11 Result(s)
within
Robert D. Finn
Bioinformatics
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Article
Open AccessA mouse model of occult intestinal colonization demonstrating antibiotic-induced outgrowth of carbapenem-resistant Enterobacteriaceae
The human intestinal microbiome is a complex community that contributes to host health and disease. In addition to normal microbiota, pathogens like carbapenem-resistant Enterobacteriaceae may be asymptomatically...
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Open AccessA unified catalog of 204,938 reference genomes from the human gut microbiome
Comprehensive, high-quality reference genomes are required for functional characterization and taxonomic assignment of the human gut microbiota. We present the Unified Human Gastrointestinal Genome (UHGG) coll...
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Article
Open AccessEstimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC
Microbial eukaryotes constitute a significant fraction of biodiversity and have recently gained more attention, but the recovery of high-quality metagenomic assembled eukaryotic genomes is limited by the curre...
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Article
Open AccessMicrobial community drivers of PK/NRP gene diversity in selected global soils
The emergence of antibiotic-resistant pathogens has created an urgent need for novel antimicrobial treatments. Advances in next-generation sequencing have opened new frontiers for discovery programmes for natu...
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Article
Open AccessA human gut bacterial genome and culture collection for improved metagenomic analyses
Understanding gut microbiome functions requires cultivated bacteria for experimental validation and reference bacterial genome sequences to interpret metagenome datasets and guide functional analyses. We prese...
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Article
Open AccessStructure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis
CA_C2195 from Clostridium acetobutylicum is a protein of unknown function. Sequence analysis predicted that part of the protein contained a metallopeptidase-related domain. There are over 200 homologs of similar ...
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Article
Open AccessSkylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models
Logos are commonly used in molecular biology to provide a compact graphical representation of the conservation pattern of a set of sequences. They render the information contained in sequence alignments or pro...
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Open AccessTwo Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila
Every genome contains a large number of uncharacterized proteins that may encode entirely novel biological systems. Many of these uncharacterized proteins fall into related sequence families. By applying seque...
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Article
Open AccessIntegrating biological data – the Distributed Annotation System
The Distributed Annotation System (DAS) is a widely adopted protocol for dynamically integrating a wide range of biological data from geographically diverse sources. DAS continues to expand its applicability a...
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Open AccessIntegrating sequence and structural biology with DAS
The Distributed Annotation System (DAS) is a network protocol for exchanging biological data. It is frequently used to share annotations of genomes and protein sequence.
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Article
Open AccessPredicting active site residue annotations in the Pfam database
Approximately 5% of Pfam families are enzymatic, but only a small fraction of the sequences within these families (<0.5%) have had the residues responsible for catalysis determined. To increase the active site...
