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Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads.
- Published in:
- Microbiome, 2017, v. 5, p. 1, doi. 10.1186/s40168-017-0233-2
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- Article
RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys.
- Published in:
- BMC Bioinformatics, 2016, v. 17, p. 277, doi. 10.1186/s12859-016-1378-x
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- Article
Comparison of functional classification systems.
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- NAR Genomics & Bioinformatics, 2022, v. 4, n. 4, p. 1, doi. 10.1093/nargab/lqac090
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- Article
Comparison of multiple metagenomes using phylogenetic networks based on ecological indices.
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- ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2010, v. 4, n. 10, p. 1236, doi. 10.1038/ismej.2010.51
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- Article
Fast and sensitive protein alignment using DIAMOND.
- Published in:
- Nature Methods, 2015, v. 12, n. 1, p. 59, doi. 10.1038/nmeth.3176
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- Article
CatReNet: interactive analysis of (auto-) catalytic reaction networks.
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- Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae515
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- Article
MeganServer: facilitating interactive access to metagenomic data on a server.
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- Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad105
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- Article
DeepToA: an ensemble deep-learning approach to predicting the theater of activity of a microbiome.
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- Bioinformatics, 2022, v. 38, n. 20, p. 4670, doi. 10.1093/bioinformatics/btac584
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- Article
A metagenomic-based survey of microbial (de)halogenation potential in a German forest soil.
- Published in:
- Scientific Reports, 2016, p. 28958, doi. 10.1038/srep28958
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- Article
MuLan-Methyl—multiple transformer-based language models for accurate DNA methylation prediction.
- Published in:
- GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad054
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- Article
CREST -- Classification Resources for Environmental Sequence Tags.
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- PLoS ONE, 2012, v. 7, n. 11, p. 1, doi. 10.1371/journal.pone.0049334
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- Article
LOCAS - A Low Coverage Assembly Tool for Resequencing Projects.
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- PLoS ONE, 2011, v. 6, n. 8, p. 1, doi. 10.1371/journal.pone.0023455
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- Article
MetaSim--A Sequencing Simulator for Genomics and Metagenomics.
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- PLoS ONE, 2008, v. 3, n. 10, p. 1, doi. 10.1371/journal.pone.0003373
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- Article
Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta- Transcriptome.
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- PLoS ONE, 2008, v. 3, n. 6, p. 1, doi. 10.1371/journal.pone.0002527
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- Article
SILVA, RDP, Greengenes, NCBI and OTT-- how do these taxonomies compare?
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- BMC Genomics, 2017, v. 18, p. 1, doi. 10.1186/s12864-017-3501-4
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- Article
Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG.
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- BMC Bioinformatics, 2011, v. 12, n. Suppl 1, p. 1, doi. 10.1186/1471-2105-12-S1-S21
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- Article
Short clones or long clones? A simulation study on the use of paired reads in metagenomics.
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- BMC Bioinformatics, 2010, v. 11, p. 1, doi. 10.1186/1471-2105-11-S1-S12
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- Article
Methods for comparative metagenomics.
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- BMC Bioinformatics, 2009, v. 10, p. 1, doi. 10.1186/1471-2105-10-S1-S12
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- Article
Dendroscope: An interactive viewer for large phylogenetic trees.
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- BMC Bioinformatics, 2007, v. 8, p. 460, doi. 10.1186/1471-2105-8-460
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- Publication type:
- Article
CrossLink: visualization and exploration of sequence relationships between (micro) RNAs.
- Published in:
- Nucleic Acids Research, 2006, v. 34, n. 11, p. w400, doi. 10.1093/nar/gkl223
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- Article
Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs).
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- Nucleic Acids Research, 2005, v. 33, n. 18, p. 5799, doi. 10.1093/nar/gki885
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- Publication type:
- Article
MAIRA- real-time taxonomic and functional analysis of long reads on a laptop.
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- BMC Bioinformatics, 2020, v. 21, n. 13, p. N.PAG, doi. 10.1186/s12859-020-03684-2
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- Publication type:
- Article
Microbiome Metabolome Integration Platform (MMIP): a web-based platform for microbiome and metabolome data integration and feature identification.
- Published in:
- Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad325
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- Article
Microbial Phylogenetic Context Using Phylogenetic Outlines.
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- Genome Biology & Evolution, 2021, v. 13, n. 9, p. 1, doi. 10.1093/gbe/evab213
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- Article
Extensive Mobilome-Driven Genome Diversification in Mouse Gut-Associated Bacteroides vulgatus mpk.
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- Genome Biology & Evolution, 2016, v. 8, n. 4, p. 1197, doi. 10.1093/gbe/evw070
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- Article
A Survey of Combinatorial Methods for Phylogenetic Networks.
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- Genome Biology & Evolution, 2011, v. 3, p. 23, doi. 10.1093/gbe/evq077
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- Article
Application of Phylogenetic Networks in Evolutionary Studies.
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- Molecular Biology & Evolution, 2006, v. 23, n. 2, p. 254, doi. 10.1093/molbev/msj030
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- Publication type:
- Article
Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing.
- Published in:
- NPJ Biofilms & Microbiomes, 2021, v. 7, n. 1, p. 1, doi. 10.1038/s41522-021-00196-6
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- Article
On the Application of Advanced Machine Learning Methods to Analyze Enhanced, Multimodal Data from Persons Infected with COVID-19.
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- Computation, 2021, v. 9, n. 1, p. 4, doi. 10.3390/computation9010004
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- Article
Analysis of Domain Architecture and Phylogenetics of Family 2 Glycoside Hydrolases (GH2).
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- PLoS ONE, 2016, v. 11, n. 12, p. 1, doi. 10.1371/journal.pone.0168035
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- Article
Characterization of the Gut Microbial Community of Obese Patients Following a Weight-Loss Intervention Using Whole Metagenome Shotgun Sequencing.
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- PLoS ONE, 2016, v. 11, n. 2, p. 1, doi. 10.1371/journal.pone.0149564
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- Article
Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks.
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- Systematic Biology, 2012, v. 61, n. 6, p. 1061, doi. 10.1093/sysbio/sys062
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- Article
Filtered Z-Closure Supernetworks for Extracting and Visualizing Recurrent Signal from Incongruent Gene Trees.
- Published in:
- Systematic Biology, 2008, v. 57, n. 6, p. 939, doi. 10.1080/10635150802552849
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- Article
Distances that Perfectly Mislead.
- Published in:
- Systematic Biology, 2004, v. 53, n. 2, p. 327, doi. 10.1080/10635150490423809
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- Article
MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data.
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- PLoS Computational Biology, 2016, v. 12, n. 6, p. 1, doi. 10.1371/journal.pcbi.1004957
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- Article
OSLay: optimal syntenic layout of unfinished assemblies.
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- Bioinformatics, 2007, v. 23, n. 13, p. 1573, doi. 10.1093/bioinformatics/btm153
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- Article
CopyCat : cophylogenetic analysis tool.
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- Bioinformatics, 2007, v. 23, n. 7, p. 898, doi. 10.1093/bioinformatics/btm027
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- Article
Identification of plant microRNA homologs.
- Published in:
- Bioinformatics, 2006, v. 22, n. 3, p. 359, doi. 10.1093/bioinformatics/bti802
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- Article
Computing recombination networks from binary sequences.
- Published in:
- Bioinformatics, 2005, v. 21, p. ii159, doi. 10.1093/bioinformatics/bti1126
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- Article
Whole-genome prokaryotic phylogeny.
- Published in:
- Bioinformatics, 2005, v. 21, n. 10, p. 2329, doi. 10.1093/bioinformatics/bth324
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- Article
VisRD—visual recombination detection.
- Published in:
- Bioinformatics, 2004, v. 20, n. 18, p. 3654, doi. 10.1093/bioinformatics/bth400
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- Article
Phylogenetic trees based on gene content.
- Published in:
- Bioinformatics, 2004, v. 20, n. 13, p. 2044, doi. 10.1093/bioinformatics/bth198
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- Article
Design of a compartmentalized shotgun assembler for the human genome.
- Published in:
- Bioinformatics, 2001, v. 17, p. 132, doi. 10.1093/bioinformatics/17.suppl_1.s132
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- Article
SplitsTree: analyzing and visualizing evolutionary data.
- Published in:
- Bioinformatics, 1998, v. 14, n. 1, p. 68, doi. 10.1093/bioinformatics/14.1.68
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- Publication type:
- Article
Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data.
- Published in:
- Microbiome, 2019, v. 7, n. 1, p. N.PAG, doi. 10.1186/s40168-019-0665-y
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- Article
Interplay of Various Evolutionary Modes in Genome Diversification and Adaptive Evolution of the Family Sulfolobaceae.
- Published in:
- Frontiers in Microbiology, 2021, v. 12, p. 1, doi. 10.3389/fmicb.2021.639995
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- Article
The Isolate Caproiciproducens sp. 7D4C2 Produces n -Caproate at Mildly Acidic Conditions From Hexoses: Genome and rBOX Comparison With Related Strains and Chain-Elongating Bacteria.
- Published in:
- Frontiers in Microbiology, 2021, v. 11, p. N.PAG, doi. 10.3389/fmicb.2020.594524
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- Article
MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs.
- Published in:
- Biology Direct, 2018, v. 13, n. 1, p. N.PAG, doi. 10.1186/s13062-018-0208-7
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- Article
Comparative analysis of four Campylobacterales.
- Published in:
- Nature Reviews Microbiology, 2004, v. 2, n. 11, p. 872, doi. 10.1038/nrmicro1024
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- Article
Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and SOLiD shotgun sequencing.
- Published in:
- BMC Genomics, 2013, v. 14, p. 1, doi. 10.1186/1471-2164-14-S5-S16
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- Article