Publications – Beiko Lab

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Range-wide parallel climate-associated genomic clines in Atlantic salmon NW Jeffery, RRE Stanley, BF Wringe, J Guijarro-Sabaniel, V Bourret, … Royal Society Open Science 4 (11), 171394	2017
SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology A Petkau, P Mabon, C Sieffert, NC Knox, J Cabral, M Iskander, M Iskander, … Microbial Genomics 3 (6)	2017
Discovery of an expanded set of avian leucosis subgroup E proviruses in chickens using Vermillion, a novel sequence capture and analysis pipeline K Rutherford, CJ Meehan, MGI Langille, SG Tyack, JC McKay, … Poultry science 96 (5), 1516-1516	2017
RAD sequencing reveals genomewide divergence between independent invasions of the European green crab (Carcinus maenas) in the Northwest Atlantic NW Jeffery, C DiBacco, M Van Wyngaarden, LC Hamilton, RRE Stanley, … Ecology and evolution 7 (8), 2513-2524	2017
Ananke: Temporal clustering reveals ecological dynamics of microbial communities MW Hall, RR Rohwer, J Perrie, KD McMahon, RG Beiko PeerJ Preprints	2017
MEGASAT: automated inference of microsatellite genotypes from sequence data L Zhan, IG Paterson, BA Fraser, B Watson, IR Bradbury, … Molecular ecology resources 17 (2), 247-256	2017
Inter-personal diversity and temporal dynamics of dental, tongue, and salivary microbiota in the healthy oral cavity MW Hall, N Singh, KF Ng, DK Lam, MB Goldberg, HC Tenenbaum, … npj Biofilms and Microbiomes 3 (1), 2	2017
Scaling Up the Phylogenetic Detection of Lateral Gene Transfer Events CX Chan, RG Beiko, MA Ragan Bioinformatics: Volume I: Data, Sequence Analysis, and Evolution, 421-432	2017
A new way to contemplate Darwin’s tangled bank: how DNA barcodes are reconnecting biodiversity science and biomonitoring M Hajibabaei, DJ Baird, NA Fahner, R Beiko, GB Golding Phil. Trans. R. Soc. B 371 (1702), 20150330	2016
Discovery of an expanded set of avian leukosis subgroup E proviruses in chickens using Vermillion, a novel sequence capture and analysis pipeline K Rutherford, CJ Meehan, MGI Langille, SG Tyack, JC McKay, … Poultry science 95 (10), 2250-2258	2016
Fixed-parameter and approximation algorithms for maximum agreement forests of multifurcating trees C Whidden, RG Beiko, N Zeh Algorithmica 74 (3), 1019-1054	2016
simDEF: definition-based semantic similarity measure of gene ontology terms for functional similarity analysis of genes A Pesaranghader, S Matwin, M Sokolova, RG Beiko Bioinformatics 32 (9), 1380-1387	2015
Microbial malaise: how can we classify the microbiome? RG Beiko Trends in microbiology 23 (11), 671-679	2015
AGING, FRAILTY AND THE MICROBIOME RG Beiko GERONTOLOGIST 55, 383-383	2015
Phylogenetic approaches to microbial community classification J Ning, RG Beiko Microbiome 3 (1), 47	2015
Correction: Genomic Comparison of Non-Typhoidal Salmonella enterica Serovars Typhimurium, Enteritidis, Heidelberg, Hadar and Kentucky Isolates from Broiler C… AS Dhanani, G Block, K Dewar, V Forgetta, E Topp, RG Beiko, MS Diarra PloS one 10 (9), e0137697	2015
Transfer of energy pathway genes in microbial enhanced biological phosphorus removal communities DHJ Wong, RG Beiko BMC genomics 16 (1), 526	2015
Genomic comparison of non-typhoidal Salmonella enterica Serovars Typhimurium, Enteritidis, Heidelberg, Hadar and Kentucky isolates from broiler chickens AS Dhanani, G Block, K Dewar, V Forgetta, E Topp, RG Beiko, MS Diarra PloS one 10 (6), e0128773	2015
Frailty and the microbiome CJ Meehan, MGI Langille, RG Beiko Frailty in Aging 41, 54-65	2015
RITA: rapid identification of high-confidence taxonomic assignments for metagenomic data NJ MacDonald, DH Parks, RG Beiko Encyclopedia of Metagenomics, 613-618	2015
STAMP: statistical analysis of metagenomic profiles DH Parks, RG Beiko Encyclopedia of Metagenomics, 641-645	2015
Microbial shifts in the aging mouse gut MGI Langille, CJ Meehan, JE Koenig, AS Dhanani, RA Rose, SE Howlett, … Microbiome 2 (1), 50	2014
Conservation and Stewardship of the Human Microbiome K O’Doherty, JD Neufeld, FSL Brinkman, H Gardner, DS Guttman, RG Beiko Proceedings of the National Academy of Sciences 111 (40), 14312-14313	2014
Bioinformatics: Hypothesis free-Or Hypotheses Freed? RG Beiko BioScience 64 (9), 844-845	2014
STAMP: statistical analysis of taxonomic and functional profiles DH Parks, GW Tyson, P Hugenholtz, RG Beiko Bioinformatics	2014
Supertrees based on the subtree prune-and-regraft distance C Whidden, N Zeh, RG Beiko Systematic Biology 63 (4), 566-581	2014
A phylogenomic view of ecological specialization in the Lachnospiraceae, a family of digestive tract-associated bacteria CJ Meehan, RG Beiko Genome Biology and Evolution 6 (3), 703-713	2014
Interactions in the microbiome: communities of organisms and communities of genes E Boon, CJ Meehan, C Whidden, DHJ Wong, MGI Langille, RG Beiko FEMS Microbiology Reviews 38 (1), 90-118	2013
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences MGI Langille, J Zaneveld, JG Caporaso, D MacDonald, D Knights, JA Reyes, JC Clemente, DE Burkepile, RLV Thurber, R Knight, RG Beiko, C Huttenhower Nature Biotechnology 31 (9), 814-821	2013
Fixed-parameter algorithms for maximum agreement forests C Whidden, RG Beiko, N Zeh SIAM Journal on Computing 42 (4), 1431-1466	2013
SPANNER: Taxonomic assignment of sequences using pyramid matching of similarity profiles MS Porter, RG Beiko Bioinformatics	2013
Supertrees based on the subtree prune-and-regraft distance C Whidden, N Zeh, RG Beiko PeerJ PrePrints	2013
GenGIS 2: Geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework RG Beiko, DH Parks, T Mankowski, S Zangooei, MS Porter, DG Armanini, DJ … PeerJ PrePrints	2013
Fixed-Parameter and Approximation Algorithms for Maximum Agreement Forests of Multifurcating Trees C Whidden, RG Beiko, N Zeh arXiv preprint arXiv:1305.0512	2013
Measuring community similarity with phylogenetic networks DH Parks, RG Beiko Molecular biology and evolution 29 (12), 3947-3958	2012
Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs BA Curtis, G Tanifuji, F Burki, A Gruber, M Irimia, S Maruyama, MC Arias, SG … Nature 492 (7427), 59-65	2012
Comparative Genomic and Phylogenetic Approaches to Characterize the Role of Genetic Recombination in Mycobacterial Evolution SE Smith, P Showers-Corneli, CN Dardenne, HH Harpending, DP Martin, RG Beiko PloS one 7 (11), e50070	2012
Lateral gene transfer of an ABC transporter complex between major constituents of the human gut microbiome CJ Meehan, RG Beiko BMC microbiology 12 (1), 248	2012
Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities DH Parks, RG Beiko The ISME Journal	2012
Rapid identification of high-confidence taxonomic assignments for metagenomic data NJ MacDonald, DH Parks, RG Beiko Nucleic acids research 40 (14), e111-e111	2012
Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation M Lommer, M Specht, AS Roy, L Kraemer, R Andreson, MA Gutowska, J Wolf, SV … Genome biology 13 (7), R66	2012
Comparative metagenomics of three Dehalococcoides-containing enrichment cultures: the role of the non-dechlorinating community L Hug, R Beiko, A Rowe, R Richardson, E Edwards BMC genomics 13 (1), 327	2012
Human microbiome: a genetic bazaar for microbes? MGI Langille, CJ Meehan, RG Beiko Current Biology 22 (1), R20-R22	2012
Fixed-parameter and approximation algorithms for maximum agreement forests C Whidden, RG Beiko, N Zeh arXiv preprint arXiv:1108.2664	2011
Classifying short genomic fragments from novel lineages using composition and homology DH Parks, NJ MacDonald, RG Beiko BMC bioinformatics 12 (1), 328	2011
Lateral transfer of genes and gene fragments in Staphylococcus extends beyond mobile elements CX Chan, RG Beiko, MA Ragan Journal of bacteriology 193 (15), 3964-3977	2011
Telling the whole story in a 10,000-genome world RG Beiko Biol Direct 6, 34	2011
Assembling networks of microbial genomes using linear programming C Holloway, RG Beiko BMC evolutionary biology 10 (1), 360	2010
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) FR Slater, CR Johnson, LL Blackall, RG Beiko, PL Bond Water research 44 (17), 4908-4923	2010
Gene sharing and genome evolution: networks in trees and trees in networks RG Beiko Biology & Philosophy 25 (4), 659-673	2010
Efficient learning of microbial genotype–phenotype association rules NJ MacDonald, RG Beiko Bioinformatics 26 (15), 1834-1840	2010
Identifying biologically relevant differences between metagenomic communities DH Parks, RG Beiko Bioinformatics 26 (6), 715-721	2010
Genetic recombination and bacterial population structure DP Martin, RG Beiko Bacterial Population Genetics in Infectious Disease, 61-85	2010
Distinguishing microbial genome fragments based on their composition: evolutionary and comparative genomic perspectives SC Perry, RG Beiko Genome biology and evolution 2, 117	2010
Fast FPT algorithms for computing rooted agreement forests: Theory and experiments C Whidden, RG Beiko, N Zeh Experimental Algorithms, 141-153	2010
GenGIS: A geospatial information system for genomic data DH Parks, M Porter, S Churcher, S Wang, C Blouin, J Whalley, S Brooks, RG Beiko Genome Research 19 (10), 1896-1904	2009
Prokaryotic evolution and the tree of life are two different things E Bapteste, MA O’Malley, RG Beiko, M Ereshefsky, JP Gogarten, L Franklin … Biol Direct 4 (1), 34	2009
SeqMonitor: Influenza Analysis Pipeline and Visualization N MacDonald, D Parks, R Beiko PLoS currents 1	2009
Tracking the evolution and geographic spread of Influenza A D Parks, N MacDonald, R Beiko PLoS currents 1	2009
Quantitative visualizations of hierarchically organized data in a geographic context DH Parks, RG Beiko Geoinformatics, 2009 17th International Conference on, 1-6	2009
Lateral genetic transfer: open issues MA Ragan, RG Beiko Philosophical Transactions of the Royal Society B: Biological Sciences 364 …	2009
Radié: visualizing taxon properties and parsimonious mappings using a radial phylogenetic tree J Whalley, S Brooks, RG Beiko Bioinformatics 25 (5), 672-673	2009
Are protein domains modules of lateral genetic transfer? CX Chan, AE Darling, RG Beiko, MA Ragan PLoS One 4 (2), e4524	2009
Untangling hybrid phylogenetic signals: horizontal gene transfer and artifacts of phylogenetic reconstruction RG Beiko, MA Ragan Horizontal Gene Transfer, 241-256	2009
Lateral transfer of genes and gene fragments in prokaryotes CX Chan, RG Beiko, AE Darling, MA Ragan Genome biology and evolution 1, 429	2009
The impact of reticulate evolution on genome phylogeny RG Beiko, WF Doolittle, RL Charlebois Systematic biology 57 (6), 844-856	2008
Large‐scale detection of recombination in nucleotide sequences CX Chan, RG Beiko, MA Ragan AIP Conference Proceedings 971, 101	2008
Spatial analysis and visualization of genetic biodiversity RG Beiko, J Whalley, S Wang, H Clair, G Smolyn, S Churcher, M Porter, C … Free and Open Source Software for Geospatial	2008
Detecting Lateral Genetic Transfer RG Beiko, MA Ragan	2008
Genetic transfer in Staphylococcus: a case study of 13 genomes CX Chan, RG Beiko, MA Ragan arXiv preprint arXiv:0709.2031	2007
Protein domains as units of genetic transfer CX Chan, RG Beiko, AE Darling, MA Ragan arXiv preprint arXiv:0709.2030	2007
Units of genetic transfer in prokaryotes CX Chan, RG Beiko, MA Ragan arXiv preprint arXiv:0709.2027	2007
A two-phase strategy for detecting recombination in nucleotide sequences CX Chan, RG Beiko, MA Ragan South African Computer Journal	2007
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 MR Davies, DJ McMillan, RG Beiko, V Barroso, R Geffers, KS Sriprakash, GS … Clinical infectious diseases 44 (11), 1442-1454	2007
A simulation test bed for hypotheses of genome evolution RG Beiko, RL Charlebois Bioinformatics 23 (7), 825-831	2007
Collapsible 3D Terrains for GIS Visualization S Wang, RG Beiko, S Brooks Geovisualization 2007	2007
Genes for the majority of group A streptococcal virulence factors and extracellular surface proteins do not confer an increased propensity to cause invasive disease DJ McMillan, RG Beiko, R Geffers, J Buer, LM Schouls, BJM Vlaminckx, WJB … Clinical infectious diseases 43 (7), 884-891	2006
Detecting recombination in evolving nucleotide sequences CX Chan, RG Beiko, MA Ragan BMC bioinformatics 7 (1), 412	2006
Searching for convergence in phylogenetic Markov chain Monte Carlo RG Beiko, JM Keith, TJ Harlow, MA Ragan Systematic biology 55 (4), 553-565	2006
Phylogenetic identification of lateral genetic transfer events R Beiko, N Hamilton BMC evolutionary biology 6 (1), 15	2006
Do different surrogate methods detect lateral genetic transfer events of different relative ages? MA Ragan, TJ Harlow, RG Beiko Trends in microbiology 14 (1), 4-8	2006
Surrogate methods for detecting laterally transferred genes MA Ragan, TJ Harlow, RG Beiko Trends in Microbiology 14 (1), 4-8	2006
Highways of gene sharing in prokaryotes RG Beiko, TJ Harlow, MA Ragan Proceedings of the National Academy of Sciences of the United States of …	2005
A word-oriented approach to alignment validation RG Beiko, CX Chan, MA Ragan Bioinformatics 21 (10), 2230-2239	2005
GANN: genetic algorithm neural networks for the detection of conserved combinations of features in DNA RG Beiko, RL Charlebois BMC bioinformatics 6 (1), 36	2005
Genome phylogenies RL Charlebois, RG Beiko, MA Ragan Organelles, genomes and eukaryote phylogeny: An evolutionary synthesis in …	2004
Characterization of species‐specific genes using a flexible, web‐based querying system RL Charlebois, GD Clarke, RG Beiko, A Jean FEMS microbiology letters 225 (2), 213-220	2003
Microbial phylogenomics: branching out RL Charlebois, RG Beiko, MA Ragan Nature 421 (6920), 217-217	2003
Expression and genomic organization of the zebrafish chaperonin gene complex CC Martin, CH Tsang, RG Beiko, PH Krone Genome 45 (5), 804-811	2002
Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores GD Clarke, RG Beiko, MA Ragan, RL Charlebois Journal of bacteriology 184 (8), 2072-2080	2002