98%
921
2 minutes
20
Summary: Data integration workflows for multiomics data take many forms across academia and industry. Efforts with limited resources often encountered in academia can easily fall short of data integration best practices for processing and combining high-content imaging, proteomics, metabolomics, and other omics data. We present Phenonaut, a Python software package designed to address the data workflow needs of migration, control, integration, and auditability in the application of literature and proprietary techniques for data source and structure agnostic workflow creation.
Availability And Implementation: Source code: https://github.com/CarragherLab/phenonaut, Documentation: https://carragherlab.github.io/phenonaut, PyPI package: https://pypi.org/project/phenonaut/.
Download full-text PDF |
Source |
---|---|
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10068743 | PMC |
http://dx.doi.org/10.1093/bioinformatics/btad143 | DOI Listing |
Eur J Radiol
September 2025
Department of Radiology, Affiliated Hospital of Hebei University, Baoding 071000, China. Electronic address:
Purpose: The present study aimed to develop a noninvasive predictive framework that integrates clinical data, conventional radiomics, habitat imaging, and deep learning for the preoperative stratification of MGMT gene promoter methylation in glioma.
Materials And Methods: This retrospective study included 410 patients from the University of California, San Francisco, USA, and 102 patients from our hospital. Seven models were constructed using preoperative contrast-enhanced T1-weighted MRI with gadobenate dimeglumine as the contrast agent.
JMIR Cancer
September 2025
iCARE Secure Data Environment & Digital Collaboration Space, NIHR Imperial Biomedical Research Centre, London, United Kingdom.
Background: Electronic health records (EHRs) are a cornerstone of modern health care delivery, but their current configuration often fragments information across systems, impeding timely and effective clinical decision-making. In gynecological oncology, where care involves complex, multidisciplinary coordination, these limitations can significantly impact the quality and efficiency of patient management. Few studies have examined how EHR systems support clinical decision-making from the perspective of end users.
View Article and Find Full Text PDFJMIR Public Health Surveill
September 2025
Department of Preventive Medicine, College of Medicine, Korea University, 73 Goryeodae-ro, Seoungbuk-gu, Seoul, 02841, Republic of Korea, 82 2-2286-1169.
Background: Scrub typhus (ST), also known as tsutsugamushi disease, is a common febrile vector-borne illness in South Korea, transmitted by trombiculid mites infected with Orientia tsutsugamushi, with rodents serving as the main hosts. Although vector-borne diseases like ST require both a One Health approach and a spatiotemporal perspective to fully understand their complex dynamics, previous studies have often lacked integrated analyses that simultaneously address disease dynamics, vectors, and environmental shifts.
Objective: We aimed to explore spatiotemporal trends, high-risk areas, and risk factors of ST by simultaneously incorporating host and environmental information.
J Chem Inf Model
September 2025
Department of Chemistry, Delaware State University, Dover, Delaware 19901, United States.
The calculation of the highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gap for chemical molecules is computationally intensive using quantum mechanics (QM) methods, while experimental determination is often costly and time-consuming. Machine Learning (ML) offers a cost-effective and rapid alternative, enabling efficient predictions of HOMO-LUMO gap values across large data sets without the need for extensive QM computations or experiments. ML models facilitate the screening of diverse molecules, providing valuable insights into complex chemical spaces and integrating seamlessly into high-throughput workflows to prioritize candidates for experimental validation.
View Article and Find Full Text PDFEur J Gastroenterol Hepatol
August 2025
Department of Gastroenterology, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi Medical Center, Nanjing Medical University, Wuxi People's Hospital, Wuxi, Jiangsu Province, China.
Background: Inflammatory bowel diseases (IBD), including Crohn's disease and ulcerative colitis, significantly impact patients' lives. Effective management often involves invasive and costly monitoring.
Objective: To evaluate the feasibility of integrating home-based fecal calprotectin testing with therapeutic drug monitoring (TDM) in managing moderate-to-severe IBD.