Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks

[1]  Paul Wilmes,et al.  Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities , 2015, Microbial biotechnology.

[2]  K. Konstantinidis,et al.  Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities. , 2014, Environmental microbiology reports.

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

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

[5]  Rob Knight,et al.  Which is more important for classifying microbial communities: who's there or what they can do? , 2014, The ISME Journal.

[6]  Pascal Bouvry,et al.  Management of an academic HPC cluster: The UL experience , 2014, 2014 International Conference on High Performance Computing & Simulation (HPCS).

[7]  Stefanie Widder,et al.  Deciphering microbial interactions and detecting keystone species with co-occurrence networks , 2014, Front. Microbiol..

[8]  Tong Zhang,et al.  Metagenomic analysis on seasonal microbial variations of activated sludge from a full-scale wastewater treatment plant over 4 years. , 2014, Environmental microbiology reports.

[9]  M. Knörnschild,et al.  Corrigendum: Bats host major mammalian paramyxoviruses , 2014, Nature Communications.

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

[11]  C. Kerepesi,et al.  AmphoraNet: the webserver implementation of the AMPHORA2 metagenomic workflow suite. , 2014, Gene.

[12]  Susumu Goto,et al.  Data, information, knowledge and principle: back to metabolism in KEGG , 2013, Nucleic Acids Res..

[13]  Elhanan Borenstein,et al.  Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities. , 2013, Current opinion in biotechnology.

[14]  P. May,et al.  Condensing the omics fog of microbial communities. , 2013, Trends in microbiology.

[15]  Kishori M. Konwar,et al.  MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information , 2013, BMC Bioinformatics.

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

[17]  G. Tyson,et al.  Rhizosphere Metatranscriptomics: Challenges and Opportunities , 2013 .

[18]  Lynne A. Goodwin,et al.  Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations , 2013, Standards in genomic sciences.

[19]  W. Verstraete,et al.  One-stage partial nitritation/anammox at 15 °C on pretreated sewage: feasibility demonstration at lab-scale , 2013, Applied Microbiology and Biotechnology.

[20]  Pelin Yilmaz,et al.  The SILVA ribosomal RNA gene database project: improved data processing and web-based tools , 2012, Nucleic Acids Res..

[21]  P. Wanichpongpan,et al.  Cultivation of microalgae (Oscillatoria okeni and Chlorella vulgaris) using tilapia-pond effluent and a comparison of their biomass removal efficiency. , 2012, Water science and technology : a journal of the International Association on Water Pollution Research.

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

[23]  É. Thébault,et al.  Ecosystem Engineers, Keystone Species , 2013 .

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

[25]  Daniel D. Sommer,et al.  MetAMOS: a modular and open source metagenomic assembly and analysis pipeline , 2013, Genome Biology.

[26]  Shilin Chen,et al.  FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads , 2012, PloS one.

[27]  N. Baliga,et al.  Genome Sequence of “Candidatus Microthrix parvicella” Bio17-1, a Long-Chain-Fatty-Acid-Accumulating Filamentous Actinobacterium from a Biological Wastewater Treatment Plant , 2012, Journal of bacteriology.

[28]  Peer Bork,et al.  MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit , 2012, PloS one.

[29]  Popular molecular markers in bacteria , 2012, Molecular Genetics, Microbiology and Virology.

[30]  Zhengwei Zhu,et al.  CD-HIT: accelerated for clustering the next-generation sequencing data , 2012, Bioinform..

[31]  J. Raes,et al.  Microbial interactions: from networks to models , 2012, Nature Reviews Microbiology.

[32]  Kevin W Eliceiri,et al.  NIH Image to ImageJ: 25 years of image analysis , 2012, Nature Methods.

[33]  R. Hettich,et al.  Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities. , 2012, Current opinion in microbiology.

[34]  Tong Zhang,et al.  454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants , 2011, The ISME Journal.

[35]  Bernard Henrissat,et al.  Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome , 2012, PLoS Comput. Biol..

[36]  Siu-Ming Yiu,et al.  IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth , 2012, Bioinform..

[37]  K. Yu,et al.  Metagenomic and Metatranscriptomic Analysis of Microbial Community Structure and Gene Expression of Activated Sludge , 2012, PloS one.

[38]  Elhanan Borenstein,et al.  Computational systems biology and in silico modeling of the human microbiome , 2012, Briefings Bioinform..

[39]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[40]  Martin Ackermann,et al.  The activity level of a microbial community function can be predicted from its metatranscriptome , 2011, The ISME Journal.

[41]  H. Flint,et al.  Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon , 2012, The ISME Journal.

[42]  Daniel G. Brown,et al.  PANDAseq: paired-end assembler for illumina sequences , 2012, BMC Bioinformatics.

[43]  Sharon I. Greenblum,et al.  Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease , 2011, Proceedings of the National Academy of Sciences.

[44]  D. Caron,et al.  Marine bacterial, archaeal and protistan association networks reveal ecological linkages , 2011, The ISME Journal.

[45]  Jane Tang,et al.  Microbial Metabolomics , 2011, Current genomics.

[46]  Natalie I. Tasman,et al.  iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates* , 2011, Molecular & Cellular Proteomics.

[47]  Hideaki Tanaka,et al.  MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads , 2011, BCB '11.

[48]  Brian C. Thomas,et al.  EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data , 2011, Genome Biology.

[49]  Albert-László Barabási,et al.  Controllability of complex networks , 2011, Nature.

[50]  A. Futschik,et al.  PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals , 2011, PloS one.

[51]  Trey Ideker,et al.  Cytoscape 2.8: new features for data integration and network visualization , 2010, Bioinform..

[52]  Sanghyuk Lee,et al.  Accurate quantification of transcriptome from RNA-Seq data by effective length normalization , 2010, Nucleic Acids Res..

[53]  Iwanka Kozarewa,et al.  96-plex molecular barcoding for the Illumina Genome Analyzer. , 2011, Methods in molecular biology.

[54]  P. Silver,et al.  Emergent cooperation in microbial metabolism , 2010, Molecular systems biology.

[55]  Leen Stougie,et al.  Graph-Based Analysis of the Metabolic Exchanges between Two Co-Resident Intracellular Symbionts, Baumannia cicadellinicola and Sulcia muelleri, with Their Insect Host, Homalodisca coagulata , 2010, PLoS Comput. Biol..

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

[57]  Sallie W. Chisholm,et al.  Unlocking Short Read Sequencing for Metagenomics , 2010, PloS one.

[58]  S. Mocali,et al.  Exploring research frontiers in microbiology: the challenge of metagenomics in soil microbiology. , 2010, Research in microbiology.

[59]  Vincent J. Denef,et al.  AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature , 2010, The ISME Journal.

[60]  O. Gascuel,et al.  New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. , 2010, Systematic biology.

[61]  Natalie I. Tasman,et al.  A guided tour of the Trans‐Proteomic Pipeline , 2010, Proteomics.

[62]  Ying Gao,et al.  Bioinformatics Applications Note Sequence Analysis Cd-hit Suite: a Web Server for Clustering and Comparing Biological Sequences , 2022 .

[63]  R. Kalscheuer.  40 Genetics of Wax Ester and Triacylglycerol Biosynthesis in Bacteria , 2010 .

[64]  K. Timmis.  Handbook of hydrocarbon and lipid microbiology , 2010 .

[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]  Jason A. Papin,et al.  Applications of genome-scale metabolic reconstructions , 2009, Molecular systems biology.

[67]  D. Stahl,et al.  Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria , 2009, Nature.

[68]  P. Wilmes,et al.  Microbial community proteomics: elucidating the catalysts and metabolic mechanisms that drive the Earth's biogeochemical cycles. , 2009, Current opinion in microbiology.

[69]  Steven J. M. Jones,et al.  Abyss: a Parallel Assembler for Short Read Sequence Data Material Supplemental Open Access , 2022 .

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

[71]  J. van Helden,et al.  Metabolic pathfinding using RPAIR annotation. , 2009, Journal of molecular biology.

[72]  Andreas Wilke,et al.  phylogenetic and functional analysis of metagenomes , 2022 .

[73]  Robert Burke,et al.  ProteoWizard: open source software for rapid proteomics tools development , 2008, Bioinform..

[74]  Ulrik Brandes,et al.  On variants of shortest-path betweenness centrality and their generic computation , 2008, Soc. Networks.

[75]  Jean-Michel Claverie,et al.  Phylogeny.fr: robust phylogenetic analysis for the non-specialist , 2008, Nucleic Acids Res..

[76]  Ruiqiang Li,et al.  SOAP: short oligonucleotide alignment program , 2008, Bioinform..

[77]  Jianhua Guo,et al.  Biological removal of nitrogen from wastewater. , 2008, Reviews of environmental contamination and toxicology.

[78]  Rick L. Stevens,et al.  The RAST Server: Rapid Annotations using Subsystems Technology , 2008, BMC Genomics.

[79]  Mihai Pop,et al.  Minimus: a fast, lightweight genome assembler , 2007, BMC Bioinformatics.

[80]  Michael Wagner,et al.  Wastewater treatment: a model system for microbial ecology. , 2006, Trends in biotechnology.

[81]  Marie-Christine Brun,et al.  TreeDyn: towards dynamic graphics and annotations for analyses of trees , 2006, BMC Bioinformatics.

[82]  S. Rossetti,et al.  Phylogeny, physiology and distribution of 'Candidatus Microthrix calida', a new Microthrix species isolated from industrial activated sludge wastewater treatment plants. , 2006, Environmental microbiology.

[83]  Dietmar Schomburg,et al.  Observing local and global properties of metabolic pathways: "load points" and "choke points" in the metabolic networks , 2006, Bioinform..

[84]  Gábor Csárdi,et al.  The igraph software package for complex network research , 2006 .

[85]  Naryttza N. Diaz,et al.  The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes , 2005, Nucleic acids research.

[86]  E. Purdom,et al.  Diversity of the Human Intestinal Microbial Flora , 2005, Science.

[87]  Robertson Craig,et al.  Open source system for analyzing, validating, and storing protein identification data. , 2004, Journal of proteome research.

[88]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[89]  Alexey I Nesvizhskii,et al.  Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. , 2002, Analytical chemistry.

[90]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[91]  Wei Qian,et al.  Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. , 2000, Molecular biology and evolution.

[92]  Michael Y. Galperin,et al.  The COG database: a tool for genome-scale analysis of protein functions and evolution , 2000, Nucleic Acids Res..

[93]  M. Klotz,et al.  Transcription of the amoC, amoA and amoB genes in Nitrosomonas europaea and Nitrosospira sp. NpAV. , 1998, FEMS microbiology letters.

[94]  Duncan J. Watts,et al.  Collective dynamics of ‘small-world’ networks , 1998, Nature.

[95]  P. Green,et al.  Consed: a graphical tool for sequence finishing. , 1998, Genome research.

[96]  A. Steinbüchel,et al.  Formation of intracytoplasmic lipid inclusions by Rhodococcus opacus strain PD630 , 1996, Archives of Microbiology.

[97]  R. Paine.  A Conversation on Refining the Concept of Keystone Species , 1995 .

[98]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[99]  T. Hvitved-Jacobsen,et al.  Measurement of pools of protein, carbohydrate and lipid in domestic wastewater , 1994 .

[100]  A. Chao.  Estimating the population size for capture-recapture data with unequal catchability. , 1987, Biometrics.

[101]  S. Fowler,et al.  Application of Nile red, a fluorescent hydrophobic probe, for the detection of neutral lipid deposits in tissue sections: comparison with oil red O. , 1985, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[102]  E. Geldreich,et al.  A new medium for the enumeration and subculture of bacteria from potable water , 1985, Applied and environmental microbiology.

[103]  H. Slijkhuis.  Microthrix parvicella, a filamentous bacterium isolated from activated sludge: cultivation in a chemically defined medium , 1983, Applied and environmental microbiology.