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Items: 1 to 50 of 75

1.

Identification of Primary Antimicrobial Resistance Drivers in Agricultural Nontyphoidal Salmonella enterica Serovars by Using Machine Learning.

Maguire F, Rehman MA, Carrillo C, Diarra MS, Beiko RG.

mSystems. 2019 Aug 6;4(4). pii: e00211-19. doi: 10.1128/mSystems.00211-19.

2.

RADProc: A computationally efficient de novo locus assembler for population studies using RADseq data.

Nadukkalam Ravindran P, Bentzen P, Bradbury IR, Beiko RG.

Mol Ecol Resour. 2019 Jan;19(1):272-282. doi: 10.1111/1755-0998.12954. Epub 2018 Dec 21.

PMID:
30312001
3.

Predicting the Functional Potential of the Microbiome from Marker Genes Using PICRUSt.

Douglas GM, Beiko RG, Langille MGI.

Methods Mol Biol. 2018;1849:169-177. doi: 10.1007/978-1-4939-8728-3_11.

PMID:
30298254
4.

16S rRNA Gene Analysis with QIIME2.

Hall M, Beiko RG.

Methods Mol Biol. 2018;1849:113-129. doi: 10.1007/978-1-4939-8728-3_8.

PMID:
30298251
5.

Cellulase-Hemicellulase Activities and Bacterial Community Composition of Different Soils from Algerian Ecosystems.

Houfani AA, Větrovský T, Navarrete OU, Štursová M, Tláskal V, Beiko RG, Boucherba N, Baldrian P, Benallaoua S, Jorquera MA.

Microb Ecol. 2019 Apr;77(3):713-725. doi: 10.1007/s00248-018-1251-8. Epub 2018 Sep 12.

PMID:
30209585
6.

Environmental extremes drive population structure at the northern range limit of Atlantic salmon in North America.

Sylvester EVA, Beiko RG, Bentzen P, Paterson I, Horne JB, Watson B, Lehnert S, Duffy S, Clément M, Robertson MJ, Bradbury IR.

Mol Ecol. 2018 Oct;27(20):4026-4040. doi: 10.1111/mec.14849. Epub 2018 Sep 17.

PMID:
30152128
7.

PMERGE: Computational filtering of paralogous sequences from RAD-seq data.

Nadukkalam Ravindran P, Bentzen P, Bradbury IR, Beiko RG.

Ecol Evol. 2018 Jun 11;8(14):7002-7013. doi: 10.1002/ece3.4219. eCollection 2018 Jul.

8.

A climate-associated multispecies cryptic cline in the northwest Atlantic.

Stanley RRE, DiBacco C, Lowen B, Beiko RG, Jeffery NW, Van Wyngaarden M, Bentzen P, Brickman D, Benestan L, Bernatchez L, Johnson C, Snelgrove PVR, Wang Z, Wringe BF, Bradbury IR.

Sci Adv. 2018 Mar 28;4(3):eaaq0929. doi: 10.1126/sciadv.aaq0929. eCollection 2018 Mar.

9.

Oceanographic variation influences spatial genomic structure in the sea scallop, Placopecten magellanicus.

Van Wyngaarden M, Snelgrove PVR, DiBacco C, Hamilton LC, Rodríguez-Ezpeleta N, Zhan L, Beiko RG, Bradbury IR.

Ecol Evol. 2018 Feb 11;8(5):2824-2841. doi: 10.1002/ece3.3846. eCollection 2018 Mar.

10.

Applications of random forest feature selection for fine-scale genetic population assignment.

Sylvester EVA, Bentzen P, Bradbury IR, Clément M, Pearce J, Horne J, Beiko RG.

Evol Appl. 2017 Sep 14;11(2):153-165. doi: 10.1111/eva.12524. eCollection 2018 Feb.

11.

Range-wide parallel climate-associated genomic clines in Atlantic salmon.

Jeffery NW, Stanley RRE, Wringe BF, Guijarro-Sabaniel J, Bourret V, Bernatchez L, Bentzen P, Beiko RG, Gilbey J, Clément M, Bradbury IR.

R Soc Open Sci. 2017 Nov 15;4(11):171394. doi: 10.1098/rsos.171394. eCollection 2017 Nov.

12.

SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology.

Petkau A, Mabon P, Sieffert C, Knox NC, Cabral J, Iskander M, Iskander M, Weedmark K, Zaheer R, Katz LS, Nadon C, Reimer A, Taboada E, Beiko RG, Hsiao W, Brinkman F, Graham M, Van Domselaar G.

Microb Genom. 2017 Jun 8;3(6):e000116. doi: 10.1099/mgen.0.000116. eCollection 2017 Jun 30.

13.

Ananke: temporal clustering reveals ecological dynamics of microbial communities.

Hall MW, Rohwer RR, Perrie J, McMahon KD, Beiko RG.

PeerJ. 2017 Sep 26;5:e3812. doi: 10.7717/peerj.3812. eCollection 2017.

14.

Scaling Up the Phylogenetic Detection of Lateral Gene Transfer Events.

Chan CX, Beiko RG, Ragan MA.

Methods Mol Biol. 2017;1525:421-432.

PMID:
27896730
15.

Discovery of an expanded set of avian leucosis subgroup E proviruses in chickens using Vermillion, a novel sequence capture and analysis pipeline.

Rutherford K, Meehan CJ, Langille MG, Tyack SG, McKay JC, McLean NL, Benkel K, Beiko RG, Benkel B.

Poult Sci. 2016 Oct 19. pii: pew404. [Epub ahead of print] No abstract available.

PMID:
27765872
16.

Discovery of an expanded set of avian leukosis subroup E proviruses in chickens using Vermillion, a novel sequence capture and analysis pipeline.

Rutherford K, Meehan CJ, Langille MG, Tyack SG, McKay JC, McLean NL, Benkel K, Beiko RG, Benkel B.

Poult Sci. 2016 Oct 1;95(10):2250-8. doi: 10.3382/ps/pew194. Epub 2016 Jun 27. Erratum in: Poult Sci. 2016 Oct 19;:.

PMID:
27354549
17.

megasat: automated inference of microsatellite genotypes from sequence data.

Zhan L, Paterson IG, Fraser BA, Watson B, Bradbury IR, Nadukkalam Ravindran P, Reznick D, Beiko RG, Bentzen P.

Mol Ecol Resour. 2017 Mar;17(2):247-256. doi: 10.1111/1755-0998.12561. Epub 2016 Jul 19.

PMID:
27333119
18.

Correction: Genomic Comparison of Non-Typhoidal Salmonella enterica Serovars Typhimurium, Enteritidis, Heidelberg, Hadar and Kentucky Isolates from Broiler Chickens.

Dhanani AS, Block G, Dewar K, Forgetta V, Topp E, Beiko RG, Diarra MS.

PLoS One. 2016 Feb 8;11(2):e0148706. doi: 10.1371/journal.pone.0148706. eCollection 2016. No abstract available.

19.

simDEF: definition-based semantic similarity measure of gene ontology terms for functional similarity analysis of genes.

Pesaranghader A, Matwin S, Sokolova M, Beiko RG.

Bioinformatics. 2016 May 1;32(9):1380-7. doi: 10.1093/bioinformatics/btv755. Epub 2015 Dec 26.

PMID:
26708333
20.

Microbial malaise: how can we classify the microbiome?

Beiko RG.

Trends Microbiol. 2015 Nov;23(11):671-679. doi: 10.1016/j.tim.2015.08.009. Epub 2015 Oct 1.

PMID:
26439295
21.

Phylogenetic approaches to microbial community classification.

Ning J, Beiko RG.

Microbiome. 2015 Oct 5;3:47. doi: 10.1186/s40168-015-0114-5.

22.

Correction: Genomic Comparison of Non-Typhoidal Salmonella enterica Serovars Typhimurium, Enteritidis, Heidelberg, Hadar and Kentucky Isolates from Broiler Chickens.

Dhanani AS, Block G, Dewar K, Forgetta V, Topp E, Beiko RG, Diarra MS.

PLoS One. 2015 Sep 9;10(9):e0137697. doi: 10.1371/journal.pone.0137697. eCollection 2015. No abstract available.

23.

Frailty and the Microbiome.

Meehan CJ, Langille MG, Beiko RG.

Interdiscip Top Gerontol Geriatr. 2015;41:54-65. doi: 10.1159/000381162. Epub 2015 Jul 17. Review.

PMID:
26301979
24.

Transfer of energy pathway genes in microbial enhanced biological phosphorus removal communities.

Wong DH, Beiko RG.

BMC Genomics. 2015 Jul 16;16:526. doi: 10.1186/s12864-015-1752-5.

25.

Genomic Comparison of Non-Typhoidal Salmonella enterica Serovars Typhimurium, Enteritidis, Heidelberg, Hadar and Kentucky Isolates from Broiler Chickens.

Dhanani AS, Block G, Dewar K, Forgetta V, Topp E, Beiko RG, Diarra MS.

PLoS One. 2015 Jun 17;10(6):e0128773. doi: 10.1371/journal.pone.0128773. eCollection 2015. Erratum in: PLoS One. 2015;10(9):e0137697. PLoS One. 2016;11(2):e0148706.

26.

Microbial shifts in the aging mouse gut.

Langille MG, Meehan CJ, Koenig JE, Dhanani AS, Rose RA, Howlett SE, Beiko RG.

Microbiome. 2014 Dec 5;2(1):50. doi: 10.1186/s40168-014-0050-9. eCollection 2014.

27.

Opinion: Conservation and stewardship of the human microbiome.

O'Doherty KC, Neufeld JD, Brinkman FS, Gardner H, Guttman DS, Beiko RG.

Proc Natl Acad Sci U S A. 2014 Oct 7;111(40):14312-3. doi: 10.1073/pnas.1413200111. No abstract available.

28.

STAMP: statistical analysis of taxonomic and functional profiles.

Parks DH, Tyson GW, Hugenholtz P, Beiko RG.

Bioinformatics. 2014 Nov 1;30(21):3123-4. doi: 10.1093/bioinformatics/btu494. Epub 2014 Jul 23.

29.

Supertrees Based on the Subtree Prune-and-Regraft Distance.

Whidden C, Zeh N, Beiko RG.

Syst Biol. 2014 Jul;63(4):566-81. doi: 10.1093/sysbio/syu023. Epub 2014 Apr 2.

30.
31.

Being Aquifex aeolicus: Untangling a hyperthermophile's checkered past.

Eveleigh RJ, Meehan CJ, Archibald JM, Beiko RG.

Genome Biol Evol. 2013;5(12):2478-97. doi: 10.1093/gbe/evt195.

32.

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.

Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C.

Nat Biotechnol. 2013 Sep;31(9):814-21. doi: 10.1038/nbt.2676. Epub 2013 Aug 25.

33.

GenGIS 2: geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework.

Parks DH, Mankowski T, Zangooei S, Porter MS, Armanini DG, Baird DJ, Langille MG, Beiko RG.

PLoS One. 2013 Jul 29;8(7):e69885. doi: 10.1371/journal.pone.0069885. Print 2013.

34.

Interactions in the microbiome: communities of organisms and communities of genes.

Boon E, Meehan CJ, Whidden C, Wong DH, Langille MG, Beiko RG.

FEMS Microbiol Rev. 2014 Jan;38(1):90-118. doi: 10.1111/1574-6976.12035. Epub 2013 Aug 28. Review.

35.

SPANNER: taxonomic assignment of sequences using pyramid matching of similarity profiles.

Porter MS, Beiko RG.

Bioinformatics. 2013 Aug 1;29(15):1858-64. doi: 10.1093/bioinformatics/btt313. Epub 2013 Jun 3.

36.

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs.

Curtis BA, Tanifuji G, Burki F, Gruber A, Irimia M, Maruyama S, Arias MC, Ball SG, Gile GH, Hirakawa Y, Hopkins JF, Kuo A, Rensing SA, Schmutz J, Symeonidi A, Elias M, Eveleigh RJ, Herman EK, Klute MJ, Nakayama T, Oborník M, Reyes-Prieto A, Armbrust EV, Aves SJ, Beiko RG, Coutinho P, Dacks JB, Durnford DG, Fast NM, Green BR, Grisdale CJ, Hempel F, Henrissat B, Höppner MP, Ishida K, Kim E, Kořený L, Kroth PG, Liu Y, Malik SB, Maier UG, McRose D, Mock T, Neilson JA, Onodera NT, Poole AM, Pritham EJ, Richards TA, Rocap G, Roy SW, Sarai C, Schaack S, Shirato S, Slamovits CH, Spencer DF, Suzuki S, Worden AZ, Zauner S, Barry K, Bell C, Bharti AK, Crow JA, Grimwood J, Kramer R, Lindquist E, Lucas S, Salamov A, McFadden GI, Lane CE, Keeling PJ, Gray MW, Grigoriev IV, Archibald JM.

Nature. 2012 Dec 6;492(7427):59-65. doi: 10.1038/nature11681. Epub 2012 Nov 28.

PMID:
23201678
37.

Comparative genomic and phylogenetic approaches to characterize the role of genetic recombination in mycobacterial evolution.

Smith SE, Showers-Corneli P, Dardenne CN, Harpending HH, Martin DP, Beiko RG.

PLoS One. 2012;7(11):e50070. doi: 10.1371/journal.pone.0050070. Epub 2012 Nov 26.

38.

Lateral gene transfer of an ABC transporter complex between major constituents of the human gut microbiome.

Meehan CJ, Beiko RG.

BMC Microbiol. 2012 Nov 1;12:248. doi: 10.1186/1471-2180-12-248.

39.

Measuring community similarity with phylogenetic networks.

Parks DH, Beiko RG.

Mol Biol Evol. 2012 Dec;29(12):3947-58. doi: 10.1093/molbev/mss200. Epub 2012 Aug 21.

PMID:
22915830
40.

Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities.

Parks DH, Beiko RG.

ISME J. 2013 Jan;7(1):173-83. doi: 10.1038/ismej.2012.88. Epub 2012 Aug 2.

41.

Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation.

Lommer M, Specht M, Roy AS, Kraemer L, Andreson R, Gutowska MA, Wolf J, Bergner SV, Schilhabel MB, Klostermeier UC, Beiko RG, Rosenstiel P, Hippler M, LaRoche J.

Genome Biol. 2012 Jul 26;13(7):R66. doi: 10.1186/gb-2012-13-7-r66.

42.

Comparative metagenomics of three Dehalococcoides-containing enrichment cultures: the role of the non-dechlorinating community.

Hug LA, Beiko RG, Rowe AR, Richardson RE, Edwards EA.

BMC Genomics. 2012 Jul 23;13:327. doi: 10.1186/1471-2164-13-327.

43.

Rapid identification of high-confidence taxonomic assignments for metagenomic data.

MacDonald NJ, Parks DH, Beiko RG.

Nucleic Acids Res. 2012 Aug;40(14):e111. doi: 10.1093/nar/gks335. Epub 2012 Apr 24.

44.

Human microbiome: a genetic bazaar for microbes?

Langille MG, Meehan CJ, Beiko RG.

Curr Biol. 2012 Jan 10;22(1):R20-2. doi: 10.1016/j.cub.2011.11.023. Review.

45.

Classifying short genomic fragments from novel lineages using composition and homology.

Parks DH, MacDonald NJ, Beiko RG.

BMC Bioinformatics. 2011 Aug 9;12:328. doi: 10.1186/1471-2105-12-328.

46.

Telling the whole story in a 10,000-genome world.

Beiko RG.

Biol Direct. 2011 Jun 30;6:34. doi: 10.1186/1745-6150-6-34.

47.

Lateral transfer of genes and gene fragments in Staphylococcus extends beyond mobile elements.

Chan CX, Beiko RG, Ragan MA.

J Bacteriol. 2011 Aug;193(15):3964-77. doi: 10.1128/JB.01524-10. Epub 2011 May 27.

48.

Assembling networks of microbial genomes using linear programming.

Holloway C, Beiko RG.

BMC Evol Biol. 2010 Nov 20;10:360. doi: 10.1186/1471-2148-10-360.

49.
50.

Efficient learning of microbial genotype-phenotype association rules.

MacDonald NJ, Beiko RG.

Bioinformatics. 2010 Aug 1;26(15):1834-40. doi: 10.1093/bioinformatics/btq305. Epub 2010 Jun 6.

PMID:
20529891

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