Robert G. Beiko, Ph.D. - Publications

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

80 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
2022 Alcock BP, Huynh W, Chalil R, Smith KW, Raphenya AR, Wlodarski MA, Edalatmand A, Petkau A, Syed SA, Tsang KK, Baker SJC, Dave M, McCarthy MC, Mukiri KM, Nasir JA, ... ... Beiko RG, et al. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Research. PMID 36263822 DOI: 10.1093/nar/gkac920  0.336
2022 Sanderson H, Gray KL, Manuele A, Maguire F, Khan A, Liu C, Navanekere Rudrappa C, Nash JHE, Robertson J, Bessonov K, Oloni M, Alcock BP, Raphenya AR, McAllister TA, Peacock SJ, ... ... Beiko RG, et al. Exploring the mobilome and resistome of in a One Health context across two continents. Microbial Genomics. 8. PMID 36129737 DOI: 10.1099/mgen.0.000880  0.689
2022 Liu C, Kenney T, Beiko RG, Gu H. The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes based on Phylogenetic Profiles. Systematic Biology. PMID 35904761 DOI: 10.1093/sysbio/syac052  0.366
2022 Kim JI, Maguire F, Tsang KK, Gouliouris T, Peacock SJ, McAllister TA, McArthur AG, Beiko RG. Machine Learning for Antimicrobial Resistance Prediction: Current Practice, Limitations, and Clinical Perspective. Clinical Microbiology Reviews. e0017921. PMID 35612324 DOI: 10.1128/cmr.00179-21  0.684
2021 Tsang KK, Maguire F, Zubyk HL, Chou S, Edalatmand A, Wright GD, Beiko RG, McArthur AG. Identifying novel β-lactamase substrate activity through prediction of antimicrobial resistance. Microbial Genomics. PMID 33416461 DOI: 10.1099/mgen.0.000500  0.647
2020 Maguire F, Jia B, Gray KL, Lau WYV, Beiko RG, Brinkman FSL. Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands. Microbial Genomics. PMID 33001022 DOI: 10.1099/mgen.0.000436  0.716
2020 Peabody MA, Lau WYV, Hoad G, Jia B, Maguire F, Gray KL, Beiko RG, Brinkman FSL. PSORTm: a bacterial and archaeal protein subcellular localization prediction tool for metagenomics data. Bioinformatics (Oxford, England). PMID 32108861 DOI: 10.1093/Bioinformatics/Btaa136  0.675
2019 Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M, Edalatmand A, Huynh W, Nguyen AV, Cheng AA, Liu S, Min SY, Miroshnichenko A, Tran HK, Werfalli RE, Nasir JA, ... ... Beiko RG, et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Research. PMID 31665441 DOI: 10.1093/Nar/Gkz935  0.689
2019 Maguire F, Rehman MA, Carrillo C, Diarra MS, Beiko RG. Identification of Primary Antimicrobial Resistance Drivers in Agricultural Nontyphoidal Salmonella enterica Serovars by Using Machine Learning. Msystems. 4. PMID 31387929 DOI: 10.1128/mSystems.00211-19  0.685
2018 Nadukkalam Ravindran P, Bentzen P, Bradbury IR, Beiko RG. RADProc: A computationally efficient de novo locus assembler for population studies using RADseq data. Molecular Ecology Resources. PMID 30312001 DOI: 10.1111/1755-0998.12954  0.365
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  0.709
2018 Hall M, Beiko RG. 16S rRNA Gene Analysis with QIIME2. Methods in Molecular Biology (Clifton, N.J.). 1849: 113-129. PMID 30298251 DOI: 10.1007/978-1-4939-8728-3_8  0.446
2018 Sylvester EVA, Beiko RG, Bentzen P, Paterson I, Horne JB, Watson B, Lehnert S, Duffy S, Clément M, Robertson MJ, Bradbury IR. Environmental extremes drive population structure at the northern range limit of Atlantic salmon in North America. Molecular Ecology. PMID 30152128 DOI: 10.1111/Mec.14849  0.353
2018 Liu C, Wright B, Allen-Vercoe E, Gu H, Beiko R. Phylogenetic clustering of genes reveals shared evolutionary trajectories and putative gene functions. Genome Biology and Evolution. PMID 30137329 DOI: 10.1093/Gbe/Evy178  0.399
2018 Nadukkalam Ravindran P, Bentzen P, Bradbury IR, Beiko RG. PMERGE: Computational filtering of paralogous sequences from RAD-seq data. Ecology and Evolution. 8: 7002-7013. PMID 30073062 DOI: 10.1002/Ece3.4219  0.424
2018 Bradbury IR, Wringe BF, Watson B, Paterson I, Horne J, Beiko R, Lehnert SJ, Clément M, Anderson EC, Jeffery NW, Duffy S, Sylvester E, Robertson M, Bentzen P. Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery. Evolutionary Applications. 11: 918-930. PMID 29928300 DOI: 10.1111/Eva.12606  0.406
2018 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. A climate-associated multispecies cryptic cline in the northwest Atlantic. Science Advances. 4: eaaq0929. PMID 29600272 DOI: 10.1126/Sciadv.Aaq0929  0.321
2018 Van Wyngaarden M, Snelgrove PVR, DiBacco C, Hamilton LC, Rodríguez-Ezpeleta N, Zhan L, Beiko RG, Bradbury IR. Oceanographic variation influences spatial genomic structure in the sea scallop,. Ecology and Evolution. 8: 2824-2841. PMID 29531698 DOI: 10.1002/Ece3.3846  0.388
2018 Sylvester EVA, Bentzen P, Bradbury IR, Clément M, Pearce J, Horne J, Beiko RG. Applications of random forest feature selection for fine-scale genetic population assignment. Evolutionary Applications. 11: 153-165. PMID 29387152 DOI: 10.1111/Eva.12524  0.334
2017 Jeffery NW, Stanley RRE, Wringe BF, Guijarro-Sabaniel J, Bourret V, Bernatchez L, Bentzen P, Beiko RG, Gilbey J, Clément M, Bradbury IR. Range-wide parallel climate-associated genomic clines in Atlantic salmon. Royal Society Open Science. 4: 171394. PMID 29291123 DOI: 10.1098/Rsos.171394  0.39
2017 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, et al. SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology. Microbial Genomics. 3: e000116. PMID 29026651 DOI: 10.1099/mgen.0.000116  0.643
2017 Hall MW, Rohwer RR, Perrie J, McMahon KD, Beiko RG. Ananke: temporal clustering reveals ecological dynamics of microbial communities. Peerj. 5: e3812. PMID 28966891 DOI: 10.7717/Peerj.3812  0.365
2017 Jeffery NW, DiBacco C, Van Wyngaarden M, Hamilton LC, Stanley RRE, Bernier R, FitzGerald J, Matheson K, McKenzie CH, Nadukkalam Ravindran P, Beiko R, Bradbury IR. RAD sequencing reveals genomewide divergence between independent invasions of the European green crab (Carcinus maenas) in the Northwest Atlantic. Ecology and Evolution. 7: 2513-2524. PMID 28428843 DOI: 10.1002/Ece3.2872  0.402
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  0.496
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  0.417
2016 Zhan L, Paterson IG, Fraser BA, Watson B, Bradbury IR, Nadukkalam Ravindran P, Reznick D, Beiko RG, Bentzen P. MEGASAT: automated inference of microsatellite genotypes from sequence data. Molecular Ecology Resources. PMID 27333119 DOI: 10.1111/1755-0998.12561  0.308
2016 Dhanani AS, Block G, Dewar K, Forgetta V, Topp E, Beiko RG, Diarra MS. Correction: Genomic Comparison of Non-Typhoidal Salmonella enterica Serovars Typhimurium, Enteritidis, Heidelberg, Hadar and Kentucky Isolates from Broiler Chickens. Plos One. 11: e0148706. PMID 26854571 DOI: 10.1371/Journal.Pone.0148706  0.415
2016 Petkau A, Bristow F, Matthews T, Adam J, Mabon P, Sieffert C, Enns E, Cabral J, Thiessen J, Knox N, Dooley D, Reimer A, Taboada E, Keddy A, Beiko RG, et al. Outbreak surveillance and investigation using IRIDA and SNVPhyl F1000research. 5. DOI: 10.7490/F1000Research.1112511.1  0.551
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  0.303
2015 Beiko RG. Microbial malaise: how can we classify the microbiome? Trends in Microbiology. 23: 671-9. PMID 26439295 DOI: 10.1016/J.Tim.2015.08.009  0.414
2015 Ning J, Beiko RG. Phylogenetic approaches to microbial community classification. Microbiome. 3: 47. PMID 26437943 DOI: 10.1186/S40168-015-0114-5  0.342
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  0.599
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  0.399
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  0.574
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  0.605
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  0.413
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  0.411
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  0.637
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  0.482
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  0.677
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  0.646
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  0.369
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  0.36
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  0.634
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  0.479
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  0.352
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  0.33
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  0.363
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  0.425
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  0.642
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  0.423
2011 Beiko RG. Telling the whole story in a 10,000-genome world. Biology Direct. 6: 34. PMID 21714939 DOI: 10.1186/1745-6150-6-34  0.451
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  0.433
2010 Holloway C, Beiko RG. Assembling networks of microbial genomes using linear programming. Bmc Evolutionary Biology. 10: 360. PMID 21092133 DOI: 10.1186/1471-2148-10-360  0.419
2010 Slater FR, Johnson CR, Blackall LL, Beiko RG, Bond PL. Monitoring associations between clade-level variation, overall community structure and ecosystem function in enhanced biological phosphorus removal (EBPR) systems using terminal-restriction fragment length polymorphism (T-RFLP). Water Research. 44: 4908-23. PMID 20701946 DOI: 10.1016/J.Watres.2010.07.028  0.32
2010 MacDonald NJ, Beiko RG. Efficient learning of microbial genotype-phenotype association rules Bioinformatics. 26: 1834-1840. PMID 20529891 DOI: 10.1093/Bioinformatics/Btq305  0.405
2010 Perry SC, Beiko RG. Distinguishing microbial genome fragments based on their composition: evolutionary and comparative genomic perspectives. Genome Biology and Evolution. 2: 117-31. PMID 20333228 DOI: 10.1093/Gbe/Evq004  0.461
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  0.346
2010 Beiko RG. Gene sharing and genome evolution: networks in trees and trees in networks Biology & Philosophy. 25: 659-673. DOI: 10.1007/S10539-010-9217-3  0.4
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  0.429
2009 MacDonald N, Parks D, Beiko R. SeqMonitor: influenza analysis pipeline and visualization. Plos Currents. 1. PMID 20025203 DOI: 10.1371/Currents.Rrn1040  0.369
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  0.421
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  0.441
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  0.444
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  0.388
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  0.702
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  0.51
2007 Davies MR, McMillan DJ, Beiko RG, Barroso V, Geffers R, Sriprakash KS, Chhatwal GS. Virulence profiling of Streptococcus dysgalactiae subspecies equisimilis isolated from infected humans reveals 2 distinct genetic lineages that do not segregate with their phenotypes or propensity to cause diseases. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. 44: 1442-54. PMID 17479940 DOI: 10.1086/516780  0.306
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  0.707
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  0.375
2006 McMillan DJ, Beiko RG, Geffers R, Buer J, Schouls LM, Vlaminckx BJM, Wannet WJB, Sriprakash KS, Chhatwal GS. Genes for the Majority of Group A Streptococcal Virulence Factors and Extracellular Surface Proteins Do Not Confer an Increased Propensity to Cause Invasive Disease Clinical Infectious Diseases. 43: 884-891. PMID 16941370 DOI: 10.1086/507537  0.341
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  0.343
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  0.369
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  0.489
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  0.324
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  0.653
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 DOI: 10.1016/S0378-1097(03)00512-3  0.697
2003 Charlebois RL, Beiko RG, Ragan MA. Microbial phylogenomics: Branching out. Nature. 421: 217. PMID 12529621 DOI: 10.1038/421217A  0.663
2002 Martin CC, Tsang CH, Beiko RG, Krone PH. Expression and genomic organization of the zebrafish chaperonin gene complex. Genome / National Research Council Canada = GéNome / Conseil National De Recherches Canada. 45: 804-11. PMID 12416612 DOI: 10.1139/G02-044  0.33
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  0.72
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