• Publications
  • Influence
IMG/M: integrated genome and metagenome comparative data analysis system
TLDR
The Integrated Microbial Genomes with Microbiome Samples (IMG/M: https://img.jgi.doe.gov/m/) system contains annotated DNA and RNA sequence data of (i) archaeal, bacterial, eukaryotic and viral genomes from cultured organisms, (ii) single cell genomes (SCG) and genomes from metagenomes (GFM) from uncultured archaea, bacteria and viruses. Expand
  • 306
  • 26
IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes
TLDR
We describe an update of IMG-ABC, which includes ClusterScout, a tool for targeted identification of custom biosynthetic gene clusters across 40 000 isolate microbial genomes, and a new search capability to query more than 700 000 BCs from isolate genomes for clusters with similar Pfam composition. Expand
  • 38
  • 3
Draft Genome Sequences of 10 Strains of the Genus Exiguobacterium
ABSTRACT High-quality draft genome sequences were determined for 10 Exiguobacterium strains in order to provide insight into their evolutionary strategies for speciation and environmental adaptation.Expand
  • 13
  • 1
Genome Sequence of Arenibacter algicola Strain TG409, a Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton
ABSTRACT Arenibacter algicola strain TG409 was isolated from Skeletonema costatum and exhibits the ability to utilize polycyclic aromatic hydrocarbons as sole sources of carbon and energy. Here, weExpand
  • 4
  • 1
  • PDF
ProDeGe: a computational protocol for fully automated decontamination of genomes
Single amplified genomes and genomes assembled from metagenomes have enabled the exploration of uncultured microorganisms at an unprecedented scale. However, both these types of products are plaguedExpand
  • 49
  • PDF
Computational Science and Engineering Online (CSE-Online): A Cyber-Infrastructure for Scientific Computing
TLDR
This paper describes the development of an extendable integrated Web-accessible simulation environment for computational science and engineering called Computational Science and Engineering Online (CSE-Online; http://cse-online.net). Expand
  • 14
  • PDF
Genome Sequence of Halomonas sp. Strain MCTG39a, a Hydrocarbon-Degrading and Exopolymeric Substance-Producing Bacterium
ABSTRACT Halomonas sp. strain MCTG39a was isolated from coastal sea surface water based on its ability to utilize n-hexadecane. During growth in marine medium the strain produces an amphiphilicExpand
  • 5
Complete Genome Sequences of Caldicellulosiruptor sp. Strain Rt8.B8, Caldicellulosiruptor sp. Strain Wai35.B1, and “Thermoanaerobacter cellulolyticus”
ABSTRACT The genus Caldicellulosiruptor contains extremely thermophilic, cellulolytic bacteria capable of lignocellulose deconstruction. Currently, complete genome sequences for elevenExpand
  • 9
  • PDF
Genome Sequence of Porticoccus hydrocarbonoclasticus Strain MCTG13d, an Obligate Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton
ABSTRACT Porticoccus hydrocarbonoclasticus strain MCTG13d is a recently discovered bacterium that is associated with marine eukaryotic phytoplankton and that almost exclusively utilizes polycyclicExpand
  • 5
Genome Sequence of Polycyclovorans algicola Strain TG408, an Obligate Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton
ABSTRACT Polycyclovorans algicola strain TG408 is a recently discovered bacterium associated with marine eukaryotic phytoplankton and exhibits the ability to utilize polycyclic aromatic hydrocarbonsExpand
  • 4