Artificial intelligence and machine learning in cancer imaging

DM Koh, N Papanikolaou, U Bick, R Illing… - Communications …, 2022 - nature.com
An increasing array of tools is being developed using artificial intelligence (AI) and machine
learning (ML) for cancer imaging. The development of an optimal tool requires …

Containers for computational reproducibility

D Moreau, K Wiebels, C Boettiger - Nature Reviews Methods Primers, 2023 - nature.com
The fast-paced development of computational tools has enabled tremendous scientific
progress in recent years. However, this rapid surge of technological capability also comes at …

Nextflow enables reproducible computational workflows

P Di Tommaso, M Chatzou, EW Floden, PP Barja… - Nature …, 2017 - nature.com
The increasing complexity of readouts for omics analyses goes hand-in-hand with concerns
about the reproducibility of experiments that analyze'big data'1, 2, 3. When analyzing very …

[HTML][HTML] Translating RNA sequencing into clinical diagnostics: opportunities and challenges

SA Byron, KR Van Keuren-Jensen… - Nature Reviews …, 2016 - nature.com
With the emergence of RNA sequencing (RNA-seq) technologies, RNA-based biomolecules
hold expanded promise for their diagnostic, prognostic and therapeutic applicability in …

[图书][B] Reproducibility and replicability in science

National Academies of Sciences, Policy, Global Affairs… - 2019 - books.google.com
One of the pathways by which the scientific community confirms the validity of a new
scientific discovery is by repeating the research that produced it. When a scientific effort fails …

BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods

KJ Gorgolewski, F Alfaro-Almagro, T Auer… - PLoS computational …, 2017 - journals.plos.org
The rate of progress in human neurosciences is limited by the inability to easily apply a wide
range of analysis methods to the plethora of different datasets acquired in labs around the …

A comparative study of containers and virtual machines in big data environment

Q Zhang, L Liu, C Pu, Q Dou, L Wu… - 2018 IEEE 11th …, 2018 - ieeexplore.ieee.org
Container technique is gaining increasing attention in recent years and has become an
alternative to traditional virtual machines. Some of the primary motivations for the enterprise …

Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing

SST Mak, S Gopalakrishnan, C Carøe, C Geng… - …, 2017 - academic.oup.com
Ancient DNA research has been revolutionized following development of next-generation
sequencing platforms. Although a number of such platforms have been applied to ancient …

The ocean sampling day consortium

A Kopf, M Bicak, R Kottmann, J Schnetzer, I Kostadinov… - Gigascience, 2015 - Springer
Abstract Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial
Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine …

IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses

S Narayanasamy, Y Jarosz, EEL Muller… - Genome biology, 2016 - Springer
Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and
often result in sub-optimal data usage. Here we present IMP, a reproducible and modular …