James H. Degnan, Ph.D. - Publications

Affiliations: 
2005 University of New Mexico, Albuquerque, NM, United States 
Area:
Statistics

28 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
2015 Zhu S, Degnan JH, Goldstien SJ, Eldon B. Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees. Bmc Bioinformatics. 16: 292. PMID 26373308 DOI: 10.1186/s12859-015-0721-y  0.88
2015 Degnan JH, Rhodes JA. There are no caterpillars in a wicked forest. Theoretical Population Biology. 105: 17-23. PMID 26365816 DOI: 10.1016/j.tpb.2015.08.007  0.88
2014 DeGiorgio M, Degnan JH. Robustness to divergence time underestimation when inferring species trees from estimated gene trees. Systematic Biology. 63: 66-82. PMID 23988674 DOI: 10.1093/sysbio/syt059  0.88
2013 Degnan JH. Anomalous unrooted gene trees. Systematic Biology. 62: 574-90. PMID 23576318 DOI: 10.1093/sysbio/syt023  0.88
2013 Degnan JH. Evaluating variations on the STAR algorithm for relative efficiency and sample sizes needed to reconstruct species trees. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 262-72. PMID 23424131  0.88
2013 Allman ES, Degnan JH, Rhodes JA. Species tree inference by the STAR method and its generalizations. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 50-61. PMID 23294273 DOI: 10.1089/cmb.2012.0101  0.88
2012 Degnan JH, Rosenberg NA, Stadler T. A characterization of the set of species trees that produce anomalous ranked gene trees. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 9: 1558-68. PMID 22868677 DOI: 10.1109/TCBB.2012.110  0.88
2012 Eldon B, Degnan JH. Multiple merger gene genealogies in two species: Monophyly, paraphyly, and polyphyly for two examples of Lambda coalescents. Theoretical Population Biology. 82: 117-30. PMID 22613063 DOI: 10.1016/j.tpb.2012.05.001  0.88
2012 Stadler T, Degnan JH. A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree. Algorithms For Molecular Biology : Amb. 7: 7. PMID 22546066 DOI: 10.1186/1748-7188-7-7  0.88
2012 Yu Y, Degnan JH, Nakhleh L. The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection. Plos Genetics. 8: e1002660. PMID 22536161 DOI: 10.1371/journal.pgen.1002660  0.88
2012 Degnan JH, Rosenberg NA, Stadler T. The probability distribution of ranked gene trees on a species tree. Mathematical Biosciences. 235: 45-55. PMID 22075548 DOI: 10.1016/j.mbs.2011.10.006  0.88
2011 Allman ES, Degnan JH, Rhodes JA. Determining species tree topologies from clade probabilities under the coalescent. Journal of Theoretical Biology. 289: 96-106. PMID 21867714 DOI: 10.1016/j.jtbi.2011.08.006  0.88
2011 DeGiorgio M, Degnan JH, Rosenberg NA. Coalescence-time distributions in a serial founder model of human evolutionary history. Genetics. 189: 579-93. PMID 21775469 DOI: 10.1534/genetics.111.129296  0.88
2011 Zhu S, Degnan JH, Steel M. Clades, clans, and reciprocal monophyly under neutral evolutionary models. Theoretical Population Biology. 79: 220-7. PMID 21420994 DOI: 10.1016/j.tpb.2011.03.002  0.88
2011 Yu Y, Than C, Degnan JH, Nakhleh L. Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting. Systematic Biology. 60: 138-49. PMID 21248369 DOI: 10.1093/sysbio/syq084  0.88
2011 Allman ES, Degnan JH, Rhodes JA. Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent. Journal of Mathematical Biology. 62: 833-62. PMID 20652704 DOI: 10.1007/s00285-010-0355-7  0.88
2011 Wang Y, Degnan JH. Performance of Matrix representation with parsimony for inferring species from gene trees Statistical Applications in Genetics and Molecular Biology. 10. DOI: 10.2202/1544-6115.1611  0.88
2010 Wang C, Szpiech ZA, Degnan JH, Jakobsson M, Pemberton TJ, Hardy JA, Singleton AB, Rosenberg NA. Comparing spatial maps of human population-genetic variation using Procrustes analysis. Statistical Applications in Genetics and Molecular Biology. 9: Article 13. PMID 20196748 DOI: 10.2202/1544-6115.1493  0.88
2010 Rosenberg NA, Degnan JH. Coalescent histories for discordant gene trees and species trees. Theoretical Population Biology. 77: 145-51. PMID 20064540 DOI: 10.1016/j.tpb.2009.12.004  0.88
2010 DeGiorgio M, Degnan JH. Fast and consistent estimation of species trees using supermatrix rooted triples. Molecular Biology and Evolution. 27: 552-69. PMID 19833741 DOI: 10.1093/molbev/msp250  0.88
2009 Degnan JH, DeGiorgio M, Bryant D, Rosenberg NA. Properties of consensus methods for inferring species trees from gene trees. Systematic Biology. 58: 35-54. PMID 20525567 DOI: 10.1093/sysbio/syp008  0.88
2009 Degnan JH, Rosenberg NA. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends in Ecology & Evolution. 24: 332-40. PMID 19307040 DOI: 10.1016/j.tree.2009.01.009  0.88
2008 Degnan JH, Lasky-Su J, Raby BA, Xu M, Molony C, Schadt EE, Lange C. Genomics and genome-wide association studies: an integrative approach to expression QTL mapping. Genomics. 92: 129-33. PMID 18586451 DOI: 10.1016/j.ygeno.2008.05.012  0.88
2008 Jakobsson M, Scholz SW, Scheet P, Gibbs JR, VanLiere JM, Fung HC, Szpiech ZA, Degnan JH, Wang K, Guerreiro R, Bras JM, Schymick JC, Hernandez DG, Traynor BJ, Simon-Sanchez J, et al. Genotype, haplotype and copy-number variation in worldwide human populations. Nature. 451: 998-1003. PMID 18288195 DOI: 10.1038/nature06742  0.88
2007 Schneiter K, Degnan JH, Corcoran C, Xu X, Laird N. EFBAT: exact family-based association tests. Bmc Genetics. 8: 86. PMID 18096066 DOI: 10.1186/1471-2156-8-86  0.88
2007 Kubatko LS, Degnan JH. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Systematic Biology. 56: 17-24. PMID 17366134 DOI: 10.1080/10635150601146041  0.88
2006 Degnan JH, Rosenberg NA. Discordance of species trees with their most likely gene trees. Plos Genetics. 2: e68. PMID 16733550 DOI: 10.1371/journal.pgen.0020068  0.88
2005 Degnan JH, Salter LA. Gene tree distributions under the coalescent process. Evolution; International Journal of Organic Evolution. 59: 24-37. PMID 15792224  0.88
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