EasyMultiProfiler: An Efficient Multi-Omics Data Integration and Analysis Workflow for Microbiome Research Article Swipe
Bingdong Liu
,
Yaxi Liu
,
Shuangbin Xu
,
Qiusheng Wu
,
Dan Wu
,
Li Zhan
,
Yunfei Liao
,
Yiu‐Wing Mai
,
Minghao Zheng
,
Shui Wang
,
Yixin Chen
,
Zhipeng Huang
,
Xiao Luo
,
Zijing Xie
,
Xiaohan Pan
,
Guangchuang Yu
,
Liwei Xie
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1101/2025.04.17.649266
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1101/2025.04.17.649266
Host-microbiome interactions are crucial in maintaining physiological homeostasis and influencing disease progression. While traditional microbiome research, focused on microbial diversity and abundance, provided essential frameworks, the integration of multi-omics approaches established a far more comprehensive, systems-level understanding of microbiome functionality. However, significant methodological challenges in multi-omics data integration remain, including inconsistent sample coverage, heterogeneous data formats, and complex downstream analytical workflows. These challenges impact the reproducibility and reliability of results and underscore the critical requirement for developing standardized, systematic workflows. Thus, we developed the EasyMultiProfiler (EMP) workflow, a streamlined and efficient analytical framework for multi-omics data analysis. EMP provides a comprehensive infrastructure based on the SummarizedExperiment and MultiAssayExperiment classes, creating a unified framework for storing and analyzing omics data. The framework's architecture comprises five interconnected functional modules: data extraction, preparation, support, analysis, and visualization. These modules are smoothly integrated into natural language-style analytical workflows, offering users an efficient and standardized solution for multi-omics analysis. EMP addresses critical challenges in multi-omics data analysis, including data integration, workflow standardization, and result reproducibility. The platform's modular architecture and intuitive interface provide researchers and clinicians with a robust, flexible workflow to systematically extract biologically relevant insights from complex multi-omics datasets.
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2025.04.17.649266
- https://www.biorxiv.org/content/biorxiv/early/2025/04/23/2025.04.17.649266.full.pdf
- OA Status
- green
- Related Works
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- OpenAlex ID
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All OpenAlex metadata
Raw OpenAlex JSON
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- DOI
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https://doi.org/10.1101/2025.04.17.649266Digital Object Identifier
- Title
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EasyMultiProfiler: An Efficient Multi-Omics Data Integration and Analysis Workflow for Microbiome ResearchWork title
- Type
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2025Year of publication
- Publication date
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2025-04-23Full publication date if available
- Authors
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Bingdong Liu, Yaxi Liu, Shuangbin Xu, Qiusheng Wu, Dan Wu, Li Zhan, Yunfei Liao, Yiu‐Wing Mai, Minghao Zheng, Shui Wang, Yixin Chen, Zhipeng Huang, Xiao Luo, Zijing Xie, Xiaohan Pan, Guangchuang Yu, Liwei XieList of authors in order
- Landing page
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https://doi.org/10.1101/2025.04.17.649266Publisher landing page
- PDF URL
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https://www.biorxiv.org/content/biorxiv/early/2025/04/23/2025.04.17.649266.full.pdfDirect link to full text PDF
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YesWhether a free full text is available
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greenOpen access status per OpenAlex
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https://www.biorxiv.org/content/biorxiv/early/2025/04/23/2025.04.17.649266.full.pdfDirect OA link when available
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Workflow, Microbiome, Data integration, Data science, Computational biology, Computer science, Omics, Biology, Bioinformatics, Data mining, DatabaseTop concepts (fields/topics) attached by OpenAlex
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0Total citation count in OpenAlex
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.disease | 10 |
| abstract_inverted_index.extract | 188 |
| abstract_inverted_index.focused | 16 |
| abstract_inverted_index.modular | 172 |
| abstract_inverted_index.modules | 135 |
| abstract_inverted_index.natural | 140 |
| abstract_inverted_index.provide | 177 |
| abstract_inverted_index.remain, | 48 |
| abstract_inverted_index.results | 69 |
| abstract_inverted_index.robust, | 183 |
| abstract_inverted_index.storing | 114 |
| abstract_inverted_index.unified | 111 |
| abstract_inverted_index.However, | 40 |
| abstract_inverted_index.classes, | 108 |
| abstract_inverted_index.creating | 109 |
| abstract_inverted_index.critical | 73, 156 |
| abstract_inverted_index.flexible | 184 |
| abstract_inverted_index.formats, | 55 |
| abstract_inverted_index.insights | 191 |
| abstract_inverted_index.modules: | 126 |
| abstract_inverted_index.offering | 144 |
| abstract_inverted_index.provided | 22 |
| abstract_inverted_index.provides | 98 |
| abstract_inverted_index.relevant | 190 |
| abstract_inverted_index.smoothly | 137 |
| abstract_inverted_index.solution | 150 |
| abstract_inverted_index.support, | 130 |
| abstract_inverted_index.workflow | 165, 185 |
| abstract_inverted_index.addresses | 155 |
| abstract_inverted_index.analysis, | 131, 161 |
| abstract_inverted_index.analysis. | 96, 153 |
| abstract_inverted_index.analyzing | 116 |
| abstract_inverted_index.comprises | 122 |
| abstract_inverted_index.coverage, | 52 |
| abstract_inverted_index.datasets. | 195 |
| abstract_inverted_index.developed | 82 |
| abstract_inverted_index.diversity | 19 |
| abstract_inverted_index.efficient | 90, 147 |
| abstract_inverted_index.essential | 23 |
| abstract_inverted_index.framework | 92, 112 |
| abstract_inverted_index.including | 49, 162 |
| abstract_inverted_index.interface | 176 |
| abstract_inverted_index.intuitive | 175 |
| abstract_inverted_index.microbial | 18 |
| abstract_inverted_index.research, | 15 |
| abstract_inverted_index.workflow, | 86 |
| abstract_inverted_index.abundance, | 21 |
| abstract_inverted_index.analytical | 59, 91, 142 |
| abstract_inverted_index.approaches | 29 |
| abstract_inverted_index.challenges | 43, 62, 157 |
| abstract_inverted_index.clinicians | 180 |
| abstract_inverted_index.developing | 76 |
| abstract_inverted_index.downstream | 58 |
| abstract_inverted_index.functional | 125 |
| abstract_inverted_index.integrated | 138 |
| abstract_inverted_index.microbiome | 14, 38 |
| abstract_inverted_index.platform's | 171 |
| abstract_inverted_index.systematic | 78 |
| abstract_inverted_index.underscore | 71 |
| abstract_inverted_index.workflows, | 143 |
| abstract_inverted_index.workflows. | 60, 79 |
| abstract_inverted_index.established | 30 |
| abstract_inverted_index.extraction, | 128 |
| abstract_inverted_index.framework's | 120 |
| abstract_inverted_index.frameworks, | 24 |
| abstract_inverted_index.homeostasis | 7 |
| abstract_inverted_index.influencing | 9 |
| abstract_inverted_index.integration | 26, 47 |
| abstract_inverted_index.maintaining | 5 |
| abstract_inverted_index.multi-omics | 28, 45, 94, 152, 159, 194 |
| abstract_inverted_index.reliability | 67 |
| abstract_inverted_index.requirement | 74 |
| abstract_inverted_index.researchers | 178 |
| abstract_inverted_index.significant | 41 |
| abstract_inverted_index.streamlined | 88 |
| abstract_inverted_index.traditional | 13 |
| abstract_inverted_index.architecture | 121, 173 |
| abstract_inverted_index.biologically | 189 |
| abstract_inverted_index.inconsistent | 50 |
| abstract_inverted_index.integration, | 164 |
| abstract_inverted_index.interactions | 1 |
| abstract_inverted_index.preparation, | 129 |
| abstract_inverted_index.progression. | 11 |
| abstract_inverted_index.standardized | 149 |
| abstract_inverted_index.comprehensive | 100 |
| abstract_inverted_index.heterogeneous | 53 |
| abstract_inverted_index.physiological | 6 |
| abstract_inverted_index.standardized, | 77 |
| abstract_inverted_index.systems-level | 35 |
| abstract_inverted_index.understanding | 36 |
| abstract_inverted_index.comprehensive, | 34 |
| abstract_inverted_index.functionality. | 39 |
| abstract_inverted_index.infrastructure | 101 |
| abstract_inverted_index.interconnected | 124 |
| abstract_inverted_index.language-style | 141 |
| abstract_inverted_index.methodological | 42 |
| abstract_inverted_index.systematically | 187 |
| abstract_inverted_index.visualization. | 133 |
| abstract_inverted_index.Host-microbiome | 0 |
| abstract_inverted_index.reproducibility | 65 |
| abstract_inverted_index.reproducibility. | 169 |
| abstract_inverted_index.standardization, | 166 |
| abstract_inverted_index.EasyMultiProfiler | 84 |
| abstract_inverted_index.MultiAssayExperiment | 107 |
| abstract_inverted_index.SummarizedExperiment | 105 |
| cited_by_percentile_year | |
| countries_distinct_count | 0 |
| institutions_distinct_count | 17 |
| citation_normalized_percentile.value | 0.13174767 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |