Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance

[1]  Kohske Takahashi,et al.  Welcome to the Tidyverse , 2019, J. Open Source Softw..

[2]  J. Huisman,et al.  Scientists’ warning to humanity: microorganisms and climate change , 2019, Nature Reviews Microbiology.

[3]  E. Muller Determining Microbial Niche Breadth in the Environment for Better Ecosystem Fate Predictions , 2019, mSystems.

[4]  S. Lücker,et al.  Metabolic Overlap in Environmentally Diverse Microbial Communities , 2019, bioRxiv.

[5]  S. Rampelli,et al.  A Multi-omics Approach to Unraveling the Microbiome-Mediated Effects of Arabinoxylan Oligosaccharides in Overweight Humans , 2019, mSystems.

[6]  S. De Vliegher,et al.  Characteristics of Escherichia coli Isolated from Bovine Mastitis Exposed to Subminimum Inhibitory Concentrations of Cefalotin or Ceftazidime , 2018, BioMed research international.

[7]  M. Domingues,et al.  Tuning culturing conditions towards the production of neutral lipids from lubricant-based wastewater in open mixed bacterial communities. , 2018, Water research.

[8]  Susana Martínez Arbas,et al.  Using metabolic networks to resolve ecological properties of microbiomes , 2018 .

[9]  Junqin Yao,et al.  Analysis of Bacterial Community Structure of Activated Sludge from Wastewater Treatment Plants in Winter , 2018, BioMed research international.

[10]  Paul Wilmes,et al.  Human Gut Microbiome: Function Matters. , 2017, Trends in microbiology.

[11]  A. Danchin,et al.  The contribution of microbial biotechnology to sustainable development goals , 2017, Microbial biotechnology.

[12]  Natalia N. Ivanova,et al.  Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea , 2017, Nature Biotechnology.

[13]  J. Banfield,et al.  dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication , 2017, The ISME Journal.

[14]  S. McIlroy,et al.  Culture-Independent Analyses Reveal Novel Anaerolineaceae as Abundant Primary Fermenters in Anaerobic Digesters Treating Waste Activated Sludge , 2017, Front. Microbiol..

[15]  Thomas Bartz-Beielstein,et al.  imputeTS: Time Series Missing Value Imputation in R , 2017, R J..

[16]  A. Heintz‐Buschart,et al.  IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses , 2016, Genome Biology.

[17]  Haixu Tang,et al.  A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics , 2016, PLoS Comput. Biol..

[18]  A. Heintz‐Buschart,et al.  Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes , 2016, Nature Microbiology.

[19]  Luiz Irber,et al.  sourmash: a library for MinHash sketching of DNA , 2016, J. Open Source Softw..

[20]  Peer Bork,et al.  Transcriptional interactions suggest niche segregation among microorganisms in the human gut , 2016, Nature Microbiology.

[21]  J. Ni,et al.  Performance Assessment of Full-Scale Wastewater Treatment Plants Based on Seasonal Variability of Microbial Communities via High-Throughput Sequencing , 2016, PloS one.

[22]  L. Lebrun,et al.  In situ phenotypic heterogeneity among single cells of the filamentous bacterium Candidatus Microthrix parvicella , 2015, The ISME Journal.

[23]  Brian D. Ondov,et al.  Mash: fast genome and metagenome distance estimation using MinHash , 2015, Genome Biology.

[24]  Kai Blin,et al.  Ten Simple Rules for Taking Advantage of Git and GitHub , 2014, bioRxiv.

[25]  H. Alvarez Triacylglycerol and wax ester-accumulating machinery in prokaryotes. , 2016, Biochimie.

[26]  Joonhong Park,et al.  The functional and taxonomic richness of wastewater treatment plant microbial communities are associated with each other and with ambient nitrogen and carbon availability. , 2015, Environmental microbiology.

[27]  Eugen Bauer,et al.  Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires , 2015, Microbiome.

[28]  K. Foster,et al.  The ecology of the microbiome: Networks, competition, and stability , 2015, Science.

[29]  Connor T. Skennerton,et al.  CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes , 2015, Genome research.

[30]  Aviaja Anna Hansen,et al.  MiDAS: the field guide to the microbes of activated sludge , 2015, Database J. Biol. Databases Curation.

[31]  Paul Wilmes,et al.  Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks , 2015, npj Biofilms and Microbiomes.

[32]  Mark P. Waldrop,et al.  Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes , 2015, Nature.

[33]  Tong Zhang,et al.  Bacterial assembly and temporal dynamics in activated sludge of a full-scale municipal wastewater treatment plant , 2014, The ISME Journal.

[34]  Christopher S. Henry,et al.  Long-term phenotypic evolution of bacteria , 2014, Nature.

[35]  Kunihiko Sadakane,et al.  MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph , 2014, Bioinform..

[36]  P. Wilmes,et al.  Lipid-based biofuel production from wastewater. , 2014, Current opinion in biotechnology.

[37]  Nitin S. Baliga,et al.  Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage , 2014, Nature Communications.

[38]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[39]  Pavel A. Pevzner,et al.  Universal database search tool for proteomics , 2014, Nature Communications.

[40]  Susannah G. Tringe,et al.  FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus , 2014, Nucleic acids research.

[41]  Lubos Polerecky,et al.  Oxygenic photosynthesis as a protection mechanism for cyanobacteria against iron-encrustation in environments with high Fe2+ concentrations , 2014, Front. Microbiol..

[42]  Torsten Seemann,et al.  Prokka: rapid prokaryotic genome annotation , 2014, Bioinform..

[43]  Damir Brdjanovic,et al.  Anticipating the next century of wastewater treatment , 2014, Science.

[44]  P. Wilmes,et al.  A hundred years of activated sludge: time for a rethink , 2014, Front. Microbiol..

[45]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[46]  Cathy H. Wu,et al.  A fast Peptide Match service for UniProt Knowledgebase , 2013, Bioinform..

[47]  Per Halkjær Nielsen,et al.  High and stable substrate specificities of microorganisms in enhanced biological phosphorus removal plants. , 2013, Environmental microbiology.

[48]  P. Hugenholtz,et al.  Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes , 2013, Nature Biotechnology.

[49]  J. Nielsen,et al.  Metabolic model for the filamentous ‘Candidatus Microthrix parvicella’ based on genomic and metagenomic analyses , 2013, The ISME Journal.

[50]  J. Comte,et al.  Links between metabolic plasticity and functional redundancy in freshwater bacterioplankton communities , 2013, Front. Microbiol..

[51]  Paul D. Cotter,et al.  Nucleic acid-based approaches to investigate microbial-related cheese quality defects , 2012, Front. Microbio..

[52]  Paul Wilmes,et al.  A biomolecular isolation framework for eco-systems biology , 2012, The ISME Journal.

[53]  Paul Wilmes,et al.  Sequential isolation of metabolites, RNA, DNA, and proteins from the same unique sample. , 2013, Methods in enzymology.

[54]  J. Prosser Ecosystem processes and interactions in a morass of diversity. , 2012, FEMS microbiology ecology.

[55]  Natalie I. Tasman,et al.  A Cross-platform Toolkit for Mass Spectrometry and Proteomics , 2012, Nature Biotechnology.

[56]  Alexandra J. Scott,et al.  Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2 , 2012, Bioinform..

[57]  Jianping Xie,et al.  The Function and Regulatory Network of WhiB and WhiB-Like Protein from Comparative Genomics and Systems Biology Perspectives , 2012, Cell Biochemistry and Biophysics.

[58]  J. Martínez,et al.  Natural Antibiotic Resistance and Contamination by Antibiotic Resistance Determinants: The Two Ages in the Evolution of Resistance to Antimicrobials , 2012, Front. Microbio..

[59]  Sean R. Eddy,et al.  Accelerated Profile HMM Searches , 2011, PLoS Comput. Biol..

[60]  W. Silver,et al.  Microbial communities acclimate to recurring changes in soil redox potential status. , 2010, Environmental microbiology.

[61]  Vincent J. Denef,et al.  Metabolome-Proteome Differentiation Coupled to Microbial Divergence , 2010, mBio.

[62]  Wael Sabra,et al.  Biosystems analysis and engineering of microbial consortia for industrial biotechnology , 2010 .

[63]  Haixu Tang,et al.  FragGeneScan: predicting genes in short and error-prone reads , 2010, Nucleic acids research.

[64]  Richard Durbin,et al.  Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..

[65]  Miriam L. Land,et al.  Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .

[66]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[67]  Dietmar Schomburg,et al.  MetaboliteDetector: comprehensive analysis tool for targeted and nontargeted GC/MS based metabolome analysis. , 2009, Analytical chemistry.

[68]  F. Arnold,et al.  Engineering microbial consortia: a new frontier in synthetic biology. , 2008, Trends in biotechnology.

[69]  Zhiguo Yuan,et al.  Advances in enhanced biological phosphorus removal: from micro to macro scale. , 2007, Water research.

[70]  B. Xie,et al.  Cause and pre-alarm control of bulking and foaming by Microthrix parvicella--a case study in triple oxidation ditch at a wastewater treatment plant. , 2007, Journal of hazardous materials.

[71]  A. Steinbüchel,et al.  Key enzymes for biosynthesis of neutral lipid storage compounds in prokaryotes: properties, function and occurrence of wax ester synthases/acyl-CoA: diacylglycerol acyltransferases. , 2007, Biochimie.

[72]  U. Bastolla,et al.  Structural approaches to sequence evolution : molecules, networks, populations , 2007 .

[73]  H Siegrist,et al.  Modelling seasonal dynamics of "Microthrix parvicella". , 2006, Water science and technology : a journal of the International Association on Water Pollution Research.

[74]  M. C. Tomei,et al.  "Microthrix parvicella", a filamentous bacterium causing bulking and foaming in activated sludge systems: a review of current knowledge. , 2005, FEMS microbiology reviews.

[75]  Dean Laslett,et al.  ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. , 2004, Nucleic acids research.

[76]  A. Steinbüchel,et al.  Triacylglycerols in prokaryotic microorganisms , 2002, Applied Microbiology and Biotechnology.

[77]  J. Nielsen,et al.  Microthrix parvicella, a specialized lipid consumer in anaerobic-aerobic activated sludge plants. , 2002, Water science and technology : a journal of the International Association on Water Pollution Research.

[78]  P. Chesson Mechanisms of Maintenance of Species Diversity , 2000 .

[79]  D. Tilman THE ECOLOGICAL CONSEQUENCES OF CHANGES IN BIODIVERSITY: A SEARCH FOR GENERAL PRINCIPLES101 , 1999 .

[80]  R M May,et al.  Niche overlap as a function of environmental variability. , 1972, Proceedings of the National Academy of Sciences of the United States of America.