John P. Huelsenbeck, Ph.D. - Publications

Affiliations: 
Integrative Biology University of California, Berkeley, Berkeley, CA 
Area:
phylogenetics
Website:
https://ib.berkeley.edu/people/faculty/huelsenbeckj

99 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
2020 Zhang C, Huelsenbeck JP, Ronquist F. Using Parsimony-Guided Tree Proposals to Accelerate Convergence in Bayesian Phylogenetic Inference. Systematic Biology. PMID 31985810 DOI: 10.1093/sysbio/syaa002  0.68
2019 Ayres DL, Cummings MP, Baele G, Darling AE, Lewis PO, Swofford DL, Huelsenbeck JP, Lemey P, Rambaut A, Suchard MA. BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics. Systematic Biology. PMID 31034053 DOI: 10.1093/sysbio/syz020  0.84
2016 Moore BR, Höhna S, May MR, Rannala B, Huelsenbeck JP. Critically evaluating the theory and performance of Bayesian analysis of macroevolutionary mixtures. Proceedings of the National Academy of Sciences of the United States of America. PMID 27512038 DOI: 10.1073/pnas.1518659113  0.88
2016 Höhna S, Landis MJ, Heath TA, Boussau B, Lartillot N, Moore BR, Huelsenbeck JP, Ronquist F. RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language. Systematic Biology. PMID 27235697 DOI: 10.1093/sysbio/syw021  0.88
2014 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. Strepsiptera, phylogenomics and the long branch attraction problem. Plos One. 9: e107709. PMID 25272037 DOI: 10.1371/journal.pone.0107709  1
2014 Heath TA, Huelsenbeck JP, Stadler T. The fossilized birth-death process for coherent calibration of divergence-time estimates. Proceedings of the National Academy of Sciences of the United States of America. 111: E2957-66. PMID 25009181 DOI: 10.1073/pnas.1319091111  1
2014 Höhna S, Heath TA, Boussau B, Landis MJ, Ronquist F, Huelsenbeck JP. Probabilistic graphical model representation in phylogenetics. Systematic Biology. 63: 753-71. PMID 24951559 DOI: 10.1093/sysbio/syu039  1
2013 Nasrallah CA, Huelsenbeck JP. A phylogenetic model for the detection of epistatic interactions. Molecular Biology and Evolution. 30: 2197-208. PMID 23748181 DOI: 10.1093/molbev/mst108  1
2013 Landis MJ, Matzke NJ, Moore BR, Huelsenbeck JP. Bayesian analysis of biogeography when the number of areas is large. Systematic Biology. 62: 789-804. PMID 23736102 DOI: 10.1093/sysbio/syt040  1
2012 Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology. 61: 539-42. PMID 22357727 DOI: 10.1093/sysbio/sys029  1
2012 Heath TA, Holder MT, Huelsenbeck JP. A dirichlet process prior for estimating lineage-specific substitution rates. Molecular Biology and Evolution. 29: 939-55. PMID 22049064 DOI: 10.1093/molbev/msr255  1
2012 Ayres DL, Darling A, Zwickl DJ, Beerli P, Holder MT, Lewis PO, Huelsenbeck JP, Ronquist F, Swofford DL, Cummings MP, Rambaut A, Suchard MA. BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics. Systematic Biology. 61: 170-3. PMID 21963610 DOI: 10.1093/sysbio/syr100  1
2011 Huelsenbeck JP, Andolfatto P, Huelsenbeck ET. Structurama: bayesian inference of population structure. Evolutionary Bioinformatics Online. 7: 55-9. PMID 21698091 DOI: 10.4137/EBO.S6761  1
2011 Huelsenbeck JP, Alfaro ME, Suchard MA. Biologically inspired phylogenetic models strongly outperform the no common mechanism model. Systematic Biology. 60: 225-32. PMID 21252385 DOI: 10.1093/sysbio/syq089  1
2011 Nasrallah CA, Mathews DH, Huelsenbeck JP. Quantifying the impact of dependent evolution among sites in phylogenetic inference. Systematic Biology. 60: 60-73. PMID 21081481 DOI: 10.1093/sysbio/syq074  1
2010 Beaumont MA, Nielsen R, Robert C, Hey J, Gaggiotti O, Knowles L, Estoup A, Panchal M, Corander J, Hickerson M, Sisson SA, Fagundes N, Chikhi L, Beerli P, Vitalis R, ... ... Huelsenbeck J, et al. In defence of model-based inference in phylogeography Molecular Ecology. 19: 436-446. DOI: 10.1111/j.1365-294X.2009.04515.x  1
2009 Bollback JP, Huelsenbeck JP. Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence. Genetics. 181: 225-34. PMID 19001294 DOI: 10.1534/genetics.107.085225  1
2008 Munch K, Boomsma W, Huelsenbeck JP, Willerslev E, Nielsen R. Statistical assignment of DNA sequences using Bayesian phylogenetics. Systematic Biology. 57: 750-7. PMID 18853361 DOI: 10.1080/10635150802422316  1
2008 Huelsenbeck JP, Joyce P, Lakner C, Ronquist F. Bayesian analysis of amino acid substitution models. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 363: 3941-53. PMID 18852098 DOI: 10.1098/rstb.2008.0175  1
2008 Huelsenbeck JP, Ané C, Larget B, Ronquist F. A Bayesian perspective on a non-parsimonious parsimony model. Systematic Biology. 57: 406-19. PMID 18570035 DOI: 10.1080/10635150802166046  1
2008 Brandley MC, Huelsenbeck JP, Wiens JJ. 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. Evolution; International Journal of Organic Evolution. 62: 2042-64. PMID 18507743 DOI: 10.1111/j.1558-5646.2008.00430.x  1
2008 Lakner C, van der Mark P, Huelsenbeck JP, Larget B, Ronquist F. Efficiency of Markov chain Monte Carlo tree proposals in Bayesian phylogenetics. Systematic Biology. 57: 86-103. PMID 18278678 DOI: 10.1080/10635150801886156  1
2008 Wong KM, Suchard MA, Huelsenbeck JP. Alignment uncertainty and genomic analysis. Science (New York, N.Y.). 319: 473-6. PMID 18218900 DOI: 10.1126/science.1151532  1
2008 Huelsenbeck JP, Bollback JP. Application of the Likelihood Function in Phylogenetic Analysis Handbook of Statistical Genetics: Third Edition. 1: 460-488. DOI: 10.1002/9780470061619.ch15  1
2007 Huelsenbeck JP, Suchard MA. A nonparametric method for accommodating and testing across-site rate variation. Systematic Biology. 56: 975-87. PMID 18075934 DOI: 10.1080/10635150701670569  1
2007 Bollback JP, Huelsenbeck JP. Clonal interference is alleviated by high mutation rates in large populations. Molecular Biology and Evolution. 24: 1397-406. PMID 17379621 DOI: 10.1093/molbev/msm056  1
2007 Huelsenbeck JP, Andolfatto P. Inference of population structure under a Dirichlet process model. Genetics. 175: 1787-802. PMID 17237522 DOI: 10.1534/genetics.106.061317  1
2007 Huelsenbeck JP. Molecular Phylogenetic Analysis Palaeobiology Ii. 522-528. DOI: 10.1002/9780470999295ch.130  1
2006 Ronquist F, Larget B, Huelsenbeck JP, Kadane JB, Simon D, van der Mark P. Comment on "Phylogenetic MCMC algorithms are misleading on mixtures of trees". Science (New York, N.Y.). 312: 367; author reply 36. PMID 16627724 DOI: 10.1126/science.1123622  1
2006 Huelsenbeck JP, Jain S, Frost SW, Pond SL. A Dirichlet process model for detecting positive selection in protein-coding DNA sequences. Proceedings of the National Academy of Sciences of the United States of America. 103: 6263-8. PMID 16606848 DOI: 10.1073/pnas.0508279103  1
2006 Alfaro ME, Huelsenbeck JP. Comparative performance of Bayesian and AIC-based measures of phylogenetic model uncertainty. Systematic Biology. 55: 89-96. PMID 16507526 DOI: 10.1080/10635150500433565  1
2004 Huelsenbeck JP, Rannala B. Frequentist properties of bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models Systematic Biology. 53: 904-913. PMID 15764559 DOI: 10.1080/10635150490522629  1
2004 Huelsenbeck JP, Dyer KA. Bayesian estimation of positively selected sites. Journal of Molecular Evolution. 58: 661-72. PMID 15461423 DOI: 10.1007/s00239-004-2588-9  1
2004 Glenner H, Hansen AJ, Sørensen MV, Ronquist F, Huelsenbeck JP, Willerslev E. Bayesian inference of the metazoan phylogeny; a combined molecular and morphological approach. Current Biology : Cb. 14: 1644-9. PMID 15380066 DOI: 10.1016/j.cub.2004.09.027  1
2004 Guindon S, Rodrigo AG, Dyer KA, Huelsenbeck JP. Modeling the site-specific variation of selection patterns along lineages. Proceedings of the National Academy of Sciences of the United States of America. 101: 12957-62. PMID 15326304 DOI: 10.1073/pnas.0402177101  1
2004 Huelsenbeck JP, Larget B, Alfaro ME. Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo. Molecular Biology and Evolution. 21: 1123-33. PMID 15034130 DOI: 10.1093/molbev/msh123  1
2004 Nylander JA, Ronquist F, Huelsenbeck JP, Nieves-Aldrey JL. Bayesian phylogenetic analysis of combined data. Systematic Biology. 53: 47-67. PMID 14965900 DOI: 10.1080/10635150490264699  1
2004 Altekar G, Dwarkadas S, Huelsenbeck JP, Ronquist F. Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics (Oxford, England). 20: 407-15. PMID 14960467 DOI: 10.1093/bioinformatics/btg427  1
2003 Huelsenbeck JP, Lander KM. Frequent inconsistency of parsimony under a simple model of cladogenesis. Systematic Biology. 52: 641-8. PMID 14530131 DOI: 10.1080/10635150390235467  1
2003 Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics (Oxford, England). 19: 1572-4. PMID 12912839 DOI: 10.1093/bioinformatics/btg180  1
2003 Huelsenbeck JP, Rannala B. Detecting correlation between characters in a comparative analysis with uncertain phylogeny. Evolution; International Journal of Organic Evolution. 57: 1237-47. PMID 12894932  1
2003 Huelsenbeck JP, Nielsen R, Bollback JP. Stochastic mapping of morphological characters. Systematic Biology. 52: 131-58. PMID 12746144 DOI: 10.1080/10635150309342  1
2002 Huelsenbeck JP, Larget B, Miller RE, Ronquist F. Potential applications and pitfalls of Bayesian inference of phylogeny. Systematic Biology. 51: 673-88. PMID 12396583 DOI: 10.1080/10635150290102366  1
2002 Huelsenbeck JP. Testing a covariotide model of DNA substitution. Molecular Biology and Evolution. 19: 698-707. PMID 11961103  1
2002 Huelsenbeck JP, Imennov NS. Geographic origin of human mitochondrial DNA: accommodating phylogenetic uncertainty and model comparison. Systematic Biology. 51: 155-65. PMID 11943098 DOI: 10.1080/106351502753475934  1
2002 Huelsenbeck JP, Bollback JP, Levine AM. Inferring the root of a phylogenetic tree. Systematic Biology. 51: 32-43. PMID 11943091 DOI: 10.1080/106351502753475862  1
2002 Nielsen R, Huelsenbeck JP. Detecting positively selected amino acid sites using posterior predictive P-values. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 576-88. PMID 11928509  1
2001 Swofford DL, Waddell PJ, Huelsenbeck JP, Foster PG, Lewis PO, Rogers JS. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Systematic Biology. 50: 525-39. PMID 12116651  1
2001 Huelsenbeck JP, Bollback JP. Empirical and hierarchical Bayesian estimation of ancestral states. Systematic Biology. 50: 351-66. PMID 12116580  1
2001 Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP. Bayesian inference of phylogeny and its impact on evolutionary biology. Science (New York, N.Y.). 294: 2310-4. PMID 11743192 DOI: 10.1126/science.1065889  1
2001 Huelsenbeck JP, Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics (Oxford, England). 17: 754-5. PMID 11524383  1
2001 Bollback JP, Huelsenbeck JP. Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (family Leviviridae). Journal of Molecular Evolution. 52: 117-28. PMID 11231891 DOI: 10.1007/s002390010140  1
2000 Huelsenbeck JP, Rannala B, Larget B. A Bayesian framework for the analysis of cospeciation. Evolution; International Journal of Organic Evolution. 54: 352-64. PMID 10937213  1
2000 Huelsenbeck JP, Rannala B, Masly JP. Accommodating phylogenetic uncertainty in evolutionary studies. Science (New York, N.Y.). 288: 2349-50. PMID 10875916 DOI: 10.1126/science.288.5475.2349  1
2000 Huelsenbeck JP, Larget B, Swofford D. A compound poisson process for relaxing the molecular clock. Genetics. 154: 1879-92. PMID 10747076  1
1999 Huelsenbeck JP, Nielsen R. Effect of nonindependent substitution on phylogenetic accuracy. Systematic Biology. 48: 317-28. PMID 12066710  1
1999 Huelsenbeck JP, Nielsen R. Variation in the pattern of nucleotide substitution across sites. Journal of Molecular Evolution. 48: 86-93. PMID 9873080 DOI: 10.1007/PL00006448  1
1998 Nielsen R, Mountain JL, Huelsenbeck JP, Slatkin M. MAXIMUM-LIKELIHOOD ESTIMATION OF POPULATION DIVERGENCE TIMES AND POPULATION PHYLOGENY IN MODELS WITHOUT MUTATION. Evolution; International Journal of Organic Evolution. 52: 669-677. PMID 28565245 DOI: 10.1111/j.1558-5646.1998.tb03692.x  1
1998 Huelsenbeck JP. Systematic bias in phylogenetic analysis: is the Strepsiptera problem solved? Systematic Biology. 47: 519-37. PMID 12066692  1
1998 Rannala B, Huelsenbeck JP, Yang Z, Nielsen R. Taxon sampling and the accuracy of large phylogenies. Systematic Biology. 47: 702-10. PMID 12066312  1
1998 Van Den Bussche RA, Baker RJ, Huelsenbeck JP, Hillis DM. Base compositional bias and phylogenetic analyses: a test of the "flying DNA" hypothesis. Molecular Phylogenetics and Evolution. 10: 408-16. PMID 10051393 DOI: 10.1006/mpev.1998.0531  1
1998 Nielsen R, Mountain JL, Huelsenbeck JP, Slatkin M. Maximum-likelihood estimation of population divergence times and population phylogeny in models without mutation Evolution. 52: 669-677.  1
1998 Nielsen R, Mountain JL, Huelsenbeck JP, Slatkin M. Maximum-likelihood estimation of population divergence times and population phylogeny in models without mutation Evolution. 52: 669-677.  1
1997 Huelsenbeck JP, Rannala B, Yang Z. STATISTICAL TESTS OF HOST-PARASITE COSPECIATION. Evolution; International Journal of Organic Evolution. 51: 410-419. PMID 28565354 DOI: 10.1111/j.1558-5646.1997.tb02428.x  0.4
1997 Huelsenbeck JP. Is the Felsenstein zone a fly trap? Systematic Biology. 46: 69-74. PMID 11975354  1
1997 Bull JJ, Badgett MR, Wichman HA, Huelsenbeck JP, Hillis DM, Gulati A, Ho C, Molineux IJ. Exceptional convergent evolution in a virus. Genetics. 147: 1497-507. PMID 9409816  1
1997 Huelsenbeck JP, Rannala B. Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science (New York, N.Y.). 276: 227-32. PMID 9092465 DOI: 10.1126/science.276.5310.227  1
1997 Huelsenbeck JP, Crandall KA. Phylogeny estimation and hypothesis testing using maximum likelihood Annual Review of Ecology and Systematics. 28: 437-466. DOI: 10.1146/annurev.ecolsys.28.1.437  1
1997 Huelsenbeck JP, Crandall KA. Phylogeny estimation and hypothesis testing using maximum likelihood Annual Review of Ecology and Systematics. 28: 437-466. DOI: 10.1146/annurev.ecolsys.28.1.437  0.96
1997 Huelsenbeck JP, Rannala B. Maximum likelihood estimation of phylogeny using stratigraphic data Paleobiology. 23: 174-180.  1
1997 Huelsenbeck JP, Rannala B. Maximum likelihood estimation of phylogeny using stratigraphic data Paleobiology. 23: 174-180.  0.4
1997 Huelsenbeck JP, Rannala B, Yang Z. Statistical tests of host-parasite cospeciation Evolution. 51: 410-419.  1
1997 Huelsenbeck JP, Rannala B, Yang Z. Statistical tests of host-parasite cospeciation Evolution. 51: 410-419.  0.4
1996 Huelsenbeck JP, Kirkpatrick M. DO PHYLOGENETIC METHODS PRODUCE TREES WITH BIASED SHAPES? Evolution; International Journal of Organic Evolution. 50: 1418-1424. PMID 28565707 DOI: 10.1111/j.1558-5646.1996.tb03915.x  1
1996 Huelsenbeck JP, Bull JJ, Cunningham CW. Reply from j.p. Huelsenbeck, j.j. Bull and C.w. Cunningham. Trends in Ecology & Evolution. 11: 335. PMID 21237868  1
1996 Huelsenbeck JP, Bull JJ, Cunningham CW. Combining data in phylogenetic analysis. Trends in Ecology & Evolution. 11: 152-8. PMID 21237790 DOI: 10.1016/0169-5347(96)10006-9  1
1996 Huelsenbeck JP, Hillis DM, Nielsen R. Likelihood-ratio test of monophyly Systematic Biology. 45: 546-558.  1
1996 Huelsenbeck JP, Hillis DM, Nielsen R. Likelihood-ratio test of monophyly Systematic Biology. 45: 546-558.  1
1996 Huelsenbeck JP, Kirkpatrick M. Do phylogenetic methods produce trees with biased shapes? Evolution. 50: 1418-1424.  1
1996 Huelsenbeck JP, Kirkpatrick M. Do phylogenetic methods produce trees with biased shapes? Evolution. 50: 1418-1424.  1
1996 Huelsenbeck JP, Bull JJ. A likelihood ratio test to detect conflicting phylogenetic signal Systematic Biology. 45: 92-98.  1
1996 Huelsenbeck JP, Bull JJ. A likelihood ratio test to detect conflicting phylogenetic signal Systematic Biology. 45: 92-98.  1
1995 Hillis DM, Huelsenbeck JP. Response. Science (New York, N.Y.). 267: 255-6. PMID 17791347 DOI: 10.1126/science.267.5195.255  1
1995 Huelsenbeck JP. The robustness of two phylogenetic methods: four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining. Molecular Biology and Evolution. 12: 843-9. PMID 7476130  1
1995 Hillis DM, Huelsenbeck JP. Assessing molecular phylogenies [7] Science. 267: 255-256.  1
1995 Hillis DM, Huelsenbeck JP. Assessing molecular phylogenies [7] Science. 267: 255-256.  1
1995 Huelsenbeck JP. Performance of phylogenetic methods in simulation Systematic Biology. 44: 17-48.  1
1994 Hillis DM, Huelsenbeck JP, Swofford DL. Hobgoblin of phylogenetics? Nature. 369: 363-4. PMID 8196763 DOI: 10.1038/369363a0  1
1994 Hillis DM, Huelsenbeck JP, Cunningham CW. Application and accuracy of molecular phylogenies. Science (New York, N.Y.). 264: 671-7. PMID 8171318  1
1994 Hillis DM, Huelsenbeck JP. Support for dental HIV transmission. Nature. 369: 24-5. PMID 8164734 DOI: 10.1038/369024a0  1
1994 Hillis DM, Huelsenbeck JP. To tree the truth: biological and numerical simulation of phylogeny. Society of General Physiologists Series. 49: 55-67. PMID 7939904  1
1994 Huelsenbeck JP. Comparing the stratigraphic record to estimates of phylogeny Paleobiology. 20: 470-483.  1
1994 Huelsenbeck JP, Swofford DL, Cunningham CW, Bull JJ, Waddell PJ. Is character weighting a panacea for the problem of data heterogeneity in phylogenetic analysis? Systematic Biology. 43: 288-291.  1
1994 Huelsenbeck JP, Swofford DL, Cunningham CW, Bull JJ, Waddell PJ. Is character weighting a panacea for the problem of data heterogeneity in phylogenetic analysis? Systematic Biology. 43: 288-291.  1
1993 Bull JJ, Huelsenbeck JP, Cunningham CW, Swofford DL, Waddell PJ. Partitioning and combining data in phylogenetic analysis Systematic Biology. 42: 384-397. DOI: 10.1093/sysbio/42.3.384  1
1993 Bull JJ, Huelsenbeck JP, Cunningham CW, Swofford DL, Waddell PJ. Partitioning and combining data in phylogenetic analysis Systematic Biology. 42: 384-397. DOI: 10.1093/sysbio/42.3.384  1
1993 Huelsenbeck JP, Hillis DM. Success of phylogenetic methods in the four-taxon case Systematic Biology. 42: 247-264.  1
1993 Huelsenbeck JP, Hillis DM. Success of phylogenetic methods in the four-taxon case Systematic Biology. 42: 247-264.  1
1992 Hillis DM, Huelsenbeck JP. Signal, noise, and reliability in molecular phylogenetic analyses. The Journal of Heredity. 83: 189-95. PMID 1624764  1
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