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 …

Molecular bases of responses to abiotic stress in trees

M Estravis-Barcala, MG Mattera… - Journal of …, 2020 - academic.oup.com
Trees are constantly exposed to climate fluctuations, which vary with both time and
geographic location. Environmental changes that are outside of the physiological favorable …

The role of software in science: a knowledge graph-based analysis of software mentions in PubMed Central

D Schindler, F Bensmann, S Dietze, F Krüger - PeerJ Computer Science, 2022 - peerj.com
Science across all disciplines has become increasingly data-driven, leading to additional
needs with respect to software for collecting, processing and analysing data. Thus …

BioCoder: a benchmark for bioinformatics code generation with contextual pragmatic knowledge

X Tang, B Qian, R Gao, J Chen, X Chen… - arXiv preprint arXiv …, 2023 - arxiv.org
Pre-trained language models like ChatGPT have significantly improved code generation. As
these models scale up, there is an increasing need for the output to handle more intricate …

Including everyone, everywhere: Understanding opportunities and challenges of geographic gender-inclusion in oss

GAA Prana, D Ford, A Rastogi, D Lo… - IEEE Transactions …, 2021 - ieeexplore.ieee.org
The gender gap is a significant concern facing the software industry as the development
becomes more geographically distributed. Widely shared reports indicate that gender …

Computational reproducibility of Jupyter notebooks from biomedical publications

S Samuel, D Mietchen - GigaScience, 2024 - academic.oup.com
Background Jupyter notebooks facilitate the bundling of executable code with its
documentation and output in one interactive environment, and they represent a popular …

AI in medical imaging grand challenges: translation from competition to research benefit and patient care

SG Armato, K Drukker, L Hadjiiski - The British Journal of …, 2023 - academic.oup.com
Artificial intelligence (AI), in one form or another, has been a part of medical imaging for
decades. The recent evolution of AI into approaches such as deep learning has dramatically …

BioCoder: a benchmark for bioinformatics code generation with large language models

X Tang, B Qian, R Gao, J Chen, X Chen… - …, 2024 - academic.oup.com
Pretrained large language models (LLMs) have significantly improved code generation. As
these models scale up, there is an increasing need for the output to handle more intricate …

Higitclass: Keyword-driven hierarchical classification of github repositories

Y Zhang, FF Xu, S Li, Y Meng, X Wang… - … Conference on Data …, 2019 - ieeexplore.ieee.org
GitHub has become an important platform for code sharing and scientific exchange. With the
massive number of repositories available, there is a pressing need for topic-based search …

Softcite dataset: A dataset of software mentions in biomedical and economic research publications

C Du, J Cohoon, P Lopez… - Journal of the Association …, 2021 - Wiley Online Library
Software contributions to academic research are relatively invisible, especially to the
formalized scholarly reputation system based on bibliometrics. In this article, we introduce a …