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Items: 1 to 50 of 72

1.

Using Parsimony-Guided Tree Proposals to Accelerate Convergence in Bayesian Phylogenetic Inference.

Zhang C, Huelsenbeck JP, Ronquist F.

Syst Biol. 2020 Jan 27. pii: syaa002. doi: 10.1093/sysbio/syaa002. [Epub ahead of print]

PMID:
31985810
2.

BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics.

Ayres DL, Cummings MP, Baele G, Darling AE, Lewis PO, Swofford DL, Huelsenbeck JP, Lemey P, Rambaut A, Suchard MA.

Syst Biol. 2019 Nov 1;68(6):1052-1061. doi: 10.1093/sysbio/syz020.

3.

Reply to Nakov et al.: Model choice requires biological insight when studying the ancestral habitat of photosynthetic eukaryotes.

Sánchez-Baracaldo P, Bianchini G, Huelsenbeck JP, Raven JA, Pisani D, Knoll AH.

Proc Natl Acad Sci U S A. 2017 Dec 12;114(50):E10608-E10609. doi: 10.1073/pnas.1717417114. Epub 2017 Dec 5. No abstract available.

4.

Critically evaluating the theory and performance of Bayesian analysis of macroevolutionary mixtures.

Moore BR, Höhna S, May MR, Rannala B, Huelsenbeck JP.

Proc Natl Acad Sci U S A. 2016 Aug 23;113(34):9569-74. doi: 10.1073/pnas.1518659113. Epub 2016 Aug 10.

5.

RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language.

Höhna S, Landis MJ, Heath TA, Boussau B, Lartillot N, Moore BR, Huelsenbeck JP, Ronquist F.

Syst Biol. 2016 Jul;65(4):726-36. doi: 10.1093/sysbio/syw021. Epub 2016 May 28.

6.

Strepsiptera, phylogenomics and the long branch attraction problem.

Boussau B, Walton Z, Delgado JA, Collantes F, Beani L, Stewart IJ, Cameron SA, Whitfield JB, Johnston JS, Holland PW, Bachtrog D, Kathirithamby J, Huelsenbeck JP.

PLoS One. 2014 Oct 1;9(10):e107709. doi: 10.1371/journal.pone.0107709. eCollection 2014.

7.

The fossilized birth-death process for coherent calibration of divergence-time estimates.

Heath TA, Huelsenbeck JP, Stadler T.

Proc Natl Acad Sci U S A. 2014 Jul 22;111(29):E2957-66. doi: 10.1073/pnas.1319091111. Epub 2014 Jul 9.

8.

Probabilistic graphical model representation in phylogenetics.

Höhna S, Heath TA, Boussau B, Landis MJ, Ronquist F, Huelsenbeck JP.

Syst Biol. 2014 Sep;63(5):753-71. doi: 10.1093/sysbio/syu039. Epub 2014 Jun 20.

9.

A phylogenetic model for the detection of epistatic interactions.

Nasrallah CA, Huelsenbeck JP.

Mol Biol Evol. 2013 Sep;30(9):2197-208. doi: 10.1093/molbev/mst108. Epub 2013 Jun 6.

10.

Bayesian analysis of biogeography when the number of areas is large.

Landis MJ, Matzke NJ, Moore BR, Huelsenbeck JP.

Syst Biol. 2013 Nov;62(6):789-804. doi: 10.1093/sysbio/syt040. Epub 2013 Jun 4.

11.

MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space.

Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP.

Syst Biol. 2012 May;61(3):539-42. doi: 10.1093/sysbio/sys029. Epub 2012 Feb 22.

12.

A dirichlet process prior for estimating lineage-specific substitution rates.

Heath TA, Holder MT, Huelsenbeck JP.

Mol Biol Evol. 2012 Mar;29(3):939-55. doi: 10.1093/molbev/msr255. Epub 2011 Nov 2.

13.

BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics.

Ayres DL, Darling A, Zwickl DJ, Beerli P, Holder MT, Lewis PO, Huelsenbeck JP, Ronquist F, Swofford DL, Cummings MP, Rambaut A, Suchard MA.

Syst Biol. 2012 Jan;61(1):170-3. doi: 10.1093/sysbio/syr100. Epub 2011 Oct 1.

14.

Structurama: bayesian inference of population structure.

Huelsenbeck JP, Andolfatto P, Huelsenbeck ET.

Evol Bioinform Online. 2011;7:55-9. doi: 10.4137/EBO.S6761. Epub 2011 Jun 2.

15.

Biologically inspired phylogenetic models strongly outperform the no common mechanism model.

Huelsenbeck JP, Alfaro ME, Suchard MA.

Syst Biol. 2011 Mar;60(2):225-32. doi: 10.1093/sysbio/syq089. Epub 2011 Jan 20.

16.

Quantifying the impact of dependent evolution among sites in phylogenetic inference.

Nasrallah CA, Mathews DH, Huelsenbeck JP.

Syst Biol. 2011 Jan;60(1):60-73. doi: 10.1093/sysbio/syq074. Epub 2010 Nov 15.

17.

Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence.

Bollback JP, Huelsenbeck JP.

Genetics. 2009 Jan;181(1):225-34. doi: 10.1534/genetics.107.085225. Epub 2008 Nov 10.

18.

Statistical assignment of DNA sequences using Bayesian phylogenetics.

Munch K, Boomsma W, Huelsenbeck JP, Willerslev E, Nielsen R.

Syst Biol. 2008 Oct;57(5):750-7. doi: 10.1080/10635150802422316.

PMID:
18853361
19.

Bayesian analysis of amino acid substitution models.

Huelsenbeck JP, Joyce P, Lakner C, Ronquist F.

Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):3941-53. doi: 10.1098/rstb.2008.0175.

20.

A Bayesian perspective on a non-parsimonious parsimony model.

Huelsenbeck JP, Ané C, Larget B, Ronquist F.

Syst Biol. 2008 Jun;57(3):406-19. doi: 10.1080/10635150802166046.

PMID:
18570035
21.

Rates and patterns in the evolution of snake-like body form in squamate reptiles: evidence for repeated re-evolution of lost digits and long-term persistence of intermediate body forms.

Brandley MC, Huelsenbeck JP, Wiens JJ.

Evolution. 2008 Aug;62(8):2042-64. doi: 10.1111/j.1558-5646.2008.00430.x. Epub 2008 May 27.

PMID:
18507743
22.

Efficiency of Markov chain Monte Carlo tree proposals in Bayesian phylogenetics.

Lakner C, van der Mark P, Huelsenbeck JP, Larget B, Ronquist F.

Syst Biol. 2008 Feb;57(1):86-103. doi: 10.1080/10635150801886156.

PMID:
18278678
23.

Alignment uncertainty and genomic analysis.

Wong KM, Suchard MA, Huelsenbeck JP.

Science. 2008 Jan 25;319(5862):473-6. doi: 10.1126/science.1151532.

24.

A nonparametric method for accommodating and testing across-site rate variation.

Huelsenbeck JP, Suchard MA.

Syst Biol. 2007 Dec;56(6):975-87.

PMID:
18075934
25.

Clonal interference is alleviated by high mutation rates in large populations.

Bollback JP, Huelsenbeck JP.

Mol Biol Evol. 2007 Jun;24(6):1397-406. Epub 2007 Mar 22.

PMID:
17379621
26.

Inference of population structure under a Dirichlet process model.

Huelsenbeck JP, Andolfatto P.

Genetics. 2007 Apr;175(4):1787-802. Epub 2007 Jan 21.

27.

Comment on "Phylogenetic MCMC algorithms are misleading on mixtures of trees".

Ronquist F, Larget B, Huelsenbeck JP, Kadane JB, Simon D, van der Mark P.

Science. 2006 Apr 21;312(5772):367; author reply 367.

28.

A Dirichlet process model for detecting positive selection in protein-coding DNA sequences.

Huelsenbeck JP, Jain S, Frost SW, Pond SL.

Proc Natl Acad Sci U S A. 2006 Apr 18;103(16):6263-8. Epub 2006 Apr 10.

29.

Comparative performance of Bayesian and AIC-based measures of phylogenetic model uncertainty.

Alfaro ME, Huelsenbeck JP.

Syst Biol. 2006 Feb;55(1):89-96.

PMID:
16507526
30.

Bayesian estimation of positively selected sites.

Huelsenbeck JP, Dyer KA.

J Mol Evol. 2004 Jun;58(6):661-72.

PMID:
15461423
31.

Bayesian inference of the metazoan phylogeny; a combined molecular and morphological approach.

Glenner H, Hansen AJ, Sørensen MV, Ronquist F, Huelsenbeck JP, Willerslev E.

Curr Biol. 2004 Sep 21;14(18):1644-9. Erratum in: Curr Biol. 2005 Feb 22;15(4):392-3.

32.

Modeling the site-specific variation of selection patterns along lineages.

Guindon S, Rodrigo AG, Dyer KA, Huelsenbeck JP.

Proc Natl Acad Sci U S A. 2004 Aug 31;101(35):12957-62. Epub 2004 Aug 23.

33.

Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo.

Huelsenbeck JP, Larget B, Alfaro ME.

Mol Biol Evol. 2004 Jun;21(6):1123-33. Epub 2004 Mar 19.

PMID:
15034130
34.

Bayesian phylogenetic analysis of combined data.

Nylander JA, Ronquist F, Huelsenbeck JP, Nieves-Aldrey JL.

Syst Biol. 2004 Feb;53(1):47-67.

PMID:
14965900
35.

Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference.

Altekar G, Dwarkadas S, Huelsenbeck JP, Ronquist F.

Bioinformatics. 2004 Feb 12;20(3):407-15. Epub 2004 Jan 22.

PMID:
14960467
36.

Frequent inconsistency of parsimony under a simple model of cladogenesis.

Huelsenbeck JP, Lander KM.

Syst Biol. 2003 Oct;52(5):641-8.

PMID:
14530131
37.

MrBayes 3: Bayesian phylogenetic inference under mixed models.

Ronquist F, Huelsenbeck JP.

Bioinformatics. 2003 Aug 12;19(12):1572-4.

PMID:
12912839
38.

Detecting correlation between characters in a comparative analysis with uncertain phylogeny.

Huelsenbeck JP, Rannala B.

Evolution. 2003 Jun;57(6):1237-47.

PMID:
12894932
39.

Stochastic mapping of morphological characters.

Huelsenbeck JP, Nielsen R, Bollback JP.

Syst Biol. 2003 Apr;52(2):131-58.

PMID:
12746144
40.

Potential applications and pitfalls of Bayesian inference of phylogeny.

Huelsenbeck JP, Larget B, Miller RE, Ronquist F.

Syst Biol. 2002 Oct;51(5):673-88. Review.

PMID:
12396583
41.

Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods.

Swofford DL, Waddell PJ, Huelsenbeck JP, Foster PG, Lewis PO, Rogers JS.

Syst Biol. 2001 Aug;50(4):525-39. No abstract available.

PMID:
12116651
42.

Empirical and hierarchical Bayesian estimation of ancestral states.

Huelsenbeck JP, Bollback JP.

Syst Biol. 2001 Jun;50(3):351-66.

PMID:
12116580
43.

Effect of nonindependent substitution on phylogenetic accuracy.

Huelsenbeck JP, Nielsen R.

Syst Biol. 1999 Jun;48(2):317-28.

PMID:
12066710
44.

Systematic bias in phylogenetic analysis: is the Strepsiptera problem solved?

Huelsenbeck JP.

Syst Biol. 1998 Sep;47(3):519-37. No abstract available.

PMID:
12066692
45.

Taxon sampling and the accuracy of large phylogenies.

Rannala B, Huelsenbeck JP, Yang Z, Nielsen R.

Syst Biol. 1998 Dec;47(4):702-10. No abstract available.

PMID:
12066312
46.

Testing a covariotide model of DNA substitution.

Huelsenbeck JP.

Mol Biol Evol. 2002 May;19(5):698-707.

PMID:
11961103
47.
48.

Inferring the root of a phylogenetic tree.

Huelsenbeck JP, Bollback JP, Levine AM.

Syst Biol. 2002 Feb;51(1):32-43.

PMID:
11943091
49.

Detecting positively selected amino acid sites using posterior predictive P-values.

Nielsen R, Huelsenbeck JP.

Pac Symp Biocomput. 2002:576-88.

50.

Bayesian inference of phylogeny and its impact on evolutionary biology.

Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP.

Science. 2001 Dec 14;294(5550):2310-4.

PMID:
11743192

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