D
Daniel Paarmann
Researcher at University of Chicago
Publications - 5
Citations - 12890
Daniel Paarmann is an academic researcher from University of Chicago. The author has contributed to research in topics: Shotgun sequencing & Gene. The author has an hindex of 5, co-authored 5 publications receiving 11296 citations. Previous affiliations of Daniel Paarmann include Bielefeld University & Argonne National Laboratory.
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Journal ArticleDOI
The RAST Server: Rapid Annotations using Subsystems Technology
Ramy K. Aziz,Ramy K. Aziz,Daniela Bartels,Aaron A. Best,Matthew DeJongh,Terrence Disz,Terrence Disz,Robert Edwards,Kevin Formsma,Svetlana Gerdes,Elizabeth M. Glass,Michael Kubal,Folker Meyer,Folker Meyer,Gary J. Olsen,Gary J. Olsen,Robert Olson,Robert Olson,Andrei L. Osterman,Ross Overbeek,Leslie Klis McNeil,Daniel Paarmann,Tobias Paczian,Bruce Parrello,Gordon D. Pusch,Claudia I. Reich,Rick Stevens,Rick Stevens,Olga Vassieva,Veronika Vonstein,Andreas Wilke,Olga Zagnitko +31 more
TL;DR: A fully automated service for annotating bacterial and archaeal genomes that identifies protein-encoding, rRNA and tRNA genes, assigns functions to the genes, predicts which subsystems are represented in the genome, uses this information to reconstruct the metabolic network and makes the output easily downloadable for the user.
Journal ArticleDOI
The Metagenomics RAST Server: A Public Resource for the Automatic Phylogenetic and Functional Analysis of Metagenomes
Folker Meyer,Folker Meyer,Daniel Paarmann,Mark D'Souza,Robert Olson,Elizabeth M. Glass,Michael Kubal,Tobias Paczian,Alexis A. Rodriguez,Rick Stevens,Rick Stevens,Andreas Wilke,Jared Wilkening,Robert Edwards,Robert Edwards +14 more
TL;DR: The open-source metagenomics RAST service provides a new paradigm for the annotation and analysis of metagenomes that is stable, extensible, and freely available to all researchers.
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The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation
Leslie Klis McNeil,Claudia I. Reich,Ramy K. Aziz,Daniela Bartels,Matthew P. Cohoon,Terry Disz,Robert Edwards,Robert Edwards,Svetlana Gerdes,Kaitlyn Hwang,Michael Kubal,Gohar Rem Margaryan,Folker Meyer,William Mihalo,Gary J. Olsen,Robert Olson,Andrei L. Osterman,Daniel Paarmann,Tobias Paczian,Bruce Parrello,Gordon D. Pusch,Dmitry A. Rodionov,Xinghua Shi,Olga Vassieva,Veronika Vonstein,Olga Zagnitko,Fangfang Xia,Jenifer F. Zinner,Ross Overbeek,Rick Stevens +29 more
TL;DR: The National Microbial Pathogen Data Resource (NMPDR) contains the complete genomes of ∼50 strains of pathogenic bacteria that are the focus of the curators, as well as >400 other genomes that provide a broad context for comparative analysis across the three phylogenetic Domains.
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The Sequence Analysis and Management System -- SAMS-2.0: data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies.
Thomas Bekel,Kolja Henckel,Helge Küster,Folker Meyer,Virginie Mittard Runte,Heiko Neuweger,Daniel Paarmann,Oliver Rupp,Martha Zakrzewski,Alfred Pühler,Jens Stoye,Alexander Goesmann +11 more
TL;DR: The Sequence Analysis and Management System (SAMS) is a bioinformatics software platform with a database backend designed to support the computational analysis of whole genome shotgun (WGS) bacterial genome sequencing, cDNA sequencing by reading expressed sequence tags (ESTs) as well as sequence data obtained by ultrafast sequencing.
Journal ArticleDOI
Under the influence of the active deodorant ingredient 4-hydroxy-3-methoxybenzyl alcohol, the skin bacterium Corynebacterium jeikeium moderately responds with differential gene expression.
Iris Brune,Anke Becker,Daniel Paarmann,Andreas Albersmeier,Jörn Kalinowski,Alfred Pühler,Andreas Tauch +6 more
TL;DR: Besides many genes encoding proteins that apparently participate in transcription and translation, the drug resistance determinant cmx and the predicted virulence factors sapA and sapD showed significantly enhanced expression levels.