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Phylogenetic approaches to microbial community classification.
- Published in:
- Microbiome, 2015, v. 3, n. 1, p. 1, doi. 10.1186/s40168-015-0114-5
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- Article
Expression and genomic organization of the zebrafish chaperonin gene complex.
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- Genome, 2002, v. 45, n. 5, p. 804, doi. 10.1139/g02-044
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- Article
Identification of key drivers of antimicrobial resistance in Enterococcus using machine learning.
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- Canadian Journal of Microbiology, 2024, v. 70, n. 10, p. 446, doi. 10.1139/cjm-2024-0049
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- Article
Compact and automated eDNA sampler for in situ monitoring of marine environments.
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- Scientific Reports, 2023, v. 13, n. 1, p. 1, doi. 10.1038/s41598-023-32310-3
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- Article
Investigating biogeographical patterns using point‐based cartograms.
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- Global Ecology & Biogeography, 2018, v. 27, n. 3, p. 380, doi. 10.1111/geb.12698
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- Article
Rapid identification of high-confidence taxonomic assignments for metagenomic data.
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- Nucleic Acids Research, 2012, v. 40, n. 14, p. e111, doi. 10.1093/nar/gks335
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- Article
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.
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- Nature Biotechnology, 2013, v. 31, n. 9, p. 814, doi. 10.1038/nbt.2676
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- Article
Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities.
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- ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2013, v. 7, n. 1, p. 173, doi. 10.1038/ismej.2012.88
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- Article
deepSimDEF: deep neural embeddings of gene products and gene ontology terms for functional analysis of genes.
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- Bioinformatics, 2022, v. 38, n. 11, p. 3051, doi. 10.1093/bioinformatics/btac304
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- Article
Environmental extremes drive population structure at the northern range limit of Atlantic salmon in North America.
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- Molecular Ecology, 2018, v. 27, n. 20, p. 4026, doi. 10.1111/mec.14849
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- Article
Correction: Genomic Comparison of Non-Typhoidal Salmonella enterica Serovars Typhimurium, Enteritidis, Heidelberg, Hadar and Kentucky Isolates from Broiler Chickens.
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- PLoS ONE, 2015, v. 10, n. 9, p. 1, doi. 10.1371/journal.pone.0137697
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- Publication type:
- Article
Genomic Comparison of Non-Typhoidal Salmonella enterica Serovars Typhimurium, Enteritidis, Heidelberg, Hadar and Kentucky Isolates from Broiler Chickens.
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- PLoS ONE, 2015, v. 10, n. 6, p. 1, doi. 10.1371/journal.pone.0128773
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- Publication type:
- Article
GenGIS 2: Geospatial Analysis of Traditional and Genetic Biodiversity, with New Gradient Algorithms and an Extensible Plugin Framework.
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- PLoS ONE, 2013, v. 8, n. 7, p. 1, doi. 10.1371/journal.pone.0069885
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- Article
Comparative Genomic and Phylogenetic Approaches to Characterize the Role of Genetic Recombination in Mycobacterial Evolution.
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- PLoS ONE, 2012, v. 7, n. 11, p. 1, doi. 10.1371/journal.pone.0050070
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- Article
Are Protein Domains Modules of Lateral Genetic Transfer?
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- PLoS ONE, 2009, v. 4, n. 2, p. 1, doi. 10.1371/journal.pone.0004524
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- Article
GANN: Genetic algorithm neural networks for the detection of conserved combinations of features in DNA.
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- BMC Bioinformatics, 2005, v. 6, p. 36, doi. 10.1186/1471-2105-6-36
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- Article
Measuring Community Similarity with Phylogenetic Networks.
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- Molecular Biology & Evolution, 2012, v. 29, n. 12, p. 3947, doi. 10.1093/molbev/mss200
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- Article
Cellulase−Hemicellulase Activities and Bacterial Community Composition of Different Soils from Algerian Ecosystems.
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- Microbial Ecology, 2019, v. 77, n. 3, p. 713, doi. 10.1007/s00248-018-1251-8
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- Article
Vaginal microbiota in women with spontaneous preterm labor versus those with term labor in Kenya: a case control study.
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- BMC Microbiology, 2022, v. 22, n. 1, p. 1, doi. 10.1186/s12866-022-02681-0
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- Article
Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation.
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- Genome Biology, 2012, v. 13, n. 7, p. 1, doi. 10.1186/gb-2012-13-7-r66
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- Article
Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation.
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- Genome Biology, 2012, v. 13, n. 7, p. 1, doi. 10.1186/gb-2012-13-7-r66
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- Article
A Phylogenomic View of Ecological Specialization in the Lachnospiraceae, a Family of Digestive Tract-Associated Bacteria.
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- Genome Biology & Evolution, 2014, v. 6, n. 3, p. 703, doi. 10.1093/gbe/evu050
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- Article
Being Aquifex aeolicus: Untangling a Hyperthermophile’s Checkered Past.
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- Genome Biology & Evolution, 2013, v. 5, n. 12, p. 2478, doi. 10.1093/gbe/evt195
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- Article
Lateral Transfer of Genes and Gene Fragments in Prokaryotes.
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- Genome Biology & Evolution, 2009, v. 1, p. 429, doi. 10.1093/gbe/evp044
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- Article
Microbial phylogenomics: Branching out.
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- Nature, 2003, v. 421, n. 6920, p. 217, doi. 10.1038/421217a
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- Publication type:
- Article
Correction: Genomic Comparison of Non-Typhoidal Salmonella enterica Serovars Typhimurium, Enteritidis, Heidelberg, Hadar and Kentucky Isolates from Broiler Chickens.
- Published in:
- PLoS ONE, 2016, v. 11, n. 2, p. 1, doi. 10.1371/journal.pone.0148706
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- Publication type:
- Article
The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes Based on Phylogenetic Profiles.
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- Systematic Biology, 2023, v. 72, n. 3, p. 559, doi. 10.1093/sysbio/syac052
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- Article
Supertrees Based on the Subtree Prune-and-Regraft Distance.
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- Systematic Biology, 2014, v. 63, n. 4, p. 566, doi. 10.1093/sysbio/syu023
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- Article
The Impact of Reticulate Evolution on Genome Phylogeny.
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- Systematic Biology, 2008, v. 57, n. 6, p. 844, doi. 10.1080/10635150802559265
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- Article
Gene sharing and genome evolution: networks in trees and trees in networks.
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- Biology & Philosophy, 2010, v. 25, n. 4, p. 659, doi. 10.1007/s10539-010-9217-3
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- Article
A simulation test bed for hypotheses of genome evolution.
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- Bioinformatics, 2007, v. 23, n. 7, p. 825, doi. 10.1093/bioinformatics/btm024
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- Article
Inter-personal diversity and temporal dynamics of dental, tongue, and salivary microbiota in the healthy oral cavity.
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- NPJ Biofilms & Microbiomes, 2017, v. 3, n. 1, p. N.PAG, doi. 10.1038/s41522-016-0011-0
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- Article
Applications of random forest feature selection for fine‐scale genetic population assignment.
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- Evolutionary Applications, 2018, v. 11, n. 2, p. 153, doi. 10.1111/eva.12524
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- Article
Integrating seascape resistances and gene flow to produce area-based metrics of functional connectivity for marine conservation planning.
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- Landscape Ecology, 2023, v. 38, n. 9, p. 2189, doi. 10.1007/s10980-023-01690-2
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- Article
RADProc: A computationally efficient de novo locus assembler for population studies using RADseq data.
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- Molecular Ecology Resources, 2019, v. 19, n. 1, p. 272, doi. 10.1111/1755-0998.12954
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- Article
megasat: automated inference of microsatellite genotypes from sequence data.
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- Molecular Ecology Resources, 2017, v. 17, n. 2, p. 247, doi. 10.1111/1755-0998.12561
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- Article
Transfer of energy pathway genes in microbial enhanced biological phosphorus removal communities.
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- BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1752-5
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- Article
Comparative metagenomics of three Dehalococcoides-containing enrichment cultures: the role of the non-dechlorinating community.
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- BMC Genomics, 2012, v. 13, n. 1, p. 327, doi. 10.1186/1471-2164-13-327
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- Article
Assembling networks of microbial genomes using linear programming.
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- BMC Evolutionary Biology, 2010, v. 10, p. 360, doi. 10.1186/1471-2148-10-360
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- Article
Phylogenetic identification of lateral genetic transfer events.
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- BMC Evolutionary Biology, 2006, v. 6, p. 15, doi. 10.1186/1471-2148-6-15
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- Article
PSORTm: a bacterial and archaeal protein subcellular localization prediction tool for metagenomics data.
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- Bioinformatics, 2020, v. 36, n. 10, p. 3043, doi. 10.1093/bioinformatics/btaa136
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- Article
simDEF: definition-based semantic similarity measure of gene ontology terms for functional similarity analysis of genes.
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- Bioinformatics, 2016, v. 32, n. 9, p. 1380, doi. 10.1093/bioinformatics/btv755
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- Article
STAMP: statistical analysis of taxonomic and functional profiles.
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- Bioinformatics, 2014, v. 30, n. 21, p. 3123, doi. 10.1093/bioinformatics/btu494
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- Article
SPANNER: taxonomic assignment of sequences using pyramid matching of similarity profiles.
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- Bioinformatics, 2013, v. 29, n. 15, p. 1858, doi. 10.1093/bioinformatics/btt313
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- Article
Efficient learning of microbial genotype–phenotype association rules.
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- Bioinformatics, 2010, v. 26, n. 15, p. 1834, doi. 10.1093/bioinformatics/btq305
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- Article
Identifying biologically relevant differences between metagenomic communities.
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- Bioinformatics, 2010, v. 26, n. 6, p. 715, doi. 10.1093/bioinformatics/btq041
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- Article
Radie: visualizing taxon properties and parsimonious mappings using a radial phylogenetic tree.
- Published in:
- Bioinformatics, 2009, v. 25, n. 5, p. 672, doi. 10.1093/bioinformatics/btp044
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- Article
PMERGE: Computational filtering of paralogous sequences from RAD‐seq data.
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- Ecology & Evolution (20457758), 2018, v. 8, n. 14, p. 7002, doi. 10.1002/ece3.4219
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- Article
Oceanographic variation influences spatial genomic structure in the sea scallop, <italic>Placopecten magellanicus</italic>.
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- Ecology & Evolution (20457758), 2018, v. 8, n. 5, p. 2824, doi. 10.1002/ece3.3846
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- Article
Mock microbial community meta‐analysis using different trimming of amplicon read lengths.
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- Environmental Microbiology, 2024, v. 26, n. 1, p. 1, doi. 10.1111/1462-2920.16566
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- Article