Search results for: Peter D’Eustachio

Items from 1 to 8 out of 8 results

article

Reactome pathway analysis: a high-performance in-memory approach

Antonio Fabregat, Konstantinos Sidiropoulos, Guilherme Viteri, Oscar Forner, more

BMC Bioinformatics > 2017 > 18 > 1 > 1-9

Background Reactome aims to provide bioinformatics tools for visualisation, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modelling, systems biology and education. Pathway analysis methods have a broad range of applications in physiological and biomedical research; one of the main problems, from the analysis methods performance point of view, is the constantly...

article

Gramene database: Navigating plant comparative genomics resources

Parul Gupta, Sushma Naithani, Marcela Karey Tello-Ruiz, Kapeel Chougule, more

Current Plant Biology > 2016 > 7-8 > C > 10-15

Gramene (http://www.gramene.org) is an online, open source, curated resource for plant comparative genomics and pathway analysis designed to support researchers working in plant genomics, breeding, evolutionary biology, system biology, and metabolic engineering. It exploits phylogenetic relationships to enrich the annotation of genomic data and provides tools to perform powerful comparative analyses...

chapter

Reactome – A Knowledgebase of Biological Pathways

Esther Schmidt, Ewan Birney, David Croft, Bernard Bono, more

Lecture Notes in Computer Science > On the Move to Meaningful Internet Systems 2006: OTM 2006 Workshops > 710-719

Reactome (www.reactome.org) is a curated database describing very diverse biological processes in a computationally accessible format. The data is provided by experts in the field and subject to a peer review process. The core unit of the Reactome data model is the reaction. The entities participating in reactions form a network of biological interactions. Reactions are grouped into pathways. Reactome...

article

Pathway Databases: Making Chemical and Biological Sense of the Genomic Data Flood

Peter D’Eustachio

Chemistry & Biology > 2013 > 20 > 5 > 629-635

Pathway databases are a means to systematically associate proteins with their functions and link them into networks that describe the reaction space of an organism. Here, the Reactome Knowledgebase provides a convenient example to illustrate strategies used to assemble such a reaction space based on manually curated experimental data, approaches to semiautomated extension of these manual annotations...

article

Human and chicken TLR pathways: manual curation and computer-based orthology analysis

Marc Gillespie, Veronica Shamovsky, Peter D’Eustachio

Mammalian Genome > 2011 > 22 > 1-2 > 130-138

The innate immune responses mediated by Toll-like receptors (TLR) provide an evolutionarily well-conserved first line of defense against microbial pathogens. In the Reactome Knowledgebase we previously integrated annotations of human TLR molecular functions with those of over 4000 other human proteins involved in processes such as adaptive immunity, DNA replication, signaling, and intermediary metabolism,...