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The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation

L. K. McNeil, C. Reich, R. K. Aziz, D. Bartels, M. Cohoon, T. Disz, R. A. Edwards, S. Gerdes, K. Hwang, M. Kubal, G. R. Margaryan, F. Meyer (+17 others)
2007 Nucleic Acids Research  
ACKNOWLEDGEMENTS This project has been funded in whole or in part with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health  ...  INTRODUCTION The National Microbial Pathogen Data Resource (NMPDR) is one of eight Bioinformatics Resource Centers funded by the National Institute of Allergy and Infectious Disease (NIAID) to provide  ...  NMPDR is both a central repository for a wide variety of scientific data on these pathogenic microorganisms and a platform for software tools that support investigator-driven data analysis.  ... 
doi:10.1093/nar/gkl947 pmid:17145713 pmcid:PMC1751540 fatcat:wgr7fnyfazfq7ptt7u2tbbynmu

Subsystems-based servers for rapid annotation of genomes and metagenomes

Ramy Aziz
2010 BMC Bioinformatics  
Chicago National Microbial Pathogen Data Resource (NMPDR) project [10] , has improved the accuracy and consistency of genome and metagenome annotation [11] .  ...  To address this challenge, researchers at San Diego State University, FIG, and the Argonne National Laboratory are developing a protein family signature-based technology (Robert A.  ... 
doi:10.1186/1471-2105-11-s4-o2 pmcid:PMC3290056 fatcat:kkxl6fcxnbdfxabsnpimseawka

National Institute of Allergy and Infectious Diseases Bioinformatics Resource Centers: New Assets for Pathogen Informatics

J. M. Greene, F. Collins, E. J. Lefkowitz, D. Roos, R. H. Scheuermann, B. Sobral, R. Stevens, O. White, V. Di Francesco
2007 Infection and Immunity  
The National Microbial Pathogen Data Resource Center (NMPDR) is focusing its annotation efforts on vertical integration across genomes that share proteins which perform the same biological functions.  ...  NMPDR is both a central repository for a wide variety of scientific data on its core pathogens and a platform for software tools that support investigator-driven data analysis.  ... 
doi:10.1128/iai.00105-07 pmid:17420237 pmcid:PMC1932942 fatcat:ywmscqywenflnlxo7frpehvnii

PATRIC, the bacterial bioinformatics database and analysis resource

Alice R. Wattam, David Abraham, Oral Dalay, Terry L. Disz, Timothy Driscoll, Joseph L. Gabbard, Joseph J. Gillespie, Roger Gough, Deborah Hix, Ronald Kenyon, Dustin Machi, Chunhong Mao (+16 others)
2013 Nucleic Acids Research  
Two of these original eight BRCs were the Pathosystems Resource Integration Center (PATRIC) (2) and the National Microbial Pathogen Data Resource (NMPDR) (3) .  ...  A single exception, the Influenza Resource Database, was initiated to specifically focus on the influenza virus.  ... 
doi:10.1093/nar/gkt1099 pmid:24225323 pmcid:PMC3965095 fatcat:isuamx5fbfap3l37l7wzvg26b4

The diversity of unique 1,4,5,6-Tetrahydro-2-methyl-4-pyrimidinecarboxylic acid coding common genes and Universal stress protein in Ectoine TRAP cluster (UspA) in 32 Halomonas species

Bhagwan Narayan Rekadwad, Wen-Jun Li, P. D. Rekha
2021 BMC Research Notes  
The presence of a superfamily of conserved ectoine-coding among members of the genus Halomonas was discovered after genome annotations of 93 Halomonas spp.  ...  As a result of the inclusion of 11 single copy ectoine coding genes in 32 Halomonas spp., genome-wide evaluations of ectoine coding genes indicate that 32 Halomonas spp. have a very strong association  ...  Acknowledgements BR is thankful to editors and the reviewers for their comment to improve manuscript in present form.  ... 
doi:10.1186/s13104-021-05689-3 pmid:34344424 pmcid:PMC8330102 fatcat:45vbqaiulrhw3ehi6mud5aclmq

Identification of Genes Encoding tRNA Modification Enzymes by Comparative Genomics [chapter]

Valérie de Crécy‐Lagard
2007 Methods in Enzymology  
This chapter reviews the methods that were used to identify these genes with a special emphasis on the comparative genomic approaches.  ...  However, the availability of hundreds of whole-genome sequences has allowed the identification of many of these missing tRNAmodification genes.  ...  Acknowledgments This work was supported in part by The National Science foundation (MCB-05169448) and by the National Institutes of Health (R01 GM70641-01).  ... 
doi:10.1016/s0076-6879(07)25007-4 pmid:17673083 pmcid:PMC3034448 fatcat:xf65ispj2bbkvgjqv5o6fujfpi

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

Ross Overbeek, Robert Olson, Gordon D. Pusch, Gary J. Olsen, James J. Davis, Terry Disz, Robert A. Edwards, Svetlana Gerdes, Bruce Parrello, Maulik Shukla, Veronika Vonstein, Alice R. Wattam (+2 others)
2013 Nucleic Acids Research  
Here we describe the interconnectedness of the SEED database and RAST, the RAST annotation pipeline and updates to both resources.  ...  In 2004, the SEED (http://pubseed.theseed.org/) was created to provide consistent and accurate genome annotations across thousands of genomes and as a platform for discovering and developing de novo annotations  ...  ACKNOWLEDGEMENTS The authors thank Bas Dutilh for helpful suggestions. FUNDING  ... 
doi:10.1093/nar/gkt1226 pmid:24293654 pmcid:PMC3965101 fatcat:oayl74ppbbgplfhsh6wle6nqdm

Comparing the genomes of Helicobacter pylori clinical strain UM032 and Mice-adapted derivatives

Yalda Khosravi, Vellaya Rehvathy, Wei Wee, Susana Wang, Primo Baybayan, Siddarth Singh, Meredith Ashby, Junxian Ong, Arlaine Amoyo, Shih Seow, Siew Choo, Tim Perkins (+7 others)
2013 Gut Pathogens  
Although not a natural host for H. pylori, mouse infection models play an important role in establishing the immunology and pathogenicity of H. pylori.  ...  Helicobacter pylori is a Gram-negative bacterium that persistently infects the human stomach inducing chronic inflammation. The exact mechanisms of pathogenesis are still not completely understood.  ...  We thank the NCBI (National Center for Biotechnology Information) rapid annotation pipeline team for providing the genome annotation services.  ... 
doi:10.1186/1757-4749-5-25 pmid:23957912 pmcid:PMC3751790 fatcat:jtg7svbam5abjdems44jvcwzpy

Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes

Christofer Karlsson, Lars Malmström, Ruedi Aebersold, Johan Malmström
2012 Nature Communications  
The proteins were grouped according to cellular functions using the National pathogen microbe data resource (NMPDR) sub-system information 27 (now part of PATRICs Bioinformatics Resource Center 28 )  ...  Based on the performance of the individual assays as a function of biological matrix, we calculated an assay score based on a rule-based assay-scoring model.  ... 
doi:10.1038/ncomms2297 pmid:23250431 pmcid:PMC3535367 fatcat:oas7vk7zmjaxbar6jmums65rwe

The smallest cells pose the biggest problems: high-performance computing and the analysis of metagenome sequence data

R A Edwards
2008 Journal of Physics, Conference Series  
Argonne National Laboratory developed the premier platform for the analysis of this new data (mg-rast), and offers a freely available service that is used by microbiologists world-wide.  ...  Increased technology such as pyrosequencing and other so-called next generation DNA sequencing platforms have resulted in huge increases in the amount of raw data that is generated.  ...  Pathogen Resource (NMPDR) for assistance, dedication, and tutelage.  ... 
doi:10.1088/1742-6596/125/1/012050 fatcat:st4rd5vqordadhwje5ukirkm6a

Annotation, comparison and databases for hundreds of bacterial genomes

Claudine Médigue, Ivan Moszer
2007 Research in Microbiology  
Software designed for the analysis and functional annotation of a single genome have, in consequence, evolved towards comparative genomics tools, bringing together the information contained in numerous  ...  This paper reviews advances in the development of bacterial annotation and comparative analysis tools, and progress in the design of novel database structures for the integration of heterogeneous biological  ...  / The VBI PathoSystems Resource Integration Center NMPDR http://www.nmpdr.org/ National Microbial Pathogen Data Resource based on subsystem annotation Phydbac http://www.igs.cnrs-mrs.fr/phydbac/ Phylogenomic  ... 
doi:10.1016/j.resmic.2007.09.009 pmid:18031997 fatcat:bfw4zslyw5bgrdtrxhozk2uc7e

How Next-Generation Sequencing and Multiscale Data Analysis Will Transform Infectious Disease Management

Theodore R. Pak, Andrew Kasarskis
2015 Clinical Infectious Diseases  
Recent reviews have examined the extent to which routine next-generation sequencing (NGS) on clinical specimens will improve the capabilities of clinical microbiology laboratories in the short term, but  ...  This review introduces a range of "omics" and patient data sources relevant to managing infections and proposes 3 potentially disruptive applications for these data in the clinical workflow.  ...  We thank Deena Altman, Shirish Huprikar, and members of the Pathogen Surveillance Program at Mount Sinai for critical suggestions on the manuscript. Financial support.  ... 
doi:10.1093/cid/civ670 pmid:26251049 pmcid:PMC4643486 fatcat:hpi3upale5ae3buqsdxahbvak4

Analytical Tools and Databases for Metagenomics in the Next-Generation Sequencing Era

Mincheol Kim, Ki-Hyun Lee, Seok-Whan Yoon, Bong-Soo Kim, Jongsik Chun, Hana Yi
2013 Genomics & Informatics  
Metagenomics has become one of the indispensable tools in microbial ecology for the last few decades, and a new revolution in metagenomic studies is now about to begin, with the help of recent advances  ...  from a bioinformatics perspective.  ...  FIGfams are sets of protein sequences and alignments that are similar along their full length and are believed to implement the same function generated from National Microbial Pathogen Data Resource (NMPDR  ... 
doi:10.5808/gi.2013.11.3.102 pmid:24124405 pmcid:PMC3794082 fatcat:lotsy2zoxzgl3mn2pd2a3zkobi

Microevolution of Group A Streptococci In Vivo: Capturing Regulatory Networks Engaged in Sociomicrobiology, Niche Adaptation, and Hypervirulence

Ramy K. Aziz, Rita Kansal, Bruce J. Aronow, William L. Taylor, Sarah L. Rowe, Michael Kubal, Gursharan S. Chhatwal, Mark J. Walker, Malak Kotb, Niyaz Ahmed
2010 PLoS ONE  
Using a murine subcutaneous chamber model to sample the bacteria prior to selection or expansion of mutants, we compared gene expression dynamics of wild type (WT) and previously isolated animal-passaged  ...  Our findings demonstrate the engagement of unique regulatory modules in niche adaptation, implicate a critical role for bacterial genetic heterogeneity that surpasses transcriptional in vivo adaptation  ...  Acknowledgments We thank the team managing the animal facilities in the VA Medical Center and William Ohr for assistance in printing the microarrays. Author Contributions  ... 
doi:10.1371/journal.pone.0009798 pmid:20418946 pmcid:PMC2854683 fatcat:uys7buzx3rhojc3nso4lwdjymy

Classification of a Hypervirulent Aeromonas hydrophila Pathotype Responsible for Epidemic Outbreaks in Warm-Water Fishes

Cody R. Rasmussen-Ivey, Mohammad J. Hossain, Sara E. Odom, Jeffery S. Terhune, William G. Hemstreet, Craig A. Shoemaker, Dunhua Zhang, De-Hai Xu, Matt J. Griffin, Yong-Jie Liu, Maria J. Figueras, Scott R. Santos (+2 others)
2016 Frontiers in Microbiology  
Collectively, these results characterize a hypervirulent A. hydrophila pathotype that affects farmed fish on multiple continents.  ...  Classification of the vAh Pathotype secretion system (T6SS).  ...  Following generation of a consensus sequence, the National Microbial Pathogen Data Resource (NMPDR) Rapid Annotations using Subsystems Technology (RAST) v2.0 server was used in conjunction with the SEED  ... 
doi:10.3389/fmicb.2016.01615 pmid:27803692 pmcid:PMC5067525 fatcat:mqc4tdobhvhhfi6cchwcm5leiq
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