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Daniel Halligan - Publications

Affiliations: 
University of Edinburgh, Edinburgh, Scotland, United Kingdom 
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29 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 Wiberg RA, Halligan DL, Ness RW, Necsulea A, Kaessmann H, Keightley PD. Assessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome. Genome Biology and Evolution. 7: 2432-44. PMID 26272717 DOI: 10.1093/gbe/evv155  0.769
2015 Deinum EE, Halligan DL, Ness RW, Zhang YH, Cong L, Zhang JX, Keightley PD. Recent Evolution in Rattus norvegicus Is Shaped by Declining Effective Population Size. Molecular Biology and Evolution. PMID 26037536 DOI: 10.1093/molbev/msv126  0.777
2015 Santpere G, Carnero-Montoro E, Petit N, Serra F, Hvilsom C, Rambla J, Heredia-Genestar JM, Halligan DL, Dopazo H, Navarro A, Bosch E. Analysis of Five Gene Sets in Chimpanzees Suggests Decoupling between the Action of Selection on Protein-Coding and on Noncoding Elements. Genome Biology and Evolution. 7: 1490-505. PMID 25977458 DOI: 10.1093/Gbe/Evv082  0.415
2014 Campos JL, Halligan DL, Haddrill PR, Charlesworth B. The relation between recombination rate and patterns of molecular evolution and variation in Drosophila melanogaster. Molecular Biology and Evolution. 31: 1010-28. PMID 24489114 DOI: 10.1093/Molbev/Msu056  0.479
2014 Kousathanas A, Halligan DL, Keightley PD. Faster-X adaptive protein evolution in house mice. Genetics. 196: 1131-43. PMID 24361937 DOI: 10.1534/Genetics.113.158246  0.756
2014 Keightley PD, Ness RW, Halligan DL, Haddrill PR. Estimation of the spontaneous mutation rate per nucleotide site in a Drosophila melanogaster full-sib family. Genetics. 196: 313-20. PMID 24214343 DOI: 10.1534/genetics.113.158758  0.772
2013 Halligan DL, Kousathanas A, Ness RW, Harr B, Eöry L, Keane TM, Adams DJ, Keightley PD. Contributions of protein-coding and regulatory change to adaptive molecular evolution in murid rodents. Plos Genetics. 9: e1003995. PMID 24339797 DOI: 10.1371/Journal.Pgen.1003995  0.762
2013 Kelleher J, Ness RW, Halligan DL. Processing genome scale tabular data with wormtable. Bmc Bioinformatics. 14: 356. PMID 24308302 DOI: 10.1186/1471-2105-14-356  0.624
2011 Keightley PD, Halligan DL. Inference of site frequency spectra from high-throughput sequence data: quantification of selection on nonsynonymous and synonymous sites in humans. Genetics. 188: 931-40. PMID 21596896 DOI: 10.1534/genetics.111.128355  0.684
2011 Halligan DL, Oliver F, Guthrie J, Stemshorn KC, Harr B, Keightley PD. Positive and negative selection in murine ultraconserved noncoding elements. Molecular Biology and Evolution. 28: 2651-60. PMID 21478460 DOI: 10.1093/molbev/msr093  0.728
2011 Keightley PD, Eöry L, Halligan DL, Kirkpatrick M. Inference of mutation parameters and selective constraint in mammalian coding sequences by approximate Bayesian computation. Genetics. 187: 1153-61. PMID 21288873 DOI: 10.1534/Genetics.110.124073  0.807
2011 Kousathanas A, Oliver F, Halligan DL, Keightley PD. Positive and negative selection on noncoding DNA close to protein-coding genes in wild house mice. Molecular Biology and Evolution. 28: 1183-91. PMID 21059791 DOI: 10.1093/Molbev/Msq299  0.793
2010 Halligan DL, Oliver F, Eyre-Walker A, Harr B, Keightley PD. Evidence for pervasive adaptive protein evolution in wild mice. Plos Genetics. 6: e1000825. PMID 20107605 DOI: 10.1371/Journal.Pgen.1000825  0.662
2010 Eory L, Halligan DL, Keightley PD. Distributions of selectively constrained sites and deleterious mutation rates in the hominid and murid genomes. Molecular Biology and Evolution. 27: 177-92. PMID 19759235 DOI: 10.1093/Molbev/Msp219  0.814
2009 Marion de Procé S, Halligan DL, Keightley PD, Charlesworth B. Patterns of DNA-sequence divergence between Drosophila miranda and D. pseudoobscura. Journal of Molecular Evolution. 69: 601-11. PMID 19859648 DOI: 10.1007/s00239-009-9298-2  0.664
2009 Keightley PD, Halligan DL. Analysis and implications of mutational variation. Genetica. 136: 359-69. PMID 18663587 DOI: 10.1007/s10709-008-9304-4  0.664
2009 Halligan DL, Keightley PD. Spontaneous Mutation Accumulation Studies in Evolutionary Genetics Annual Review of Ecology, Evolution, and Systematics. 40: 151-172. DOI: 10.1146/ANNUREV.ECOLSYS.39.110707.173437  0.619
2008 Pannebakker BA, Halligan DL, Reynolds KT, Ballantyne GA, Shuker DM, Barton NH, West SA. Effects of spontaneous mutation accumulation on sex ratio traits in a parasitoid wasp. Evolution; International Journal of Organic Evolution. 62: 1921-35. PMID 18522711 DOI: 10.1111/J.1558-5646.2008.00434.X  0.33
2008 Haag-Liautard C, Dorris M, Maside X, MacAskill S, Halligan DL, Houle D, Charlesworth B, Keightley PD. Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila (Nature (2007) 445, (82-85)) Nature. 453: 128. DOI: 10.1038/nature06946  0.679
2007 Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, ... ... Halligan DL, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/Nature06341  0.658
2007 Wang J, Keightley PD, Halligan DL. Effect of divergence time and recombination rate on molecular evolution of Drosophila INE-1 transposable elements and other candidates for neutrally evolving sites. Journal of Molecular Evolution. 65: 627-39. PMID 17896069 DOI: 10.1007/s00239-007-9028-6  0.688
2007 Haddrill PR, Halligan DL, Tomaras D, Charlesworth B. Reduced efficacy of selection in regions of the Drosophila genome that lack crossing over. Genome Biology. 8: R18. PMID 17284312 DOI: 10.1186/gb-2007-8-2-r18  0.441
2007 Haag-Liautard C, Dorris M, Maside X, Macaskill S, Halligan DL, Houle D, Charlesworth B, Keightley PD. Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila. Nature. 445: 82-5. PMID 17203060 DOI: 10.1038/Nature05388  0.713
2006 Halligan DL, Keightley PD. Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison. Genome Research. 16: 875-84. PMID 16751341 DOI: 10.1101/gr.5022906  0.688
2005 Keightley PD, Kryukov GV, Sunyaev S, Halligan DL, Gaffney DJ. Evolutionary constraints in conserved nongenic sequences of mammals. Genome Research. 15: 1373-8. PMID 16204190 DOI: 10.1101/Gr.3942005  0.814
2005 Haddrill PR, Charlesworth B, Halligan DL, Andolfatto P. Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content. Genome Biology. 6: R67. PMID 16086849 DOI: 10.1186/Gb-2005-6-8-R67  0.428
2004 Halligan DL, Eyre-Walker A, Andolfatto P, Keightley PD. Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila. Genome Research. 14: 273-9. PMID 14762063 DOI: 10.1101/Gr.1329204  0.719
2003 Halligan DL, Peters AD, Keightley PD. Estimating numbers of EMS-induced mutations affecting life history traits in Caenorhabditis elegans in crosses between inbred sublines. Genetical Research. 82: 191-205. PMID 15134198  0.642
2003 Halligan DL, Keightley PD. How many lethal alleles? Trends in Genetics : Tig. 19: 57-9. PMID 12547508 DOI: 10.1016/S0168-9525(02)00045-8  0.573
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