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Dose-finding clinical trials in oncology aim to estimate the maximum tolerated dose (MTD), based on safety traditionally obtained from the clinician's perspective. While the collection of patient-reported outcomes (PROs) has been advocated…
Monitoring the safety of medical products is a core concern of contemporary pharmacovigilance. To support drug safety assessment, Spontaneous Reporting Systems (SRS) collect reports of suspected adverse events of approved medical products…
The change of two orders of magnitude in the 'new DCF' of NIST's SRE'10, relative to the 'old DCF' evaluation criterion, posed a difficult challenge for participants and evaluator alike. Initially, participants were at a loss as to how to…
Over time, the performance of clinical prediction models may deteriorate due to changes in clinical management, data quality, disease risk and/or patient mix. Such prediction models must be updated in order to remain useful. Here, we…
This manuscript introduces an \proglang{R} package called \pkg{trialr} that implements a collection of clinical trial methods in \proglang{Stan} and \proglang{R}. In this article, we explore three methods in detail. The first is the…
The rapid growth of biomedical knowledge has outpaced our ability to efficiently extract insights and generate novel hypotheses. Large language models (LLMs) have emerged as a promising tool to revolutionize knowledge interaction and…
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to…
Large-scale ad hoc analytics of genomic data is popular using the R-programming language supported by 671 software packages provided by Bioconductor. More recently, analytical jobs are benefitting from on-demand computing and storage, their…
Bayesian networks are a class of models that are widely used for risk assessment of complex operational systems. There are now multiple approaches, as well as implemented software, that guide their construction via data learning or expert…
We introduce two new tools to assess the validity of statistical distributions. These tools are based on components derived from a new statistical quantity, the $comparison$ $curve$. The first tool is a graphical representation of these…
Background: Assessment of long-term survival for health technology assessment often necessitates extrapolation beyond the duration of a clinical trial. Without robust methods and external data, extrapolations are unreliable. Flexible…
AI algorithms are being used with increased frequency in SE research and practice. Such algorithms are usually commissioned and certified using data from outside the SE domain. Can we assume that such algorithms can be used…
The rapid growth of scientific software has created practical barriers for bioinformatics research. Although powerful statistical, artificial intelligence (AI)-based methods are now widely available, their effective use is often hindered by…
Biomedical researchers use ontologies to annotate their data with ontology terms, enabling better data integration and interoperability. However, the number, variety and complexity of current biomedical ontologies make it cumbersome for…
Methods for evaluating the quality of genomic and metagenomic data are essential to aid genome assembly and to correctly interpret the results of subsequent analyses. BUSCO estimates the completeness and redundancy of processed genomic data…
Phase 1-2 designs provide a methodological advance over phase 1 designs for dose finding by using both clinical response and toxicity. A phase 1-2 trial still may fail to select a truly optimal dose. because early response is not a perfect…
The limits of TDF (time, dose, and fractionation) and linear quadratic models have been known for a long time. Medical physicists and physicians are required to provide fast and reliable interpretations regarding the delivered doses or any…
Structural identifiability and observability are desirable properties of systems biology models. Many software toolboxes have been developed for their analysis in the last decades. STRIKE-GOLDD is a generally applicable tool that can…
An important objective in biomedical risk assessment is estimation of minimum exposure levels that induce a pre-specified adverse response in a target population. The exposure/dose points in such settings are known as Benchmark Doses…
Biological regulatory networks can be represented by computational models, which allow the study and analysis of biological behaviours, therefore providing a better understanding of a given biological process. However, as new information is…