Related papers: A data-supported history of bioinformatics tools
Benchmarking, which involves collecting reference datasets and demonstrating method performances, is a requirement for the development of new computational tools, but also becomes a domain of its own to achieve neutral comparisons of…
Deciphering cell type heterogeneity is crucial for systematically understanding tissue homeostasis and its dysregulation in diseases. Computational deconvolution is an efficient approach estimating cell type abundances from a variety of…
The continuous development of artificial intelligence has a profound impact on biomedicine and other fields, providing new research ideas and technical methods. Brain-inspired computing is an important intersection between multimodal…
Like hardware, evolution of software has had a major impact on the field of particle simulations. This paper illustrates how simulation software has evolved, and where it can go. In addition, with the various ongoing Virtual Observatory…
Biological processes involve a variety of spatial and temporal scales. A holistic understanding of many biological processes therefore requires multi-scale models which capture the relevant properties on all these scales. In this manuscript…
Artificial intelligence has provided us with an exploration of a whole new research era. As more data and better computational power become available, the approach is being implemented in various fields. The demand for it in health…
A main challenge of data-driven sciences is how to make maximal use of the progressively expanding databases of experimental datasets in order to keep research cumulative. We introduce the idea of a modeling-based dataset retrieval engine…
In this paper we present Simgrid, a toolkit for the versatile simulation of large scale distributed systems, whose development effort has been sustained for the last fifteen years. Over this time period SimGrid has evolved from a…
Multimodal data modeling has emerged as a powerful approach in clinical research, enabling the integration of diverse data types such as imaging, genomics, wearable sensors, and electronic health records. Despite its potential to improve…
Advancements in artificial intelligence (AI) have transformed many scientific fields, with microbiology and microbiome research now experiencing significant breakthroughs through machine learning applications. This review provides a…
Researchers in biomedical research, public health, and the life sciences often spend weeks or months discovering, accessing, curating, and integrating data from disparate sources, significantly delaying the onset of actual analysis and…
Just as in eukaryotes, high-throughput chromosome conformation capture (Hi-C) data have revealed nested organizations of bacterial chromosomes into overlapping interaction domains. In this chapter, we present a multiscale analysis framework…
We analyzed Medical Subject Headings (MeSH) from 21.6 million research articles indexed by PubMed to map this vast space of entities and their relations, providing insights into the origins and future of biomedical convergence. Detailed…
Computational intelligence is broadly defined as biologically-inspired computing. Usually, inspiration is drawn from neural systems. This article shows how to analyze neural systems using information theory to obtain constraints that help…
Recent technological advances have expanded the availability of high-throughput biological datasets, enabling the reliable design of digital twins of biomedical systems or patients. Such computational tools represent key reaction networks…
Across biological subdisciplines, the last decade has seen an explosion of high-dimensional datasets, including datasets for cells, species, immune systems, neurons and behaviour. At the ICTS workshop 'Unifying Theories in High-Dimensional…
Denoising diffusion models have emerged as one of the most powerful generative models in recent years. They have achieved remarkable success in many fields, such as computer vision, natural language processing (NLP), and bioinformatics.…
The twenty-first century has ushered in the age of big data and data economy, in which data DNA, which carries important knowledge, insights and potential, has become an intrinsic constituent of all data-based organisms. An appropriate…
Computer simulations have become a very powerful tool for scientific research. Given the vast complexity that comes with many open scientific questions, a purely analytical or experimental approach is often not viable. For example,…
Biomedical research yields a wealth of information, much of which is only accessible through the literature. Consequently, literature search is an essential tool for building on prior knowledge in clinical and biomedical research. Although…