论文信息 - Connecting genotype to phenotype in the era of high-throughput sequencing. - 字舞流文

Connecting genotype to phenotype in the era of high-throughput sequencing.

Rick L. Stevens | Kevin P. Keegan | R. Overbeek | M. D'Souza | J. Gilbert | C. Henry | M. DeJongh | A. Best | R. Stevens | R. Edwards | Folker Meyer | R. Olson | E. Glass | D. Bartels | Fangfang Xia | V. Vonstein | T. Disz | Andreas Wilke | Scott Devoid | P. Larsen | N. Desai | J. Wilkening | Jared Wilkening

[1] Folker Meyer,et al. The Future of microbial metagenomics (or is ignorance bliss?) , 2011, The ISME Journal.

[2] Ronan M. T. Fleming,et al. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 , 2007, Nature Protocols.

[3] Huzefa Rangwala,et al. Evaluation of short read metagenomic assembly , 2010, 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

[4] Rick L. Stevens,et al. High-throughput generation, optimization and analysis of genome-scale metabolic models , 2010, Nature Biotechnology.

[5] A. Goesmann,et al. CARMEN - Comparative Analysis and in silico Reconstruction of organism-specific MEtabolic Networks. , 2010, Genetics and molecular research : GMR.

[6] Neil Swainston,et al. Integration of metabolic databases for the reconstruction of genome-scale metabolic networks , 2010, BMC Systems Biology.

[7] Robert Olson,et al. Accessing the SEED Genome Databases via Web Services API: Tools for Programmers , 2010, BMC Bioinformatics.

[8] Weiwen Zhang,et al. Reconstruction of xylose utilization pathway and regulons in Firmicutes , 2010, BMC Genomics.

[9] Bruce J. Aronow,et al. Microevolution of Group A Streptococci In Vivo: Capturing Regulatory Networks Engaged in Sociomicrobiology, Niche Adaptation, and Hypervirulence , 2010, PloS one.

[10] Costas D. Maranas,et al. OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions , 2010, PLoS Comput. Biol..

[11] Damian Szklarczyk,et al. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations , 2009, Nucleic Acids Res..

[12] Inna Dubchak,et al. MicrobesOnline: an integrated portal for comparative and functional genomics , 2009, Nucleic Acids Res..

[13] B. Palsson,et al. A protocol for generating a high-quality genome-scale metabolic reconstruction , 2010 .

[14] Miguel Rocha,et al. OptFlux: an open-source software platform for in silico metabolic engineering , 2010, BMC Systems Biology.

[15] Andreas Wilke,et al. Using clouds for metagenomics: A case study , 2009, 2009 IEEE International Conference on Cluster Computing and Workshops.

[16] R. Overbeek,et al. FIGfams: yet another set of protein families , 2009, Nucleic acids research.

[17] Rick L Stevens,et al. iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations , 2009, Genome Biology.

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

[19] Vinay Satish Kumar,et al. GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions , 2009, PLoS Comput. Biol..

[20] Joakim Lundeberg,et al. Generations of sequencing technologies. , 2009, Genomics.

[21] Adam M. Feist,et al. Reconstruction of biochemical networks in microorganisms , 2009, Nature Reviews Microbiology.

[22] Vinay Satish Kumar,et al. A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189 , 2009, PLoS Comput. Biol..

[23] M. Gerstein,et al. RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.

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

[25] Grigoriy E. Pinchuk,et al. Towards environmental systems biology of Shewanella , 2008, Nature Reviews Microbiology.

[26] Adam M. Feist,et al. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli , 2008, Nature Biotechnology.

[27] C. Nusbaum,et al. ALLPATHS: de novo assembly of whole-genome shotgun microreads. , 2008, Genome research.

[28] David Hernández,et al. De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. , 2008, Genome research.

[29] E. Birney,et al. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[30] Rick L. Stevens,et al. Functional metagenomic profiling of nine biomes , 2008, Nature.

[31] Mark J. P. Chaisson,et al. Short read fragment assembly of bacterial genomes. , 2008, Genome research.

[32] Yoshihiro Yamanishi,et al. KEGG for linking genomes to life and the environment , 2007, Nucleic Acids Res..

[33] I-Min A. Chen,et al. IMG/M: a data management and analysis system for metagenomes , 2007, Nucleic Acids Res..

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

[35] Juliane C. Dohm,et al. SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. , 2007, Genome research.

[36] Vincent J. Magrini,et al. Extending assembly of short DNA sequences to handle error , 2007, Bioinform..

[37] Peter Salamon,et al. Metagenomic and Small-Subunit rRNA Analyses Reveal the Genetic Diversity of Bacteria, Archaea, Fungi, and Viruses in Soil , 2007, Applied and Environmental Microbiology.

[38] Neil Hall,et al. Advanced sequencing technologies and their wider impact in microbiology , 2007, Journal of Experimental Biology.

[39] D. Stahl,et al. Molecular Systems Biology 3; Article number 92; doi:10.1038/msb4100131 Citation: Molecular Systems Biology 3:92 , 2022 .

[40] V. Hatzimanikatis,et al. Thermodynamics-based metabolic flux analysis. , 2007, Biophysical journal.

[41] S. Kravitz,et al. CAMERA: A Community Resource for Metagenomics , 2007, PLoS biology.

[42] Alexander F. Auch,et al. MEGAN analysis of metagenomic data. , 2007, Genome research.

[43] Michelle G. Giglio,et al. TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes , 2006, Nucleic Acids Res..

[44] Fangfang Xia,et al. The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation , 2006, Nucleic Acids Res..

[45] Vinay Satish Kumar,et al. Optimization based automated curation of metabolic reconstructions , 2007, BMC Bioinformatics.

[46] John Gould,et al. Toward the automated generation of genome-scale metabolic networks in the SEED , 2007, BMC Bioinformatics.

[47] Steffen Klamt,et al. Structural and functional analysis of cellular networks with CellNetAnalyzer , 2007, BMC Systems Biology.

[48] Matthias Heinemann,et al. Systematic assignment of thermodynamic constraints in metabolic network models , 2006, BMC Bioinformatics.

[49] B. Palsson,et al. Systems approach to refining genome annotation , 2006, Proceedings of the National Academy of Sciences.

[50] S. Panke,et al. Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data , 2006, Molecular systems biology.

[51] Matthew D. Jankowski,et al. Genome-scale thermodynamic analysis of Escherichia coli metabolism. , 2006, Biophysical journal.

[52] Cathy H. Wu,et al. The Universal Protein Resource (UniProt): an expanding universe of protein information , 2005, Nucleic Acids Res..

[53] Inna Dubchak,et al. The integrated microbial genomes (IMG) system , 2005, Nucleic Acids Res..

[54] Hongfang Liu,et al. BioThesaurus: a web-based thesaurus of protein and gene names , 2006, Bioinform..

[55] Forest Rohwer,et al. An application of statistics to comparative metagenomics , 2006, BMC Bioinformatics.

[56] M. Breitbart,et al. Using pyrosequencing to shed light on deep mine microbial ecology , 2006, BMC Genomics.

[57] 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.

[58] Tao Cai,et al. Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary , 2005, Bioinform..

[59] E. Ruppin,et al. Regulatory on/off minimization of metabolic flux changes after genetic perturbations. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[60] Owen White,et al. Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics , 2005, Bioinform..

[61] Rick L. Stevens,et al. The SEED: a peer-to-peer environment for genome annotation , 2004, CACM.

[62] J. Banfield,et al. Community structure and metabolism through reconstruction of microbial genomes from the environment , 2004, Nature.

[63] Markus J. Herrgård,et al. Reconstruction of microbial transcriptional regulatory networks. , 2004, Current opinion in biotechnology.

[64] A. Burgard,et al. Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization , 2003, Biotechnology and bioengineering.

[65] Darren A. Natale,et al. The COG database: an updated version includes eukaryotes , 2003, BMC Bioinformatics.

[66] Ron D. Appel,et al. ExPASy: the proteomics server for in-depth protein knowledge and analysis , 2003, Nucleic Acids Res..

[67] G. Church,et al. Analysis of optimality in natural and perturbed metabolic networks , 2002 .

[68] B. Palsson,et al. Transcriptional regulation in constraints-based metabolic models of Escherichia coli Covert , 2002 .

[69] R. Jensen. Orthologs and paralogs - we need to get it right , 2001, Genome Biology.

[70] B. Palsson,et al. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[71] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[72] Susumu Goto,et al. KEGG: Kyoto Encyclopedia of Genes and Genomes , 2000, Nucleic Acids Res..

[73] Keith F. Tipton,et al. History of the enzyme nomenclature system , 2000, Bioinform..

[74] J. Handelsman,et al. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. , 1998, Chemistry & biology.

[75] A. Douglas,et al. Nutritional interactions in insect-microbial symbioses: aphids and their symbiotic bacteria Buchnera. , 1998, Annual review of entomology.

[76] Hans-Werner Mewes,et al. The PIR-International Protein Sequence Database , 1992, Nucleic Acids Res..

[77] G. Schuler,et al. Entrez: molecular biology database and retrieval system. , 1996, Methods in enzymology.

[78] B. Palsson,et al. Metabolic Flux Balancing: Basic Concepts, Scientific and Practical Use , 1994, Bio/Technology.

[79] B. Palsson,et al. Metabolic Capabilities of Escherichia coli II. Optimal Growth Patterns , 1993 .

[80] B. Palsson,et al. Metabolic capabilities of Escherichia coli: I. synthesis of biosynthetic precursors and cofactors. , 1993, Journal of theoretical biology.

[81] N. Pace,et al. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. , 1985, Proceedings of the National Academy of Sciences of the United States of America.