Related papers: A data-supported history of bioinformatics tools
Advances in information technology and its widespread growth in several areas of business, engineering, medical and scientific studies are resulting in information/data explosion. Knowledge discovery and decision making from such rapidly…
Documentation is one of the most neglected activities in Software Engineering, although it is an important method of assuring quality and understanding. Bioinformatics software is generally written by researchers from fields other than…
Increasingly sophisticated experiments, coupled with large-scale computational models, have the potential to systematically test biological hypotheses to drive our understanding of multicellular systems. In this short review, we explore key…
Despite the success of large language models (LLMs) on general-purpose tasks, their performance in highly specialized domains such as biomedicine remains unsatisfactory. A key limitation is the inability of LLMs to effectively leverage…
Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by…
The surge in high-throughput omics data has reshaped the landscape of biological research, underlining the need for powerful, user-friendly data analysis and interpretation tools. This paper presents GenoCraft, a web-based comprehensive…
In recent years, deep learning revolutionized machine learning and its applications, producing results comparable to human experts in several domains, including neuroscience. Each year, hundreds of scientific publications present…
Enumerated threat agent lists have long driven biodefense priorities. The global SARS-CoV-2 pandemic demonstrated the limitations of searching for known threat agents as compared to a more agnostic approach. Recent technological advances…
Genomic data and biomedical imaging data are undergoing exponential growth. However, our understanding of the phenotype-genotype connection linking the two types of data is lagging behind. While there are many types of software that enable…
The field of single-cell biology is growing rapidly and is generating large amounts of data from a variety of species, disease conditions, tissues, and organs. Coordinated efforts such as CZI CELLxGENE, HuBMAP, Broad Institute Single Cell…
The histological assessment of human tissue has emerged as the key challenge for detection and treatment of cancer. A plethora of different data sources ranging from tissue microarray data to gene expression, proteomics or metabolomics data…
The objective of this short report is to reconsider the subject of bioinformatics as just being a tool of experimental biological science. To do that, we introduce three examples to show how bioinformatics could be considered as an…
With many advancements in in silico biology in recent years, the paramount challenge is to translate the accumulated knowledge into exciting industry partnerships and clinical applications. Achieving models that characterize the link of…
Biomedical information extraction (BioIE) is important to many applications, including clinical decision support, integrative biology, and pharmacovigilance, and therefore it has been an active research. Unlike existing reviews covering a…
Under the data-driven research paradigm, research software has come to play crucial roles in nearly every stage of scientific inquiry. Scholars are advocating for the formal citation of software in academic publications, treating it on par…
Biclustering is a data mining technique which searches for local patterns in numeric tabular data with main application in bioinformatics. This technique has shown promise in multiple areas, including development of biomarkers for cancer,…
Nowadays, the amount of heterogeneous biomedical data is increasing more and more thanks to novel sensing techniques and high-throughput technologies. In reference to biomedical image analysis, the advances in image acquisition modalities…
Animal vocalisations and natural soundscapes are fascinating objects of study, and contain valuable evidence about animal behaviours, populations and ecosystems. They are studied in bioacoustics and ecoacoustics, with signal processing and…
Biologists are increasingly using databases for storing and managing their data. Biological databases typically consist of a mixture of raw data, metadata, sequences, annotations, and related data obtained from various sources. Current…
A key goal of bioinformatics is to create database systems and software platforms capable of storing and analysing large sets of biological data. Hundreds of biological databases are now available and provide access to huge amount of…