. Bioinformatics (Oxford, England). 30: 123-4. PMID 24191071 DOI: 10.1093/Bioinformatics/Btt635  0.8
2013 Volz EM, Koelle K, Bedford T. Viral phylodynamics. Plos Computational Biology. 9: e1002947. PMID 23555203 DOI: 10.1371/journal.pcbi.1002947  0.8
2013 Zinder D, Bedford T, Gupta S, Pascual M. The roles of competition and mutation in shaping antigenic and genetic diversity in influenza. Plos Pathogens. 9: e1003104. PMID 23300455 DOI: 10.1371/Journal.Ppat.1003104  0.8
2012 Bedford T, Rambaut A, Pascual M. Canalization of the evolutionary trajectory of the human influenza virus. Bmc Biology. 10: 38. PMID 22546494 DOI: 10.1186/1741-7007-10-38  0.8
2012 Baele G, Lemey P, Bedford T, Rambaut A, Suchard MA, Alekseyenko AV. Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. Molecular Biology and Evolution. 29: 2157-67. PMID 22403239 DOI: 10.1093/Molbev/Mss084  0.8
2011 Baskerville EB, Dobson AP, Bedford T, Allesina S, Anderson TM, Pascual M. Spatial guilds in the Serengeti food web revealed by a Bayesian group model. Plos Computational Biology. 7: e1002321. PMID 22219719 DOI: 10.1371/Journal.Pcbi.1002321  0.8
2011 Bedford T, Cobey S, Pascual M. Strength and tempo of selection revealed in viral gene genealogies. Bmc Evolutionary Biology. 11: 220. PMID 21787390 DOI: 10.1186/1471-2148-11-220  0.8
2010 Rogers RL, Bedford T, Lyons AM, Hartl DL. Adaptive impact of the chimeric gene Quetzalcoatl in Drosophila melanogaster. Proceedings of the National Academy of Sciences of the United States of America. 107: 10943-8. PMID 20534482 DOI: 10.1073/Pnas.1006503107  0.8
2010 Bedford T, Cobey S, Beerli P, Pascual M. Global migration dynamics underlie evolution and persistence of human influenza A (H3N2). Plos Pathogens. 6: e1000918. PMID 20523898 DOI: 10.1371/Journal.Ppat.1000918  0.8
2009 Bedford T, Hartl DL. Optimization of gene expression by natural selection. Proceedings of the National Academy of Sciences of the United States of America. 106: 1133-8. PMID 19139403 DOI: 10.1073/Pnas.0812009106  0.8
2009 Rogers RL, Bedford T, Hartl DL. Formation and longevity of chimeric and duplicate genes in Drosophila melanogaster. Genetics. 181: 313-22. PMID 19015547 DOI: 10.1534/Genetics.108.091538  0.8
2008 Bedford T, Wapinski I, Hartl DL. Overdispersion of the molecular clock varies between yeast, Drosophila and mammals. Genetics. 179: 977-84. PMID 18505862 DOI: 10.1534/Genetics.108.089185  0.8
2008 Bedford T, Hartl DL. Overdispersion of the molecular clock: temporal variation of gene-specific substitution rates in Drosophila. Molecular Biology and Evolution. 25: 1631-8. PMID 18480070 DOI: 10.1093/Molbev/Msn112  0.8
2007 Volkman SK, Lozovsky E, Barry AE, Bedford T, Bethke L, Myrick A, Day KP, Hartl DL, Wirth DF, Sawyer SA. Genomic heterogeneity in the density of noncoding single-nucleotide and microsatellite polymorphisms in Plasmodium falciparum. Gene. 387: 1-6. PMID 17005334 DOI: 10.1016/J.Gene.2006.07.026  0.8
2004 Castillo-Davis CI, Bedford TB, Hartl DL. Accelerated rates of intron gain/loss and protein evolution in duplicate genes in human and mouse malaria parasites. Molecular Biology and Evolution. 21: 1422-7. PMID 15084679 DOI: 10.1093/Molbev/Msh143  0.8
2003 Nielsen KM, Kasper J, Choi M, Bedford T, Kristiansen K, Wirth DF, Volkman SK, Lozovsky ER, Hartl DL. Gene conversion as a source of nucleotide diversity in Plasmodium falciparum. Molecular Biology and Evolution. 20: 726-34. PMID 12679555 DOI: 10.1093/Molbev/Msg076  0.8
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