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Understanding cellular metabolism is important across biotechnology and biomedical research and has critical implications in a broad range of normal and pathological conditions. Here, we introduce the user-friendly web-based platform ImmCellFie, which allows the comprehensive analysis of metabolic functions inferred from transcriptomic or proteomic data. We explain how to set up a run using publicly available omics data and how to visualize the results. The ImmCellFie algorithm pushes beyond conventional statistical enrichment and incorporates complex biological mechanisms to quantify cell activity. For complete details on the use and execution of this protocol, please refer to Richelle et al. (2021)..
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http://dx.doi.org/10.1016/j.xpro.2023.102069 | DOI Listing |
J Eval Clin Pract
September 2025
Health Technology Assessment Unit, Acute and Hospital-Based Care Portfolio, Ontario Health, Toronto, Ontario, Canada.
Rationale: Systematic reviews are essential for evidence-based healthcare decision-making. While it is relatively straightforward to quantitatively assess random errors in systematic reviews, as these are typically reported in primary studies, the assessment of biases often remains narrative. Primary studies seldom provide quantitative estimates of biases and their uncertainties, resulting in systematic reviews rarely including such measurements.
View Article and Find Full Text PDFJMIR Res Protoc
September 2025
Suzanne Dworak-Peck School of Social Work, University of Southern California, Los Angeles, CA, United States.
Background: The past decade has seen a substantial increase in the number of people experiencing unsheltered homelessness. The unsheltered population faces heightened health and social risks, yet research on their experiences remains limited.
Objective: This paper presents the protocol for the Periodic Assessment of Trajectories of Housing, Homelessness, and Health Study (PATHS), a longitudinal study that leverages mobile phone technology and web-based surveys to track the housing and health trajectories of people experiencing unsheltered homelessness in Los Angeles County.
J Comput Chem
September 2025
Laboratório de Bioinformática e Química Medicinal, Fundação Oswaldo Cruz Rondônia (LABIOQUIM-Fiocruz-RO), Porto Velho, Rondônia, Brazil.
Virtual screening through molecular docking represents a fundamental computational methodology extensively employed in the identification of therapeutic compounds for malaria and other parasitic diseases. Although numerous software platforms are available, including AutodockGPU, the command-line interface requirements present significant barriers to non-specialized users, while multi-target screening protocols introduce additional complexity in receptor preparation procedures. To address these limitations, we developed Plasmodocking, a comprehensive web-based platform designed to automate molecular docking simulations against predefined Plasmodium falciparum targets (https://plasmodocking-unir.
View Article and Find Full Text PDFBioinform Adv
August 2025
Department of Anatomy and Cell Biology, Medical School OWL, Bielefeld University, Bielefeld 33615, Germany.
Motivation: The growing use of transcriptomic data from platforms like Nanostring GeoMx DSP demands accessible and flexible tools for differential gene expression analysis and heatmap generation. Current web-based tools often lack transparency, modifiability, and independence from external servers creating barriers for researchers seeking customizable workflows, as well as data privacy and security. Additionally, tools that can be utilized by individuals with minimal bioinformatics expertise provide an inclusive solution, empowering a broader range of users to analyze complex data effectively.
View Article and Find Full Text PDFJ Adv Res
August 2025
Microbiology and intelligent biomanufacturing Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan 610041, China. Electronic address:
Introduction: Small non-coding RNAs (sncRNAs) have been proven to play crucial roles in various biological processes such as development, stress responses, virulence, and pathogenicity. However, to the best of our knowledge, none of the currently available databases can store, manage, and analyze the vast amounts of sncRNA sequencing data. A comprehensive web-based platform for the integration and analysis of sncRNAs in fungi and their potential functions is still lacking.
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