Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities

M Chiara, AM D'Erchia, C Gissi… - Briefings in …, 2021 - academic.oup.com
Various next generation sequencing (NGS) based strategies have been successfully used in
the recent past for tracing origins and understanding the evolution of infectious agents …

Challenges and best practices in omics benchmarking

TG Brooks, NF Lahens, A Mrčela, GR Grant - Nature Reviews Genetics, 2024 - nature.com
Technological advances enabling massively parallel measurement of biological features—
such as microarrays, high-throughput sequencing and mass spectrometry—have ushered in …

The nf-core framework for community-curated bioinformatics pipelines

PA Ewels, A Peltzer, S Fillinger, H Patel… - Nature …, 2020 - nature.com
To the Editor—The standardization, portability and reproducibility of analysis pipelines are
key issues within the bioinformatics community. Most bioinformatics pipelines are designed …

The EMBL-EBI search and sequence analysis tools APIs in 2019

F Madeira, YM Park, J Lee, N Buso, T Gur… - Nucleic acids …, 2019 - academic.oup.com
The EMBL-EBI provides free access to popular bioinformatics sequence analysis
applications as well as to a full-featured text search engine with powerful cross-referencing …

Making sense of big data in health research: towards an EU action plan

C Auffray, R Balling, I Barroso, L Bencze, M Benson… - Genome medicine, 2016 - Springer
Medicine and healthcare are undergoing profound changes. Whole-genome sequencing
and high-resolution imaging technologies are key drivers of this rapid and crucial …

Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities

S Cohen-Boulakia, K Belhajjame, O Collin… - Future Generation …, 2017 - Elsevier
With the development of new experimental technologies, biologists are faced with an
avalanche of data to be computationally analyzed for scientific advancements and …

[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 …

[HTML][HTML] Four simple recommendations to encourage best practices in research software

RC Jiménez, M Kuzak, M Alhamdoosh, M Barker… - …, 2017 - ncbi.nlm.nih.gov
Scientific research relies on computer software, yet software is not always developed
following practices that ensure its quality and sustainability. This manuscript does not aim to …

Actively triggerable metals via liquid metal embrittlement for biomedical applications

VR Feig, E Remlova, B Muller… - Advanced …, 2023 - Wiley Online Library
Actively triggerable materials, which break down upon introduction of an exogenous
stimulus, enable precise control over the lifetime of biomedical technologies, as well as …

Current RNA-seq methodology reporting limits reproducibility

J Simoneau, S Dumontier, R Gosselin… - Briefings in …, 2021 - academic.oup.com
Ribonucleic acid sequencing (RNA-seq) identifies and quantifies RNA molecules from a
biological sample. Transformation from raw sequencing data to meaningful gene or isoform …