Water Research, Journal Year: 2025, Volume and Issue: 279, P. 123437 - 123437
Published: March 6, 2025
Language: Английский
iMeta, Journal Year: 2024, Volume and Issue: 3(5)
Published: Aug. 1, 2024
The OmicShare tools platform is a user-friendly online resource for data analysis and visualization, encompassing 161 bioinformatic tools. Users can easily track the progress of projects in real-time through an overview interface. has powerful interactive graphics engine that allows custom-tailored modification charts generated from analyses. visually appealing produced by improve interpretability meet requirements publication. It been acknowledged over 4000 publications available https://www.omicshare.com/tools/. Advances high-throughput sequencing technologies have resulted exponential increase volume biological data, creating significant challenges biologists analyzing extensive sets extracting meaningful insights them [1]. Typically, process initial acquisition to dissemination research findings involves three key stages: statistical analysis, creation charts, graphical enhancement. Many bioinformatics platforms or high throughput omics such as Majorbio Cloud [2], SangerBox [3], ImageGP [4], Wekemo [5], Evenn [6], Circos TBtools [7], complexHeatmap [8], ggVennDiagram [9], emerged. Most these were developed specific research, especially metagenomics transcriptomics, some provide solutions special problems. However, default graphic outputs often require fine-tuning using editing software (such Adobe Illustrator Photoshop) attain standard suitable Furthermore, many visualizing lack interfaces, which makes more complicated rather than simple mouse clicks [10]. To bridge this gap empower all researchers, including those without programming skills, smoothly navigate refinement one continuous workflow, we present (https://www.omicshare.com/tools/). This acts zero-code, portal streamlines granting researchers capability easy, adaptable, individualized exploration their data. suite robust collection utilities designed address multifaceted needs research. These span wide array functions, nucleic acid protein sequence gene function annotation, differential expression assessment, clustering evaluation, custom output creation. rich assortment offers full methods meticulous visualization depicted Figure 1A. Within framework, effortlessly carry out enrichment utilizing databases like Gene Ontology (GO), Kyoto Encyclopedia Genes Genomes (KEGG), Disease Ontology, Reactome. In addition, encompasses comprehensive set tests, correlation, variance, principal component (PCA), together with survival analysis. also facilitates production publication-ready graphics, heatmaps, Venn diagrams, scatter plots, cater standards scientific communication. suite, 129 offer features simplify imagery enable conceive visualizations. Examples include generating various specialized diagrams: grouped bar GO enrichment, correlation network composite plots Set Enrichment Analysis, PCA confidence intervals, diagrams comparing multiple cohorts, ridge displayed 1B–K. Additionally, integrated are exceptionally diverse detailed. For instance, KEGG tool does not just generate bubble (Figure 1E), it creates visuals circular 1H,K), offering variety ways display aid management adhere formatting analyses, format conversion utilities. streamline normalization standardization, facilitating IDs across different nomenclatures species accommodate transformation between "long" "wide" formats ease use enhance efficiency begin selecting best suits needs, uploading via interface, configuring necessary parameters launch 2A). successful arrange files fulfills tool. Each within accompanied sample file download users. encouraged templates own according avoid any mistakes 2B). Proper guidance provided setting parameter tool's instructional documentation. case utilities, users advised retain settings optimal results. feature monitoring system tracks task identifies errors. Once initiated, monitor its progression on project dashboard 2C). After completion, results immediate preview 2D). error, error-checking facility provides potential cause error. additional support, consult detailed documentation contact customer service team. proactively verify upon submission. Failure criteria will prevent initiation, triggering helpful error prompt. support formats, ensuring broad compatibility common types, FASTA files, tab-separated comma-separated value text Excel spreadsheets. possess advanced engine, crafted JavaScript dynamic chart customization community. presents range be modified allowing tweaks elements axes, fonts, themes, color schemes. selection predefined schemes, spanning 23 gradient colors 15 categorized palettes, added option concoct if defaults unsatisfactory. diagram tool, adjustments readily accessible, enabling alter visual aspects nodes edges, shape, size, color, transparency, label style, line thickness, curvature, style savable, swift reinstatement previous configurations revisiting interface transitioning tasks. By default, styles calibrated publication standards, produce presentation-ready minimal effort. Visual primed inclusion academic manuscripts, conforming quality publications. afforded flexibility personalize elements, refining preset suit preferences. supports export both bitmap images (JPG, PNG, BMP, TIF) vector (PDF, SVG), latter further modifications Illustrator, Inkscape, CorelDRAW. serves zero-coding, interactive, providing standards. facilitate seamless integration into scholarly articles mitigating steep learning curve commonly associated complex software. renowned heatmaps [11, 12], performing pathway analyses [13-15], conducting [16-18], [19, 20]. Since April 2016, garnered citations SCI-indexed papers. evolution characterized enhancements expansions. Despite tools, certain exhibit incomplete categorization, necessitating optimization adjustment. Future updates expected incorporate types analytical techniques, single-cell clinical Concurrently, efforts directed toward user settings, thereby enhancing accessibility limited expertise. platform, JavaScript, HTML, Bootstrap front-end development, responsive accessible On backend, web framework ThinkPHP employed preprocessing Some utilize R Python languages graphing, incorporating packages ggplot2, complexHeatmap, edgeR, DESeq2; integral evaluations high-quality Meanwhile, other leverage custom-developed drawing plugins, unique tailored representations directly based user-specific platform. Huangkai Zhou, Chuan Gao, Peng Ai conceived idea. Wenjie Huang Hongyan Mu functional modules interfaces. Jianzhou Chen, Gui Huang, Shimiao Hong completed process, cloud server development. wrote manuscript. Meiying Deng Zhou responsible revising All authors read final manuscript approved We would express our gratitude reports suggestions, well developers who technical project. declare no conflict interest. No animals humans involved study. at Supporting information (scripts, abstract, slides, videos, Chinese translated version, update materials) may found DOI iMeta Science https://www.imeta.science/.
Language: Английский
Citations
58
iMeta, Journal Year: 2025, Volume and Issue: unknown
Published: Feb. 17, 2025
Abstract The rapid growth of microbiome research has generated an unprecedented amount multi‐omics data, presenting challenges in data analysis and visualization. To address these issues, we present MicrobiomeStatPlots, a comprehensive platform offering streamlined, reproducible tools for This integrates essential bioinformatics workflows with pipelines provides 82 distinct visualization cases interpreting datasets. By incorporating basic tutorials advanced R‐based strategies, MicrobiomeStatPlots enhances accessibility usability researchers. Users can customize plots, contribute to the platform's expansion, access wealth knowledge freely on GitHub ( https://github.com/YongxinLiu/MicrobiomeStatPlot ). Future plans include extending support metabolomics, viromics, metatranscriptomics, along seamless integration into omics workflows. bridges gaps visualization, paving way more efficient, impactful research.
Language: Английский
Citations
3
Environmental Science & Technology, Journal Year: 2025, Volume and Issue: unknown
Published: Jan. 21, 2025
The plastisphere, defined as the ecological niche for microbial colonization of plastic debris, has been recognized a hotspot pathogenic and antibiotic-resistant bacteria. However, interactions between bacteria phages facilitated by well their impact on risks to public health, remain unclear. Here, we analyzed metagenomic data from 180 plastisphere environmental samples, stemming four different habitats two types (biodegradable nonbiodegradable plastics) obtained 611 nonredundant metagenome-assembled genomes (MAGs) 4061 phage contigs. community exhibited decreased diversity virulent proportion compared those found in environments. Indexes phage-host interaction networks indicated significant associations with (ARB), particularly biodegradable plastics. Known phage-encoded auxiliary metabolic genes (AMGs) were involved nutrient metabolism, antibiotic production, quorum sensing, biofilm formation which contributed enhanced competition survival pathogens ARB hosts. Phages also carried transcriptionally active virulence factor (VFGs) resistance (ARGs), could mediate horizontal transfer communities. Overall, these discoveries suggest that form symbiotic relationships hosts, encoding AMGs mediating gene (HGT) increase source plastisphere.
Language: Английский
Citations
2
iMeta, Journal Year: 2024, Volume and Issue: 3(5)
Published: Sept. 12, 2024
Abstract ImageGP is an extensively utilized, open‐access platform for online data visualization and analysis. Over the past 7 years, it has catered to more than 700,000 usages globally, garnering substantial user feedback. The updated version, 2 (available at https://www.bic.ac.cn/BIC ), introduces a redesigned interface leveraging cutting‐edge web technologies enhance functionality interaction. Key enhancements include following: (i) Addition of modules format transformation, facilitating operations such as matrix merging, subsetting, transformation between long wide formats. (ii) Streamlined workflows with features like preparameter selection validation grouping parameters similar attributes. (iii) Expanded repertoire functions analysis tools, including Weighted Gene Co‐Expression Network Analysis, differential gene expression analysis, FASTA sequence processing. (iv) Personalized space uploading large sets, tracking history, sharing reproducible data, scripts, results. (v) Enhanced support through simplified error debugging feature accessible single click. (vi) Introduction R package, ImageGP, enabling local These updates position versatile tool serving both wet‐lab dry‐lab researchers expanded capabilities.
Language: Английский
Citations
11
GigaScience, Journal Year: 2025, Volume and Issue: 14
Published: Jan. 1, 2025
Abstract Converting multiomics datasets into gene sets facilitates data integration that leads to knowledge discovery. Although there are tools developed analyze sets, only a few offer the management of from multiple sources. GeneSetCart is an interactive web-based platform enables investigators gather various sources; augment these with gene–gene coexpression correlations and protein–protein interactions; perform set operations on such as union, consensus, intersection; visualize all in one place. supports upload single or well fetching by searching PubMed for genes comentioned terms publications. Venn diagrams, heatmaps, Uniform Manifold Approximation Projection (UMAP) plots, SuperVenn UpSet plots can session summarize similarity overlap among sets. Users also enrichment analysis their assembled external tools. All be saved user account reanalysis sharing collaborators. has library crossing feature created several National Institutes Health Common Fund programs. For top overlapping pairs programs, large language model (LLM) prompted propose possible reasons high overlap. Using this feature, two use cases presented. In addition, users produce publication-ready reports uploaded Text supplemented LLM. Overall, useful resource enabling biologists without programming expertise facilitate hypothesis generation.
Language: Английский
Citations
1
International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(16), P. 9093 - 9093
Published: Aug. 22, 2024
Bacteria of the Thiothrix morphotype, comprising genera Thiothrix, Thiolinea and Thiofilum, are frequently encountered in domestic industrial wastewater treatment systems, but they usually not clearly differentiated due to marked similarity their morphologies. Methods ranging from light microscopy, FISH PCR modern high-throughput sequencing used identify them. The development these bacteria systems has both advantages disadvantages. On one hand, explosive growth can lead activated sludge bulking or clogging system’s membranes, with a consequent decrease water efficiency. other members morphotype improve quality granular increase This may be capacity for sulfide oxidation, denitrification combined oxidation reduced sulfur compounds, enhanced biological phosphate removal possibly denitrifying removal. recently obtained pangenome genus allows explanation, at genomic level, experimental results various studies. Moreover, this review summarizes data on factors affecting proliferation representatives morphotype.
Language: Английский
Citations
7
Plants, Journal Year: 2024, Volume and Issue: 13(16), P. 2275 - 2275
Published: Aug. 15, 2024
Central Asia (CA) is located in the interior of Eurasian continent and consists five countries—Kazakhstan, Kyrgyzstan, Tajikistan, Turkmenistan, Uzbekistan. It contains largest concentration temperate deserts mountains CA biodiversity hotspots. However, regionwide floristic diversity sorely lacking, nationwide seriously outdated this region. Using data collected by Mapping Plants (MAP) project, we describe analyze diverse characteristics plant at both regional national levels, including dominant families genera, endemic taxa, similarity. The results allow compilation a new checklist vascular plants CA, 9643 taxa (1198 genera within 139 families) 3409 (414 66 families). We confirm that there are 5695, 4036, 4542, 3005, 4222 species countries, which 532, 326, 505, 175, 301 Kazakhstan, Uzbekistan, respectively. region’s notable for its high degree endemism—up to 35.35%—which contributes uniqueness irreplaceability CA. encompassing most area mountains, has highest density (3.19/100 km2) endemism (11.12%) among countries. Neighboring countries such as Tajikistan Kazakhstan Kyrgyzstan share more common, while Turkmenistan less overlap with other four Trends total consistent. This comprehensive inventory novel, revealing CA’s two dimensions providing solid foundation subsequent research will be beneficial transboundary conservation sustainable use resources
Language: Английский
Citations
4
iMetaOmics., Journal Year: 2024, Volume and Issue: 1(2)
Published: Nov. 20, 2024
Abstract The advent of next‐generation sequencing has revolutionized microbiome research, enabling in‐depth exploration microbial communities through amplicon sequencing. widespread adoption across diverse fields, coupled with decreasing costs, underscores the critical need for validated, fully automated, reproducible, and adaptable analysis pipelines. However, analyzing these high‐throughput datasets often necessitates extensive bioinformatics expertize, hindering accessibility many researchers. To address this challenge, in 2023 we developed EasyAmplicon, a comprehensive, user‐friendly pipeline that integrates popular tools such as USEARCH VSEARCH, offering streamlined workflow from raw data to results. Remarkably, EasyAmplicon garnered significant recognition within year, evidenced by 127 citations date. further facilitate researchers enhance usability, present detailed protocol video recording guides users each step pipeline, including preprocessing (quality filtering, chimera removal), sequence variant analysis, diversity visualization. is designed ease use, documented, allowing execute without requiring complex scripting skills. freely available on GitHub ( https://github.com/YongxinLiu/EasyAmplicon ).
Language: Английский
Citations
4
International Journal of Food Sciences and Nutrition, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 15
Published: Feb. 3, 2025
Environmental factors can play fundamental role in health childhood and adulthood during critical developmental periods like lactation. The maternal intake of probiotics kefir lactation could benefit newborns' intestinal health. This study aimed to evaluate the effects on bacterial breast milk composition gut microbiota offspring Wistar male rats at weaning. Lactating their pups were divided into four groups based litter size intake. Sequencing 16S rRNA gene revealed predominance Proteobacteria, Firmicutes, Actinobacteriota phyla. Offspring exhibited clustering tendencies with varying genus abundance. Additionally, led increased levels butyrate acid faeces (> +30%, p > 0.05). These findings show that period be a window opportunity program through modulation.
Language: Английский
Citations
0
Current Issues in Molecular Biology, Journal Year: 2025, Volume and Issue: 47(2), P. 127 - 127
Published: Feb. 16, 2025
MicroRNAs play crucial roles in regulating inflammatory responses and disease progression. Since its identification on chromosome 17q11.2 2005, miR-451 has emerged as a key regulator of multiple physiological pathological processes. While role cancer been extensively documented, accumulating evidence reveals miR-451's broader significance conditions through the regulation NF-κB, AMPK, PI3K signaling pathways. This comprehensive review systematically analyzes multifaceted functions diseases, with particular focus ischemia-reperfusion injury, arthritis, acute organ injuries. We present compelling for potential diagnostic biomarker, demonstrating distinctive expression patterns across various biological specimens states. Furthermore, we elucidate how modulates immune cell populations, including microglia activation, macrophage polarization, neutrophil chemotaxis. By integrating current bioinformatic analyses, establish theoretical framework linking molecular mechanisms to therapeutic applications. not only synthesizes understanding diseases but also provides critical insights developing novel tools strategies.
Language: Английский
Citations
0