A5058460697- Biomedical Text Mining and Ontologies
- Scientific Computing and Data Management
- Cell Image Analysis Techniques
- Monoclonal and Polyclonal Antibodies Research
- Semantic Web and Ontologies
- Research Data Management Practices
- Neuroscience and Neuropharmacology Research
- Genetics, Bioinformatics, and Biomedical Research
- Meta-analysis and systematic reviews
- Advanced Biosensing Techniques and Applications
- Academic Publishing and Open Access
- Neural dynamics and brain function
- Bioinformatics and Genomic Networks
- Advanced Proteomics Techniques and Applications
- Functional Brain Connectivity Studies
- Biosimilars and Bioanalytical Methods
- scientometrics and bibliometrics research
- Advanced Memory and Neural Computing
- Viral Infectious Diseases and Gene Expression in Insects
- 3D Printing in Biomedical Research
- Gene expression and cancer classification
- Receptor Mechanisms and Signaling
- Ion channel regulation and function
- Single-cell and spatial transcriptomics
- Cognitive Computing and Networks
University of California, San Diego
2015-2025
Developmental Studies Hybridoma Bank
2024
University of Toronto
2024
McGill University
2024
University of Leicester
2024
Cell Signaling Technology (United States)
2024
UC San Diego Health System
2024
Emory University
2024
University of San Diego
2021
Universidad Cristiana Autónoma de Nicaragua
2020
The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies provide a representation biomedical knowledge from Open Biological Ontologies (OBO) project adds ability this was derived. We here state several applications using it, such as adding semantic expressivity existing databases, building data entry forms,...
Recent advances in 'omic' technologies have created unprecedented opportunities for biological research, but current software and database resources are extremely fragmented. OMICtools is a manually curated metadatabase that provides an overview of more than 4400 web-accessible tools related to genomics, transcriptomics, proteomics metabolomics. All been classified by omic (next-generation sequencing, microarray, mass spectrometry nuclear magnetic resonance) associated with published...
Antibodies are critical reagents to detect and characterize proteins. It is commonly understood that many commercial antibodies do not recognize their intended targets, but information on the scope of problem remains largely anecdotal, as such, feasibility goal at least one potent specific antibody targeting each protein in a proteome cannot be assessed. Focusing for human proteins, we have scaled standardized characterization approach using parental knockout cell lines (Laflamme et al.,...
Brain connectomics research has rapidly expanded using functional MRI (fMRI) and diffusion-weighted (dwMRI). A common product of these varied analyses is a connectivity matrix (CM). CM stores the connection strength between any two regions ("nodes") in brain network. This format useful for several reasons: (1) it highly distilled, with minimal data size complexity, (2) graph theory can be applied to characterize network's topology, (3) retains sufficient information capture individual...
Antibodies are ubiquitous key biological research resources yet tricky to use as they prone performance issues and represent a major source of variability across studies. Understanding what antibody was used in published study is therefore necessary repeat and/or interpret given study. However, reagents still frequently not cited with sufficient detail determine which experiments. The Antibody Registry public, open database that enables citation antibodies by providing persistent record for...
Preprints, versions of scientific manuscripts that precede peer review, are growing in popularity. They offer an opportunity to democratize and accelerate research, as they have no publication costs or a lengthy review process. Preprints often later published peer-reviewed venues, but these publications the original preprints frequently not linked any way. To this end, we developed tool, PreprintMatch, find matches between their corresponding papers, if exist. This tool outperforms existing...
Characterizing cellular diversity at different levels of biological organization and across data modalities is a prerequisite to understanding the function cell types in brain. Classification neurons also essential manipulate controlled ways understand their variation vulnerability brain disorders. The BRAIN Initiative Cell Census Network (BICCN) an integrated network data-generating centers, archives, standards developers, with goal systematic multimodal type profiling characterization....
Antibodies are critical reagents to detect and characterize proteins. It is commonly understood that many commercial antibodies do not recognize their intended targets, but information on the scope of problem remains largely anecdotal, as such, feasibility goal at least one potent specific antibody targeting each protein in a proteome cannot be assessed. Focusing for human proteins, we have scaled standardized characterization approach using parental knockout cell lines (Laflamme et al.,...
Conversations about open science have reached the mainstream, yet many practices such as data sharing remain uncommon. Our efforts towards openness therefore need to increase in scale and aim for a more ambitious target. We an ecosystem not only where research outputs are openly shared but also which transparency permeates process from start lends itself rigorous collaborative research. To support this vision, Essay provides overview of selection initiatives past 2 decades, focusing on...
Abstract Antibody-based research applications are critical for biological discovery. Yet, there no industry standards to compare the performance of antibodies in various applications. We describe a knockout cell line-based antibody characterization platform, developed, and approved jointly by academic researchers that enables systematic comparison western blot, immunoprecipitation, immunofluorescence procedures. The scalable protocols consist (i) identification appropriate lines studies,...
<ns4:p>A central tenet in support of research reproducibility is the ability to uniquely identify resources, i.e., reagents, tools, and materials that are used perform experiments. However, current reporting practices for resources insufficient allow humans algorithms exact reported or answer basic questions such as “What other studies resource X?” To address this issue, Resource Identification Initiative was launched a pilot project improve standards methods sections papers thereby...
The reproducibility crisis is a multifaceted problem involving ingrained practices within the scientific community. Fortunately, some causes are addressed by author's adherence to rigor and criteria, implemented via checklists at various journals. We developed an automated tool (SciScore) that evaluates research articles based on their key including NIH criteria RRIDs, unprecedented scale. show despite steady improvements, less than half of scoring such as blinding or power analysis,...
The Data and Resource Center (DRC) of the NIH-funded SPARC program is developing databases, connectivity maps, simulation tools for mammalian autonomic nervous system. experimental data mathematical models supplied to DRC by consortium are curated, annotated semantically linked via a single knowledgebase. A portal has been developed that allows discovery both semantic search an interface includes Google Map-like 2D flatmaps displaying connectivity, 3D anatomical organ scaffolds provide...
In this paper, we describe the neuroscience gateway (NSG), which facilitates access to high performance computing resources for computational neuroscientists. Through a simple web-based portal, NSG provides streamlined environment uploading models, specifying HPC job parameters, querying running status, receiving completion notices, and storing retrieving output data. The architecture transparently distributes user jobs appropriate available through XSEDE organization.
An initiative of the NIH Blueprint for neuroscience research, Neuroscience Information Framework (NIF) project advances by enabling discovery and access to public research data tools worldwide through an open source, semantically enhanced search portal. One critical components overall NIF system, Standardized Ontologies (NIFSTD), provides extensive collection standard concepts along with their synonyms relationships. The knowledge models defined in NIFSTD ontologies enable effective...
In the wake of reproducibility crisis and numerous discussions on how commercially available antibodies as research tool contribute to it, The Antibody Society developed a series 10 webinars address issues involved. were delivered by speakers with both academic commercial backgrounds. This report highlights problems, offers solutions help scientific community appropriately identify right validate them for their development projects. Despite various proposed here, they must be applied...
Many-author non-empirical papers include “how to” articles, recommendations or consensus statements, roadmaps for future research, catalogs of ideas, calls to action. These benefit the research community and broader academic ecosystem by addressing unmet needs introducing new perspectives approaches. Large, diverse authorship teams that examine an issue from many different can create valuable resources individual co-authors could not develop independently, in smaller groups. Realizing...
Abstract Background Tables are useful information artifacts that allow easy detection of missing data and have been deployed by several publishers to improve the amount present for key resources reagents such as antibodies, cell lines, other tools constitute inputs a study. STAR*Methods resource tables increased “findability” these resources, improving transparency paper warning authors (before publication) about any problems, cannot be uniquely identified or those known problematic, but...