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Results: 1 to 20 of 117

1.

Empirical calibrated radiocarbon sampler: a tool for incorporating radiocarbon-date and calibration error into Bayesian phylogenetic analyses of ancient DNA.

Molak M, Suchard MA, Ho SY, Beilman DW, Shapiro B.

Mol Ecol Resour. 2014 Jun 25. doi: 10.1111/1755-0998.12295. [Epub ahead of print]

PMID:
24964386
[PubMed - as supplied by publisher]
2.

OutbreakTools: a new platform for disease outbreak analysis using the R software.

Jombart T, Aanensen DM, Baguelin M, Birrell P, Cauchemez S, Camacho A, Colijn C, Collins C, Cori A, Didelot X, Fraser C, Frost S, Hens N, Hugues J, Höhle M, Opatowski L, Rambaut A, Ratmann O, Soubeyrand S, Suchard MA, Wallinga J, Ypma R, Ferguson N.

Epidemics. 2014 Jun;7:28-34. doi: 10.1016/j.epidem.2014.04.003. Epub 2014 Apr 18.

PMID:
24928667
[PubMed - in process]
Free PMC Article
3.

πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios.

Bielejec F, Lemey P, Carvalho LM, Baele G, Rambaut A, Suchard MA.

BMC Bioinformatics. 2014 May 7;15:133. doi: 10.1186/1471-2105-15-133.

PMID:
24885610
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Air travel is associated with intracontinental spread of dengue virus serotypes 1-3 in Brazil.

Nunes MR, Palacios G, Faria NR, Sousa EC Jr, Pantoja JA, Rodrigues SG, Carvalho VL, Medeiros DB, Savji N, Baele G, Suchard MA, Lemey P, Vasconcelos PF, Lipkin WI.

PLoS Negl Trop Dis. 2014 Apr 17;8(4):e2769. doi: 10.1371/journal.pntd.0002769. eCollection 2014 Apr.

PMID:
24743730
[PubMed - in process]
Free PMC Article
5.

BEAST 2: a software platform for Bayesian evolutionary analysis.

Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ.

PLoS Comput Biol. 2014 Apr 10;10(4):e1003537. doi: 10.1371/journal.pcbi.1003537. eCollection 2014 Apr.

PMID:
24722319
[PubMed - in process]
Free PMC Article
6.

The genealogical population dynamics of HIV-1 in a large transmission chain: bridging within and among host evolutionary rates.

Vrancken B, Rambaut A, Suchard MA, Drummond A, Baele G, Derdelinckx I, Van Wijngaerden E, Vandamme AM, Van Laethem K, Lemey P.

PLoS Comput Biol. 2014 Apr 3;10(4):e1003505. doi: 10.1371/journal.pcbi.1003505. eCollection 2014 Apr.

PMID:
24699231
[PubMed - in process]
Free PMC Article
7.

Inferring heterogeneous evolutionary processes through time: from sequence substitution to phylogeography.

Bielejec F, Lemey P, Baele G, Rambaut A, Suchard MA.

Syst Biol. 2014 Jul;63(4):493-504. doi: 10.1093/sysbio/syu015. Epub 2014 Mar 12.

PMID:
24627184
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Unifying viral genetics and human transportation data to predict the global transmission dynamics of human influenza H3N2.

Lemey P, Rambaut A, Bedford T, Faria N, Bielejec F, Baele G, Russell CA, Smith DJ, Pybus OG, Brockmann D, Suchard MA.

PLoS Pathog. 2014 Feb 20;10(2):e1003932. doi: 10.1371/journal.ppat.1003932. eCollection 2014 Feb.

PMID:
24586153
[PubMed - in process]
Free PMC Article
9.

Integrating influenza antigenic dynamics with molecular evolution.

Bedford T, Suchard MA, Lemey P, Dudas G, Gregory V, Hay AJ, McCauley JW, Russell CA, Smith DJ, Rambaut A.

Elife. 2014;3:e01914. doi: 10.7554/eLife.01914. Epub 2014 Feb 4.

PMID:
24497547
[PubMed]
Free PMC Article
10.

On the biogeography of Centipeda: a species-tree diffusion approach.

Nylinder S, Lemey P, De Bruyn M, Suchard MA, Pfeil BE, Walsh N, Anderberg AA.

Syst Biol. 2014 Mar;63(2):178-91. doi: 10.1093/sysbio/syt102. Epub 2013 Dec 12.

PMID:
24335493
[PubMed - indexed for MEDLINE]
11.

The spread of type 2 Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) in North America: a phylogeographic approach.

Shi M, Lemey P, Singh Brar M, Suchard MA, Murtaugh MP, Carman S, D'Allaire S, Delisle B, Lambert MÈ, Gagnon CA, Ge L, Qu Y, Yoo D, Holmes EC, Chi-Ching Leung F.

Virology. 2013 Dec;447(1-2):146-54. doi: 10.1016/j.virol.2013.08.028. Epub 2013 Sep 27.

PMID:
24210109
[PubMed - indexed for MEDLINE]
12.

The impact of drug and outcome prevalence on the feasibility and performance of analytical methods for a risk identification and analysis system.

Reich CG, Ryan PB, Suchard MA.

Drug Saf. 2013 Oct;36 Suppl 1:S195-204. doi: 10.1007/s40264-013-0112-0.

PMID:
24166235
[PubMed - indexed for MEDLINE]
13.

A comparison of the empirical performance of methods for a risk identification system.

Ryan PB, Stang PE, Overhage JM, Suchard MA, Hartzema AG, DuMouchel W, Reich CG, Schuemie MJ, Madigan D.

Drug Saf. 2013 Oct;36 Suppl 1:S143-58. doi: 10.1007/s40264-013-0108-9.

PMID:
24166231
[PubMed - indexed for MEDLINE]
14.

Empirical performance of the self-controlled case series design: lessons for developing a risk identification and analysis system.

Suchard MA, Zorych I, Simpson SE, Schuemie MJ, Ryan PB, Madigan D.

Drug Saf. 2013 Oct;36 Suppl 1:S83-93. doi: 10.1007/s40264-013-0100-4.

PMID:
24166226
[PubMed - indexed for MEDLINE]
15.

Multiple self-controlled case series for large-scale longitudinal observational databases.

Simpson SE, Madigan D, Zorych I, Schuemie MJ, Ryan PB, Suchard MA.

Biometrics. 2013 Dec;69(4):893-902. doi: 10.1111/biom.12078. Epub 2013 Oct 11.

PMID:
24117144
[PubMed - indexed for MEDLINE]
16.

High-dimensional, massive sample-size Cox proportional hazards regression for survival analysis.

Mittal S, Madigan D, Burd RS, Suchard MA.

Biostatistics. 2014 Apr;15(2):207-21. doi: 10.1093/biostatistics/kxt043. Epub 2013 Oct 4.

PMID:
24096388
[PubMed - in process]
17.

Discussion: An estimate of the science-wise false discovery rate and application to the top medical literature.

Schuemie MJ, Ryan PB, Suchard MA, Shahn Z, Madigan D.

Biostatistics. 2014 Jan;15(1):36-9; discussion 39-45. doi: 10.1093/biostatistics/kxt037. Epub 2013 Sep 25. No abstract available.

PMID:
24068252
[PubMed - indexed for MEDLINE]
18.

Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts.

Mather AE, Reid SW, Maskell DJ, Parkhill J, Fookes MC, Harris SR, Brown DJ, Coia JE, Mulvey MR, Gilmour MW, Petrovska L, de Pinna E, Kuroda M, Akiba M, Izumiya H, Connor TR, Suchard MA, Lemey P, Mellor DJ, Haydon DT, Thomson NR.

Science. 2013 Sep 27;341(6153):1514-7. doi: 10.1126/science.1240578. Epub 2013 Sep 12.

PMID:
24030491
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Interpreting observational studies: why empirical calibration is needed to correct p-values.

Schuemie MJ, Ryan PB, DuMouchel W, Suchard MA, Madigan D.

Stat Med. 2014 Jan 30;33(2):209-18. doi: 10.1002/sim.5925. Epub 2013 Jul 30.

PMID:
23900808
[PubMed - indexed for MEDLINE]
20.

Stability-mediated epistasis constrains the evolution of an influenza protein.

Gong LI, Suchard MA, Bloom JD.

Elife. 2013 May 14;2:e00631. doi: 10.7554/eLife.00631.

PMID:
23682315
[PubMed]
Free PMC Article

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