Bruce H. Rannala, PhD - Publications

Affiliations: 
University of California, Davis, Davis, CA 

64 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
2022 Flouri T, Huang J, Jiao X, Kapli P, Rannala B, Yang Z. Bayesian Phylogenetic Inference using Relaxed-clocks and the Multispecies Coalescent. Molecular Biology and Evolution. 39. PMID 35907248 DOI: 10.1093/molbev/msac161  0.392
2022 Gao J, May MR, Rannala B, Moore BR. New Phylogenetic Models Incorporating Interval-Specific Dispersal Dynamics Improve Inference of Disease Spread. Molecular Biology and Evolution. PMID 35861314 DOI: 10.1093/molbev/msac159  0.301
2020 Jiao X, Flouris T, Rannala B, Yang Z. The Impact of Cross-Species Gene Flow on Species Tree Estimation. Systematic Biology. PMID 31977022 DOI: 10.1093/Sysbio/Syaa001  0.466
2019 Flouris T, Jiao X, Rannala B, Yang Z. A Bayesian implementation of the multispecies coalescent model with introgression for phylogenomic analysis. Molecular Biology and Evolution. PMID 31825513 DOI: 10.1093/Molbev/Msz296  0.487
2018 Flouri T, Jiao X, Rannala B, Yang Z. Species Tree Inference with bpp Using Genomic Sequences and the Multispecies Coalescent. Molecular Biology and Evolution. PMID 30053098 DOI: 10.1093/Molbev/Msy147  0.482
2018 Leaché AD, Zhu T, Rannala B, Yang Z. The Spectre of Too Many Species. Systematic Biology. PMID 29982825 DOI: 10.1093/Sysbio/Syy051  0.485
2017 Yang Z, Rannala B. Bayesian Species Identification under the Multispecies Coalescent Provides Significant Improvements to DNA Barcoding Analyses. Molecular Ecology. PMID 28281309 DOI: 10.1111/Mec.14093  0.444
2017 Rannala B, Yang Z. Efficient Bayesian species tree inference under the multispecies coalescent. Systematic Biology. PMID 28053140 DOI: 10.1093/Sysbio/Syw119  0.495
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  0.457
2016 Rannala B. Conceptual issues in Bayesian divergence time estimation Philosophical Transactions of the Royal Society B. 371: 20150134. PMID 27325831 DOI: 10.1098/Rstb.2015.0134  0.473
2015 Rannala B. The art and science of species delimitation Current Zoology. 61: 846-853. DOI: 10.1093/Czoolo/61.5.846  0.412
2014 Yang Z, Rannala B. Unguided species delimitation using DNA sequence data from multiple Loci. Molecular Biology and Evolution. 31: 3125-35. PMID 25274273 DOI: 10.1093/Molbev/Msu279  0.457
2014 Wang Y, Rannala B. Bayesian inference of shared recombination hotspots between humans and chimpanzees. Genetics. 198: 1621-8. PMID 25261696 DOI: 10.1534/Genetics.114.168377  0.374
2014 Zhang C, Rannala B, Yang Z. Bayesian species delimitation can be robust to guide-tree inference errors. Systematic Biology. 63: 993-1004. PMID 25096853 DOI: 10.1093/Sysbio/Syu052  0.408
2014 Leaché AD, Harris RB, Rannala B, Yang Z. The influence of gene flow on species tree estimation: a simulation study. Systematic Biology. 63: 17-30. PMID 23945075 DOI: 10.1093/Sysbio/Syt049  0.463
2013 Rannala B, Yang Z. Improved reversible jump algorithms for Bayesian species delimitation. Genetics. 194: 245-53. PMID 23502678 DOI: 10.1534/Genetics.112.149039  0.427
2013 Padhukasahasram B, Rannala B. Meiotic gene-conversion rate and tract length variation in the human genome. European Journal of Human Genetics : Ejhg. PMID 23443031 DOI: 10.1038/Ejhg.2013.30  0.43
2012 Yang Z, Rannala B. Molecular phylogenetics: principles and practice. Nature Reviews. Genetics. 13: 303-14. PMID 22456349 DOI: 10.1038/Nrg3186  0.421
2012 Zhang C, Rannala B, Yang Z. Robustness of compound Dirichlet priors for Bayesian inference of branch lengths. Systematic Biology. 61: 779-84. PMID 22328570 DOI: 10.1093/Sysbio/Sys030  0.404
2012 Rannala B, Zhu T, Yang Z. Tail paradox, partial identifiability, and influential priors in Bayesian branch length inference. Molecular Biology and Evolution. 29: 325-35. PMID 21890479 DOI: 10.1093/Molbev/Msr210  0.43
2011 Padhukasahasram B, Rannala B. Bayesian population genomic inference of crossing over and gene conversion. Genetics. 189: 607-19. PMID 21840857 DOI: 10.1534/Genetics.111.130195  0.459
2011 Leaché AD, Rannala B. The accuracy of species tree estimation under simulation: a comparison of methods. Systematic Biology. 60: 126-37. PMID 21088009 DOI: 10.1093/Sysbio/Syq073  0.495
2010 Yang Z, Rannala B. Bayesian species delimitation using multilocus sequence data. Proceedings of the National Academy of Sciences of the United States of America. 107: 9264-9. PMID 20439743 DOI: 10.1073/Pnas.0913022107  0.49
2009 Wang Y, Rannala B. Population genomic inference of recombination rates and hotspots. Proceedings of the National Academy of Sciences of the United States of America. 106: 6215-6219. PMID 19342488 DOI: 10.1073/Pnas.0900418106  0.41
2008 Wang Y, Rannala B. Bayesian inference of fine-scale recombination rates using population genomic data Philosophical Transactions of the Royal Society B. 363: 3921-3930. PMID 18852101 DOI: 10.1098/Rstb.2008.0172  0.464
2008 Fetterman CD, Rannala B, Walter MA. Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies Bmc Evolutionary Biology. 8: 261-261. PMID 18816404 DOI: 10.1186/1471-2148-8-261  0.308
2008 Rannala B, Yang Z. Phylogenetic inference using whole genomes. Annual Review of Genomics and Human Genetics. 9: 217-31. PMID 18767964 DOI: 10.1146/Annurev.Genom.9.081307.164407  0.456
2008 Mateiu LM, Rannala BH. Bayesian inference of errors in ancient DNA caused by postmortem degradation. Molecular Biology and Evolution. 25: 1503-11. PMID 18420593 DOI: 10.1093/Molbev/Msn095  0.356
2007 Cranston KA, Rannala B. Summarizing a posterior distribution of trees using agreement subtrees. Systematic Biology. 56: 578-90. PMID 17654363 DOI: 10.1080/10635150701485091  0.697
2007 Ro S, Rannala B. Inferring somatic mutation rates using the stop-enhanced green fluorescent protein mouse Genetics. 177: 9-16. PMID 17603123 DOI: 10.1534/Genetics.106.069310  0.374
2007 Rannala B, Yang Z. Inferring speciation times under an episodic molecular clock. Systematic Biology. 56: 453-66. PMID 17558967 DOI: 10.1080/10635150701420643  0.527
2006 Mateiu L, Rannala B. Inferring Complex DNA Substitution Processes on Phylogenies Using Uniformization and Data Augmentation Systematic Biology. 55: 259-269. PMID 16551582 DOI: 10.1080/10635150500541599  0.422
2006 Yang Z, Rannala B. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Molecular Biology and Evolution. 23: 212-26. PMID 16177230 DOI: 10.1093/Molbev/Msj024  0.484
2005 Yang Z, Rannala B. Branch-length prior influences Bayesian posterior probability of phylogeny. Systematic Biology. 54: 455-70. PMID 16012111 DOI: 10.1080/10635150590945313  0.521
2005 Wang Y, Rannala B. In Silico Analysis of Disease-Association Mapping Strategies Using the Coalescent Process and Incorporating Ascertainment and Selection American Journal of Human Genetics. 76: 1066-1073. PMID 15818531 DOI: 10.1086/430472  0.351
2005 Cranston K, Rannala B. Closing the gap between rocks and clocks Heredity. 94: 461-462. PMID 15714220 DOI: 10.1038/Sj.Hdy.6800644  0.716
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  0.491
2004 Beaumont MA, Rannala B. The Bayesian revolution in genetics. Nature Reviews. Genetics. 5: 251-61. PMID 15131649 DOI: 10.1038/Nrg1318  0.335
2004 Wilson GA, Rannala B. Bayesian inference of recent migration rates using multilocus genotypes. Genetics. 163: 1177-91. PMID 12663554 DOI: 10.1093/genetics/163.3.1177  0.345
2003 Rannala B, Yang Z. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics. 164: 1645-56. PMID 12930768  0.447
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 DOI: 10.1111/J.0014-3820.2003.Tb00332.X  0.453
2002 Rannala B. Identifiability of parameters in MCMC Bayesian inference of phylogeny. Systematic Biology. 51: 754-760. PMID 12396589 DOI: 10.1080/10635150290102429  0.411
2002 Fisher MC, Rannala B, Chaturvedi V, Taylor JW. Disease surveillance in recombining pathogens: multilocus genotypes identify sources of human Coccidioides infections. Proceedings of the National Academy of Sciences of the United States of America. 99: 9067-71. PMID 12084944 DOI: 10.1073/Pnas.132178099  0.315
2002 Reeve JP, Rannala B. DMLE+: Bayesian linkage disequilibrium gene mapping. Bioinformatics. 18: 894-895. PMID 12075030 DOI: 10.1093/Bioinformatics/18.6.894  0.373
2001 Rannala B. Finding genes influencing susceptibility to complex diseases in the post-genome era. American Journal of Pharmacogenomics. 1: 203-221. PMID 12083968 DOI: 10.2165/00129785-200101030-00005  0.35
2001 Rannala B, Bertorelle G. Using linked markers to infer the age of a mutation. Human Mutation. 18: 87-100. PMID 11462233 DOI: 10.1002/Humu.1158  0.418
2001 Rannala B, Reeve JP. High-Resolution Multipoint Linkage-Disequilibrium Mapping in the Context of a Human Genome Sequence American Journal of Human Genetics. 69: 159-178. PMID 11410841 DOI: 10.1086/321279  0.387
2000 Slatkin M, Rannala B. Estimating allele age. Annual Review of Genomics and Human Genetics. 1: 225-49. PMID 11701630 DOI: 10.1146/Annurev.Genom.1.1.225  0.382
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  0.441
1999 Knowles LL, Futuyma DJ, Eanes WF, Rannala B. INSIGHT INTO SPECIATION FROM HISTORICAL DEMOGRAPHY IN THE PHYTOPHAGOUS BEETLE GENUS OPHRAELLA. Evolution; International Journal of Organic Evolution. 53: 1846-1856. PMID 28565438 DOI: 10.1111/j.1558-5646.1999.tb04567.x  0.3
1998 Bertorelle G, Rannala B. Using rare mutations to estimate population divergence times: A maximum likelihood approach Proceedings of the National Academy of Sciences of the United States of America. 95: 15452-15457. PMID 9860989 DOI: 10.1073/Pnas.95.26.15452  0.417
1998 Rannala B, Slatkin M. Likelihood analysis of disequilibrium mapping, and related problems. American Journal of Human Genetics. 62: 459-73. PMID 9463316 DOI: 10.1086/301709  0.43
1998 Yang Z, Rannala B. Bayesian estimation of molecular evolutionary trees. Annals of Human Genetics. 62: 453-464. DOI: 10.1111/J.1469-1809.1998.Ahg625_0453_16.X  0.429
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  0.427
1997 Rannala B. On the Genealogy of a Rare Allele Theoretical Population Biology. 52: 216-223. PMID 9466962 DOI: 10.1006/Tpbi.1997.1332  0.38
1997 Rannala B, Mountain JL. Detecting immigration by using multilocus genotypes Proceedings of the National Academy of Sciences of the United States of America. 94: 9197-9201. PMID 9256459 DOI: 10.1073/Pnas.94.17.9197  0.347
1997 Yang Z, Rannala B. Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method. Molecular Biology and Evolution. 14: 717-24. PMID 9214744 DOI: 10.1093/Oxfordjournals.Molbev.A025811  0.513
1997 Rannala B. Gene Genealogy In A Population Of Variable Size Heredity. 78: 417-423. PMID 9134707 DOI: 10.1038/Hdy.1997.65  0.37
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  0.359
1997 Rannala B, Yang Z. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. Journal of Molecular Evolution. 43: 304-11. PMID 8703097 DOI: 10.1007/Bf02338839  0.547
1997 Huelsenbeck JP, Rannala B. Maximum likelihood estimation of phylogeny using stratigraphic data Paleobiology. 23: 174-180. DOI: 10.1017/S0094837300016778  0.526
1996 Rannala B. The Sampling Theory of Neutral Alleles in an Island Population of Fluctuating Size Theoretical Population Biology. 50: 91-104. PMID 8813016 DOI: 10.1006/Tpbi.1996.0024  0.35
1996 Rannala B, Hartigan JA. Estimating gene flow in island populations. Genetical Research. 67: 147-58. PMID 8801187 DOI: 10.1017/S0016672300033607  0.473
1995 Rannala B. Polymorphic Characters and Phylogenetic Analysis: A Statistical Perspective Systematic Biology. 44: 421-429. DOI: 10.1093/Sysbio/44.3.421  0.341
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