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Correction: Sex solves Haldane's dilemma.

Hickey DA, Golding GB.

Genome. 2020 Jan 16:1. doi: 10.1139/gen-2019-0225. [Epub ahead of print] No abstract available.


Sex solves Haldane's dilemma.

Hickey DA, Golding GB.

Genome. 2019 Nov;62(11):761-768. doi: 10.1139/gen-2019-0051. Epub 2019 Sep 3. Erratum in: Genome. 2020 Jan 16;:1.


The Caribou (Rangifer tarandus) Genome.

Taylor RS, Horn RL, Zhang X, Golding GB, Manseau M, Wilson PJ.

Genes (Basel). 2019 Jul 17;10(7). pii: E540. doi: 10.3390/genes10070540.


Molecular Traits of Long Non-protein Coding RNAs from Diverse Plant Species Show Little Evidence of Phylogenetic Relationships.

Simopoulos CMA, Weretilnyk EA, Golding GB.

G3 (Bethesda). 2019 Aug 8;9(8):2511-2520. doi: 10.1534/g3.119.400201.


Genetic resiliency and the Black Death: No apparent loss of mitogenomic diversity due to the Black Death in medieval London and Denmark.

Klunk J, Duggan AT, Redfern R, Gamble J, Boldsen JL, Golding GB, Walter BS, Eaton K, Stangroom J, Rouillard JM, Devault A, DeWitte SN, Poinar HN.

Am J Phys Anthropol. 2019 Jun;169(2):240-252. doi: 10.1002/ajpa.23820. Epub 2019 Apr 9.


Divergent subgenome evolution after allopolyploidization in African clawed frogs (Xenopus).

Furman BLS, Dang UJ, Evans BJ, Golding GB.

J Evol Biol. 2018 Dec;31(12):1945-1958. doi: 10.1111/jeb.13391. Epub 2018 Nov 12.


Prediction of plant lncRNA by ensemble machine learning classifiers.

Simopoulos CMA, Weretilnyk EA, Golding GB.

BMC Genomics. 2018 May 2;19(1):316. doi: 10.1186/s12864-018-4665-2.


Inter-replicon Gene Flow Contributes to Transcriptional Integration in the Sinorhizobium meliloti Multipartite Genome.

diCenzo GC, Wellappili D, Golding GB, Finan TM.

G3 (Bethesda). 2018 May 4;8(5):1711-1720. doi: 10.1534/g3.117.300405.


The advantage of recombination when selection is acting at many genetic Loci.

Hickey DA, Golding GB.

J Theor Biol. 2018 Apr 7;442:123-128. doi: 10.1016/j.jtbi.2018.01.018.


Human-Specific Mutations and Positively Selected Sites in MARCO Confer Functional Changes.

Novakowski KE, Yap NVL, Yin C, Sakamoto K, Heit B, Golding GB, Bowdish DME.

Mol Biol Evol. 2018 Feb 1;35(2):440-450. doi: 10.1093/molbev/msx298.


Genetic Discontinuity between the Maritime Archaic and Beothuk Populations in Newfoundland, Canada.

Duggan AT, Harris AJT, Marciniak S, Marshall I, Kuch M, Kitchen A, Renaud G, Southon J, Fuller B, Young J, Fiedel S, Golding GB, Grimes V, Poinar H.

Curr Biol. 2017 Oct 23;27(20):3149-3156.e11. doi: 10.1016/j.cub.2017.08.053. Epub 2017 Oct 12.


Evolution of the Largest Mammalian Genome.

Evans BJ, Upham NS, Golding GB, Ojeda RA, Ojeda AA.

Genome Biol Evol. 2017 Jun 1;9(6):1711-1724. doi: 10.1093/gbe/evx113.


Shotgun metagenomic sequencing reveals freshwater beach sands as reservoir of bacterial pathogens.

Mohiuddin MM, Salama Y, Schellhorn HE, Golding GB.

Water Res. 2017 May 15;115:360-369. doi: 10.1016/j.watres.2017.02.057. Epub 2017 Mar 1.


A molecular portrait of maternal sepsis from Byzantine Troy.

Devault AM, Mortimer TD, Kitchen A, Kiesewetter H, Enk JM, Golding GB, Southon J, Kuch M, Duggan AT, Aylward W, Gardner SN, Allen JE, King AM, Wright G, Kuroda M, Kato K, Briggs DE, Fornaciari G, Holmes EC, Poinar HN, Pepperell CS.

Elife. 2017 Jan 10;6. pii: e20983. doi: 10.7554/eLife.20983.


17th Century Variola Virus Reveals the Recent History of Smallpox.

Duggan AT, Perdomo MF, Piombino-Mascali D, Marciniak S, Poinar D, Emery MV, Buchmann JP, DuchĂȘne S, Jankauskas R, Humphreys M, Golding GB, Southon J, Devault A, Rouillard JM, Sahl JW, Dutour O, Hedman K, Sajantila A, Smith GL, Holmes EC, Poinar HN.

Curr Biol. 2016 Dec 19;26(24):3407-3412. doi: 10.1016/j.cub.2016.10.061. Epub 2016 Dec 8.


Estimation of Gene Insertion/Deletion Rates with Missing Data.

Dang UJ, Devault AM, Mortimer TD, Pepperell CS, Poinar HN, Golding GB.

Genetics. 2016 Oct;204(2):513-529. Epub 2016 Aug 26.


A new way to contemplate Darwin's tangled bank: how DNA barcodes are reconnecting biodiversity science and biomonitoring.

Hajibabaei M, Baird DJ, Fahner NA, Beiko R, Golding GB.

Philos Trans R Soc Lond B Biol Sci. 2016 Sep 5;371(1702). pii: 20150330. doi: 10.1098/rstb.2015.0330. Review.


Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus.

Bos KI, Herbig A, Sahl J, Waglechner N, Fourment M, Forrest SA, Klunk J, Schuenemann VJ, Poinar D, Kuch M, Golding GB, Dutour O, Keim P, Wagner DM, Holmes EC, Krause J, Poinar HN.

Elife. 2016 Jan 21;5:e12994. doi: 10.7554/eLife.12994.


Ribosomal DNA and Plastid Markers Used to Sample Fungal and Plant Communities from Wetland Soils Reveals Complementary Biotas.

Porter TM, Shokralla S, Baird D, Golding GB, Hajibabaei M.

PLoS One. 2016 Jan 5;11(1):e0142759. doi: 10.1371/journal.pone.0142759. eCollection 2016.


markophylo: Markov chain analysis on phylogenetic trees.

Dang UJ, Golding GB.

Bioinformatics. 2016 Jan 1;32(1):130-2. doi: 10.1093/bioinformatics/btv541. Epub 2015 Sep 11.


The Evolution of the Scavenger Receptor Cysteine-Rich Domain of the Class A Scavenger Receptors.

Yap NV, Whelan FJ, Bowdish DM, Golding GB.

Front Immunol. 2015 Jul 6;6:342. doi: 10.3389/fimmu.2015.00342. eCollection 2015.


Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform.

Shokralla S, Porter TM, Gibson JF, Dobosz R, Janzen DH, Hallwachs W, Golding GB, Hajibabaei M.

Sci Rep. 2015 Apr 17;5:9687. doi: 10.1038/srep09687.


Examination of prokaryotic multipartite genome evolution through experimental genome reduction.

diCenzo GC, MacLean AM, Milunovic B, Golding GB, Finan TM.

PLoS Genet. 2014 Oct 23;10(10):e1004742. doi: 10.1371/journal.pgen.1004742. eCollection 2014 Oct.


FuncPatch: a web server for the fast Bayesian inference of conserved functional patches in protein 3D structures.

Huang YF, Golding GB.

Bioinformatics. 2015 Feb 15;31(4):523-31. doi: 10.1093/bioinformatics/btu673. Epub 2014 Oct 15.


Increased substitution rates surrounding low-complexity regions within primate proteins.

Lenz C, Haerty W, Golding GB.

Genome Biol Evol. 2014 Mar;6(3):655-65. doi: 10.1093/gbe/evu042.


Phylogenetic Gaussian process model for the inference of functionally important regions in protein tertiary structures.

Huang YF, Golding GB.

PLoS Comput Biol. 2014 Jan;10(1):e1003429. doi: 10.1371/journal.pcbi.1003429. Epub 2014 Jan 16.


Second-pandemic strain of Vibrio cholerae from the Philadelphia cholera outbreak of 1849.

Devault AM, Golding GB, Waglechner N, Enk JM, Kuch M, Tien JH, Shi M, Fisman DN, Dhody AN, Forrest S, Bos KI, Earn DJ, Holmes EC, Poinar HN.

N Engl J Med. 2014 Jan 23;370(4):334-40. doi: 10.1056/NEJMoa1308663. Epub 2014 Jan 8.


A guide to bioinformatics for immunologists.

Whelan FJ, Yap NV, Surette MG, Golding GB, Bowdish DM.

Front Immunol. 2013 Dec 4;4:416. doi: 10.3389/fimmu.2013.00416. Review.


RNA-Seq effectively monitors gene expression in Eutrema salsugineum plants growing in an extreme natural habitat and in controlled growth cabinet conditions.

Champigny MJ, Sung WW, Catana V, Salwan R, Summers PS, Dudley SA, Provart NJ, Cameron RK, Golding GB, Weretilnyk EA.

BMC Genomics. 2013 Aug 28;14:578. doi: 10.1186/1471-2164-14-578.


Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small-scale reproducibility.

Porter TM, Golding GB, King C, Froese D, Zazula G, Poinar HN.

Mol Ecol Resour. 2013 Sep;13(5):798-810. doi: 10.1111/1755-0998.12124. Epub 2013 May 20.


BOND: Basic OligoNucleotide Design.

Ilie L, Mohamadi H, Golding GB, Smyth WF.

BMC Bioinformatics. 2013 Feb 27;14:69. doi: 10.1186/1471-2105-14-69.


The evolution of the class A scavenger receptors.

Whelan FJ, Meehan CJ, Golding GB, McConkey BJ, Bowdish DM.

BMC Evol Biol. 2012 Nov 27;12:227. doi: 10.1186/1471-2148-12-227.


Transcriptomic and metabolomic analysis of Yukon Thellungiella plants grown in cabinets and their natural habitat show phenotypic plasticity.

Guevara DR, Champigny MJ, Tattersall A, Dedrick J, Wong CE, Li Y, Labbe A, Ping CL, Wang Y, Nuin P, Golding GB, McCarry BE, Summers PS, Moffatt BA, Weretilnyk EA.

BMC Plant Biol. 2012 Oct 1;12:175. doi: 10.1186/1471-2229-12-175.


The effect of sampling from subdivided populations on species identification with DNA barcodes using a Bayesian statistical approach.

Lou M, Golding GB.

Mol Phylogenet Evol. 2012 Nov;65(2):765-73. doi: 10.1016/j.ympev.2012.07.033. Epub 2012 Aug 11.


Factors that affect large subunit ribosomal DNA amplicon sequencing studies of fungal communities: classification method, primer choice, and error.

Porter TM, Golding GB.

PLoS One. 2012;7(4):e35749. doi: 10.1371/journal.pone.0035749. Epub 2012 Apr 27. Erratum in: PLoS One. 2012;7(8). doi:10.1371/annotation/188edbe7-9f2e-4031-9155-d4a9337e6257.


Inferring sequence regions under functional divergence in duplicate genes.

Huang YF, Golding GB.

Bioinformatics. 2012 Jan 15;28(2):176-83. doi: 10.1093/bioinformatics/btr635. Epub 2011 Nov 26.


A draft genome of Yersinia pestis from victims of the Black Death.

Bos KI, Schuenemann VJ, Golding GB, Burbano HA, Waglechner N, Coombes BK, McPhee JB, DeWitte SN, Meyer M, Schmedes S, Wood J, Earn DJ, Herring DA, Bauer P, Poinar HN, Krause J.

Nature. 2011 Oct 12;478(7370):506-10. doi: 10.1038/nature10549. Erratum in: Nature. 2011 Dec 8;480(7376):278.


Antibiotic resistance is ancient.

D'Costa VM, King CE, Kalan L, Morar M, Sung WW, Schwarz C, Froese D, Zazula G, Calmels F, Debruyne R, Golding GB, Poinar HN, Wright GD.

Nature. 2011 Aug 31;477(7365):457-61. doi: 10.1038/nature10388.


Are similarity- or phylogeny-based methods more appropriate for classifying internal transcribed spacer (ITS) metagenomic amplicons?

Porter TM, Golding GB.

New Phytol. 2011 Nov;192(3):775-82. doi: 10.1111/j.1469-8137.2011.03838.x. Epub 2011 Aug 2.


The LysR-type PcaQ protein regulates expression of a protocatechuate-inducible ABC-type transport system in Sinorhizobium meliloti.

MacLean AM, Haerty W, Golding GB, Finan TM.

Microbiology. 2011 Sep;157(Pt 9):2522-2533. doi: 10.1099/mic.0.050542-0. Epub 2011 Jun 23.


Increased polymorphism near low-complexity sequences across the genomes of Plasmodium falciparum isolates.

Haerty W, Golding GB.

Genome Biol Evol. 2011;3:539-50. doi: 10.1093/gbe/evr045. Epub 2011 May 21.


"Patchy-tachy" leads to false positives for recombination.

Sun S, Evans BJ, Golding GB.

Mol Biol Evol. 2011 Sep;28(9):2549-59. doi: 10.1093/molbev/msr076. Epub 2011 Apr 15.


Pervasive cryptic epistasis in molecular evolution.

Lunzer M, Golding GB, Dean AM.

PLoS Genet. 2010 Oct 21;6(10):e1001162. doi: 10.1371/journal.pgen.1001162. Erratum in: PLoS Genet. 2010;6(11). doi: 10.1371/annotation/d618ce28-5010-47df-a44e-148ecdc0fef6.


Low-complexity sequences and single amino acid repeats: not just "junk" peptide sequences.

Haerty W, Golding GB.

Genome. 2010 Oct;53(10):753-62. doi: 10.1139/g10-063. Review.


Inferring bacterial genome flux while considering truncated genes.

Hao W, Golding GB.

Genetics. 2010 Sep;186(1):411-26. doi: 10.1534/genetics.110.118448. Epub 2010 Jun 15.


Assigning sequences to species in the absence of large interspecific differences.

Lou M, Golding GB.

Mol Phylogenet Evol. 2010 Jul;56(1):187-94. doi: 10.1016/j.ympev.2010.01.002. Epub 2010 Jan 11.


Genome-wide evidence for selection acting on single amino acid repeats.

Haerty W, Golding GB.

Genome Res. 2010 Jun;20(6):755-60. doi: 10.1101/gr.101246.109. Epub 2010 Jan 7.


Does gene translocation accelerate the evolution of laterally transferred genes?

Hao W, Golding GB.

Genetics. 2009 Aug;182(4):1365-75. doi: 10.1534/genetics.109.104216. Epub 2009 May 27.



Golding GB, Hanner R, Hebert PD.

Mol Ecol Resour. 2009 May;9 Suppl s1:iv-vi. doi: 10.1111/j.1755-0998.2009.02654.x. No abstract available.


Nucleotide substitution bias within the genus Drosophila affects the pattern of proteome evolution.

Albu M, Min XJ, Golding GB, Hickey D.

Genome Biol Evol. 2009 Aug 4;1:288-93. doi: 10.1093/gbe/evp028.

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