Human Ageing Genomic Resources - Revision history

Dmitry Dzhagarov: /* THE REJUVENATION ROADMAP */

2024-09-16T18:34:08Z

THE REJUVENATION ROADMAP

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	== [https://www.lifespan.io/road-maps/the-rejuvenation-roadmap/ THE REJUVENATION ROADMAP] ==		== [https://www.lifespan.io/road-maps/the-rejuvenation-roadmap/ THE REJUVENATION ROADMAP] ==

			== The cell rejuvenation atlas ==
			'''SINGULAR (Single-cell RNA-seq Investigation of Rejuvenation Agents and Longevity)''', a cell rejuvenation atlas that provides a unified system biology analysis of diverse rejuvenation strategies across multiple organs at single-cell resolution.<ref>Hodar, J. A., Jung, S., Soudy, M., Barvaux, S., & Del Sol, A. (2024). The cell rejuvenation atlas: leveraging network biology to identify master regulators of rejuvenation strategies. Aging. 16(17), 12168—12190 PMID: 39264584 [https://doi.org/10.18632/aging.206105 DOI: 10.18632/aging.206105]</ref>

			Code for the processing pipeline and auxiliary functions in the workflow is available at https://github.com/jarcoshodar/singularsource.

			SINGULAR is available as a publicly available interactive database at https://singular.lcsb.uni.lu/. Source code for a local install and exploration of the data is available at https://git-r3lab.uni.lu/mohamed.soudy/singular.

	== References ==		== References ==

Dmitry Dzhagarov: /* GenAge */

2024-08-01T10:36:23Z

GenAge

← Older revision		Revision as of 10:36, 1 August 2024
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	=== Aging-related gene sets ===		=== Aging-related gene sets ===
	Functions for aging-related gene sets. All included genes are collected from aging-related literature and manually annotated. All gene sets are divided into ten sub-categories. The species currently listed include humans and mice.<ref>[https://ngdc.cncb.ac.cn/aging/age_related_genes Aging-related gene sets]</ref>		Functions for aging-related gene sets. All included genes are collected from aging-related literature and manually annotated. All gene sets are divided into ten sub-categories. The species currently listed include humans and mice.<ref>[https://ngdc.cncb.ac.cn/aging/age_related_genes Aging-related gene sets]</ref>

			== CodeKeeper™ ==
			[https://bioviva-codekeeper.com '''CodeKeeper'''™] is BioViva's open access database for gene therapy. It is designed for anyone interested in what is happening in the gene therapy space. Advanced tools are available for universities, companies, independent researchers, and anyone else who is interested in understanding or contributing to the state-of-the-art.

	=== Senescence promoting genes ===		=== Senescence promoting genes ===

Dmitry Dzhagarov: /* A metabolic atlas of mouse aging */

2024-06-18T09:20:12Z

A metabolic atlas of mouse aging

← Older revision		Revision as of 09:20, 18 June 2024
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	== [http://mengwanglab.org/atlas Cell Atlas of Worm Aging (CAWA)]		== [http://mengwanglab.org/atlas Cell Atlas of Worm Aging (CAWA)] ==

	<ref>Gao, S.M., Qi, Y., Zhang, Q. et al. Aging atlas reveals cell-type-specific effects of pro-longevity strategies. Nat Aging (2024). https://doi.org/10.1038/s43587-024-00631-1</ref>		<ref>Gao, S.M., Qi, Y., Zhang, Q. et al. Aging atlas reveals cell-type-specific effects of pro-longevity strategies. Nat Aging (2024). https://doi.org/10.1038/s43587-024-00631-1</ref>

Dmitry Dzhagarov: /* A metabolic atlas of mouse aging */

2024-06-18T09:19:24Z

A metabolic atlas of mouse aging

← Older revision		Revision as of 09:19, 18 June 2024
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	<ref>Steven E Pilley, et al., (2024). A metabolic atlas of mouse aging. bioRxiv; doi: https://doi.org/10.1101/2024.05.04.592445</ref>		<ref>Steven E Pilley, et al., (2024). A metabolic atlas of mouse aging. bioRxiv; doi: https://doi.org/10.1101/2024.05.04.592445</ref>


			== [http://mengwanglab.org/atlas Cell Atlas of Worm Aging (CAWA)]

			<ref>Gao, S.M., Qi, Y., Zhang, Q. et al. Aging atlas reveals cell-type-specific effects of pro-longevity strategies. Nat Aging (2024). https://doi.org/10.1038/s43587-024-00631-1</ref>

	== [https://db.cngb.org/cdcp/hlma/ Human Muscle Ageing Cell Atlas (HMA)] ==		== [https://db.cngb.org/cdcp/hlma/ Human Muscle Ageing Cell Atlas (HMA)] ==

Dmitry Dzhagarov: /* Biolearn, an open-source library for biomarkers of aging */

2024-05-10T17:07:25Z

Biolearn, an open-source library for biomarkers of aging

← Older revision		Revision as of 17:07, 10 May 2024
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	3. provision of computational methodologies to assess any harmonized biomarker against unified datasets.		3. provision of computational methodologies to assess any harmonized biomarker against unified datasets.

			== [https://doi.org/10.1101/2024.05.04.592445 A metabolic atlas of mouse aging] ==

			<ref>Steven E Pilley, et al., (2024). A metabolic atlas of mouse aging. bioRxiv; doi: https://doi.org/10.1101/2024.05.04.592445</ref>

	== [https://db.cngb.org/cdcp/hlma/ Human Muscle Ageing Cell Atlas (HMA)] ==		== [https://db.cngb.org/cdcp/hlma/ Human Muscle Ageing Cell Atlas (HMA)] ==

Dmitry Dzhagarov: /* Biolearn, an open-source library for biomarkers of aging */

2024-04-26T11:10:39Z

Biolearn, an open-source library for biomarkers of aging

← Older revision		Revision as of 11:10, 26 April 2024
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	3. provision of computational methodologies to assess any harmonized biomarker against unified datasets.		3. provision of computational methodologies to assess any harmonized biomarker against unified datasets.

			== [https://db.cngb.org/cdcp/hlma/ Human Muscle Ageing Cell Atlas (HMA)] ==
			The Human Muscle Ageing Cell Atlas provides a series of integrated cellular and molecular explanations for sarcopenia and frailty development in advanced ages.<ref>Lai, Y., Ramírez-Pardo, I., Isern, J. et al. (2024). Multimodal cell atlas of the ageing human skeletal muscle. Nature https://doi.org/10.1038/s41586-024-07348-6 </ref><ref>[https://db.cngb.org/cdcp/hlma/ Human Muscle Ageing Cell Atlas (HMA)]</ref>

	== [http://www.thua45.cn/geredb-wp/ Gene Expression Regulation Database (GREDB)] ==		== [http://www.thua45.cn/geredb-wp/ Gene Expression Regulation Database (GREDB)] ==

Dmitry Dzhagarov: /* voyAGEr: free web interface for the analysis of age-related gene expression alterations in human tissues */

2024-04-03T21:00:58Z

voyAGEr: free web interface for the analysis of age-related gene expression alterations in human tissues

← Older revision		Revision as of 21:00, 3 April 2024
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	== voyAGEr: free web interface for the analysis of age-related gene expression alterations in human tissues ==		== voyAGEr: free web interface for the analysis of age-related gene expression alterations in human tissues ==
	'''voyAGEr''' is an online graphical interface to explore age-related gene expression alterations in 49 human tissues.<ref>Schneider A.L., Martins-Silva R., Kaizeler A., Saraiva-Agostinho N., Barbosa-Morais N. (2023). voyAGEr: free web interface for the analysis of age-related gene expression alterations in human tissues. bioRxiv, 521681. [https://doi.org/10.1101/2022.12.22.521681 doi: 10.1101/2022.12.22.521681]</ref>		'''voyAGEr''' is an online graphical interface to explore age-related gene expression alterations in 49 human tissues.<ref>Schneider A.L., Martins-Silva R., Kaizeler A., Saraiva-Agostinho N., Barbosa-Morais N. (2023). voyAGEr: free web interface for the analysis of age-related gene expression alterations in human tissues. bioRxiv, 521681. [https://doi.org/10.1101/2022.12.22.521681 doi: 10.1101/2022.12.22.521681]; eLife 12:RP88623. https://doi.org/10.7554/eLife.88623.3</ref>
	voyAGEr was created to assist researchers with no expertise in bioinformatics, providing a supportive framework for elaborating, testing and refining their hypotheses on the molecular nature of human ageing and its association with pathologies, thereby also aiding in the discovery of novel therapeutic targets. voyAGEr is freely available at https://compbio.imm.medicina.ulisboa.pt/app/voyAGEr.		voyAGEr was created to assist researchers with no expertise in bioinformatics, providing a supportive framework for elaborating, testing and refining their hypotheses on the molecular nature of human ageing and its association with pathologies, thereby also aiding in the discovery of novel therapeutic targets. voyAGEr is freely available at https://compbio.imm.medicina.ulisboa.pt/app/voyAGEr.
	voyAGEr reveals transcriptomic signatures of the known asynchronous ageing between tissues, allowing the observation of tissue-specific age-periods of major transcriptional changes, associated with alterations in different biological pathways, cellular composition, and disease conditions.		voyAGEr reveals transcriptomic signatures of the known asynchronous ageing between tissues, allowing the observation of tissue-specific age-periods of major transcriptional changes, associated with alterations in different biological pathways, cellular composition, and disease conditions.

Dmitry Dzhagarov: /* voyAGEr: free web interface for the analysis of age-related gene expression alterations in human tissues */

2023-12-13T16:47:18Z

voyAGEr: free web interface for the analysis of age-related gene expression alterations in human tissues

← Older revision		Revision as of 16:47, 13 December 2023
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	GereDB is an comprehensive cohort of gene expression regulation relationships curiated from published literatures. Geredb has been continually devepleted for more than 4 years, making it the one of the most trusted and complete collection of gene expression regulation database in the community.<ref>Huang, T., Huang, X., Shi, B. & Yao, M. (2019). GEREDB: Gene expression regulation database curated by mining abstracts from literature. Journal of Bioinformatics and Computational Biology 17, 1950024 https://www.ncbi.nlm.nih.gov/pubmed/31617460</ref>		GereDB is an comprehensive cohort of gene expression regulation relationships curiated from published literatures. Geredb has been continually devepleted for more than 4 years, making it the one of the most trusted and complete collection of gene expression regulation database in the community.<ref>Huang, T., Huang, X., Shi, B. & Yao, M. (2019). GEREDB: Gene expression regulation database curated by mining abstracts from literature. Journal of Bioinformatics and Computational Biology 17, 1950024 https://www.ncbi.nlm.nih.gov/pubmed/31617460</ref>

	== ~~[https://compbio.imm.medicina.ulisboa.pt/app/voyAGEr.~~ voyAGEr: free web interface for the analysis of age-related gene expression alterations in human tissues] ==		== voyAGEr: free web interface for the analysis of age-related gene expression alterations in human tissues ==
	'''voyAGEr''' is an online graphical interface to explore age-related gene expression alterations in 49 human tissues.<ref>Schneider A.L., Martins-Silva R., Kaizeler A., Saraiva-Agostinho N., Barbosa-Morais N. (2023). voyAGEr: free web interface for the analysis of age-related gene expression alterations in human tissues. bioRxiv, 521681. [https://doi.org/10.1101/2022.12.22.521681 doi: 10.1101/2022.12.22.521681]</ref>		'''voyAGEr''' is an online graphical interface to explore age-related gene expression alterations in 49 human tissues.<ref>Schneider A.L., Martins-Silva R., Kaizeler A., Saraiva-Agostinho N., Barbosa-Morais N. (2023). voyAGEr: free web interface for the analysis of age-related gene expression alterations in human tissues. bioRxiv, 521681. [https://doi.org/10.1101/2022.12.22.521681 doi: 10.1101/2022.12.22.521681]</ref>
	voyAGEr was created to assist researchers with no expertise in bioinformatics, providing a supportive framework for elaborating, testing and refining their hypotheses on the molecular nature of human ageing and its association with pathologies, thereby also aiding in the discovery of novel therapeutic targets. voyAGEr is freely available at https://compbio.imm.medicina.ulisboa.pt/app/voyAGEr.		voyAGEr was created to assist researchers with no expertise in bioinformatics, providing a supportive framework for elaborating, testing and refining their hypotheses on the molecular nature of human ageing and its association with pathologies, thereby also aiding in the discovery of novel therapeutic targets. voyAGEr is freely available at https://compbio.imm.medicina.ulisboa.pt/app/voyAGEr.

Dmitry Dzhagarov: /* Gene Expression Regulation Database (GREDB) */

2023-12-13T16:44:51Z

Gene Expression Regulation Database (GREDB)

← Older revision		Revision as of 16:44, 13 December 2023
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	== [http://www.thua45.cn/geredb-wp/ Gene Expression Regulation Database (GREDB)] ==		== [http://www.thua45.cn/geredb-wp/ Gene Expression Regulation Database (GREDB)] ==
	GereDB is an comprehensive cohort of gene expression regulation relationships curiated from published literatures. Geredb has been continually devepleted for more than 4 years, making it the one of the most trusted and complete collection of gene expression regulation database in the community.<ref>Huang, T., Huang, X., Shi, B. & Yao, M. (2019). GEREDB: Gene expression regulation database curated by mining abstracts from literature. Journal of Bioinformatics and Computational Biology 17, 1950024 https://www.ncbi.nlm.nih.gov/pubmed/31617460</ref>		GereDB is an comprehensive cohort of gene expression regulation relationships curiated from published literatures. Geredb has been continually devepleted for more than 4 years, making it the one of the most trusted and complete collection of gene expression regulation database in the community.<ref>Huang, T., Huang, X., Shi, B. & Yao, M. (2019). GEREDB: Gene expression regulation database curated by mining abstracts from literature. Journal of Bioinformatics and Computational Biology 17, 1950024 https://www.ncbi.nlm.nih.gov/pubmed/31617460</ref>

			== [https://compbio.imm.medicina.ulisboa.pt/app/voyAGEr. voyAGEr: free web interface for the analysis of age-related gene expression alterations in human tissues] ==
			'''voyAGEr''' is an online graphical interface to explore age-related gene expression alterations in 49 human tissues.<ref>Schneider A.L., Martins-Silva R., Kaizeler A., Saraiva-Agostinho N., Barbosa-Morais N. (2023). voyAGEr: free web interface for the analysis of age-related gene expression alterations in human tissues. bioRxiv, 521681. [https://doi.org/10.1101/2022.12.22.521681 doi: 10.1101/2022.12.22.521681]</ref>
			voyAGEr was created to assist researchers with no expertise in bioinformatics, providing a supportive framework for elaborating, testing and refining their hypotheses on the molecular nature of human ageing and its association with pathologies, thereby also aiding in the discovery of novel therapeutic targets. voyAGEr is freely available at https://compbio.imm.medicina.ulisboa.pt/app/voyAGEr.
			voyAGEr reveals transcriptomic signatures of the known asynchronous ageing between tissues, allowing the observation of tissue-specific age-periods of major transcriptional changes, associated with alterations in different biological pathways, cellular composition, and disease conditions.

	== GenAge ==		== GenAge ==

Dmitry Dzhagarov: /* HALL: a comprehensive database for human aging and longevity studies */

2023-12-07T08:46:31Z

HALL: a comprehensive database for human aging and longevity studies

← Older revision		Revision as of 08:46, 7 December 2023
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	'''The Human Ageing Genomic Resources (HAGR)''' is a collection of databases and tools designed to help researchers study the genetics of human ageing using modern approaches such as functional genomics, network analyses, systems biology and evolutionary analyses.<ref>[https://genomics.senescence.info Human Ageing Genomic Resources]</ref>		'''The Human Ageing Genomic Resources (HAGR)''' is a collection of databases and tools designed to help researchers study the genetics of human ageing using modern approaches such as functional genomics, network analyses, systems biology and evolutionary analyses.<ref>[https://genomics.senescence.info Human Ageing Genomic Resources]</ref>

	== HALL: a comprehensive database for human aging and longevity studies ==		== [https://ngdc.cncb.ac.cn/hall/index HALL: a comprehensive database for human aging and longevity studies] ==
	Human Aging and Longevity Landscape (HALL), a comprehensive multi-omics repository encompassing a diverse spectrum of human cohorts, spanning from young adults to centenarians. The core objective of HALL is to foster healthy aging by offering an extensive repository of information on biomarkers that gauge the trajectory of human aging. Moreover, the database facilitates the development of diagnostic tools for aging-related conditions and empowers targeted interventions to enhance longevity. HALL is publicly available at https://ngdc.cncb.ac.cn/hall/index.<ref>Li, H., Wu, S., Li, J., Xiong, Z., Yang, K., Ye, W., ... & Zhang, W. (2023). HALL: a comprehensive database for human aging and longevity studies. Nucleic Acids Research, gkad880. [https://doi.org/10.1093/nar/gkad880 DOI: 10.1093/nar/gkad880]</ref><ref>[https://~~ngdc~~.~~cncb~~.ac.~~cn/hall/index HALL]~~</ref>		Human Aging and Longevity Landscape (HALL), a comprehensive multi-omics repository encompassing a diverse spectrum of human cohorts, spanning from young adults to centenarians. The core objective of HALL is to foster healthy aging by offering an extensive repository of information on biomarkers that gauge the trajectory of human aging. Moreover, the database facilitates the development of diagnostic tools for aging-related conditions and empowers targeted interventions to enhance longevity. HALL is publicly available at https://ngdc.cncb.ac.cn/hall/index.<ref>Li, H., Wu, S., Li, J., Xiong, Z., Yang, K., Ye, W., ... & Zhang, W. (2023). HALL: a comprehensive database for human aging and longevity studies. Nucleic Acids Research, gkad880. [https://doi.org/10.1093/nar/gkad880 DOI: 10.1093/nar/gkad880]</ref>

			== [https://Bio-Learn.github.io/ Biolearn, an open-source library for biomarkers of aging] ==
			Identifying and validating biomarkers of aging is pivotal for understanding the aging process and testing longevity interventions.
			Biolearn is an open-source library (freely available at https://Bio-Learn.github.io/) dedicated to the implementation and application of aging biomarkers.<ref>Ying, K., Paulson, S., Perez-Guevara, M., Emamifar, M., Casas Martinez, M., Kwon, D., ... & Gladyshev, V. N. (2023). Biolearn, an open-source library for biomarkers of aging. bioRxiv, 2023-12. https://doi.org/10.1101/2023.12.02.569722</ref>

			'''Biolearn facilitates''':

			1. harmonization of existing aging biomarkers, while presenting a structured framework for novel biomarkers in standardized formats;

			2. unification of public datasets, ensuring coherent structuring and formatting, thus simplifying cross-population validation studies; and

			3. provision of computational methodologies to assess any harmonized biomarker against unified datasets.

	== [http://www.thua45.cn/geredb-wp/ Gene Expression Regulation Database (GREDB)] ==		== [http://www.thua45.cn/geredb-wp/ Gene Expression Regulation Database (GREDB)] ==