[HTML][HTML] The role of metadata in reproducible computational research

J Leipzig, D Nüst, CT Hoyt, K Ram, J Greenberg - Patterns, 2021 - cell.com
Reproducible computational research (RCR) is the keystone of the scientific method for in
silico analyses, packaging the transformation of raw data to published results. In addition to …

Associations between blood type and COVID-19 infection, intubation, and death

M Zietz, J Zucker, NP Tatonetti - Nature communications, 2020 - nature.com
The rapid global spread of the novel coronavirus SARS-CoV-2 has strained healthcare and
testing resources, making the identification and prioritization of individuals most at-risk a …

Scaling tree-based automated machine learning to biomedical big data with a feature set selector

TT Le, W Fu, JH Moore - Bioinformatics, 2020 - academic.oup.com
Abstract Motivation Automated machine learning (AutoML) systems are helpful data science
assistants designed to scan data for novel features, select appropriate supervised learning …

From open data to open science

R Ramachandran, K Bugbee… - Earth and Space …, 2021 - Wiley Online Library
The open science movement continues to gain momentum, attention, and discussion.
However, there are a number of different interpretations, viewpoints, and perspectives as to …

sPlotOpen–An environmentally balanced, open‐access, global dataset of vegetation plots

FM Sabatini, J Lenoir, T Hattab, EA Arnst… - Global Ecology and …, 2021 - Wiley Online Library
Motivation Assessing biodiversity status and trends in plant communities is critical for
understanding, quantifying and predicting the effects of global change on ecosystems …

Not just for programmers: How GitHub can accelerate collaborative and reproducible research in ecology and evolution

PHP Braga, K Hébert, EJ Hudgins… - Methods in Ecology …, 2023 - Wiley Online Library
Researchers in ecology and evolutionary biology are increasingly dependent on
computational code to conduct research. Hence, the use of efficient methods to share …

Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager

JAF Yates, TC Lamnidis, M Borry, AA Valtueña… - PeerJ, 2021 - peerj.com
The broadening utilisation of ancient DNA to address archaeological, palaeontological, and
biological questions is resulting in a rising diversity in the size of laboratories and scale of …

The LOTUS initiative for open knowledge management in natural products research

A Rutz, M Sorokina, J Galgonek, D Mietchen… - Elife, 2022 - elifesciences.org
Contemporary bioinformatic and chemoinformatic capabilities hold promise to reshape
knowledge management, analysis and interpretation of data in natural products research …

Unifying the identification of biomedical entities with the Bioregistry

CT Hoyt, M Balk, TJ Callahan, D Domingo-Fernández… - Scientific data, 2022 - nature.com
The standardized identification of biomedical entities is a cornerstone of interoperability,
reuse, and data integration in the life sciences. Several registries have been developed to …

[HTML][HTML] A publishing infrastructure for AI-assisted academic authoring

M Pividori, CS Greene - BioRxiv, 2023 - ncbi.nlm.nih.gov
In this work we investigate how models with advanced natural language processing
capabilities can be used to reduce the time-consuming process of writing and revising …