iSMOD: an integrative browser for image-based single-cell multi-omics data Article Swipe
Weihang Zhang
,
Jinli Suo
,
Yan Yan
,
Runzhao Yang
,
Yi-Ming Lu
,
Yiqi Jin
,
Shuochen Gao
,
Shao Li
,
Juntao Gao
,
Michael Q. Zhang
,
Qionghai Dai
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1093/nar/gkad580
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1093/nar/gkad580
Genomic and transcriptomic image data, represented by DNA and RNA fluorescence in situ hybridization (FISH), respectively, together with proteomic data, particularly that related to nuclear proteins, can help elucidate gene regulation in relation to the spatial positions of chromatins, messenger RNAs, and key proteins. However, methods for image-based multi-omics data collection and analysis are lacking. To this end, we aimed to develop the first integrative browser called iSMOD (image-based Single-cell Multi-omics Database) to collect and browse comprehensive FISH and nucleus proteomics data based on the title, abstract, and related experimental figures, which integrates multi-omics studies focusing on the key players in the cell nucleus from 20 000+ (still growing) published papers. We have also provided several exemplar demonstrations to show iSMOD’s wide applications—profiling multi-omics research to reveal the molecular target for diseases; exploring the working mechanism behind biological phenomena using multi-omics interactions, and integrating the 3D multi-omics data in a virtual cell nucleus. iSMOD is a cornerstone for delineating a global view of relevant research to enable the integration of scattered data and thus provides new insights regarding the missing components of molecular pathway mechanisms and facilitates improved and efficient scientific research.
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- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/nar/gkad580
- https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad580/50875702/gkad580.pdf
- OA Status
- gold
- Cited By
- 3
- References
- 103
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4384119489
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Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4384119489Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1093/nar/gkad580Digital Object Identifier
- Title
-
iSMOD: an integrative browser for image-based single-cell multi-omics dataWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
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2023Year of publication
- Publication date
-
2023-07-13Full publication date if available
- Authors
-
Weihang Zhang, Jinli Suo, Yan Yan, Runzhao Yang, Yi-Ming Lu, Yiqi Jin, Shuochen Gao, Shao Li, Juntao Gao, Michael Q. Zhang, Qionghai DaiList of authors in order
- Landing page
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https://doi.org/10.1093/nar/gkad580Publisher landing page
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https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad580/50875702/gkad580.pdfDirect link to full text PDF
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad580/50875702/gkad580.pdfDirect OA link when available
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Biology, Omics, Proteomics, Computational biology, Data integration, Bioinformatics, Data science, Computer science, Gene, Genetics, Data miningTop concepts (fields/topics) attached by OpenAlex
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3Total citation count in OpenAlex
- Citations by year (recent)
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2025: 1, 2024: 2Per-year citation counts (last 5 years)
- References (count)
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103Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.browser | 66 |
| abstract_inverted_index.collect | 74 |
| abstract_inverted_index.develop | 62 |
| abstract_inverted_index.methods | 46 |
| abstract_inverted_index.missing | 180 |
| abstract_inverted_index.nuclear | 25 |
| abstract_inverted_index.nucleus | 80, 104 |
| abstract_inverted_index.papers. | 111 |
| abstract_inverted_index.pathway | 184 |
| abstract_inverted_index.players | 100 |
| abstract_inverted_index.related | 23, 89 |
| abstract_inverted_index.several | 116 |
| abstract_inverted_index.spatial | 36 |
| abstract_inverted_index.studies | 95 |
| abstract_inverted_index.virtual | 151 |
| abstract_inverted_index.working | 135 |
| abstract_inverted_index.Abstract | 0 |
| abstract_inverted_index.However, | 45 |
| abstract_inverted_index.analysis | 53 |
| abstract_inverted_index.exemplar | 117 |
| abstract_inverted_index.figures, | 91 |
| abstract_inverted_index.focusing | 96 |
| abstract_inverted_index.growing) | 109 |
| abstract_inverted_index.improved | 188 |
| abstract_inverted_index.insights | 177 |
| abstract_inverted_index.lacking. | 55 |
| abstract_inverted_index.nucleus. | 153 |
| abstract_inverted_index.provided | 115 |
| abstract_inverted_index.provides | 175 |
| abstract_inverted_index.relation | 33 |
| abstract_inverted_index.relevant | 164 |
| abstract_inverted_index.research | 125, 165 |
| abstract_inverted_index.together | 17 |
| abstract_inverted_index.Database) | 72 |
| abstract_inverted_index.abstract, | 87 |
| abstract_inverted_index.diseases; | 132 |
| abstract_inverted_index.efficient | 190 |
| abstract_inverted_index.elucidate | 29 |
| abstract_inverted_index.exploring | 133 |
| abstract_inverted_index.iSMOD’s | 121 |
| abstract_inverted_index.mechanism | 136 |
| abstract_inverted_index.messenger | 40 |
| abstract_inverted_index.molecular | 129, 183 |
| abstract_inverted_index.phenomena | 139 |
| abstract_inverted_index.positions | 37 |
| abstract_inverted_index.proteins, | 26 |
| abstract_inverted_index.proteins. | 44 |
| abstract_inverted_index.proteomic | 19 |
| abstract_inverted_index.published | 110 |
| abstract_inverted_index.regarding | 178 |
| abstract_inverted_index.research. | 192 |
| abstract_inverted_index.scattered | 171 |
| abstract_inverted_index.biological | 138 |
| abstract_inverted_index.collection | 51 |
| abstract_inverted_index.components | 181 |
| abstract_inverted_index.integrates | 93 |
| abstract_inverted_index.mechanisms | 185 |
| abstract_inverted_index.proteomics | 81 |
| abstract_inverted_index.regulation | 31 |
| abstract_inverted_index.scientific | 191 |
| abstract_inverted_index.Multi-omics | 71 |
| abstract_inverted_index.Single-cell | 70 |
| abstract_inverted_index.chromatins, | 39 |
| abstract_inverted_index.cornerstone | 157 |
| abstract_inverted_index.delineating | 159 |
| abstract_inverted_index.facilitates | 187 |
| abstract_inverted_index.image-based | 48 |
| abstract_inverted_index.integrating | 144 |
| abstract_inverted_index.integration | 169 |
| abstract_inverted_index.integrative | 65 |
| abstract_inverted_index.multi-omics | 49, 94, 124, 141, 147 |
| abstract_inverted_index.represented | 6 |
| abstract_inverted_index.(image-based | 69 |
| abstract_inverted_index.experimental | 90 |
| abstract_inverted_index.fluorescence | 11 |
| abstract_inverted_index.particularly | 21 |
| abstract_inverted_index.comprehensive | 77 |
| abstract_inverted_index.hybridization | 14 |
| abstract_inverted_index.interactions, | 142 |
| abstract_inverted_index.respectively, | 16 |
| abstract_inverted_index.demonstrations | 118 |
| abstract_inverted_index.transcriptomic | 3 |
| abstract_inverted_index.applications—profiling | 123 |
| cited_by_percentile_year.max | 96 |
| cited_by_percentile_year.min | 91 |
| corresponding_author_ids | https://openalex.org/A5102943651, https://openalex.org/A5058814283, https://openalex.org/A5080722708 |
| countries_distinct_count | 2 |
| institutions_distinct_count | 11 |
| corresponding_institution_ids | https://openalex.org/I4210148697, https://openalex.org/I99065089 |
| citation_normalized_percentile.value | 0.69322866 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |