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Items: 39

1.

Exploring the Evolution of Virulence Factors through Bioinformatic Data Mining.

Doxey AC, Mansfield MJ, Lobb B.

mSystems. 2019 May 21;4(3). pii: e00162-19. doi: 10.1128/mSystems.00162-19.

2.

AnnoTree: visualization and exploration of a functionally annotated microbial tree of life.

Mendler K, Chen H, Parks DH, Lobb B, Hug LA, Doxey AC.

Nucleic Acids Res. 2019 May 21;47(9):4442-4448. doi: 10.1093/nar/gkz246.

3.

Bioinformatic discovery of a toxin family in Chryseobacterium piperi with sequence similarity to botulinum neurotoxins.

Mansfield MJ, Wentz TG, Zhang S, Lee EJ, Dong M, Sharma SK, Doxey AC.

Sci Rep. 2019 Feb 7;9(1):1634. doi: 10.1038/s41598-018-37647-8.

4.

The impact of cigarette smoke exposure, COPD, or asthma status on ABC transporter gene expression in human airway epithelial cells.

Aguiar JA, Tamminga A, Lobb B, Huff RD, Nguyen JP, Kim Y, Dvorkin-Gheva A, Stampfli MR, Doxey AC, Hirota JA.

Sci Rep. 2019 Jan 17;9(1):153. doi: 10.1038/s41598-018-36248-9.

5.

Metagenomic Sequencing of Wastewater from a South African Research Farm.

Lobb B, Adegoke AA, Ma K, Doxey AC, Aiyegoro OA.

Microbiol Resour Announc. 2018 Oct 25;7(16). pii: e01323-18. doi: 10.1128/MRA.01323-18. eCollection 2018 Oct.

6.

Identification of a diphtheria toxin-like gene family beyond the Corynebacterium genus.

Mansfield MJ, Sugiman-Marangos SN, Melnyk RA, Doxey AC.

FEBS Lett. 2018 Aug;592(16):2693-2705. doi: 10.1002/1873-3468.13208. Epub 2018 Aug 16.

PMID:
30058084
7.

Draft Genome Sequences of Two Novel Cellulolytic Streptomyces Strains Isolated from South African Rhizosphere Soil.

Adegboye MF, Lobb B, Babalola OO, Doxey AC, Ma K.

Genome Announc. 2018 Jun 28;6(26). pii: e00632-18. doi: 10.1128/genomeA.00632-18.

8.

Genomic insights into the evolution and ecology of botulinum neurotoxins.

Mansfield MJ, Doxey AC.

Pathog Dis. 2018 Jun 1;76(4). doi: 10.1093/femspd/fty040.

PMID:
29684130
9.

Discovery of novel bacterial toxins by genomics and computational biology.

Doxey AC, Mansfield MJ, Montecucco C.

Toxicon. 2018 Jun 1;147:2-12. doi: 10.1016/j.toxicon.2018.02.002. Epub 2018 Feb 10. Review.

PMID:
29438679
10.

Identification of a Botulinum Neurotoxin-like Toxin in a Commensal Strain of Enterococcus faecium.

Zhang S, Lebreton F, Mansfield MJ, Miyashita SI, Zhang J, Schwartzman JA, Tao L, Masuyer G, Martínez-Carranza M, Stenmark P, Gilmore MS, Doxey AC, Dong M.

Cell Host Microbe. 2018 Feb 14;23(2):169-176.e6. doi: 10.1016/j.chom.2017.12.018. Epub 2018 Jan 27.

11.

Aerobic proteobacterial methylotrophs in Movile Cave: genomic and metagenomic analyses.

Kumaresan D, Stephenson J, Doxey AC, Bandukwala H, Brooks E, Hillebrand-Voiculescu A, Whiteley AS, Murrell JC.

Microbiome. 2018 Jan 2;6(1):1. doi: 10.1186/s40168-017-0383-2.

12.

Epigenetic profiling of growth plate chondrocytes sheds insight into regulatory genetic variation influencing height.

Guo M, Liu Z, Willen J, Shaw CP, Richard D, Jagoda E, Doxey AC, Hirschhorn J, Capellini TD.

Elife. 2017 Dec 5;6. pii: e29329. doi: 10.7554/eLife.29329.

13.

Rainbow trout exposed to benzo[a]pyrene yields conserved microRNA binding sites in DNA methyltransferases across 500 million years of evolution.

Kuc C, Richard DJ, Johnson S, Bragg L, Servos MR, Doxey AC, Craig PM.

Sci Rep. 2017 Dec 4;7(1):16843. doi: 10.1038/s41598-017-17236-x.

14.

Transcriptome Analysis of Polyhydroxybutyrate Cycle Mutants Reveals Discrete Loci Connecting Nitrogen Utilization and Carbon Storage in Sinorhizobium meliloti.

D'Alessio M, Nordeste R, Doxey AC, Charles TC.

mSystems. 2017 Sep 12;2(5). pii: e00035-17. doi: 10.1128/mSystems.00035-17. eCollection 2017 Sep-Oct.

15.

Discovery of a proteolytic flagellin family in diverse bacterial phyla that assembles enzymatically active flagella.

Eckhard U, Bandukwala H, Mansfield MJ, Marino G, Cheng J, Wallace I, Holyoak T, Charles TC, Austin J, Overall CM, Doxey AC.

Nat Commun. 2017 Sep 12;8(1):521. doi: 10.1038/s41467-017-00599-0.

16.

Estrogen Receptor β Is a Novel Target in Acute Myeloid Leukemia.

Rota SG, Roma A, Dude I, Ma C, Stevens R, MacEachern J, Graczyk J, Espiritu SMG, Rao PN, Minden MD, Kreinin E, Hess DA, Doxey AC, Spagnuolo PA.

Mol Cancer Ther. 2017 Nov;16(11):2618-2626. doi: 10.1158/1535-7163.MCT-17-0292. Epub 2017 Aug 23.

17.

Metagenomic data-mining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems.

Jameson E, Doxey AC, Airs R, Purdy KJ, Murrell JC, Chen Y.

Microb Genom. 2016 Sep 20;2(9):e000080. doi: 10.1099/mgen.0.000080. eCollection 2016 Sep.

18.

The Skin Microbiome of Cohabiting Couples.

Ross AA, Doxey AC, Neufeld JD.

mSystems. 2017 Jul 20;2(4). pii: e00043-17. doi: 10.1128/mSystems.00043-17. eCollection 2017 Jul-Aug.

19.

Ancient selection for derived alleles at a GDF5 enhancer influencing human growth and osteoarthritis risk.

Capellini TD, Chen H, Cao J, Doxey AC, Kiapour AM, Schoor M, Kingsley DM.

Nat Genet. 2017 Aug;49(8):1202-1210. doi: 10.1038/ng.3911. Epub 2017 Jul 3.

20.

Functional metagenomics reveals novel β-galactosidases not predictable from gene sequences.

Cheng J, Romantsov T, Engel K, Doxey AC, Rose DR, Neufeld JD, Charles TC.

PLoS One. 2017 Mar 8;12(3):e0172545. doi: 10.1371/journal.pone.0172545. eCollection 2017.

21.

Lineage-specific mutational clustering in protein structures predicts evolutionary shifts in function.

Adams J, Mansfield MJ, Richard DJ, Doxey AC.

Bioinformatics. 2017 May 1;33(9):1338-1345. doi: 10.1093/bioinformatics/btw815.

PMID:
28052926
22.

Agricultural soil denitrifiers possess extensive nitrite reductase gene diversity.

Coyotzi S, Doxey AC, Clark ID, Lapen DR, Van Cappellen P, Neufeld JD.

Environ Microbiol. 2017 Mar;19(3):1189-1208. doi: 10.1111/1462-2920.13643. Epub 2017 Feb 1.

PMID:
27943515
23.

Novel function discovery through sequence and structural data mining.

Lobb B, Doxey AC.

Curr Opin Struct Biol. 2016 Jun;38:53-61. doi: 10.1016/j.sbi.2016.05.017. Epub 2016 Jun 10. Review.

PMID:
27289211
24.

MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes.

Petrenko P, Lobb B, Kurtz DA, Neufeld JD, Doxey AC.

BMC Biol. 2015 Nov 5;13:92. doi: 10.1186/s12915-015-0195-4.

25.

Remote homology and the functions of metagenomic dark matter.

Lobb B, Kurtz DA, Moreno-Hagelsieb G, Doxey AC.

Front Genet. 2015 Jul 21;6:234. doi: 10.3389/fgene.2015.00234. eCollection 2015.

26.

Botulinum neurotoxin homologs in non-Clostridium species.

Mansfield MJ, Adams JB, Doxey AC.

FEBS Lett. 2015 Jan 30;589(3):342-8. doi: 10.1016/j.febslet.2014.12.018. Epub 2014 Dec 23.

27.

mimicMe: a web server for prediction and analysis of host-like proteins in microbial pathogens.

Petrenko P, Doxey AC.

Bioinformatics. 2015 Feb 15;31(4):590-2. doi: 10.1093/bioinformatics/btu681. Epub 2014 Oct 17.

PMID:
25399027
28.

Aquatic metagenomes implicate Thaumarchaeota in global cobalamin production.

Doxey AC, Kurtz DA, Lynch MD, Sauder LA, Neufeld JD.

ISME J. 2015 Feb;9(2):461-71. doi: 10.1038/ismej.2014.142. Epub 2014 Aug 15.

29.

Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements.

Guturu H, Doxey AC, Wenger AM, Bejerano G.

Philos Trans R Soc Lond B Biol Sci. 2013 Nov 11;368(1632):20130029. doi: 10.1098/rstb.2013.0029. Print 2013 Dec 19.

30.

Prediction of molecular mimicry candidates in human pathogenic bacteria.

Doxey AC, McConkey BJ.

Virulence. 2013 Aug 15;4(6):453-66. doi: 10.4161/viru.25180. Epub 2013 May 28.

31.

Horizontal gene transfer contributed to the evolution of extracellular surface structures: the freshwater polyp Hydra is covered by a complex fibrous cuticle containing glycosaminoglycans and proteins of the PPOD and SWT (sweet tooth) families.

Böttger A, Doxey AC, Hess MW, Pfaller K, Salvenmoser W, Deutzmann R, Geissner A, Pauly B, Altstätter J, Münder S, Heim A, Gabius HJ, McConkey BJ, David CN.

PLoS One. 2012;7(12):e52278. doi: 10.1371/journal.pone.0052278. Epub 2012 Dec 27.

32.

Modular evolution and the origins of symmetry: reconstruction of a three-fold symmetric globular protein.

Broom A, Doxey AC, Lobsanov YD, Berthin LG, Rose DR, Howell PL, McConkey BJ, Meiering EM.

Structure. 2012 Jan 11;20(1):161-71. doi: 10.1016/j.str.2011.10.021. Epub 2011 Dec 15.

33.

Nuclear targeting of methyl-recycling enzymes in Arabidopsis thaliana is mediated by specific protein interactions.

Lee S, Doxey AC, McConkey BJ, Moffatt BA.

Mol Plant. 2012 Jan;5(1):231-48. doi: 10.1093/mp/ssr083. Epub 2011 Oct 5.

34.

Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d.

Doxey AC, Cheng Z, Moffatt BA, McConkey BJ.

BMC Struct Biol. 2010 Aug 3;10:23. doi: 10.1186/1472-6807-10-23.

35.

Assessing the evolution of gene expression using microarray data.

Woody OZ, Doxey AC, McConkey BJ.

Evol Bioinform Online. 2008 Apr 24;4:139-52.

36.

Insights into the evolutionary origins of clostridial neurotoxins from analysis of the Clostridium botulinum strain A neurotoxin gene cluster.

Doxey AC, Lynch MD, Müller KM, Meiering EM, McConkey BJ.

BMC Evol Biol. 2008 Nov 14;8:316. doi: 10.1186/1471-2148-8-316.

37.

Functional divergence in the Arabidopsis beta-1,3-glucanase gene family inferred by phylogenetic reconstruction of expression states.

Doxey AC, Yaish MW, Moffatt BA, Griffith M, McConkey BJ.

Mol Biol Evol. 2007 Apr;24(4):1045-55. Epub 2007 Feb 1.

PMID:
17272678
38.

Ordered surface carbons distinguish antifreeze proteins and their ice-binding regions.

Doxey AC, Yaish MW, Griffith M, McConkey BJ.

Nat Biotechnol. 2006 Jul;24(7):852-5. Epub 2006 Jul 2.

PMID:
16823370
39.

Cold-active winter rye glucanases with ice-binding capacity.

Yaish MW, Doxey AC, McConkey BJ, Moffatt BA, Griffith M.

Plant Physiol. 2006 Aug;141(4):1459-72. Epub 2006 Jun 30.

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