Bayesian statistics and modelling

R van de Schoot, S Depaoli, R King, B Kramer… - Nature Reviews …, 2021 - nature.com
Bayesian statistics is an approach to data analysis based on Bayes' theorem, where
available knowledge about parameters in a statistical model is updated with the information …

Bayesian analysis reporting guidelines

JK Kruschke - Nature human behaviour, 2021 - nature.com
Previous surveys of the literature have shown that reports of statistical analyses often lack
important information, causing lack of transparency and failure of reproducibility. Editors and …

[HTML][HTML] Empowering biomedical discovery with AI agents

S Gao, A Fang, Y Huang, V Giunchiglia, A Noori… - Cell, 2024 - cell.com
We envision" AI scientists" as systems capable of skeptical learning and reasoning that
empower biomedical research through collaborative agents that integrate AI models and …

Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers

L Wratten, A Wilm, J Göke - Nature methods, 2021 - nature.com
The rapid growth of high-throughput technologies has transformed biomedical research.
With the increasing amount and complexity of data, scalability and reproducibility have …

Therapeutics data commons: Machine learning datasets and tasks for drug discovery and development

K Huang, T Fu, W Gao, Y Zhao, Y Roohani… - arxiv preprint arxiv …, 2021 - arxiv.org
Therapeutics machine learning is an emerging field with incredible opportunities for
innovatiaon and impact. However, advancement in this field requires formulation of …

Packaging research artefacts with RO-Crate

S Soiland-Reyes, P Sefton, M Crosas… - Data …, 2022 - journals.sagepub.com
An increasing number of researchers support reproducibility by including pointers to and
descriptions of datasets, software and methods in their publications. However, scientific …

A large-scale study on research code quality and execution

A Trisovic, MK Lau, T Pasquier, M Crosas - Scientific Data, 2022 - nature.com
This article presents a study on the quality and execution of research code from publicly-
available replication datasets at the Harvard Dataverse repository. Research code is …

RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12

H Salgado, S Gama-Castro, P Lara… - Nucleic Acids …, 2024 - academic.oup.com
RegulonDB is a database that contains the most comprehensive corpus of knowledge of the
regulation of transcription initiation of Escherichia coli K-12, including data from both …

Eleven quick tips for data cleaning and feature engineering

D Chicco, L Oneto, E Tavazzi - PLOS Computational Biology, 2022 - journals.plos.org
Applying computational statistics or machine learning methods to data is a key component of
many scientific studies, in any field, but alone might not be sufficient to generate robust and …

Metabolomics and multi-omics integration: a survey of computational methods and resources

T Eicher, G Kinnebrew, A Patt, K Spencer, K Ying, Q Ma… - Metabolites, 2020 - mdpi.com
As researchers are increasingly able to collect data on a large scale from multiple clinical
and omics modalities, multi-omics integration is becoming a critical component of …