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Jeremy M. Brown, Ph.D. - Publications

Affiliations: 
Biological Sciences Louisiana State University, Baton Rouge, LA, United States 
Area:
phylogenetics, molecular evolution, phylogeography
Website:
http://www.phyleauxgenetics.org
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27 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 Hime PM, Lemmon AR, Lemmon ECM, Prendini E, Brown JM, Thomson RC, Kratovil JD, Noonan BP, Pyron RA, Peloso PLV, Kortyna ML, Keogh JS, Donnellan SC, Mueller RL, Raxworthy CJ, et al. Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life. Systematic Biology. PMID 32359157 DOI: 10.1093/Sysbio/Syaa034  0.705
2018 Richards EJ, Brown JM, Barley AJ, Chong RA, Thomson RC. Variation across mitochondrial gene trees provides evidence for systematic error: How much gene tree variation is biological? Systematic Biology. PMID 29471536 DOI: 10.1093/Sysbio/Syy013  0.36
2018 Brown JM, Thomson RC. The behavior of Metropolis-coupled Markov chains when sampling rugged phylogenetic distributions. Systematic Biology. PMID 29462409 DOI: 10.1093/Sysbio/Syy008  0.376
2017 Höhna S, Coghill LM, Mount GG, Thomson RC, Brown JM. P3: Phylogenetic Posterior Prediction in RevBayes. Molecular Biology and Evolution. PMID 29136211 DOI: 10.1093/Molbev/Msx286  0.333
2017 Barley AJ, Brown JM, Thomson RC. Impact of Model Violations on the Inference of Species Boundaries Under the Multispecies. Systematic Biology. PMID 28945903 DOI: 10.1093/Sysbio/Syx073  0.396
2016 Brown JM, Thomson RC. Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses. Systematic Biology. PMID 28003531 DOI: 10.1093/Sysbio/Syw101  0.418
2016 Huang W, Zhou G, Marchand M, Ash JR, Morris D, Van Dooren P, Brown JM, Gallivan KA, Wilgenbusch JC. TreeScaper: visualizing and extracting phylogenetic signal from sets of trees. Molecular Biology and Evolution. PMID 27634869 DOI: 10.1093/Molbev/Msw196  0.318
2016 Engebretsen KN, Barrow LN, Rittmeyer EN, Brown JM, Moriarty Lemmon E. Quantifying the spatiotemporal dynamics in a chorus frog (Pseudacris) hybrid zone over 30 years. Ecology and Evolution. 6: 5013-31. PMID 27547330 DOI: 10.1002/Ece3.2232  0.31
2016 Andersen JJ, Nelson BJ, Brown JM. EmpPrior: using outside empirical data to inform branch-length priors for Bayesian phylogenetics. Bmc Bioinformatics. 17: 253. PMID 27342194 DOI: 10.1186/S12859-016-1132-4  0.39
2015 Doyle VP, Young RE, Naylor GJ, Brown JM. Can we identify genes with increased phylogenetic reliability? Systematic Biology. PMID 26099258 DOI: 10.1093/Sysbio/Syv041  0.324
2015 Nelson BJ, Andersen JJ, Brown JM. Deflating trees: improving Bayesian branch-length estimates using informed priors. Systematic Biology. 64: 441-7. PMID 25595363 DOI: 10.1093/Sysbio/Syv003  0.365
2014 Doyle VP, Andersen JJ, Nelson BJ, Metzker ML, Brown JM. Untangling the influences of unmodeled evolutionary processes on phylogenetic signal in a forensically important HIV-1 transmission cluster. Molecular Phylogenetics and Evolution. 75: 126-37. PMID 24589520 DOI: 10.1016/J.Ympev.2014.02.022  0.381
2014 Brown JM. Detection of implausible phylogenetic inferences using posterior predictive assessment of model fit. Systematic Biology. 63: 334-48. PMID 24415681 DOI: 10.1093/Sysbio/Syu002  0.414
2014 Reid NM, Hird SM, Brown JM, Pelletier TA, McVay JD, Satler JD, Carstens BC. Poor fit to the multispecies coalescent is widely detectable in empirical data. Systematic Biology. 63: 322-33. PMID 23985785 DOI: 10.1093/Sysbio/Syt057  0.383
2012 Fong JJ, Brown JM, Fujita MK, Boussau B. A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic lissamphibia. Plos One. 7: e48990. PMID 23145043 DOI: 10.1371/Journal.Pone.0048990  0.685
2011 Boussau B, Brown JM, Fujita MK. Nonadaptive evolution of mitochondrial genome size. Evolution; International Journal of Organic Evolution. 65: 2706-11. PMID 21884067 DOI: 10.1111/J.1558-5646.2011.01322.X  0.647
2011 Brown JM, Savidge K, McTavish EJ. DIM SUM: demography and individual migration simulated using a Markov chain. Molecular Ecology Resources. 11: 358-63. PMID 21429144 DOI: 10.1111/J.1755-0998.2010.02925.X  0.717
2010 Scaduto DI, Brown JM, Haaland WC, Zwickl DJ, Hillis DM, Metzker ML. Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences. Proceedings of the National Academy of Sciences of the United States of America. 107: 21242-7. PMID 21078965 DOI: 10.1073/Pnas.1015673107  0.708
2010 Brown JM, Hedtke SM, Lemmon AR, Lemmon EM. When trees grow too long: investigating the causes of highly inaccurate bayesian branch-length estimates. Systematic Biology. 59: 145-61. PMID 20525627 DOI: 10.1093/Sysbio/Syp081  0.718
2009 Lemmon AR, Brown JM, Stanger-Hall K, Lemmon EM. The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Systematic Biology. 58: 130-45. PMID 20525573 DOI: 10.1093/Sysbio/Syp017  0.736
2009 Brown JM, ElDabaje R. PuMA: Bayesian analysis of partitioned (and unpartitioned) model adequacy. Bioinformatics (Oxford, England). 25: 537-8. PMID 19098028 DOI: 10.1093/Bioinformatics/Btn651  0.342
2008 Rabeling C, Brown JM, Verhaagh M. Newly discovered sister lineage sheds light on early ant evolution. Proceedings of the National Academy of Sciences of the United States of America. 105: 14913-7. PMID 18794530 DOI: 10.1073/Pnas.0806187105  0.354
2007 Brown JM, Lemmon AR. The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics. Systematic Biology. 56: 643-55. PMID 17661232 DOI: 10.1080/10635150701546249  0.703
2005 Brown JM, Pauly GB. Increased rates of molecular evolution in an equatorial plant clade: an effect of environment or phylogenetic nonindependence? Evolution; International Journal of Organic Evolution. 59: 238-42. PMID 15792244 DOI: 10.1554/04-360  0.726
2004 Agrawal AF, Brown JM, Brodie ED. On the social structure of offspring rearing in the burrower bug, Sehirus cinctus (Hemiptera: Cydnidae) Behavioral Ecology and Sociobiology. 57: 139-148. DOI: 10.1007/S00265-004-0841-2  0.47
2003 Brown JM, Agrawal AF, Brodie ED. An analysis of single clutch paternity in the burrower bug Sehirus cinctus using microsatellites Journal of Insect Behavior. 16: 731-745. DOI: 10.1023/B:Joir.0000018317.55712.D3  0.493
2001 Agrawal AF, Brodie ED, Brown J. Parent-offspring coadaptation and the dual genetic control of maternal care. Science (New York, N.Y.). 292: 1710-2. PMID 11387474 DOI: 10.1126/Science.1059910  0.447
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