14 papers · ranked by Valyu relevance
Nicolas Mongiardino Koch, Pablo Milla Carmona
Much of our understanding of the history of life hinges upon time calibration, the process of assigning absolute times to cladogenetic events. Bayesian approaches to time scaling phylogenetic trees have dramatically grown in complexity, and depend today upon numerous methodological choices. Arriving at objective…
Margaret Jane Moore, Chris Rorden, Gail A. Robinson, Jason B. Mattingley + 1 more
Lesion mapping results can vary substantially as a function of specific analysis parameters, but the extent to which individual methodological choices interact to modulate the sensitivity and specificity of results is not clear. Here, we employed a large-scale simulation approach to inform practical recommendations for…
Jonathan Rondeau-Leclaire, F. Guillaume Blanchet, Pierre-Étienne Jacques, Isabelle Laforest-Lapointe
Estimating taxonomic profiles is a central task in microbiome research. Several bioinformatic tools have been developed for this purpose, differing in algorithmic strategy, reference database flexibility, sensitivity parameters, and the type of abundance they estimate. As a result, taxonomic profiles carry an unwanted…
Seyyed Mahmood Ghasem, Johannes F. Fahrmann, Samir Hanash, Kim-Anh Do + 2 more
Logistic regression has demonstrated its utility in classifying binary labeled datasets through the maximum likelihood approach. However, in numerous biological and clinical contexts, the aim is often to determine coefficients that yield the highest sensitivity at the pre-specified specificity or vice versa. Therefore…
Rachel Mester, Alfonso Landeros, Chris Rackauckas, Kenneth Lange
Differential sensitivity analysis is indispensable in fitting parameters, understanding uncertainty, and forecasting the results of both thought and lab experiments. Although there are many methods currently available for performing differential sensitivity analysis of biological models, it can be difficult to…
Daniel R. Bergman, Trachette Jackson, Harsh Vardhan Jain, Kerri-Ann Norton
Agent-based models (ABMs) have become essential tools for simulating complex biological, ecological, and social systems where emergent behaviors arise from the interactions among individual agents. Quantifying uncertainty through global sensitivity analysis is crucial for assessing the robustness and reliability of ABM…
Joanna Emerson, Ari Panzer, Joshua T. Cohen, Kalipso Chalkidou + 6 more
The iDSI reference case, originally published in 2014, aims to improve the quality and comparability of cost-effectiveness analyses (CEAs). This study assesses whether the development of the guideline has improved the reporting and methodology for CEAs using disability-adjusted life-years (DALYs). We analyzed the Tufts…
Gorm E. Shackelford, Philip A. Martin, Amelia S. C. Hood, Alec P. Christie + 2 more
Meta-analysis is often used to make generalizations across all available evidence at the global scale. But how can these global generalizations be used for evidence-based decision making at the local scale, if only the local evidence is perceived to be relevant to a local decision? We show how an interactive method of…
Matthias Steinfath, Silvia Vogl, Norman Violet, Franziska Schwarz + 4 more
Assessing the impact of recommendations rectifying the reproducibility crisis (publishing both positive and “negative” results and increasing statistical power) on competing objectives, such as discovering causal relationships, avoiding publishing false positive results, and reducing resource consumption, we developed…
Laura Fancello, Thomas Burger
Proteogenomics aims at identifying variant or unknown proteins in bottom-up proteomics, searching transcriptome- or genome-derived custom protein databases. However, empirical observations reported that the large size of these proteogenomic databases is associated to lower sensitivity of peptide identifications.…
Ben Lambert, David J. Gavaghan, Simon Tavener
Biological systems have evolved a degree of robustness with respect to perturbations in their environment and this capability is essential for their survival. In applications ranging from therapeutics to conservation, it is important to understand not only the sensitivity of biological systems to changes in their…
Berna Devezer, Danielle J. Navarro, Joachim Vandekerckhove, Erkan Ozge Buzbas
Current attempts at methodological reform in sciences come in response to an overall lack of rigor in methodological and scientific practices in experimental sciences. However, some of these reform attempts suffer from the same mistakes and over-generalizations they purport to address. Considering the costs of allowing…
Kai Standvoss, Vartan Kazezian, Britta R. Lewke, Kathleen Bastian + 12 more
Methods sections are often missing critical details needed to reproduce an experiment. Methodological shortcut citations, in which authors cite previous papers instead of describing the method in detail, may contribute to this problem. This meta-research study used three approaches to systematically examine the use of…
Yefeng Yang, Coralie Williams, Alistair M. Senior, Kyle Morrison + 4 more
Meta-analytic modelling plays a pivotal role in synthesizing research and informing relevant policies. Yet researchers face many analytical challenges. In environmental and biological sciences, one of the most common yet unrecognised issues is the selection between two common effect size metrics, log response ratio…