Robert G. Beiko, Ph.D. - Publications

2003 University of Ottawa, Ottawa, ON, Canada 
Molecular Biology, Genetics, Artificial Intelligence

55 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
2018 Douglas GM, Beiko RG, Langille MGI. Predicting the Functional Potential of the Microbiome from Marker Genes Using PICRUSt. Methods in Molecular Biology (Clifton, N.J.). 1849: 169-177. PMID 30298254 DOI: 10.1007/978-1-4939-8728-3_11  0.6
2017 Chan CX, Beiko RG, Ragan MA. Scaling Up the Phylogenetic Detection of Lateral Gene Transfer Events. Methods in Molecular Biology (Clifton, N.J.). 1525: 421-432. PMID 27896730 DOI: 10.1007/978-1-4939-6622-6_16  0.52
2016 Rutherford K, Meehan CJ, Langille MG, Tyack SG, McKay JC, McLean NL, Benkel K, Beiko RG, Benkel B. Discovery of an expanded set of avian leucosis subgroup E proviruses in chickens using Vermillion, a novel sequence capture and analysis pipeline. Poultry Science. PMID 27765872 DOI: 10.3382/ps/pew404  0.6
2016 Rutherford K, Meehan CJ, Langille MG, Tyack SG, McKay JC, McLean NL, Benkel K, Beiko RG, Benkel B. Discovery of an expended set of avian leukosis subroup E proviruses in chickens using Vermillion, a novel sequence capture and analysis pipeline. Poultry Science. PMID 27354549 DOI: 10.3382/ps/pew194  0.6
2016 Whidden C, Beiko RG, Zeh N. Fixed-Parameter and Approximation Algorithms for Maximum Agreement Forests of Multifurcating Trees Algorithmica. 74: 1019-1054. DOI: 10.1007/s00453-015-9983-z  0.68
2015 Pesaranghader A, Matwin S, Sokolova M, Beiko RG. simDEF: definition-based semantic similarity measure of gene ontology terms for functional similarity analysis of genes. Bioinformatics (Oxford, England). PMID 26708333 DOI: 10.1093/bioinformatics/btv755  0.68
2015 Meehan CJ, Langille MG, Beiko RG. Frailty and the Microbiome. Interdisciplinary Topics in Gerontology and Geriatrics. 41: 54-65. PMID 26301979 DOI: 10.1159/000381162  0.6
2015 Wong DH, Beiko RG. Transfer of energy pathway genes in microbial enhanced biological phosphorus removal communities. Bmc Genomics. 16: 526. PMID 26173980 DOI: 10.1186/s12864-015-1752-5  0.68
2015 Meehan CJ, Langille MGI, Beiko RG. Frailty and the microbiome Frailty in Aging: Biological, Clinical and Social Implications. 108: 54-65. DOI: 10.1159/000381162  0.68
2014 Langille MG, Meehan CJ, Koenig JE, Dhanani AS, Rose RA, Howlett SE, Beiko RG. Microbial shifts in the aging mouse gut. Microbiome. 2: 50. PMID 25520805 DOI: 10.1186/s40168-014-0050-9  0.68
2014 O'Doherty KC, Neufeld JD, Brinkman FS, Gardner H, Guttman DS, Beiko RG. Opinion: Conservation and stewardship of the human microbiome. Proceedings of the National Academy of Sciences of the United States of America. 111: 14312-3. PMID 25294925 DOI: 10.1073/pnas.1413200111  0.68
2014 Parks DH, Tyson GW, Hugenholtz P, Beiko RG. STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics (Oxford, England). 30: 3123-4. PMID 25061070 DOI: 10.1093/bioinformatics/btu494  0.68
2014 Whidden C, Zeh N, Beiko RG. Supertrees Based on the Subtree Prune-and-Regraft Distance. Systematic Biology. 63: 566-81. PMID 24695589 DOI: 10.1093/sysbio/syu023  0.68
2014 Meehan CJ, Beiko RG. A phylogenomic view of ecological specialization in the lachnospiraceae, a family of digestive tract-associated bacteria Genome Biology and Evolution. 6: 703-713. PMID 24625961 DOI: 10.1093/gbe/evu050  0.68
2014 Boon E, Meehan CJ, Whidden C, Wong DH, Langille MG, Beiko RG. Interactions in the microbiome: communities of organisms and communities of genes. Fems Microbiology Reviews. 38: 90-118. PMID 23909933 DOI: 10.1111/1574-6976.12035  0.68
2013 Eveleigh RJ, Meehan CJ, Archibald JM, Beiko RG. Being Aquifex aeolicus: Untangling a hyperthermophile's checkered past. Genome Biology and Evolution. 5: 2478-97. PMID 24281050 DOI: 10.1093/gbe/evt195  0.68
2013 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. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature Biotechnology. 31: 814-21. PMID 23975157 DOI: 10.1038/nbt.2676  0.68
2013 Parks DH, Mankowski T, Zangooei S, Porter MS, Armanini DG, Baird DJ, Langille MG, Beiko RG. GenGIS 2: geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework. Plos One. 8: e69885. PMID 23922841 DOI: 10.1371/journal.pone.0069885  0.68
2013 Porter MS, Beiko RG. SPANNER: taxonomic assignment of sequences using pyramid matching of similarity profiles. Bioinformatics (Oxford, England). 29: 1858-64. PMID 23732273 DOI: 10.1093/bioinformatics/btt313  0.68
2013 Parks DH, Beiko RG. Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities. The Isme Journal. 7: 173-83. PMID 22855211 DOI: 10.1038/ismej.2012.88  0.68
2013 Whidden C, Beiko RG, Zeh N. Fixed-parameter algorithms for maximum agreement forests Siam Journal On Computing. 42: 1431-1466. DOI: 10.1137/110845045  0.68
2012 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, ... ... Beiko RG, et al. Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature. 492: 59-65. PMID 23201678 DOI: 10.1038/nature11681  0.68
2012 Smith SE, Showers-Corneli P, Dardenne CN, Harpending HH, Martin DP, Beiko RG. Comparative genomic and phylogenetic approaches to characterize the role of genetic recombination in mycobacterial evolution. Plos One. 7: e50070. PMID 23189179 DOI: 10.1371/journal.pone.0050070  0.68
2012 Meehan CJ, Beiko RG. Lateral gene transfer of an ABC transporter complex between major constituents of the human gut microbiome Bmc Microbiology. 12. PMID 23116195 DOI: 10.1186/1471-2180-12-248  0.68
2012 Parks DH, Beiko RG. Measuring community similarity with phylogenetic networks. Molecular Biology and Evolution. 29: 3947-58. PMID 22915830 DOI: 10.1093/molbev/mss200  0.68
2012 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 and low-iron response of an oceanic diatom adapted to chronic iron limitation. Genome Biology. 13: R66. PMID 22835381 DOI: 10.1186/gb-2012-13-7-r66  0.68
2012 Hug LA, Beiko RG, Rowe AR, Richardson RE, Edwards EA. Comparative metagenomics of three Dehalococcoides-containing enrichment cultures: the role of the non-dechlorinating community. Bmc Genomics. 13: 327. PMID 22823523 DOI: 10.1186/1471-2164-13-327  0.68
2012 MacDonald NJ, Parks DH, Beiko RG. Rapid identification of high-confidence taxonomic assignments for metagenomic data Nucleic Acids Research. 40. PMID 22532608 DOI: 10.1093/nar/gks335  0.68
2012 Langille MGI, Meehan CJ, Beiko RG. Human microbiome: A genetic bazaar for microbes? Current Biology. 22: R20-R22. PMID 22240474 DOI: 10.1016/j.cub.2011.11.023  0.68
2011 Parks DH, MacDonald NJ, Beiko RG. Classifying short genomic fragments from novel lineages using composition and homology Bmc Bioinformatics. 12. PMID 21827705 DOI: 10.1186/1471-2105-12-328  0.68
2011 Chan CX, Beiko RG, Ragan MA. Lateral transfer of genes and gene fragments in Staphylococcus extends beyond mobile elements. Journal of Bacteriology. 193: 3964-77. PMID 21622749 DOI: 10.1128/JB.01524-10  0.68
2010 MacDonald NJ, Beiko RG. Efficient learning of microbial genotype-phenotype association rules Bioinformatics. 26: 1834-1840. PMID 20529891 DOI: 10.1093/bioinformatics/btq305  0.68
2010 Parks DH, Beiko RG. Identifying biologically relevant differences between metagenomic communities. Bioinformatics (Oxford, England). 26: 715-21. PMID 20130030 DOI: 10.1093/bioinformatics/btq041  0.68
2010 Whidden C, Beiko RG, Zeh N. Fast FPT algorithms for computing rooted agreement forests: Theory and experiments (Extended Abstract) Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6049: 141-153. DOI: 10.1007/978-3-642-13193-6_13  0.68
2009 Chan CX, Beiko RG, Darling AE, Ragan MA. Lateral transfer of genes and gene fragments in prokaryotes. Genome Biology and Evolution. 1: 429-38. PMID 20333212 DOI: 10.1093/gbe/evp044  0.52
2009 Bapteste E, O'Malley MA, Beiko RG, Ereshefsky M, Gogarten JP, Franklin-Hall L, Lapointe FJ, Dupré J, Dagan T, Boucher Y, Martin W. Prokaryotic evolution and the tree of life are two different things. Biology Direct. 4: 34. PMID 19788731 DOI: 10.1186/1745-6150-4-34  0.68
2009 Parks DH, Porter M, Churcher S, Wang S, Blouin C, Whalley J, Brooks S, Beiko RG. GenGIS: A geospatial information system for genomic data. Genome Research. 19: 1896-904. PMID 19635847 DOI: 10.1101/gr.095612.109  0.68
2009 Ragan MA, Beiko RG. Lateral genetic transfer: open issues. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 364: 2241-51. PMID 19571244 DOI: 10.1098/rstb.2009.0031  0.68
2009 Beiko RG, Ragan MA. Untangling hybrid phylogenetic signals: horizontal gene transfer and artifacts of phylogenetic reconstruction. Methods in Molecular Biology (Clifton, N.J.). 532: 241-56. PMID 19271189 DOI: 10.1007/978-1-60327-853-9_14  0.68
2009 Chan CX, Darling AE, Beiko RG, Ragan MA. Are protein domains modules of lateral genetic transfer? Plos One. 4: e4524. PMID 19229333 DOI: 10.1371/journal.pone.0004524  0.68
2009 Parks DH, Beiko RG. Quantitative visualizations of hierarchically organized data in a geographic context 2009 17th International Conference On Geoinformatics, Geoinformatics 2009. DOI: 10.1109/GEOINFORMATICS.2009.5293552  0.68
2008 Beiko RG, Doolittle WF, Charlebois RL. The impact of reticulate evolution on genome phylogeny. Systematic Biology. 57: 844-56. PMID 19085328 DOI: 10.1080/10635150802559265  0.68
2008 Beiko RG, Ragan MA. Detecting lateral genetic transfer : a phylogenetic approach. Methods in Molecular Biology (Clifton, N.J.). 452: 457-69. PMID 18566777 DOI: 10.1007/978-1-60327-159-2_21  0.68
2007 Beiko RG, Charlebois RL. A simulation test bed for hypotheses of genome evolution. Bioinformatics (Oxford, England). 23: 825-31. PMID 17267425 DOI: 10.1093/bioinformatics/btm024  0.88
2007 Chan CX, Beiko RG, Ragan MA. Large-scale detection of recombination in nucleotide sequences Aip Conference Proceedings. 971: 101-104. DOI: 10.1063/1.2883829  0.68
2006 Chan CX, Beiko RG, Ragan MA. Detecting recombination in evolving nucleotide sequences. Bmc Bioinformatics. 7: 412. PMID 16978423 DOI: 10.1186/1471-2105-7-412  0.68
2006 Beiko RG, Keith JM, Harlow TJ, Ragan MA. Searching for convergence in phylogenetic Markov chain Monte Carlo. Systematic Biology. 55: 553-65. PMID 16857650 DOI: 10.1080/10635150600812544  0.68
2006 Beiko RG, Hamilton N. Phylogenetic identification of lateral genetic transfer events. Bmc Evolutionary Biology. 6: 15. PMID 16472400 DOI: 10.1186/1471-2148-6-15  0.68
2006 Ragan MA, Harlow TJ, Beiko RG. Do different surrogate methods detect lateral genetic transfer events of different relative ages? Trends in Microbiology. 14: 4-8. PMID 16356716 DOI: 10.1016/j.tim.2005.11.004  0.68
2005 Beiko RG, Harlow TJ, Ragan MA. Highways of gene sharing in prokaryotes. Proceedings of the National Academy of Sciences of the United States of America. 102: 14332-7. PMID 16176988 DOI: 10.1073/pnas.0504068102  0.68
2005 Beiko RG, Chan CX, Ragan MA. A word-oriented approach to alignment validation. Bioinformatics (Oxford, England). 21: 2230-9. PMID 15728118 DOI: 10.1093/bioinformatics/bti335  0.68
2005 Beiko RG, Charlebois RL. GANN: genetic algorithm neural networks for the detection of conserved combinations of features in DNA. Bmc Bioinformatics. 6: 36. PMID 15725347 DOI: 10.1186/1471-2105-6-36  0.88
2003 Charlebois RL, Clarke GD, Beiko RG, St Jean A. Characterization of species-specific genes using a flexible, web-based querying system. Fems Microbiology Letters. 225: 213-20. PMID 12951244  0.88
2003 Charlebois RL, Beiko RG, Ragan MA. Microbial phylogenomics: Branching out. Nature. 421: 217. PMID 12529621 DOI: 10.1038/421217a  0.68
2002 Clarke GD, Beiko RG, Ragan MA, Charlebois RL. Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores. Journal of Bacteriology. 184: 2072-80. PMID 11914337 DOI: 10.1128/JB.184.8.2072-2080.2002  0.68
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