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