相关论文: OMICtools: a community-driven search engine for bi…
We present a system that constructs and maintains an up-to-date co-occurrence network of medical concepts based on continuously mining the latest biomedical literature. Users can explore this network visually via a concise online interface…
A major barrier to medical imaging research and in particular the development of artificial intelligence (AI) is a lack of large databases of medical images which share images with other researchers. Without such databases it is not…
Materials discovery and biomedical translation increasingly require models that can reason across composition, processing, structure, biological response, manufacturability, safety, and governance constraints. Existing materials and…
Open source software is a rapidly evolving center for distributed work, and understanding the characteristics of this work across its different contexts is vital for informing policy, economics, and the design of enabling software. The…
PubMed is a freely accessible system for searching the biomedical literature, with approximately 2.5 million users worldwide on an average workday. We have recently developed PubMed Labs (www.pubmed.gov/labs), an experimental platform for…
Machine learning classification problems are widespread in bioinformatics, but the technical knowledge required to perform model training, optimization, and inference can prevent researchers from utilizing this technology. This article…
Open source software (OSS) is essential for modern society and, while substantial research has been done on individual (typically central) projects, only a limited understanding of the periphery of the entire OSS ecosystem exists. For…
Study reproducibility is essential to corroborate, build on, and learn from the results of scientific research but is notoriously challenging in bioinformatics, which often involves large data sets and complex analytic workflows involving…
Advances in molecular technologies underlie an enormous growth in the size of data sets pertaining to biology and biomedicine. These advances parallel those in the deep learning subfield of machine learning. Components in the differentiable…
Modern biomedical applications often involve time-series data, from high-throughput phenotyping of model organisms, through to individual disease diagnosis and treatment using biomedical data streams. Data and tools for time-series analysis…
We present SciClaims, an interactive web-based system for end-to-end scientific claim analysis in the biomedical domain. Designed for high-stakes use cases such as systematic literature reviews and patent validation, SciClaims extracts…
Datasets together with active scientific communities prepared to leverage them can contribute to scientific progress and facilitate making research more equitable. In this study we found that MIMIC, despite its limited amount of funding,…
Motivation: Bioinformatics is faced with a variety of problems that require human involvement. Tasks like genome annotation, image analysis, knowledge-base construction and protein structure determination all benefit from human input. In…
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics…
Scientific research increasingly relies on specialized computational tools, yet effectively utilizing these tools demands substantial domain expertise. While Large Language Models (LLMs) show promise in tool automation, they struggle to…
The NIAID Data Ecosystem Discovery Portal (https://data.niaid.nih.gov) provides a unified search interface for over 4 million datasets relevant to infectious and immune-mediated disease (IID) research. Integrating metadata from…
High-dimensional omics data contains intrinsic biomedical information that is crucial for personalised medicine. Nevertheless, it is challenging to capture them from the genome-wide data due to the large number of molecular features and…
With the increasing amount of data and use of computation in science, software has become an important component in many different domains. Computing is now being used more often and in more aspects of scientific work including data…
Background: Biomedical research projects deal with data management requirements from multiple sources like funding agencies' guidelines, publisher policies, discipline best practices, and their own users' needs. We describe functional and…
SimOmics is an R package designed to generate realistic, multivariate, and multi-omics synthetic datasets. It is intended for use in benchmarking, method development, and reproducibility in bioinformatics, particularly in the context of…