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Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
TLDR
By following this protocol, investigators are able to gain an in-depth understanding of the biological themes in lists of genes that are enriched in genome-scale studies.
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
TLDR
The survey will help tool designers/developers and experienced end users understand the underlying algorithms and pertinent details of particular tool categories/tools, enabling them to make the best choices for their particular research interests.
The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists
TLDR
The DAVID Gene Functional Classification Tool uses a novel agglomeration algorithm to condense a list of genes or associated biological terms into organized classes of related genes or biology, called biological modules, for efficient interpretation of gene lists in a network context.
DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists
TLDR
The expanded DAVID Knowledgebase now integrates almost all major and well-known public bioinformatics resources centralized by the DAVID Gene Concept, a single-linkage method to agglomerate tens of millions of diverse gene/protein identifiers and annotation terms from a variety of public bio informatics databases.
DAVID-WS: a stateful web service to facilitate gene/protein list analysis
TLDR
DAVID, the database for annotation, visualization and integrated discovery (DAVID), is a web-based online bioinformatics resource that aims to provide tools for the functional interpretation of large lists of genes/proteins.
DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis
TLDR
The DAVID Knowledgebase is designed to facilitate high throughput gene functional analysis, and not only provides the quick accessibility to a wide range of heterogeneous annotation data in a centralized location, but also enriches the level of biological information for an individual gene.
Cutting Edge: Ku70 Is a Novel Cytosolic DNA Sensor That Induces Type III Rather Than Type I IFN
TLDR
Ku70 mediates type III IFN induction by DNA for the first time, and is identified as a novel DNA sensor inducing the IFN-lambda1 activation.
Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts
TLDR
The findings suggest that Pneumocystis has developed unique mechanisms of adaptation to life exclusively in mammalian hosts, including dependence on the lungs for gas and nutrients and highly efficient strategies to escape both host innate and acquired immune defenses.
A Benchmark Study on Error Assessment and Quality Control of CCS Reads Derived from the PacBio RS.
TLDR
This benchmark study indicates that even though CCS reads are post error-corrected it is still necessary to perform appropriate QC on C CS reads in order to produce successful downstream bioinformatics analytical results.
Evolution of the Pygmy Phenotype: Evidence of Positive Selection from Genome-wide Scans in African, Asian, and Melanesian Pygmies
TLDR
It is found that negritos in the Philippines and Papua New Guinea are genetically more similar to their nonpygmy neighbors than to one another and have experienced positive selection at different genes, indicating that geographically distant pygmy groups are likely to have evolved their short stature independently.
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