Stanley J. F. Laulederkind
A5037400577- Biomedical Text Mining and Ontologies
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Genomics and Phylogenetic Studies
- Inflammatory mediators and NSAID effects
- Genomics and Rare Diseases
- Metabolomics and Mass Spectrometry Studies
- Molecular Biology Techniques and Applications
- Estrogen and related hormone effects
- Sphingolipid Metabolism and Signaling
- Computational Drug Discovery Methods
- Genetic Mapping and Diversity in Plants and Animals
- NF-κB Signaling Pathways
- Cancer Genomics and Diagnostics
- Semantic Web and Ontologies
- Lipid Membrane Structure and Behavior
- Cholinesterase and Neurodegenerative Diseases
- Pharmacogenetics and Drug Metabolism
- RNA Research and Splicing
- Genetics, Bioinformatics, and Biomedical Research
- RNA modifications and cancer
- Receptor Mechanisms and Signaling
- Microbial Metabolic Engineering and Bioproduction
- RNA and protein synthesis mechanisms
- Cell Adhesion Molecules Research
Medical College of Wisconsin
2015-2025
Phoenix Bioinformatics
2018-2023
University College London
2018-2023
University of Padua
2023
SIB Swiss Institute of Bioinformatics
2023
Stanford University
2023
University at Buffalo, State University of New York
2023
University of Southern California
2023
Marquette University
2017-2019
University of Cambridge
2014-2018
Abstract The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding functions of genes and gene products. Here, we report advances consortium over past two years. new GO-CAM annotation framework was notably improved, formalized model with a computational schema to check validate rapidly increasing repository 2838 GO-CAMs. In addition, describe impacts several collaborations refine GO 10% increase in number annotations,...
The Human Phenotype Ontology (HPO)—a standardized vocabulary of phenotypic abnormalities associated with 7000+ diseases—is used by thousands researchers, clinicians, informaticians and electronic health record systems around the world. Its detailed descriptions clinical computable disease definitions have made HPO de facto standard for deep phenotyping in field rare disease. HPO's interoperability other ontologies has enabled it to be improve diagnostic accuracy incorporating model organism...
RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences, collating information on ncRNA sequences all types from broad range organisms. We have recently added new genome mapping pipeline that identifies genomic locations for in 296 species. also several functional annotations, such as tRNA secondary structures, Gene Ontology and miRNA-target interactions. A quality control mechanism based Rfam family assignments potential contamination, incomplete more. The has become...
The Rat Genome Database (RGD, http://rgd.mcw.edu) provides the most comprehensive data repository and informatics platform related to laboratory rat, one of important model organisms for disease studies. RGD maintains updates datasets genomic elements such as genes, transcripts increasingly in recent years, sequence variations, well map positions multiple assemblies information. Functional annotations are curated from published literature, submitted by researchers integrated other public...
The Alliance of Genome Resources (the Alliance) is a combined effort 7 knowledgebase projects: Saccharomyces Database, WormBase, FlyBase, Mouse the Zebrafish Information Network, Rat and Gene Ontology Resource. seeks to provide several benefits: better service various communities served by these projects; harmonized view data for all biomedical researchers, bioinformaticians, clinicians, students; more sustainable infrastructure. has cross-organism useful comparative views gene function,...
Abstract The Rat Genome Database (RGD, https://rgd.mcw.edu) has evolved from simply a resource for rat genetic markers, maps, and genes, by adding multiple genomic data types extensive disease phenotype annotations developing tools to effectively mine, analyze, visualize the available data, empower investigators in their hypothesis-driven research. Leveraging its robust flexible infrastructure, RGD added human eight other model organisms (mouse, 13-lined ground squirrel, chinchilla, naked...
Abstract The Alliance of Genome Resources (Alliance) is an extensible coalition knowledgebases focused on the genetics and genomics intensively studied model organisms. organized as individual knowledge centers with strong connections to their research communities a centralized software infrastructure, discussed here. Model organisms currently represented in are budding yeast, Caenorhabditis elegans, Drosophila, zebrafish, frog, laboratory mouse, rat, Gene Ontology Consortium. project rapid...
Formed in late 1999, the Rat Genome Database (RGD, https://rgd.mcw.edu) will be 20 2020, Year of Rat. Because laboratory rat, Rattus norvegicus, has been used as a model for complex human diseases such cardiovascular disease, diabetes, cancer, neurological disorders and arthritis, among others, >150 years, RGD always disease-focused committed to providing data tools researchers doing comparative genomics translational studies. At its inception, before sequencing rat genome, started with only...
The Pathway Ontology (PW) developed at the Rat Genome Database (RGD), covers all types of biological pathways, including altered and disease pathways captures relationships between them within hierarchical structure a directed acyclic graph. ontology allows for standardized annotation rat, human mouse genes to pathway terms. It also constitutes vehicle easy navigation gene report pages, reports interactive diagrams, directly connected diagram those that are globally related in suites suite...
Fully automated text mining (TM) systems promote efficient literature searching, retrieval, and review but are not sufficient to produce ready-to-consume curated documents. These meant replace biocurators, instead assist them in one or more curation steps. To do so, the user interface is an important aspect that needs be considered for tool adoption. The BioCreative Interactive task (IAT) a track designed exploring user-system interactions, promoting development of useful TM tools, providing...
Prostaglandin E2 (PGE2) production in immortalized, nontransformed cells derived from wild-type, cyclooxygenase 1–deficient (COX-1−/−) or 2–deficient (COX-2−/−) mice was examined after treatment with interleukin (IL)-1β, tumor necrosis factor α, acidic fibroblast growth factor, and phorbol ester (phorbol myristate acetate). Compared their wild-type counterparts, COX-1−/− COX-2−/− exhibited substantially enhanced expression of the remaining functional COX gene. Furthermore, both basal...
Model organisms are vital to uncovering the mechanisms of human disease and developing new therapeutic tools. Researchers collecting integrating relevant model organism and/or data often apply disparate terminologies (vocabularies ontologies), making larger scale comparisons inferences challenging at best. A single ontology that connects annotated using diverse terminologies, in which terminology relationships applicable animal models continuously maintained, is needed. The Mouse Genome...
The Rat Genome Database (RGD, http://rgd.mcw.edu) was developed to provide a core resource for rat researchers combining genetic, genomic, pathway, phenotype and strain information with focus on disease. RGD users are provided access structured curated data from the molecular level through of whole organism, including variations associated disease phenotypes. To fully support use as translational model biological systems human disease, continues curate these datasets while enhancing...
The Rat Genome Database (RGD) was started >10 years ago to provide a core genomic resource for rat researchers. Currently, RGD combines genetic, genomic, pathway, phenotype and strain information with focus on disease. users are provided access structured curated data from the molecular level through organismal level. Those all over world. End not only researchers but also working mouse human data. Translational research is supported by RGD's comparative genetics/genomics in disease portals,...
Gene ontology (GO) annotation is a common task among model organism databases (MODs) for capturing gene function data from journal articles. It time-consuming and labor-intensive task, thus often considered as one of the bottlenecks in literature curation. There growing need semiautomated or fully automated GO curation techniques that will help database curators to rapidly accurately identify information full-length Despite multiple attempts past, few studies have proven be useful with...
Abstract The Rat Genome Database (RGD) is a multispecies knowledgebase which integrates genetic, multiomic, phenotypic, and disease data across 10 mammalian species. To support cross-species, multiomics studies to enhance expand on manually extracted from the biomedical literature by RGD team of expert curators, imports multiple sources. These include major databases substantial number domain-specific resources, as well direct submissions individual researchers. incorporation these diverse...
Abstract A comprehensive, computable representation of the functional repertoire all macromolecules encoded within human genome is a foundational resource for biology and biomedical research. The Gene Ontology Consortium has been working towards this goal by generating structured body information about gene functions, which now includes experimental findings reported in more than 175,000 publications genes experimentally tractable model organisms 1,2 . Here, we describe results large,...
We previously reported that ceramide, the immediate product of sphingomyelin hydrolysis, increases in response to interleukin (IL)-1 beta and plays a role modulating IL-1 beta-mediated prostaglandin E2 production cyclooxygenase gene expression human fibroblasts (Ballou, L. R., C. P. Chao, M. A. Holness, S. Barker, R. Raghow. 1992. J. Biol. Chem. 267:20044-20050). Here we describe effects ceramide another process these cells, induction IL-6 production. found submicromolar concentrations...
Abstract The cytokine-mediated stimulation of sphingomyelin (SM) metabolism is emerging as an important signal transduction pathway via the generation ceramide and sphingosine, products which have been shown to affect a wide variety biological processes. Because SM-mediated initiated hydrolysis integral membrane phospholipid by phospholipase C-like enzyme (sphingomyelinase) yield lipids modulate protein kinase C activity, SM phosphatidylinositol (PI) signaling pathways share certain...
Gene function curation via Ontology (GO) annotation is a common task among Model Organism Database groups. Owing to its manual nature, this considered one of the bottlenecks in literature curation. There have been many previous attempts at automatic identification GO terms and supporting information from full text. However, few systems delivered an accuracy that comparable with humans. One recognized challenge developing such lack marked sentence-level evidence text provides basis for making...