A5063972221- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- Gene expression and cancer classification
- Computational Drug Discovery Methods
- Microbial Metabolic Engineering and Bioproduction
- Genomics and Phylogenetic Studies
- Gene Regulatory Network Analysis
- Microbial Natural Products and Biosynthesis
- Immune Cell Function and Interaction
- Scientific Computing and Data Management
- Genetics, Bioinformatics, and Biomedical Research
- MicroRNA in disease regulation
- T-cell and B-cell Immunology
- RNA Research and Splicing
- Wikis in Education and Collaboration
- Semantic Web and Ontologies
- Machine Learning in Bioinformatics
- RNA modifications and cancer
- Advanced biosensing and bioanalysis techniques
- CRISPR and Genetic Engineering
- CAR-T cell therapy research
- Cardiac Valve Diseases and Treatments
- Genomics and Rare Diseases
- Circular RNAs in diseases
- Neuroinflammation and Neurodegeneration Mechanisms
Gladstone Institutes
2013-2023
University of California, San Francisco
2004-2023
Abcam (United States)
2018
Massachusetts General Hospital
2018
University of Michigan–Ann Arbor
2018
University of Missouri
2012-2013
Chinese Academy of Sciences
2013
Beijing Institute of Genomics
2013
Maastricht University
2008-2012
Agilent Technologies (United States)
2012
WikiPathways (wikipathways.org) captures the collective knowledge represented in biological pathways. By providing a database curated, machine readable way, omics data analysis and visualization is enabled. other pathway databases are used to analyze experimental by research groups many fields. Due open collaborative nature of platform, our content keeps growing getting more accurate, making reliable rich database. Previously, however, focus was primarily on genes proteins, leaving...
Abstract WikiPathways (https://www.wikipathways.org) is a biological pathway database known for its collaborative nature and open science approaches. With the core idea of scientific community developing curating knowledge in models, lowers all barriers accessing using content. Increasingly more content creators, initiatives, projects tools have started WikiPathways. Central this growth increased use are various communities that focus on particular subsets molecular pathways such as rare...
The exponential growth of diverse types biological data presents the research community with an unprecedented challenge and opportunity. is to stay afloat in flood data, keeping it as accessible, up-to-date, integrated possible. opportunity cultivate new models curation exchange that take advantage direct participation by a greater portion community. This combination especially relevant task collecting pathway information. Pathways are critical understanding functions individual genes...
Here, we describe the development of WikiPathways (http://www.wikipathways.org), a public wiki for pathway curation, since it was first published in 2008. New features are discussed, as well developments community contributors. include zoomable viewer, support ontology annotations, ability to mark pathways private limited time and availability stable hyperlinks elements therein. content is freely available variety formats such BioPAX standard, increasingly adopted by external databases...
WikiPathways (http://www.wikipathways.org) is an open, collaborative platform for capturing and disseminating models of biological pathways data visualization analysis. Since our last NAR update, 4 years ago, has experienced massive growth in content, which continues to be contributed by hundreds individuals each year. New aspects the diversity depth collected are described from perspective researchers interested using pathway information their studies. We provide updates on extensions...
Biological pathways are a useful abstraction of biological concepts, and software tools to deal with pathway diagrams can help research. PathVisio is new visualization tool for that mimics the popular GenMAPP completely Java implementation allows better integration other open source projects. The MAPP file format replaced by GPML, XML provides seamless exchange graphical information among multiple programs. be combined bioinformatics up three possible uses: visual compilation knowledge,...
We introduce GO-Elite, a flexible and powerful pathway analysis tool for wide array of species, identifiers (IDs), pathways, ontologies gene sets. In addition to the Gene Ontology (GO), GO-Elite allows user perform over-representation on any structured ontology annotations, database or biological IDs (e.g. gene, protein metabolite). exploits nature report minimal set non-overlapping terms. The results can be visualized WikiPathways as networks. Built-in support is provided over 60 species 50...
WikiPathways (wikipathways.org) is an open-source biological pathway database. Collaboration and open science are pivotal to the success of WikiPathways. Here we highlight continuing efforts supporting WikiPathways, content growth collaboration among researchers. As evolving database, there a growing need for address overcome technical challenges. In this direction, has undergone major restructuring, enabling renewed approach sharing curating knowledge, thus providing stability future...
Abstract Background Microarray technologies have evolved rapidly, enabling biologists to quantify genome-wide levels of gene expression, alternative splicing, and sequence variations for a variety species. Analyzing displaying these data present significant challenge. Pathway-based approaches analyzing microarray proven useful presenting generating testable hypotheses. Results To address the growing needs community we released version 2 Gene Map Annotator Pathway Profiler (GenMAPP), new...
Many complementary solutions are available for the identifier mapping problem. This creates an opportunity bioinformatics tool developers. Tools can be made to flexibly support multiple services or could combined get broader coverage. approach requires interface layer between tools and services. Here we present BridgeDb, a software framework gene, protein metabolite mapping. provides standardized through which connected different makes it easier developers Mapping merged multi-omics...
DNA microarrays produced by deposition (or `spotting')of a single long oligonucleotide probe for each gene may be an attractive alternative to other types of arrays. We spotted arrays using two large collections ∼70-mer probes, and used these analyze expression in dissimilar human RNA samples. These samples were also analyzed situ synthesis sets multiple short (25-mer)oligonucleotides (Affymetrix GeneChips). compared measurements 7344 genes that represented both the situ-synthesized 25-mer...
Wikidata is a community-maintained knowledge base that has been assembled from repositories in the fields of genomics, proteomics, genetic variants, pathways, chemical compounds, and diseases, adheres to FAIR principles findability, accessibility, interoperability reusability. Here we describe breadth depth biomedical contained within Wikidata, discuss open-source tools have built add information synchronize it with source databases. We also demonstrate several use cases for including...
Insulin resistance (IR) is a hallmark of obesity and metabolic disease. Circulating extracellular RNAs (ex-RNAs), stable RNA molecules in plasma, may play role IR, though most studies on ex-RNAs IR are small. We sought to characterize the relationship between phenotypes large community-based human cohort.We measured circulating plasma 2,317 participants without diabetes Framingham Heart Study (FHS) Offspring Cohort at cycle 8 defined associations (measured by insulin level). association...
We need to effectively combine the knowledge from surging literature with complex datasets propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets intervention. Here, we describe a large-scale community effort build an open access, interoperable computable repository COVID-19 molecular mechanisms. The Disease Map (C19DMap) is graphical, interactive representation disease-relevant mechanisms linking many sources. Notably, it computational...
WikiPathways is a platform for creating, updating, and sharing biological pathways [1]. Pathways can be edited downloaded using the wiki-style website. Here we present SOAP web service that provides programmatic access to complementary We describe functionality this offers discuss several use cases in detail. Exposing through opens up new ways of utilizing pathway information assisting community curation process.
The role of alternative splicing in self-renewal, pluripotency and tissue lineage specification human embryonic stem cells (hESCs) is largely unknown. To better define these regulatory cues, we modified the H9 hESC line to allow selection pluripotent hESCs by neomycin resistance cardiac progenitors puromycin resistance. Exon-level microarray expression data from undifferentiated neural precursors were used identify splice isoforms with cardiac-restricted or common cardiac/neural...
To develop a comprehensive catalogue of phenotypic and functional parameters human CD4(+) T cell differentiation stages, we have performed microarray gene expression profiling on subpopulations thymocytes circulating naive cells, including CD3(-)CD4(+)CD8(-) intrathymic progenitor CD3(int)CD4(+)CD8(+) 'double positive' thymocytes, CD3(high)CD4(+)CD8(-) 'single CD3(+)CD4(+)CD8(-) CD45RA(+)CD62L(+) cells from cord blood adult blood. These were sort-purified to >98% purity their expressed RNAs...
Reactome and WikiPathways are two of the most popular freely available databases for biological pathways. pathways centrally curated with periodic input from selected domain experts. is a community-based platform where created continually by any interested party. The nascent collaboration between illustrates mutual benefits combining these approaches. We format converter that converts to GPML used in WikiPathways. In addition, we developed ComplexViz plugin PathVisio which simplifies looking...
Background: Plasma extracellular RNAs have recently garnered interest as biomarkers in heart failure (HF). Most studies HF focus on single related to phenotypes and outcomes, few describe their functional roles. We hypothesized that clusters of plasma microRNAs (miRNAs) associated with left ventricular (LV) remodeling human would identify novel subsets genes involved animal models. Methods Results: prospectively measured circulating miRNAs 64 patients systolic (mean age, 64.8 years; 91% men;...
Abstract Thousands of pathway diagrams are published each year as static figures inaccessible to computational queries and analyses. Using a combination machine learning, optical character recognition, manual curation, we identified 64,643 between 1995 2019 extracted 1,112,551 instances human genes, comprising 13,464 unique NCBI participating in wide variety biological processes. This collection represents an order magnitude more genes than found the text same papers, thousands missing from...