Research graph
References from Systems-based approaches to unravel multi-species microbial community functioning. Local targets link to admitted publications; unresolved targets remain external evidence.
The microbiome as a human organ
10.1111/j.1469-0691.2012.03916.x · 2012 · External reference
2020 visions
10.1038/463026a · 2010 · External reference
A biomolecular isolation framework for eco-systems biology
2012 · External reference
10.1038/nature08883
10.1038/nature08883 · External reference
10.1002/pmic.201200576
10.1002/pmic.201200576 · External reference
10.1111/j.1574-6941.2011.01284.x
10.1111/j.1574-6941.2011.01284.x · External reference
10.1021/ac1011574
10.1021/ac1011574 · External reference
10.1038/nature02340
10.1038/nature02340 · External reference
10.1038/ismej.2010.185
10.1038/ismej.2010.185 · External reference
10.1038/nature12375
10.1038/nature12375 · External reference
10.1126/science.1243768
10.1126/science.1243768 · External reference
10.1038/nmeth.f.303
10.1038/nmeth.f.303 · External reference
10.1128/aem.01541-09
10.1128/aem.01541-09 · External reference
Computational methods for high-throughput comparative analyses of natural microbial communities
10.1016/b978-0-12-407863-5.00018-6 · 2013 · External reference
10.1038/nbt.2676
10.1038/nbt.2676 · External reference
A user's guide to quantitative and comparative analysis of metagenomic datasets
10.1016/b978-0-12-407863-5.00023-x · 2013 · External reference
10.1093/bioinformatics/btr216
10.1093/bioinformatics/btr216 · External reference
10.1089/cmb.2010.0245
10.1089/cmb.2010.0245 · External reference
10.1093/nar/gks678
10.1093/nar/gks678 · External reference
10.1089/cmb.2011.0276
10.1089/cmb.2011.0276 · 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
MetaCluster-TA: taxonomic annotation for metagenomic data based on assembly-assisted binning
10.1186/1471-2164-15-s1-s12 · 2014 · External reference
MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm
2014 · External reference
10.1186/gb-2009-10-8-r85
10.1186/gb-2009-10-8-r85 · External reference
10.1101/gr.142315.112
10.1101/gr.142315.112 · External reference
Unresolved reference
2014 · External reference
10.1038/nmeth.3103
10.1038/nmeth.3103 · External reference
10.1186/1471-2105-9-386
10.1186/1471-2105-9-386 · External reference
Analysis and comparison of very large metagenomes with fast clustering and functional annotation
10.1186/1471-2105-10-359 · 2009 · External reference
10.1093/nar/gku702
10.1093/nar/gku702 · External reference
10.1371/journal.pcbi.1002358
10.1371/journal.pcbi.1002358 · External reference
An iterative workflow for mining the human intestinal metaproteome
10.1186/1471-2164-12-6 · 2011 · External reference
Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset
10.1186/2042-5783-1-4 · 2011 · External reference
10.1128/aem.71.10.6319-6324.2005
10.1128/aem.71.10.6319-6324.2005 · External reference
10.1038/nbt.2579
10.1038/nbt.2579 · 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
Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment
10.1038/ncomms3120 · 2013 · External reference
Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling
10.1186/2049-2618-1-22 · 2013 · External reference
Discovery of a novel methanogen prevalent in thawing permafrost
10.1038/ncomms4212 · 2014 · External reference
10.1038/ncomms1597
10.1038/ncomms1597 · External reference
Metabolic synergy: increasing biosynthetic capabilities by network cooperation
2007 · External reference
Metabolic modeling of a mutualistic microbial community
10.1038/msb4100131 · 2007 · External reference
10.1371/journal.pcbi.1001002
10.1371/journal.pcbi.1001002 · External reference
Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity
10.1038/nrg2695 · 2009 · External reference
10.1038/nature08390
10.1038/nature08390 · External reference
10.1101/gad.1030302
10.1101/gad.1030302 · External reference
The role of small RNAs in quorum sensing
10.1016/j.mib.2007.03.009 · 2007 · External reference
10.1016/j.mib.2007.03.004
10.1016/j.mib.2007.03.004 · External reference
10.1038/nature08055
10.1038/nature08055 · External reference
10.1371/journal.pone.0036009
10.1371/journal.pone.0036009 · External reference
IDBA-MT: de novo assembler for metatranscriptomic data generated from next-generation sequencing technology
10.1089/cmb.2013.0042 · 2013 · External reference
10.1093/bioinformatics/bts721
10.1093/bioinformatics/bts721 · External reference
10.1111/j.1462-2920.2010.02400.x
10.1111/j.1462-2920.2010.02400.x · External reference
10.1016/j.cell.2012.10.052
10.1016/j.cell.2012.10.052 · External reference
10.1073/pnas.1402782111
10.1073/pnas.1402782111 · External reference
Metaproteomics: extracting and mining proteome information to characterize metabolic activities in microbial communities
10.1002/0471250953.bi1326s46 · 2014 · External reference
Microbial community analysis using MEGAN
10.1016/b978-0-12-407863-5.00021-6 · 2013 · External reference
10.1371/journal.pcbi.1000465
10.1371/journal.pcbi.1000465 · External reference
10.1371/journal.pcbi.1002981
10.1371/journal.pcbi.1002981 · External reference
10.1007/s00216-012-5918-6
10.1007/s00216-012-5918-6 · External reference
Quantitative shotgun proteomics using a protease with broad specificity and normalized spectral abundance factors
10.1039/b701483j · 2007 · External reference
Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology
10.1038/ismej.2013.78 · 2013 · External reference
Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics
10.1093/bioinformatics/btu267 · 2014 · External reference
10.1371/journal.pone.0068465
10.1371/journal.pone.0068465 · External reference
10.1038/ismej.2012.28
10.1038/ismej.2012.28 · External reference
10.1038/ismej.2009.139
10.1038/ismej.2009.139 · External reference
10.1038/ismej.2011.137
10.1038/ismej.2011.137 · External reference
Metaproteogenomic analysis of a sulfate-reducing enrichment culture reveals genomic organization of key enzymes in the m-xylene degradation pathway and metabolic activity of proteobacteria
10.1016/j.syapm.2014.07.005 · 2014 · External reference
10.1073/pnas.1322132111
10.1073/pnas.1322132111 · External reference
10.1038/nature11708
10.1038/nature11708 · External reference
10.5936/csbj.201301004 · Admitted local publication
10.1016/j.numecd.2009.04.018
10.1016/j.numecd.2009.04.018 · External reference
Metabolomics: from small molecules to big ideas
10.1038/nmeth0211-117 · 2011 · External reference
Practical approach for the identification and isomer elucidation of biomarkers detected in a metabonomic study for the discovery of individuals at risk for diabetes by integrating the chromatographic and mass spectrometric information
10.1021/ac702089h · 2008 · External reference
Metabolomic analyses of faeces reveals malabsorption in cirrhotic patients
10.1016/j.dld.2013.01.001 · 2013 · External reference
Metabolites associated with adaptation of microorganisms to an acidophilic, metal-rich environment identified by stable-isotope-enabled metabolomics
10.1128/mbio.00484-12 · 2013 · External reference
10.1021/ac502045j
10.1021/ac502045j · External reference
Development and in silico evaluation of large-scale metabolite identification methods using functional group detection for metabolomics
2014 · External reference
10.1021/pr500494u
10.1021/pr500494u · External reference
10.1007/s11306-014-0629-y
10.1007/s11306-014-0629-y · External reference
In situ proteo-metabolomics reveals metabolite secretion by the acid mine drainage bio-indicator, Euglena mutabilis
10.1038/ismej.2011.198 · 2012 · External reference
10.1038/ismej.2007.30
10.1038/ismej.2007.30 · External reference
The use of nucleic acid based stable isotope probing to identify the microorganisms responsible for anaerobic benzene and toluene biodegradation
10.1016/j.mimet.2011.02.011 · 2011 · External reference
Multisubstrate isotope labeling and metagenomic analysis of active soil bacterial communities
10.1128/mbio.01157-14 · 2014 · External reference
10.1139/cjm-2014-0193
10.1139/cjm-2014-0193 · External reference
Using stable isotope probing to obtain a targeted metatranscriptome of aerobic methanotrophs in lake sediment
10.1111/1758-2229.12078 · 2013 · External reference
Unresolved reference
2014 · External reference
Exploring the limits of robust detection of incorporation of 13C by mass spectrometry in protein-based stable isotope probing (protein-SIP)
10.1007/s00216-011-5289-4 · 2011 · External reference
Quantitative tracking of isotope flows in proteomes of microbial communities
2011 · External reference
Elucidation of in situ polycyclic aromatic hydrocarbon degradation by functional metaproteomics (protein-SIP)
10.1002/pmic.201200569 · 2013 · External reference
10.3390/metabo4010036
10.3390/metabo4010036 · External reference
10.1016/j.physa.2010.02.047
10.1016/j.physa.2010.02.047 · External reference
10.1089/cmb.2008.06tt
10.1089/cmb.2008.06tt · External reference
10.1002/biot.200900303
10.1002/biot.200900303 · External reference
10.1016/j.jtbi.2011.03.008
10.1016/j.jtbi.2011.03.008 · External reference
Sybil—efficient constraint-based modelling in R
10.1186/1752-0509-7-125 · 2013 · External reference
10.1093/bioinformatics/btq183
10.1093/bioinformatics/btq183 · External reference
10.1016/j.celrep.2014.03.070
10.1016/j.celrep.2014.03.070 · External reference
10.1186/gb-2011-12-6-r60
10.1186/gb-2011-12-6-r60 · External reference
Reverse ecology: from systems to environments and back
10.1007/978-1-4614-3567-9_15 · 2012 · External reference
10.1073/pnas.1300926110
10.1073/pnas.1300926110 · External reference
10.1073/pnas.1116053109
10.1073/pnas.1116053109 · External reference
Use of internal standards for quantitative metatranscriptome and metagenome analysis
10.1016/b978-0-12-407863-5.00012-5 · 2013 · External reference
