Bioinformatic approaches for studying the microbiome of fermented food

LH Walsh, M Coakley, AM Walsh… - Critical Reviews in …, 2023 - Taylor & Francis
High-throughput DNA sequencing-based approaches continue to revolutionise our
understanding of microbial ecosystems, including those associated with fermented foods …

Illuminating the druggable genome: Pathways to progress

KR Sharma, CM Colvis, GP Rodgers, DM Sheeley - Drug discovery today, 2023 - Elsevier
There are∼ 4500 genes within the 'druggable genome', the subset of the human genome
that expresses proteins able to bind drug-like molecules, yet existing drugs only target a few …

[HTML][HTML] Assessment of transparency indicators across the biomedical literature: How open is open?

S Serghiou, DG Contopoulos-Ioannidis… - PLoS …, 2021 - journals.plos.org
Recent concerns about the reproducibility of science have led to several calls for more open
and transparent research practices and for the monitoring of potential improvements over …

[HTML][HTML] New trends in bibliometric APIs: A comparative analysis

A Velez-Estevez, IJ Perez, P García-Sánchez… - Information Processing …, 2023 - Elsevier
The science of science practice requires the analysis of large and complex bibliometric data.
Traditional data exporting from companies' websites is not sufficient, so APIs are used to …

OpenCitations, an infrastructure organization for open scholarship

S Peroni, D Shotton - Quantitative Science Studies, 2020 - direct.mit.edu
OpenCitations is an infrastructure organization for open scholarship dedicated to the
publication of open citation data as Linked Open Data using Semantic Web technologies …

[HTML][HTML] Entrez direct: E-utilities on the UNIX command line

J Kans - Entrez programming utilities help [Internet], 2024 - ncbi.nlm.nih.gov
Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases
(publication, sequence, structure, gene, variation, expression, etc.) from a Unix terminal …

Continued use of retracted papers: Temporal trends in citations and (lack of) awareness of retractions shown in citation contexts in biomedicine

TK Hsiao, J Schneider - Quantitative Science Studies, 2021 - direct.mit.edu
We present the first database-wide study on the citation contexts of retracted papers, which
covers 7,813 retracted papers indexed in PubMed, 169,434 citations collected from iCite …

A network-based normalized impact measure reveals successful periods of scientific discovery across disciplines

Q Ke, AJ Gates, AL Barabási - Proceedings of the National …, 2023 - National Acad Sciences
The impact of a scientific publication is often measured by the number of citations it receives
from the scientific community. However, citation count is susceptible to well-documented …

[HTML][HTML] Robustness of evidence reported in preprints during peer review

L Nelson, H Ye, A Schwenn, S Lee, S Arabi… - The Lancet Global …, 2022 - thelancet.com
Scientists have expressed concern that the risk of flawed decision making is increased
through the use of preprint data that might change after undergoing peer review. This Health …

[HTML][HTML] Predicting translational progress in biomedical research

BI Hutchins, MT Davis, RA Meseroll… - PLoS biology, 2019 - journals.plos.org
Fundamental scientific advances can take decades to translate into improvements in human
health. Shortening this interval would increase the rate at which scientific discoveries lead to …