Research graph
References from Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics. Local targets link to admitted publications; unresolved targets remain external evidence.
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10.1126/science.1070633 · External reference
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Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms
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Marine metagenomics: strategies for the discovery of novel enzymes with biotechnological applications from marine environments
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10.1093/dnares/dsm018
10.1093/dnares/dsm018 · External reference
Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data
10.1038/srep25373 · 2016 · External reference
Metagenomics, metatranscriptomics, and metabolomics approaches for microbiome analysis
2016 · External reference
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10.1038/nbt.2676 · External reference
10.1111/j.1365-294x.2010.04948.x
10.1111/j.1365-294x.2010.04948.x · External reference
10.1093/bib/bbr019
10.1093/bib/bbr019 · External reference
Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies
2012 · External reference
Bipartite graphs for visualization analysis of microbiome data
2016 · External reference
An introduction to the analysis of shotgun metagenomic data
10.3389/fpls.2014.00209 · 2014 · External reference
10.1016/j.molcel.2015.05.004
10.1016/j.molcel.2015.05.004 · External reference
10.1073/pnas.171285098
10.1073/pnas.171285098 · External reference
10.1016/s0022-2836(05)80360-2
10.1016/s0022-2836(05)80360-2 · External reference
10.1101/gr.229202
10.1101/gr.229202 · External reference
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
10.1186/gb-2009-10-3-r25 · 2009 · External reference
10.1093/bioinformatics/btp698
10.1093/bioinformatics/btp698 · External reference
10.1093/nar/gkv1344
10.1093/nar/gkv1344 · External reference
Alignment-free sequence comparison—a review
10.1093/bioinformatics/btg005 · 2003 · External reference
Current opportunities and challenges in microbial metagenome analysis—a bioinformatic perspective
10.1093/bib/bbs039 · 2012 · External reference
Database resources of the National Center for Biotechnology Information
10.1093/nar/gkp382 · 2009 · External reference
Classification of metagenomic sequences: methods and challenges
10.1093/bib/bbs054 · 2012 · External reference
10.1186/gb-2009-10-8-r85
10.1186/gb-2009-10-8-r85 · External reference
10.1109/isb.2011.6033147
10.1109/isb.2011.6033147 · 2011 · External reference
10.1007/s10142-015-0433-4
10.1007/s10142-015-0433-4 · External reference
TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences
10.1186/1471-2105-5-163 · 2004 · External reference
Unsupervised statistical clustering of environmental shotgun sequences
10.1186/1471-2105-10-316 · 2009 · External reference
Clustering metagenomic sequences with interpolated Markov models
10.1186/1471-2105-11-544 · 2010 · External reference
CompostBin: a DNA composition-based algorithm for binning environmental shotgun reads
10.1007/978-3-540-78839-3_3 · 2008 · External reference
Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life
10.1186/2049-2618-1-30 · 2013 · External reference
10.1126/science.1224041
10.1126/science.1224041 · External reference
Visualization of genome signatures of eukaryote genomes by batch-learning self-organizing map with a special emphasis on Drosophila genomes
10.1155/2014/985706 · 2014 · External reference
Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples
10.1093/dnares/dsi015 · 2006 · External reference
Development of self-compressing BLSOM for comprehensive analysis of big sequence data
10.1155/2015/506052 · 2015 · External reference
10.1109/5.58325
10.1109/5.58325 · External reference
VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data
10.1186/s40168-014-0066-1 · 2015 · External reference
Accelerating t-SNE using tree-based algorithms
2014 · External reference
Alignment-free visualization of metagenomic data by nonlinear dimension reduction
10.1038/srep04516 · 2014 · External reference
Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition
10.1093/nar/gkr1204 · 2011 · External reference
The oligonucleotide frequency derived error gradient and its application to the binning of metagenome fragments
10.1186/1471-2164-10-s3-s10 · 2009 · External reference
The binning of metagenomic contigs for microbial physiology of mixed cultures
10.3389/fmicb.2012.00410 · 2012 · External reference
10.1089/cmb.2010.0245
10.1089/cmb.2010.0245 · External reference
MBBC: an efficient approach for metagenomic binning based on clustering
10.1186/s12859-015-0473-8 · 2015 · External reference
10.1038/nbt.2939
10.1038/nbt.2939 · External reference
10.1016/0888-7543(88)90007-9
10.1016/0888-7543(88)90007-9 · External reference
10.1371/journal.pone.0047656
10.1371/journal.pone.0047656 · External reference
10.1038/nmeth.3103
10.1038/nmeth.3103 · External reference
Variational Bayesian model selection for mixture distributions
2001 · External reference
COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge
2016 · External reference
Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes
10.1038/srep24175 · 2016 · External reference
MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation–maximization algorithm
10.1186/2049-2618-2-26 · 2014 · External reference
10.7717/peerj.1165
10.7717/peerj.1165 · External reference
10.1093/bioinformatics/btv638
10.1093/bioinformatics/btv638 · External reference
10.7717/peerj.603
10.7717/peerj.603 · External reference
10.1038/nbt.2579
10.1038/nbt.2579 · External reference
cy3sabiork: a Cytoscape app for visualizing kinetic data from SABIO-RK
10.12688/f1000research.9211.1 · 2016 · External reference
MetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample
10.1093/bioinformatics/bts397 · 2012 · External reference
10.1089/cmb.2011.0276
10.1089/cmb.2011.0276 · External reference
MetaCluster-TA: taxonomic annotation for metagenomic data based on assembly-assisted binning
10.1186/1471-2164-15-s1-s12 · 2014 · External reference
10.1016/j.gpb.2015.08.002
10.1016/j.gpb.2015.08.002 · External reference
A first look at the Oxford Nanopore MinION sequencer
10.1111/1755-0998.12324 · 2014 · External reference
10.1111/j.1365-294x.2012.05538.x
10.1111/j.1365-294x.2012.05538.x · External reference
10.1186/2047-217x-1-18
10.1186/2047-217x-1-18 · External reference
10.1073/pnas.171285098
10.1073/pnas.171285098 · External reference
10.1101/gr.074492.107
10.1101/gr.074492.107 · External reference
10.1093/nar/gks678
10.1093/nar/gks678 · External reference
10.1093/bioinformatics/bts174
10.1093/bioinformatics/bts174 · External reference
Ray Meta: scalable de novo metagenome assembly and profiling
10.1186/gb-2012-13-12-r122 · 2012 · External reference
Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization
10.1101/gr.142315.112 · 2012 · External reference
Unresolved reference
2013 · External reference
GTM: the generative topographic mapping
10.1162/089976698300017953 · 1998 · External reference
Visualizing high-dimensional data using t-SNE
2008 · External reference
IMP: a pipeline for reproducible metagenomic and metatranscriptomic analyses
2016 · External reference
