Showing papers by "Fiona S. L. Brinkman published in 2012"
University of California, Los Angeles1, J. Craig Venter Institute2, Swiss Institute of Bioinformatics3, University of Rome Tor Vergata4, Simon Fraser University5, University of Edinburgh6, Centre national de la recherche scientifique7, Ontario Institute for Cancer Research8, University of British Columbia9, University of Toronto10, Claude Bernard University Lyon 111, Mount Sinai Hospital, Toronto12, Virginia Commonwealth University13, University of Lausanne14
TL;DR: The International Molecular Exchange consortium is an international collaboration between major public interaction data providers to share literature-curation efforts and make a nonredundant set of protein interactions available in a single search interface on a common website.
Abstract: The International Molecular Exchange (IMEx) consortium is an international collaboration between major public interaction data providers to share literature-curation efforts and make a nonredundant set of protein interactions available in a single search interface on a common website (http://www.imexconsortium.org/). Common curation rules have been developed, and a central registry is used to manage the selection of articles to enter into the dataset. We discuss the advantages of such a service to the user, our quality-control measures and our data-distribution practices.
490 citations
TL;DR: The authors adapted the murine Plasmodium berghei ANKA ECM model to serve as a preclinical drug-screening platform by combining antimalarial drug intervention in established malarial infections with iterative mouse-human bioinformatic analysis of early transcriptional changes in co-regulated gene sets.
Abstract: Case fatality rates for severe malaria remain high even in the best clinical settings because antimalarial drugs act against the parasite without alleviating life-threatening inflammation. We assessed the potential for host-directed therapy of severe malaria of a new class of anti-inflammatory drugs, the innate defense regulator (IDR) peptides, based on host defense peptides. The Plasmodium berghei ANKA model of experimental cerebral malaria was adapted to use as a preclinical screen by combining late-stage intervention in established infections with advanced bioinformatic analysis of early transcriptional changes in co-regulated gene sets. Coadministration of IDR-1018 with standard first-line antimalarials increased survival of infected mice while down-regulating key inflammatory networks associated with fatality. Thus, IDR peptides provided host-directed adjunctive therapy for severe disease in combination with antimalarial treatment.
88 citations
TL;DR: Raloxifene, a drug currently used in the prevention of osteoporosis and/or invasive breast cancer in post-menopausal women, was predicted from a computational screening approach to discover drug repurposing opportunities and found to strongly attenuate P. aeruginosa virulence in a Caenorhabditis elegans model of infection.
85 citations
TL;DR: MicrobeDB provides a foundation for analysis of microbial genomes by the automation of downloading published, completed bacterial and archaeal genomes from key sources, parsing annotations of all genomes into a local database, and allowing interaction with the database through an easy to use programming interface.
Abstract: Summary: Analysis of microbial genomes often requires the general organization and comparison of tens to thousands of genomes both from public repositories and unpublished sources. MicrobeDB provides a foundation for such projects by the automation of downloading published, completed bacterial and archaeal genomes from key sources, parsing annotations of all genomes (both public and private) into a local database, and allowing interaction with the database through an easy to use programming interface. MicrobeDB creates a simple to use, easy to maintain, centralized local resource for various large-scale comparative genomic analyses and a back-end for future microbial application design.
Availability: MicrobeDB is freely available under the GNU-GPL at: http://github.com/mlangill/microbedb/
Contact: moc.liamg@ellignal.i.g.nagrom
20 citations
TL;DR: It is suggested that high SSC among B cells may serve as a useful biomarker to identify patients with DLBCL at high risk for relapse and is of particular interest because this biomarker is readily available in most clinical laboratories without significant alteration to existing routine diagnostic strategies or incurring additional costs.
Abstract: Despite advances in the understanding of diffuse large B-cell lymphoma (DLBCL) biology, only the clinically based International Prognostic Index (IPI) is used routinely for risk stratification at diagnosis. To find novel prognostic markers, we analyzed flow cytometric data from 229 diagnostic DLBCL samples using an automated multiparameter data analysis approach developed in our laboratory. By using the developed automated data analysis pipeline, we identified 71 of 229 cases as having more than 35% B cells with a high side scatter (SSC) profile, a parameter reflecting internal cellular complexity. This high SSC B-cell feature was associated with inferior overall and progression-free survival ( P = .001 and P = .01, respectively) and remained a significant predictor of overall survival in multivariate Cox regression analysis (IPI, P = .001; high SSC, P = .004; rituximab, P = .53).
This study suggests that high SSC among B cells may serve as a useful biomarker to identify patients with DLBCL at high risk for relapse. This is of particular interest because this biomarker is readily available in most clinical laboratories without significant alteration to existing routine diagnostic strategies or incurring additional costs.
12 citations
TL;DR: The International Molecular Exchange (IMEx) consortium curates protein interaction data curation as discussed by the authors, which is based on the International Journal of Protein Interaction Data (IJPDD).
Abstract: Corrigendum: Protein interaction data curation: the International Molecular Exchange (IMEx) consortium
5 citations