Publications
Selected publications
- How ageing processes influence cancer (Journal article - 2013)
- Insights into the evolution of longevity from the bowhead whale genome. (Journal article - 2015)
- A Network Pharmacology Approach Reveals New Candidate Caloric Restriction Mimetics in C. Elegans (Journal article - 2016)
- An integrative analysis of the age-associated multi-omic landscape across cancers (Journal article - 2021)
- A multidimensional systems biology analysis of cellular senescence in aging and disease (Journal article - 2020)
- Cellular reprogramming and the rise of rejuvenation biotech (Journal article - 2022)
- Gene co-expression analysis for functional classification and gene-disease predictions. (Journal article - 2018)
- Human Ageing Genomic Resources: new and updated databases (Journal article - 2017)
2024
Sex-specific insights into drug-induced lifespan extension and weight loss in mice
Predicting Mouse Lifespan-Extending Chemical Compounds with Machine Learning
Mosaic Regulation of Stress Pathways Underlies Senescent Cell Heterogeneity
Leonard Hayflick (1928-2024).
West, M. D., de Magalhães, J. P., & Olshansky, S. J. (2024). Leonard Hayflick (1928-2024).. Nature aging. doi:10.1038/s43587-024-00720-1
Somatic mutations in human ageing: New insights from DNA sequencing and inherited mutations.
Chatsirisupachai, K., & de Magalhães, J. P. (2024). Somatic mutations in human ageing: New insights from DNA sequencing and inherited mutations.. Ageing research reviews, 96, 102268. doi:10.1016/j.arr.2024.102268
Distinguishing between driver and passenger mechanisms of aging.
de Magalhães, J. P. (2024). Distinguishing between driver and passenger mechanisms of aging.. Nature genetics, 56(2), 204-211. doi:10.1038/s41588-023-01627-0
Human Ageing Genomic Resources: updates on key databases in ageing research.
de Magalhães, J. P., Abidi, Z., Dos Santos, G. A., Avelar, R. A., Barardo, D., Chatsirisupachai, K., . . . To, P. K. P. (2024). Human Ageing Genomic Resources: updates on key databases in ageing research.. Nucleic acids research, 52(D1), D900-D908. doi:10.1093/nar/gkad927
The longevity bottleneck hypothesis: Could dinosaurs have shaped ageing in present-day mammals?
de Magalhães, J. P. (2024). The longevity bottleneck hypothesis: Could dinosaurs have shaped ageing in present-day mammals?. BioEssays : news and reviews in molecular, cellular and developmental biology, 46(1), e2300098. doi:10.1002/bies.202300098
2023
scDiffCom: a tool for differential analysis of cell-cell interactions provides a mouse atlas of aging changes in intercellular communication.
Lagger, C., Ursu, E., Equey, A., Avelar, R. A., Pisco, A. O., Tacutu, R., & de Magalhães, J. P. (2023). scDiffCom: a tool for differential analysis of cell-cell interactions provides a mouse atlas of aging changes in intercellular communication.. Nature aging, 3(11), 1446-1461. doi:10.1038/s43587-023-00514-x
Transcriptomic analysis reveals a tissue-specific loss of identity during ageing and cancer.
Dos Santos, G. A., Chatsirisupachai, K., Avelar, R. A., & de Magalhães, J. P. (2023). Transcriptomic analysis reveals a tissue-specific loss of identity during ageing and cancer.. BMC genomics, 24(1), 644. doi:10.1186/s12864-023-09756-w
m7GHub V2.0: an updated database for decoding the N7-methylguanosine (m<SUP>7</SUP>G) epitranscriptome
Wang, X., Zhang, Y., Chen, K., Liang, Z., Ma, J., Xia, R., . . . Song, B. (2023). m7GHub V2.0: an updated database for decoding the N7-methylguanosine (m<SUP>7</SUP>G) epitranscriptome. NUCLEIC ACIDS RESEARCH. doi:10.1093/nar/gkad789
Transcriptomics age acceleration in prolonged treated HIV infection
Mikaeloff, F., Gelpi, M., Escos, A., Knudsen, A. D., Hogh, J., Benfield, T., . . . Neogi, U. (2023). Transcriptomics age acceleration in prolonged treated HIV infection. AGING CELL, 22(10). doi:10.1111/acel.13951
m6A-TSHub: Unveiling the Context-specific m<sup>6</sup>A Methylation and m<sup>6</sup>A-affecting Mutations in 23 Human Tissues.
Song, B., Huang, D., Zhang, Y., Wei, Z., Su, J., Pedro de Magalhães, J., . . . Chen, K. (2023). m6A-TSHub: Unveiling the Context-specific m<sup>6</sup>A Methylation and m<sup>6</sup>A-affecting Mutations in 23 Human Tissues.. Genomics, proteomics & bioinformatics, 21(4), 678-694. doi:10.1016/j.gpb.2022.09.001
Predicting lifespan-extending chemical compounds for C. elegans with machine learning and biologically interpretable features
Ribeiro, C., Farmer, C. K., de Magalhaes, J. P., & Freitas, A. A. (2023). Predicting lifespan-extending chemical compounds for C. elegans with machine learning and biologically interpretable features. AGING-US, 15(13), 6073-6099. Retrieved from https://www.webofscience.com/
Interpretable Ensembles of Classifiers for Uncertain Data With Bioinformatics Applications
Maia, M. R. D. H., Plastino, A., Freitas, A., & de Magalhaes, J. P. (2023). Interpretable Ensembles of Classifiers for Uncertain Data With Bioinformatics Applications. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 20(3), 1829-1841. doi:10.1109/TCBB.2022.3218588
Epigenetic fidelity in complex biological systems and implications for ageing
Ageing as a software design flaw
de Magalhaes, J. P. (2023). Ageing as a software design flaw. GENOME BIOLOGY, 24(1). doi:10.1186/s13059-023-02888-y
Rilmenidine extends lifespan and healthspan in<i> Caenorhabditis</i><i> elegans</i> via a nischarin I1-imidazoline receptor
Bennett, D. F., Goyala, A., Statzer, C., Beckett, C. W., Tyshkovskiy, A., Gladyshev, V. N., . . . de Magalhaes, J. P. (2023). Rilmenidine extends lifespan and healthspan in<i> Caenorhabditis</i><i> elegans</i> via a nischarin I1-imidazoline receptor. AGING CELL, 22(2). doi:10.1111/acel.13774
RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication
Song, B., Wang, X., Liang, Z., Ma, J., Huang, D., Wang, Y., . . . Wei, Z. (2023). RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication. NUCLEIC ACIDS RESEARCH, 51(D1), D1388-D1396. doi:10.1093/nar/gkac750
2022
GeneFriends: gene co-expression databases and tools for humans and model organisms
Raina, P., Guinea, R., Chatsirisupachai, K., Lopes, I., Farooq, Z., Guinea, C., . . . de Magalhaes, J. P. (2022). GeneFriends: gene co-expression databases and tools for humans and model organisms. NUCLEIC ACIDS RESEARCH. doi:10.1093/nar/gkac1031
Predicting Lifespan-Extending Chemical Compounds with Machine Learning and Biologically Interpretable Features
DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology.
Zhang, Y., Jiang, J., Ma, J., Wei, Z., Wang, Y., Song, B., . . . Chen, K. (2022). DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology.. Nucleic acids research, gkac1061. doi:10.1093/nar/gkac1061
Intercellular communication analysis of the human retinal pigment epithelial and choroidal cells predicts pathways associated with aging, cellular senescence and age-related macular degeneration
Dhirachaikulpanich, D., Lagger, C., Chatsirisupachai, K., de Magalhaes, J. P., & Paraoan, L. (2022). Intercellular communication analysis of the human retinal pigment epithelial and choroidal cells predicts pathways associated with aging, cellular senescence and age-related macular degeneration. FRONTIERS IN AGING NEUROSCIENCE, 14. doi:10.3389/fnagi.2022.1016293
Age-associated differences in the cancer molecular landscape.
Chatsirisupachai, K., Lagger, C., & de Magalhães, J. P. (2022). Age-associated differences in the cancer molecular landscape.. Trends in cancer, 8(11), 962-971. doi:10.1016/j.trecan.2022.06.007
Skin Aging in Long-Lived Naked Mole-Rats Is Accompanied by Increased Expression of Longevity-Associated and Tumor Suppressor Genes
Fatima, I., Chen, G., Botchkareva, N. V., Sharov, A. A., Thornton, D., Wilkinson, H. N., . . . Botchkarev, V. A. (2022). Skin Aging in Long-Lived Naked Mole-Rats Is Accompanied by Increased Expression of Longevity-Associated and Tumor Suppressor Genes. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 142(11), 2853-+. doi:10.1016/j.jid.2022.04.028
Geographic encoding of transcripts enabled high-accuracy and isoform-aware deep learning of RNA methylation
Huang, D., Chen, K., Song, B., Wei, Z., Su, J., Coenen, F., . . . Meng, J. (2022). Geographic encoding of transcripts enabled high-accuracy and isoform-aware deep learning of RNA methylation. NUCLEIC ACIDS RESEARCH, 50(18), 10290-10310. doi:10.1093/nar/gkac830
WHISTLE server: A high-accuracy genomic coordinate-based machine learning platform for RNA modification prediction
Liu, L., Song, B., Chen, K., Zhang, Y., de Magalhaes, J. P., Rigden, D. J., . . . Wei, Z. (2022). WHISTLE server: A high-accuracy genomic coordinate-based machine learning platform for RNA modification prediction. METHODS, 203, 378-382. doi:10.1016/j.ymeth.2021.07.003
Cellular reprogramming and the rise of rejuvenation biotech
de Magalhaes, J. P., & Ocampo, A. (2022). Cellular reprogramming and the rise of rejuvenation biotech. TRENDS IN BIOTECHNOLOGY, 40(6), 639-642. doi:10.1016/j.tibtech.2022.01.011
Single-cell gene regulation across aging tissues
Lagger, C., & de Magalhaes, J. P. (2022). Single-cell gene regulation across aging tissues. NATURE AGING, 2(6), 468-470. doi:10.1038/s43587-022-00238-4
Identifying Novel Osteoarthritis-Associated Genes in Human Cartilage Using a Systematic Meta-Analysis and a Multi-Source Integrated Network
Shorter, E., Avelar, R., Zachariou, M., Spyrou, G. M., Raina, P., Smagul, A., . . . Poulet, B. (n.d.). Identifying Novel Osteoarthritis-Associated Genes in Human Cartilage Using a Systematic Meta-Analysis and a Multi-Source Integrated Network. International Journal of Molecular Sciences, 23(8), 4395. doi:10.3390/ijms23084395
Targeting aging mechanisms: pharmacological perspectives
Moskalev, A., Guvatova, Z., Lopes, I. D. A., Beckett, C. W., Kennedy, B. K., De Magalhaes, J. P., & Makarov, A. A. (2022). Targeting aging mechanisms: pharmacological perspectives. TRENDS IN ENDOCRINOLOGY AND METABOLISM, 33(4), 266-280. doi:10.1016/j.tem.2022.01.007
Every gene can (and possibly will) be associated with cancer
de Magalhaes, J. P. (2022). Every gene can (and possibly will) be associated with cancer. TRENDS IN GENETICS, 38(3), 216-217. doi:10.1016/j.tig.2021.09.005
Positive Selection and Enhancer Evolution Shaped Lifespan and Body Mass in Great Apes
Tejada-Martinez, D., Avelar, R. A., Lopes, I., Zhang, B., Novoa, G., de Magalhaes, J. P., & Trizzino, M. (2022). Positive Selection and Enhancer Evolution Shaped Lifespan and Body Mass in Great Apes. MOLECULAR BIOLOGY AND EVOLUTION, 39(2). doi:10.1093/molbev/msab369
Sex-specific aging in animals: Perspective and future directions
Bronikowski, A. M., Meisel, R. P., Biga, P. R., Walters, J. R., Mank, J. E., Larschan, E., . . . Riddle, N. C. (2022). Sex-specific aging in animals: Perspective and future directions. AGING CELL, 21(2). doi:10.1111/acel.13542
m6A-TSHub: unveiling the context-specific m6A methylation and m6A-affecting mutations in 23 human tissues
Trans cohort metabolic reprogramming towards glutaminolysis in long-term successfully treated HIV-infection
Mikaeloff, F., Akusjarvi, S. S., Ikomey, G. M., Krishnan, S., Sperk, M., Gupta, S., . . . Neogi, U. (2022). Trans cohort metabolic reprogramming towards glutaminolysis in long-term successfully treated HIV-infection. COMMUNICATIONS BIOLOGY, 5(1). doi:10.1038/s42003-021-02985-3
m5C-Atlas: a comprehensive database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome.
Ma, J., Song, B., Wei, Z., Huang, D., Zhang, Y., Su, J., . . . Chen, K. (2022). m5C-Atlas: a comprehensive database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome.. Nucleic acids research, 50(D1), D196-D203. doi:10.1093/nar/gkab1075
Machine learning-based predictions of dietary restriction associations across ageing-related genes
Magdaleno, G. D. V., Bespalov, V., Zheng, Y., Freitas, A. A., & de Magalhaes, J. P. (2022). Machine learning-based predictions of dietary restriction associations across ageing-related genes. BMC BIOINFORMATICS, 23(1). doi:10.1186/s12859-021-04523-8
2021
ConsRM: collection and large-scale prediction of the evolutionarily conserved RNA methylation sites, with implications for the functional epitranscriptome
Song, B., Chen, K., Tang, Y., Wei, Z., Su, J., de Magalhaes, J. P., . . . Meng, J. (2021). ConsRM: collection and large-scale prediction of the evolutionarily conserved RNA methylation sites, with implications for the functional epitranscriptome. BRIEFINGS IN BIOINFORMATICS, 22(6). doi:10.1093/bib/bbab088
Rilmenidine mimics caloric restriction via the nischarin I1-imidazoline receptor to extend lifespan in<i>C. elegans</i>
Bennett, D., Goyala, A., Statzer, C., Beckett, C., Tyshkovskiy, A., Gladyshev, V., . . . de Magalhães, J. P. (2021). Rilmenidine mimics caloric restriction via the nischarin I1-imidazoline receptor to extend lifespan in<i>C. elegans</i>. doi:10.1101/2021.10.13.464294
Targeting immune dysfunction in aging
Borgoni, S., Kudryashova, K. S., Burka, K., & de Magalhaes, J. P. (2021). Targeting immune dysfunction in aging. AGEING RESEARCH REVIEWS, 70. doi:10.1016/j.arr.2021.101410
The hoverfly and the wasp: A critique of the hallmarks of aging as a paradigm
Gems, D., & de Magalha, P. J. (2021). The hoverfly and the wasp: A critique of the hallmarks of aging as a paradigm. AGEING RESEARCH REVIEWS, 70. doi:10.1016/j.arr.2021.101407
The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS (vol 118, e2010632118, 2021)
Orkin, J. D., Montague, M. J., Tejada-Martinez, D., de Manuel, M., del Campo, J., Hernandez, S. C., . . . Melin, A. D. (2021). The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS (vol 118, e2010632118, 2021). PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 118(34). doi:10.1073/pnas.2112613118
scAgeCom: a murine atlas of age-related changes in intercellular communication inferred with the package scDiffCom
Machine-learning-based predictions of caloric restriction associations across ageing-related genes
Longevity pharmacology comes of age
de Magalhaes, J. P. (2021). Longevity pharmacology comes of age. DRUG DISCOVERY TODAY, 26(7), 1559-1562. doi:10.1016/j.drudis.2021.02.015
Attention-based multi-label neural networks for integrated prediction and interpretation of twelve widely occurring RNA modifications
Song, Z., Huang, D., Song, B., Chen, K., Song, Y., Liu, G., . . . Meng, J. (2021). Attention-based multi-label neural networks for integrated prediction and interpretation of twelve widely occurring RNA modifications. NATURE COMMUNICATIONS, 12(1). doi:10.1038/s41467-021-24313-3
Evolution, structure and emerging roles of C1ORF112 in DNA replication, DNA damage responses, and cancer
Edogbanya, J., Tejada-Martinez, D., Jones, N. J., Jaiswal, A., Bell, S., Cordeiro, R., . . . de Magalhaes, J. P. (2021). Evolution, structure and emerging roles of C1ORF112 in DNA replication, DNA damage responses, and cancer. CELLULAR AND MOLECULAR LIFE SCIENCES, 78(9), 4365-4376. doi:10.1007/s00018-021-03789-8
An integrative analysis of the age-associated multi-omic landscape across cancers
Chatsirisupachai, K., Lesluyes, T., Paraoan, L., Van Loo, P., & de Magalhães, J. P. (2021). An integrative analysis of the age-associated multi-omic landscape across cancers. Nature Communications, 12(1). doi:10.1038/s41467-021-22560-y
Winter is coming: the future of cryopreservation
Bojic, S., Murray, A., Bentley, B. L., Spindler, R., Pawlik, P., Cordeiro, J. L., . . . de Magalhaes, J. P. (2021). Winter is coming: the future of cryopreservation. BMC BIOLOGY, 19(1). doi:10.1186/s12915-021-00976-8
Positive selection and gene duplications in tumour suppressor genes reveal clues about how cetaceans resist cancer
Tejada-Martinez, D., de Magalhaes, J. P., & Opazo, J. C. (2021). Positive selection and gene duplications in tumour suppressor genes reveal clues about how cetaceans resist cancer. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 288(1945). doi:10.1098/rspb.2020.2592
The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS
Orkin, J. D., Montague, M. J., Tejada-Martinez, D., de Manuel, M., del Campo, J., Hernandez, S. C., . . . Melin, A. D. (2021). The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 118(7). doi:10.1073/pnas.2010632118
Ageing transcriptome meta-analysis reveals similarities and differences between key mammalian tissues
Palmer, D., Fabris, F., Doherty, A., Freitas, A. A., & de Magalhaes, J. P. (2021). Ageing transcriptome meta-analysis reveals similarities and differences between key mammalian tissues. AGING-US, 13(3), 3313-3341. Retrieved from https://www.webofscience.com/
Gene Size Matters: An Analysis of Gene Length in the Human Genome
Lopes, I., Altab, G., Raina, P., & de Magalhaes, J. P. (2021). Gene Size Matters: An Analysis of Gene Length in the Human Genome. FRONTIERS IN GENETICS, 12. doi:10.3389/fgene.2021.559998
RMDisease: a database of genetic variants that affect RNA modifications, with implications for epitranscriptome pathogenesis
Chen, K., Song, B., Tang, Y., Wei, Z., Xu, Q., Su, J., . . . Meng, J. (2021). RMDisease: a database of genetic variants that affect RNA modifications, with implications for epitranscriptome pathogenesis. NUCLEIC ACIDS RESEARCH, 49(D1), D1396-D1404. doi:10.1093/nar/gkaa790
m<SUP>6</SUP>A-Atlas: a comprehensive knowledgebase for unraveling the <i>N</i><SUP>6</SUP>-methyladenosine (m<SUP>6</SUP>A) epitranscriptome
Tang, Y., Chen, K., Song, B., Ma, J., Wu, X., Xu, Q., . . . Meng, J. (2021). m<SUP>6</SUP>A-Atlas: a comprehensive knowledgebase for unraveling the <i>N</i><SUP>6</SUP>-methyladenosine (m<SUP>6</SUP>A) epitranscriptome. NUCLEIC ACIDS RESEARCH, 49(D1), D134-D143. doi:10.1093/nar/gkaa692
2020
SynergyAge, a curated database for synergistic and antagonistic interactions of longevity-associated genes
Bunu, G., Toren, D., Ion, C. -F., Barardo, D., Sârghie, L., Grigore, L. G., . . . Tacutu, R. (2020). SynergyAge, a curated database for synergistic and antagonistic interactions of longevity-associated genes. Scientific Data, 7(1). doi:10.1038/s41597-020-00710-z
A method for the permeabilization of live <i>Drosophila melanogaster</i> larvae to small molecules and cryoprotectants
Murray, A., Palmer, D., Bennett, D., Dwarampudi, V., & Pedro de Magalhaes, J. (2020). A method for the permeabilization of live <i>Drosophila melanogaster</i> larvae to small molecules and cryoprotectants. FLY, 14(1-4), 29-33. doi:10.1080/19336934.2020.1724051
Vulnerability of progeroid smooth muscle cells to biomechanical forces is mediated by MMP13
Pitrez, P. R., Estronca, L., Monteiro, L. M., Colell, G., Vazao, H., Santinha, D., . . . Ferreira, L. (2020). Vulnerability of progeroid smooth muscle cells to biomechanical forces is mediated by MMP13. NATURE COMMUNICATIONS, 11(1). doi:10.1038/s41467-020-17901-2
A scan for genes associated with cancer mortality and longevity in pedigree dog breeds.
Doherty, A., Lopes, I., Ford, C. T., Monaco, G., Guest, P., & de Magalhães, J. P. (2020). A scan for genes associated with cancer mortality and longevity in pedigree dog breeds.. Mammalian genome : official journal of the International Mammalian Genome Society. doi:10.1007/s00335-020-09845-1
Biohorology and biomarkers of aging: Current state-of-the-art, challenges and opportunities
Galkin, F., Mamoshina, P., Aliper, A., de Magalhaes, J. P., Gladyshev, V. N., & Zhavoronkov, A. (2020). Biohorology and biomarkers of aging: Current state-of-the-art, challenges and opportunities. AGEING RESEARCH REVIEWS, 60. doi:10.1016/j.arr.2020.101050
m7GHub: deciphering the location, regulation and pathogenesis of internal mRNA N7-methylguanosine (m7G) sites in human
Song, B., Tang, Y., Chen, K., Wei, Z., Rong, R., Lu, Z., . . . Meng, J. (2020). m7GHub: deciphering the location, regulation and pathogenesis of internal mRNA N7-methylguanosine (m7G) sites in human. Bioinformatics, 36(11), 3528-3536. doi:10.1093/bioinformatics/btaa178
Comparing enrichment analysis and machine learning for identifying gene properties that discriminate between gene classes
Fabris, F., Palmer, D., de Magalhaes, J. P., & Freitas, A. A. (2020). Comparing enrichment analysis and machine learning for identifying gene properties that discriminate between gene classes. BRIEFINGS IN BIOINFORMATICS, 21(3), 803-814. doi:10.1093/bib/bbz028
A multidimensional systems biology analysis of cellular senescence in aging and disease
Avelar, R. A., Ortega, J. G., Tacutu, R., Tyler, E. J., Bennett, D., Binetti, P., . . . de Magalhaes, J. P. (2020). A multidimensional systems biology analysis of cellular senescence in aging and disease. Genome Biology, 21(1). doi:10.1186/s13059-020-01990-9
Using deep learning to associate human genes with age-related diseases
Fabris, F., Palmer, D., Salama, K. M., de Magalhaes, J. P., & Freitas, A. A. (2020). Using deep learning to associate human genes with age-related diseases. BIOINFORMATICS, 36(7), 2202-2208. doi:10.1093/bioinformatics/btz887
miRNA-31 Improves Cognition and Abolishes Amyloid-β Pathology by Targeting APP and BACE1 in an Animal Model of Alzheimer's Disease
Barros-Viegas, A. T., Carmona, V., Ferreiro, E., Guedes, J., Cardoso, A. M., Cunha, P., . . . Cardoso, A. L. (2020). miRNA-31 Improves Cognition and Abolishes Amyloid-β Pathology by Targeting APP and BACE1 in an Animal Model of Alzheimer's Disease. MOLECULAR THERAPY-NUCLEIC ACIDS, 19, 1219-1236. doi:10.1016/j.omtn.2020.01.010
Ageing-associated changes in the expression of lncRNAs in human tissues reflect a transcriptional modulation in ageing pathways
Marttila, S., Chatsirisupachai, K., Palmer, D., & de Magalhaes, J. P. (2020). Ageing-associated changes in the expression of lncRNAs in human tissues reflect a transcriptional modulation in ageing pathways. MECHANISMS OF AGEING AND DEVELOPMENT, 185. doi:10.1016/j.mad.2019.111177
Bioinformatics approaches for deciphering the epitranscriptome: Recent progress and emerging topics
Liu, L., Song, B., Ma, J., Song, Y., Zhang, S. -Y., Tang, Y., . . . Meng, J. (2020). Bioinformatics approaches for deciphering the epitranscriptome: Recent progress and emerging topics. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 18, 1587-1604. doi:10.1016/j.csbj.2020.06.010
2019
A human tissue-specific transcriptomic analysis reveals a complex relationship between aging, cancer, and cellular senescence
Chatsirisupachai, K., Palmer, D., Ferreira, S., & de Magalhaes, J. P. (2019). A human tissue-specific transcriptomic analysis reveals a complex relationship between aging, cancer, and cellular senescence. AGING CELL, 18(6). doi:10.1111/acel.13041
To help aging populations, classify organismal senescence.
Calimport, S. R. G., Bentley, B. L., Stewart, C., Pawelec, G., Scuteri, A., Vinciguerra, M., . . . Church, G. (2019). To help aging populations, classify organismal senescence. SCIENCE, 366(6465), 576-+. doi:10.1126/science.aay7319
The fog of genetics: what is known, unknown and unknowable in the genetics of complex traits and diseases
de Magalhaes, J. P., & Wang, J. (2019). The fog of genetics: what is known, unknown and unknowable in the genetics of complex traits and diseases. EMBO REPORTS, 20(11). doi:10.15252/embr.201948054
A Multidimensional Systems Biology Analysis of Cellular Senescence in Ageing and Disease
WHISTLE: a high-accuracy map of the human N<SUP>6</SUP>-methyladenosine (m<SUP>6</SUP>A) epitranscriptome predicted using a machine learning approach
Chen, K., Wei, Z., Zhang, Q., Wu, X., Rong, R., Lu, Z., . . . Meng, J. (2019). WHISTLE: a high-accuracy map of the human N<SUP>6</SUP>-methyladenosine (m<SUP>6</SUP>A) epitranscriptome predicted using a machine learning approach. NUCLEIC ACIDS RESEARCH, 47(7). doi:10.1093/nar/gkz074
RNA-Seq signatures normalized by mRNA abundance allow absolute deconvolution of human immune cell types
Monaco, G., Lee, B., Xu, W., Mustafah, S., Hwang, Y. Y., Carré, C., . . . Larbi, A. (2019). RNA-Seq signatures normalized by mRNA abundance allow absolute deconvolution of human immune cell types. Cell Reports, 26(06), 1627-1640.E7. doi:10.1016/j.celrep.2019.01.041
2018
Biological Processes Modulating Longevity across Primates: A Phylogenetic Genome-Phenome Analysis
Muntane, G., Farre, X., Rodriguez, J. A., Pegueroles, C., Hughes, D. A., de Magalhaes, J. P., . . . Navarro, A. (2018). Biological Processes Modulating Longevity across Primates: A Phylogenetic Genome-Phenome Analysis. Molecular Biology and Evolution, 35(8), 1990-2004. doi:10.1093/molbev/msy105
From humans to hydra: patterns of cancer across the tree of life
Albuquerque, T. A. F., do Val, L. D., Doherty, A., & de Magalhaes, J. P. (2018). From humans to hydra: patterns of cancer across the tree of life. BIOLOGICAL REVIEWS, 93(3), 1715-1734. doi:10.1111/brv.12415
Gene co-expression analysis for functional classification and gene-disease predictions.
van Dam, S., Vosa, U., van der Graaf, A., Franke, L., & de Magalhaes, J. P. (2018). Gene co-expression analysis for functional classification and gene-disease predictions. BRIEFINGS IN BIOINFORMATICS, 19(4), 575-592. doi:10.1093/bib/bbw139
A new approach for interpreting Random Forest models and its application to the biology of ageing
Fabris, F., Doherty, A., Palmer, D., de Magalhaes, J. P., & Freitas, A. A. (2018). A new approach for interpreting Random Forest models and its application to the biology of ageing. BIOINFORMATICS, 34(14), 2449-2456. doi:10.1093/bioinformatics/bty087
Enhancing Epitranscriptome Module Detection from m<SUP>6</SUP>A-Seq Data Using Threshold-Based Measurement Weighting Strategy
Chen, K., Wei, Z., Liu, H., de Magalhaes, J. P., Rong, R., Lu, Z., & Meng, J. (2018). Enhancing Epitranscriptome Module Detection from m<SUP>6</SUP>A-Seq Data Using Threshold-Based Measurement Weighting Strategy. BIOMED RESEARCH INTERNATIONAL, 2018. doi:10.1155/2018/2075173
Topological Characterization of Human and Mouse m<SUP>5</SUP>C Epitranscriptome Revealed by Bisulfite Sequencing
Wei, Z., Panneerdoss, S., Timilsina, S., Zhu, J., Mohammad, T. A., Lu, Z. -L., . . . Meng, J. (2018). Topological Characterization of Human and Mouse m<SUP>5</SUP>C Epitranscriptome Revealed by Bisulfite Sequencing. INTERNATIONAL JOURNAL OF GENOMICS, 2018. doi:10.1155/2018/1351964
Circulating MicroRNAs in Young Patients with Acute Coronary Syndrome
Tong, K. -L., Zuhdi, A. S. M., Ahmad, W. A. W., Vanhoutte, P. M., de Magalhaes, J. P., Mustafa, M. R., & Wong, P. -F. (2018). Circulating MicroRNAs in Young Patients with Acute Coronary Syndrome. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 19(5). doi:10.3390/ijms19051467
A Reassessment of Genes Modulating Aging in Mice Using Demographic Measurements of the Rate of Aging
de Magalhaes, J. P., Thompson, L., de Lima, I., Gaskill, D., Li, X., Thornton, D., . . . Palmer, D. (2018). A Reassessment of Genes Modulating Aging in Mice Using Demographic Measurements of the Rate of Aging. GENETICS, 208(4), 1617-1630. doi:10.1534/genetics.118.300821
Vive la radiorésistance!: converging research in radiobiology and biogerontology to enhance human radioresistance for deep space exploration and colonization.
Cortese, F., Klokov, D., Osipov, A., Stefaniak, J., Moskalev, A., Schastnaya, J., . . . Zhavoronkov, A. (2018). Vive la radiorésistance!: converging research in radiobiology and biogerontology to enhance human radioresistance for deep space exploration and colonization.. Oncotarget, 9(18), 14692-14722. doi:10.18632/oncotarget.24461
Stress, cell senescence and organismal ageing
de Magalhaes, J. P., & Passos, J. F. (2018). Stress, cell senescence and organismal ageing. MECHANISMS OF AGEING AND DEVELOPMENT, 170, 2-9. doi:10.1016/j.mad.2017.07.001
Naked mole rats can undergo developmental, oncogene-induced and DNA damage-induced cellular senescence
Zhao, Y., Tyshkovskiy, A., Muñoz-Espín, D., Tian, X., Serrano, M., De Magalhaes, J. P., . . . Gorbunova, V. (2018). Naked mole rats can undergo developmental, oncogene-induced and DNA damage-induced cellular senescence. Proceedings of the National Academy of Sciences of USA, 115(8), 1801-1806. doi:10.1073/pnas.1721160115
2017
Human Ageing Genomic Resources: new and updated databases
Tacutu, R., Thornton, D., Johnson, E., Budovsky, A., Barardo, D., Craig, T., . . . de Magalhaes, J. P. (2017). Human Ageing Genomic Resources: new and updated databases. NUCLEIC ACIDS RESEARCH, 46(D1), D1083-D1090. doi:10.1093/nar/gkx1042
The Business of Anti-Aging Science
de Magalhaes, J. P., Stevens, M., & Thornton, D. (2017). The Business of Anti-Aging Science. TRENDS IN BIOTECHNOLOGY, 35(11), 1062-1073. doi:10.1016/j.tibtech.2017.07.004
Identification of polymorphisms in cancer patients that differentially affect survival with age
Doherty, A., Kernogitski, Y., Kulminski, A. M., & de Magalhaes, J. P. (2017). Identification of polymorphisms in cancer patients that differentially affect survival with age. AGING-US, 9(10), 2114-+. doi:10.18632/aging.101305
Machine learning for predicting lifespan-extending chemical compounds
Barardo, D. G., Newby, D., Thornton, D., Ghafourian, T., de Magalhaes, J. P., & Freitas, A. A. (2017). Machine learning for predicting lifespan-extending chemical compounds. AGING-US, 9(7), 1721-1737. doi:10.18632/aging.101264
The DrugAge database of aging-related drugs.
Barardo, D., Thornton, D., Thoppil, H., Walsh, M., Sharifi, S., Ferreira, S., . . . de Magalhães, J. P. (2017). The DrugAge database of aging-related drugs.. Aging Cell, 16(3), 594-597. doi:10.1111/acel.12585
A review of supervised machine learning applied to ageing research
Fabris, F., de Magalhes, J. P., & Freitas, A. A. (2017). A review of supervised machine learning applied to ageing research. BIOGERONTOLOGY, 18(2), 171-188. doi:10.1007/s10522-017-9683-y
Analysis of the FGF gene family provides insights into aquatic adaptation in cetaceans
Nam, K., Lee, K. W., Chung, O., Yim, H. -S., Cha, S. -S., Lee, S. -W., . . . Jeong, J. -Y. (2017). Analysis of the FGF gene family provides insights into aquatic adaptation in cetaceans. SCIENTIFIC REPORTS, 7. doi:10.1038/srep40233
2016
Has gene duplication impacted the evolution of Eutherian longevity?
Doherty, A., & de Magalhaes, J. P. (2016). Has gene duplication impacted the evolution of Eutherian longevity?. AGING CELL, 15(5), 978-980. doi:10.1111/acel.12503
Longer lifespan in male mice treated with a weakly estrogenic agonist, an antioxidant, an -glucosidase inhibitor or a Nrf2-inducer
Strong, R., Miller, R. A., Antebi, A., Astle, C. M., Bogue, M., Denzel, M. S., . . . Harrison, D. E. (2016). Longer lifespan in male mice treated with a weakly estrogenic agonist, an antioxidant, an -glucosidase inhibitor or a Nrf2-inducer. AGING CELL, 15(5), 872-884. doi:10.1111/acel.12496
Systematic analysis of the gerontome reveals links between aging and age-related diseases.
Fernandes, M., Wan, C., Tacutu, R., Barardo, D., Rajput, A., Wang, J., . . . de Magalhães, J. P. (2016). Systematic analysis of the gerontome reveals links between aging and age-related diseases.. Human molecular genetics, 25(21), 4804-4818. doi:10.1093/hmg/ddw307
Fish oil supplements, longevity and aging
de Magalhaes, J. P., Mueller, M., Rainger, G. E., & Steegenga, W. (2016). Fish oil supplements, longevity and aging. AGING-US, 8(8), 1578-1582. doi:10.18632/aging.101021
Reductions in hypothalamic Gfap expression, glial cells and α-tanycytes in lean and hypermetabolic Gnasxl-deficient mice
Holmes, A. P., Wong, S. Q., Pulix, M., Johnson, K., Horton, N. S., Thomas, P., . . . Plagge, A. (2016). Reductions in hypothalamic Gfap expression, glial cells and α-tanycytes in lean and hypermetabolic Gnasxl-deficient mice. Molecular Brain, 9(1), 1-13. doi:10.1186/s13041-016-0219-1
A Network Pharmacology Approach Reveals New Candidate Caloric Restriction Mimetics in C. Elegans
Calvert, S., Tacutu, R., Sharifi, S., Teixeira, R., Ghosh, P., & De Magalhaes, J. P. (2016). A Network Pharmacology Approach Reveals New Candidate Caloric Restriction Mimetics in C. Elegans. Aging cell, 15(2), 256-266. doi:10.1111/acel.12432
Integrative Genomics of Aging
de Magalhães, J. P., & Tacutu, R. (2016). Integrative Genomics of Aging. In Handbook of the Biology of Aging (pp. 263-285). Elsevier. doi:10.1016/b978-0-12-411596-5.00009-5
2015
Transcriptome analysis in calorie-restricted rats implicates epigenetic and post-translational mechanisms in neuroprotection and aging.
Wood, S. H., van Dam, S., Craig, T., Tacutu, R., O'Toole, A., Merry, B. J., & De Magalhaes, J. P. (2015). Transcriptome analysis in calorie-restricted rats implicates epigenetic and post-translational mechanisms in neuroprotection and aging.. Genome biology, 16(1). doi:10.1186/s13059-015-0847-2
Insights on cryoprotectant toxicity from gene expression profiling of endothelial cells exposed to ethylene glycol
Cordeiro, R. M., Stirling, S., Fahy, G. M., & De Magalhaes, J. P. (2015). Insights on cryoprotectant toxicity from gene expression profiling of endothelial cells exposed to ethylene glycol. Cryobiology, 71(03), 405-412. doi:10.1016/j.cryobiol.2015.10.142
A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels.
Monaco, G., van Dam, S., Casal Novo Ribeiro, J. L., Larbi, A., & De Magalhaes, J. P. (2015). A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels.. BMC evolutionary biology, 15(1). doi:10.1186/s12862-015-0534-7
A direct communication proposal to test the Zoo Hypothesis
de Magalhaes, J. P. (2016). A direct communication proposal to test the Zoo Hypothesis. SPACE POLICY, 38, 22-26. doi:10.1016/j.spacepol.2016.06.001
Geroprotectors.org: a new, structured and curated database of current therapeutic interventions in aging and age-related disease
Moskalev, A., Chernyagina, E., de Magalhaes, J. P., Barardo, D., Thoppil, H., Shaposhnikov, M., . . . Zhavoronkov, A. (2015). Geroprotectors.org: a new, structured and curated database of current therapeutic interventions in aging and age-related disease. AGING-US, 7(9), 616-628. doi:10.18632/aging.100799
Being cool: how body temperature influences ageing and longevity
Keil, G., Cummings, E., & de Magalhaes, J. P. (2015). Being cool: how body temperature influences ageing and longevity. BIOGERONTOLOGY, 16(4), 383-397. doi:10.1007/s10522-015-9571-2
The big, the bad and the ugly <i>Extreme animals as inspiration for biomedical research</i>
de Magalhaes, J. P. (2015). The big, the bad and the ugly <i>Extreme animals as inspiration for biomedical research</i>. EMBO REPORTS, 16(7), 771-776. doi:10.15252/embr.201540606
Meet the Editorial Board Members.
de Magalhães, J. P., & Pandey, G. K. (2015). Meet the Editorial Board Members.. Current Genomics, 16(3), 139-140. doi:10.2174/138920291603150409100245
Mathematical Study of Mortality Dynamics in Heterogeneous Population Composed of Subpopulations Following the Exponential Law
Arnold (-Gaille), S., Vasiev, B., Avraam, D., & de Magalhaes, J. P. (2015). Mathematical Study of Mortality Dynamics in Heterogeneous Population Composed of Subpopulations Following the Exponential Law.
Predicting the Pro-Longevity or Anti-Longevity Effect of Model Organism Genes with New Hierarchical Feature Selection Methods
Wan, C., Freitas, A. A., & de Magalhaes, J. P. (2015). Predicting the Pro-Longevity or Anti-Longevity Effect of Model Organism Genes with New Hierarchical Feature Selection Methods. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 12(2), 262-275. doi:10.1109/TCBB.2014.2355218
GeneFriends: a human RNA-seq-based gene and transcript co-expression database
van Dam, S., Craig, T., & De Magalhaes, J. P. (2015). GeneFriends: a human RNA-seq-based geneand transcript co-expression database. Nucleic Acids Research, 43(D1), D1124-D1132. doi:10.1093/nar/gku1042
The Digital Ageing Atlas: integrating the diversity of age-related changes into a unified resource
Craig, T., Smelick, C., Tacutu, R., Wuttke, D., Wood, S. H., Stanley, H., . . . De Magalhaes, J. P. (2015). The Digital Ageing Atlas: integrating the diversity of age-related changes into a unified resource. Nucleic Acids Research, 43(D1), D873-D878. doi:10.1093/nar/gku843
Insights into the evolution of longevity from the bowhead whale genome.
Keane, M., Semeiks, J., Webb, A. E., Li, Y. I., Quesada, V., Craig, T., . . . De Magalhaes, J. P. (2015). Insights into the evolution of longevity from the bowhead whale genome.. Cell reports, 10(1), 112-122. doi:10.1016/j.celrep.2014.12.008
Dissecting the role of microRNAs and their therapeutic potential in Alzheimer's disease
Viegas, A. T., Carmona, V., Pereira de Almeida, L., de Magalhaes, J. P., & Cardoso, A. L. (2015). Dissecting the role of microRNAs and their therapeutic potential in Alzheimer's disease. In FEBS JOURNAL Vol. 282 (pp. 217). Retrieved from https://www.webofscience.com/
2014
The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations
Keane, M., Craig, T., Alfoeldi, J., Berlin, A. M., Johnson, J., Seluanov, A., . . . de Magalhaes, J. P. (2014). The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations. BIOINFORMATICS, 30(24), 3558-3560. doi:10.1093/bioinformatics/btu579
The Scientific Quest for Lasting Youth: Prospects for Curing Aging
de Magalhaes, J. P. (2014). The Scientific Quest for Lasting Youth: Prospects for Curing Aging. REJUVENATION RESEARCH, 17(5), 458-467. doi:10.1089/rej.2014.1580
Why genes extending lifespan in model organisms have not been consistently associated with human longevity and what it means to translation research
de Magalhaes, J. P. (2014). Why genes extending lifespan in model organisms have not been consistently associated with human longevity and what it means to translation research. CELL CYCLE, 13(17), 2671-2673. doi:10.4161/15384101.2014.950151
2013
LongevityMap: a database of human genetic variants associated with longevity
Budovsky, A., Craig, T., Wang, J., Tacutu, R., Csordas, A., Lourenco, J., . . . de Magalhaes, J. P. (2013). LongevityMap: a database of human genetic variants associated with longevity. TRENDS IN GENETICS, 29(10), 559-560. doi:10.1016/j.tig.2013.08.003
A mathematical model of mortality dynamics across the lifespan combining heterogeneity and stochastic effects
Avraam, D., de Magalhaes, J. P., & Vasiev, B. (2013). A mathematical model of mortality dynamics across the lifespan combining heterogeneity and stochastic effects. EXPERIMENTAL GERONTOLOGY, 48(8), 801-811. doi:10.1016/j.exger.2013.05.054
A mathematical model of mortality dynamics across the lifespan combining heterogeneity and stochastic effects
Avraam, D., de Magalhaes, J. P., & Vasiev, B. (2013). A mathematical model of mortality dynamics across the lifespan combining heterogeneity and stochastic effects. Experimental Gerontology, 48(8), 801-811. doi:10.1016/j.exger.2013.05.054
A-to-I RNA editing does not change with age in the healthy male rat brain
Holmes, A. P., Wood, S. H., Merry, B. J., & de Magalhaes, J. P. (2013). A-to-I RNA editing does not change with age in the healthy male rat brain. BIOGERONTOLOGY, 14(4), 395-400. doi:10.1007/s10522-013-9433-8
Endless paces of degeneration-applying comparative genomics to study evolution's moulding of longevity
de Magalhaes, J. P., & Keane, M. (2013). Endless paces of degeneration-applying comparative genomics to study evolution's moulding of longevity. EMBO REPORTS, 14(8), 661-662. doi:10.1038/embor.2013.96
<i>MYCN/LIN28B/Let-7/HMGA2</i> pathway implicated by meta-analysis of GWAS in suppression of post-natal proliferation thereby potentially contributing to aging
Keane, M., & de Magalhaes, J. P. (2013). <i>MYCN/LIN28B/Let-7/HMGA2</i> pathway implicated by meta-analysis of GWAS in suppression of post-natal proliferation thereby potentially contributing to aging. MECHANISMS OF AGEING AND DEVELOPMENT, 134(7-8), 346-348. doi:10.1016/j.mad.2013.04.006
Whole transcriptome sequencing of the aging rat brain reveals dynamic RNA changes in the dark matter of the genome
Wood, S. H., Craig, T., Li, Y., Merry, B., & de Magalhaes, J. P. (2013). Whole transcriptome sequencing of the aging rat brain reveals dynamic RNA changes in the dark matter of the genome. AGE, 35(3), 763-776. doi:10.1007/s11357-012-9410-1
How ageing processes influence cancer
de Magalhaes, J. P. (2013). How ageing processes influence cancer. NATURE REVIEWS CANCER, 13(5), 357-365. doi:10.1038/nrc3497
Accelerated protein evolution analysis reveals genes and pathways associated with the evolution of mammalian longevity
Li, Y., & de Magalhaes, J. P. (2013). Accelerated protein evolution analysis reveals genes and pathways associated with the evolution of mammalian longevity. AGE, 35(2), 301-314. doi:10.1007/s11357-011-9361-y
An analysis and validation pipeline for large-scale RNAi-based screens
Plank, M., Hu, G., Silva, A. S., Wood, S. H., Hesketh, E. E., Janssens, G., . . . Church, G. M. (2013). An analysis and validation pipeline for large-scale RNAi-based screens. SCIENTIFIC REPORTS, 3. doi:10.1038/srep01076
Human Ageing Genomic Resources: Integrated databases and tools for the biology and genetics of ageing
Tacutu, R., Craig, T., Budovsky, A., Wuttke, D., Lehmann, G., Taranukha, D., . . . de Magalhaes, J. P. (2013). Human Ageing Genomic Resources: Integrated databases and tools for the biology and genetics of ageing. NUCLEIC ACIDS RESEARCH, 41(D1), D1027-D1033. doi:10.1093/nar/gks1155
Whole transcriptome sequencing of the aging rat brain reveals dynamic RNA changes in the dark matter of the genome
Wood, S. H., Craig, T., Li, Y., Merry, B., & de Magalhães, J. P. (2013). Whole transcriptome sequencing of the aging rat brain reveals dynamic RNA changes in the dark matter of the genome.
2012
Programmatic features of aging originating in development: aging mechanisms beyond molecular damage?
de Magalhaes, J. P. (2012). Programmatic features of aging originating in development: aging mechanisms beyond molecular damage?. FASEB JOURNAL, 26(12), 4821-4826. doi:10.1096/fj.12-210872
Prediction of <i>C</i>. <i>elegans</i> Longevity Genes by Human and Worm Longevity Networks
Tacutu, R., Shore, D. E., Budovsky, A., de Magalhaes, J. P., Ruvkun, G., Fraifeld, V. E., & Curran, S. P. (2012). Prediction of <i>C</i>. <i>elegans</i> Longevity Genes by Human and Worm Longevity Networks. PLOS ONE, 7(10). doi:10.1371/journal.pone.0048282
GeneFriends: An online co-expression analysis tool to identify novel gene targets for aging and complex diseases
van Dam, S., Cordeiro, R., Craig, T., van Dam, J., Wood, S. H., & de Magalhaes, J. P. (2012). GeneFriends: An online co-expression analysis tool to identify novel gene targets for aging and complex diseases. BMC GENOMICS, 13. doi:10.1186/1471-2164-13-535
The Role of DNA Methylation in Aging, Rejuvenation, and Age-Related Disease
Johnson, A. A., Akman, K., Calimport, S. R. G., Wuttke, D., Stolzing, A., & de Magalhaes, J. P. (2012). The Role of DNA Methylation in Aging, Rejuvenation, and Age-Related Disease. REJUVENATION RESEARCH, 15(5), 483-494. doi:10.1089/rej.2012.1324
Dissecting the Gene Network of Dietary Restriction to Identify Evolutionarily Conserved Pathways and New Functional Genes
Wuttke, D., Connor, R., Vora, C., Craig, T., Li, Y., Wood, S., . . . de Magalhaes, J. P. (2012). Dissecting the Gene Network of Dietary Restriction to Identify Evolutionarily Conserved Pathways and New Functional Genes. PLOS GENETICS, 8(8). doi:10.1371/journal.pgen.1002834
Osh6 links yeast vacuolar functions to lifespan extension and TOR
Wuttke, D., & de Magalhaes, J. P. (2012). Osh6 links yeast vacuolar functions to lifespan extension and TOR. CELL CYCLE, 11(13), 2419-2420. doi:10.4161/cc.21069
Mutational Bias Plays an Important Role in Shaping Longevity-Related Amino Acid Content in Mammalian mtDNA-Encoded Proteins
Carlos Aledo, J., Valverde, H., & de Magalhaes, J. P. (2012). Mutational Bias Plays an Important Role in Shaping Longevity-Related Amino Acid Content in Mammalian mtDNA-Encoded Proteins. JOURNAL OF MOLECULAR EVOLUTION, 74(5-6), 332-341. doi:10.1007/s00239-012-9510-7
A meta-analysis of caloric restriction gene expression profiles to infer common signatures and regulatory mechanisms
Plank, M., Wuttke, D., van Dam, S., Clarkea, S. A., & de Magalhaes, J. P. (2012). A meta-analysis of caloric restriction gene expression profiles to infer common signatures and regulatory mechanisms. MOLECULAR BIOSYSTEMS, 8(4), 1339-1349. doi:10.1039/c2mb05255e
Genome-Wide Patterns of Genetic Distances Reveal Candidate Loci Contributing to Human Population-Specific Traits
de Magalhaes, J. P., & Matsuda, A. (2012). Genome-Wide Patterns of Genetic Distances Reveal Candidate Loci Contributing to Human Population-Specific Traits. ANNALS OF HUMAN GENETICS, 76, 142-158. doi:10.1111/j.1469-1809.2011.00695.x
Dissecting the gene network of dietary restriction to identify evolutionarily conserved pathways and new functional genes
Wuttke, D., Connor, R., Vora, C., Craig, T., Li, Y., Wood, S., . . . de Magalhães, J. P. (2012). Dissecting the gene network of dietary restriction to identify evolutionarily conserved pathways and new functional genes.
Genome-Environment Interactions That Modulate Aging: Powerful Targets for Drug Discovery
de Magalhaes, J. P., Wuttke, D., Wood, S. H., Plank, M., & Vora, C. (2012). Genome-Environment Interactions That Modulate Aging: Powerful Targets for Drug Discovery. PHARMACOLOGICAL REVIEWS, 64(1), 88-101. doi:10.1124/pr.110.004499
Genome-environment interactions that modulate aging: powerful targets for drug discovery
de Magalhães, J. P., Wuttke, D., Wood, S. H., Plank, M., & Vora, C. (2012). Genome-environment interactions that modulate aging: powerful targets for drug discovery.
2011
A data mining approach for classifying DNA repair genes into ageing-related or non-ageing-related
Freitas, A. A., Vasieva, O., & de Magalhães, J. P. (2011). A data mining approach for classifying DNA repair genes into ageing-related or non-ageing-related. BMC Genomics, 12(1). doi:10.1186/1471-2164-12-27
Gathering insights on disease etiology from gene expression profiles of healthy tissues
Silva, A. S., Wood, S. H., van Dam, S., Berres, S., McArdle, A., & de Magalhães, J. P. (2011). Gathering insights on disease etiology from gene expression profiles of healthy tissues. Bioinformatics, 27(23), 3300-3305. doi:10.1093/bioinformatics/btr559
Gathering insights on disease etiology from gene expression profiles of healthy tissues
Silva, A. S., Wood, S. H., van Dam, S., Berres, S., McArdle, A., & de Magalhaes, J. P. (2011). Gathering insights on disease etiology from gene expression profiles of healthy tissues. BIOINFORMATICS, 27(23), 3300-3305. doi:10.1093/bioinformatics/btr559
RNA Sequencing Reveals Differential Expression of Mitochondrial and Oxidation Reduction Genes in the Long-Lived Naked Mole-Rat When Compared to Mice
Yu, C., Li, Y., Holmes, A., Szafranski, K., Faulkes, C. G., Coen, C. W., . . . Church, G. M. (2011). RNA Sequencing Reveals Differential Expression of Mitochondrial and Oxidation Reduction Genes in the Long-Lived Naked Mole-Rat When Compared to Mice. PLOS ONE, 6(11). doi:10.1371/journal.pone.0026729
A review and appraisal of the DNA damage theory of ageing
Freitas, A. A., & de Magalhaes, J. P. (2011). A review and appraisal of the DNA damage theory of ageing. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH, 728(1-2), 12-22. doi:10.1016/j.mrrev.2011.05.001
A role for Ras signaling in modulating mammalian aging by the GH/IGF1 axis
de Magalhaes, J. P. (2011). A role for Ras signaling in modulating mammalian aging by the GH/IGF1 axis. AGING-US, 3(4), 336-337. doi:10.18632/aging.100309
Mitochondrially encoded methionine is inversely related to longevity in mammals
Carlos Aledo, J., Li, Y., Pedro de Magalhaes, J., Ruiz-Camacho, M., & Antonio Perez-Claros, J. (2011). Mitochondrially encoded methionine is inversely related to longevity in mammals. AGING CELL, 10(2), 198-207. doi:10.1111/j.1474-9726.2010.00657.x
The biology of ageing
de Magalhães, J. P. (2011). The biology of ageing. In An Introduction to Gerontology (pp. 21-47). Cambridge University Press. doi:10.1017/cbo9780511973697.002
A data mining approach for classifying DNA repair genes into ageing-related or non-ageing-related
Freitas, A. A., Vasieva, O., & de Magalhaes, J. P. (2011). A data mining approach for classifying DNA repair genes into ageing-related or non-ageing-related. BMC GENOMICS, 12. doi:10.1186/1471-2164-12-27
A data mining approach for classifying DNA repair genes into ageing-related or non-ageing-related
Freitas, A. A., Vasieva, O., & de Magalhaes, J. P. (2011). A data mining approach for classifying DNA repair genes into ageing-related or non-ageing-related. BMC Genomics.
Paternal genome effects on aging: Evidence for a role of <i>Rasgrf1</i> in longevity determination?
de Magalhaes, J. P. (2011). Paternal genome effects on aging: Evidence for a role of <i>Rasgrf1</i> in longevity determination?. MECHANISMS OF AGEING AND DEVELOPMENT, 132(1-2), 72-73. doi:10.1016/j.mad.2010.11.004
The Biology of Ageing: A Primer
de Magalhães, J. P. (2011). The Biology of Ageing: A Primer. In I. Stuart-Hamilton (Ed.), An Introduction to Gerontology (pp. 21-47). Cambridge: Cambridge University Press,.
2010
Bioinformatics in aging research: a workshop report.
Fuellen, G., Adjaye, J., de Grey, A., Lepperdinger, G., de Magalhães, J. P., Sühnel, J., & Wipat, A. (2010). Bioinformatics in aging research: a workshop report.. In Rejuvenation research Vol. 13 (pp. 763-767). doi:10.1089/rej.2010.1125
Ecological, biomedical and epidemiological approaches to understanding oxidative balance and ageing: what they can teach each other
Cohen, A. A., de Magalhaes, J. P., & Gohil, K. (2010). Ecological, biomedical and epidemiological approaches to understanding oxidative balance and ageing: what they can teach each other. FUNCTIONAL ECOLOGY, 24(5), 997-1006. doi:10.1111/j.1365-2435.2010.01761.x
Cell resilience in species life spans: a link to inflammation?
Finch, C. E., Morgan, T. E., Longo, V. D., & de Magalhaes, J. P. (2010). Cell resilience in species life spans: a link to inflammation?. Aging cell, 9(4), 519-526.
Next-generation sequencing in aging research: Emerging applications, problems, pitfalls and possible solutions
de Magalhaes, J. P., Finch, C. E., & Janssens, G. (2010). Next-generation sequencing in aging research: Emerging applications, problems, pitfalls and possible solutions. AGEING RESEARCH REVIEWS, 9(3), 315-323. doi:10.1016/j.arr.2009.10.006
Age-related gene-specific changes of A-to-I mRNA editing in the human brain
Nicholas, A., de Magalhaes, J. P., Kraytsberg, Y., Richfield, E. K., Levanon, E. Y., & Khrapko, K. (2010). Age-related gene-specific changes of A-to-I mRNA editing in the human brain. MECHANISMS OF AGEING AND DEVELOPMENT, 131(6), 445-447. doi:10.1016/j.mad.2010.06.001
Systems Biology and Longevity: An Emerging Approach to Identify Innovative Anti-Aging Targets and Strategies
Cevenini, E., Bellavista, E., Tieri, P., Castellani, G., Lescai, F., Francesconi, M., . . . Franceschi, C. (2010). Systems Biology and Longevity: An Emerging Approach to Identify Innovative Anti-Aging Targets and Strategies. CURRENT PHARMACEUTICAL DESIGN, 16(7), 802-813. doi:10.2174/138161210790883660
Cell resilience in species life spans: a link to inflammation?
Finch, C. E., Morgan, T. E., Longo, V. D., & de Magalhaes, J. P. (2010). Cell resilience in species life spans: a link to inflammation?. AGING CELL, 9(4), 519-526. doi:10.1111/j.1474-9726.2010.00578.x
2009
A database of vertebrate longevity records and their relation to other life-history traits
de Magalhaes, J. P., & Costa, J. (2009). A database of vertebrate longevity records and their relation to other life-history traits. JOURNAL OF EVOLUTIONARY BIOLOGY, 22(8), 1770-1774. doi:10.1111/j.1420-9101.2009.01783.x
Meta-analysis of age-related gene expression profiles identifies common signatures of aging
de Magalhaes, J. P., Curado, J., & Church, G. M. (2009). Meta-analysis of age-related gene expression profiles identifies common signatures of aging. BIOINFORMATICS, 25(7), 875-881. doi:10.1093/bioinformatics/btp073
The Human Ageing Genomic Resources: online databases and tools for biogerontologists
de Magalhaes, J. P., Budovsky, A., Lehmann, G., Costa, J., Li, Y., Fraifeld, V., & Church, G. M. (2009). The Human Ageing Genomic Resources: online databases and tools for biogerontologists. AGING CELL, 8(1), 65-72. doi:10.1111/j.1474-9726.2008.00442.x
The Human Ageing Genomic Resources: online databases and tools for biogerontologists
De Magalhães, J. P., Budovsky, A., Lehmann, G., Costa, J., Li, Y., Fraifeld, V., & Church, G. M. (2009). The Human Ageing Genomic Resources: online databases and tools for biogerontologists. Aging Cell, 8(1), 65-72. doi:10.1111/j.1474-9726.2008.00442.x
Ageing research in the post-genome era: New technologies for an old problem
De Magalhães, J. P. (2009). Ageing research in the post-genome era: New technologies for an old problem. In Redox Metabolism and Longevity Relationships in Animals and Plants (pp. 99-115).
Ageing research in the post-genome era: new technologies for an old problem.
de Magalhães, J. P. (2009). Ageing research in the post-genome era: new technologies for an old problem.. SEB experimental biology series, 62, 99-115.
Meta-analysis of age-related gene expression profiles identifies common signatures of aging
de Magalhães, J. P., Curado, J., & Church, G. M. (2009). Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics.
2008
Cell divisions and mammalian aging: integrative biology insights from genes that regulate longevity
de Magalhaes, J. P., & Faragher, R. G. A. (2008). Cell divisions and mammalian aging: integrative biology insights from genes that regulate longevity. BIOESSAYS, 30(6), 567-578. doi:10.1002/bies.20760
2007
A proposal to sequence genomes of unique interest for research on aging
de Magalhaes, J. P., Sedivy, J. M., Finch, C. E., Austad, S. N., & Church, G. M. (2007). A proposal to sequence genomes of unique interest for research on aging. JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES, 62(6), 583-584. Retrieved from https://www.webofscience.com/
Analyses of human-chimpanzee orthologous gene pairs to explore evolutionary hypotheses of aging
de Magalhaes, J. P., & Church, G. M. (2007). Analyses of human-chimpanzee orthologous gene pairs to explore evolutionary hypotheses of aging. MECHANISMS OF AGEING AND DEVELOPMENT, 128(5-6), 355-364. doi:10.1016/j.mad.2007.03.004
An analysis of the relationship between metabolism, developmental schedules, and longevity using phylogenetic independent contrasts
de Magalhaes, J. P., Costa, J., & Church, G. M. (2007). An analysis of the relationship between metabolism, developmental schedules, and longevity using phylogenetic independent contrasts. JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES, 62(2), 149-160. Retrieved from https://www.webofscience.com/
2006
Cells discover fire: Employing reactive oxygen species in development and consequences for aging
de Magalhaes, J. P., & Church, G. (2006). Cells discover fire: Employing reactive oxygen species in development and consequences for aging. EXPERIMENTAL GERONTOLOGY, 41(1), 1-10. doi:10.1016/j.exger.2005.09.002
Species Selection in Comparative Studies of Aging and Antiaging Research
de Magalhães, J. P. (2006). Species Selection in Comparative Studies of Aging and Antiaging Research. In Handbook of Models for Human Aging (pp. 9-20). Elsevier. doi:10.1016/b978-012369391-4/50003-5
2005
Cognitive aging as an extension of brain development: A model linking learning, brain plasticity, and neurodegeneration
de Magalhaes, J. P., & Sandberg, A. (2005). Cognitive aging as an extension of brain development: A model linking learning, brain plasticity, and neurodegeneration. MECHANISMS OF AGEING AND DEVELOPMENT, 126(10), 1026-1033. doi:10.1016/j.mad.2005.04.004
Human disease-associated mitochondrial mutations fixed in nonhuman primates
de Magalhaes, J. P. (2005). Human disease-associated mitochondrial mutations fixed in nonhuman primates. JOURNAL OF MOLECULAR EVOLUTION, 61(4), 491-497. doi:10.1007/s00239-004-0258-6
Genomes optimize reproduction: Aging as a consequence of the developmental program
de Magalhaes, J. P., & Church, G. M. (2005). Genomes optimize reproduction: Aging as a consequence of the developmental program. PHYSIOLOGY, 20, 252-259. doi:10.1152/physiol.00010.2005
HAGR: the human ageing genomic resources
de Magalhaes, J. P., Costa, J., & Toussaint, O. (2005). HAGR: the human ageing genomic resources. NUCLEIC ACIDS RESEARCH, 33, D537-D543. doi:10.1093/nar/gki017
Open-minded scepticism: inferring the causal mechanisms of human ageing from genetic perturbations
de Magalhaes, J. P. (2005). Open-minded scepticism: inferring the causal mechanisms of human ageing from genetic perturbations. AGEING RESEARCH REVIEWS, 4(1), 1-22. doi:10.1016/j.arr.2004.05.003
The influence of genes on the aging process of mice: A statistical assessment of the genetics of aging
de Magalhaes, J. P., Cabral, J. A. S., & Magalhaes, D. (2005). The influence of genes on the aging process of mice: A statistical assessment of the genetics of aging. GENETICS, 169(1), 265-274. doi:10.1534/genetics.104.032292
2004
From cells to ageing: a review of models and mechanisms of cellular senescence and their impact on human ageing
de Magalhaes, J. P. (2004). From cells to ageing: a review of models and mechanisms of cellular senescence and their impact on human ageing. EXPERIMENTAL CELL RESEARCH, 300(1), 1-10. doi:10.1016/j.yexcr.2004.07.006
Gene expression and regulation in H<sub>2</sub>O<sub>2</sub>-induced premature senescence of human foreskin fibroblasts expressing or not telomerase
de Magalhaes, J. P., Chainiaux, F., de Longueville, F., Mainfroid, V., Migeot, V., Marcq, L., . . . Toussaint, O. (2004). Gene expression and regulation in H<sub>2</sub>O<sub>2</sub>-induced premature senescence of human foreskin fibroblasts expressing or not telomerase. EXPERIMENTAL GERONTOLOGY, 39(9), 1379-1389. doi:10.1016/j.exger.2004.06.004
GenAge: a genomic and proteomic network map of human ageing
de Magalhaes, J. P., & Toussaint, O. (2004). GenAge: a genomic and proteomic network map of human ageing. FEBS LETTERS, 571(1-3), 243-247. doi:10.1016/j.febslet.2004.07.006
Telomeres and telomerase: A modern fountain of youth?
de Magalhaes, J. P., & Toussaint, O. (2004). Telomeres and telomerase: A modern fountain of youth?. REJUVENATION RESEARCH, 7(2), 126-133. doi:10.1089/1549168041553044
Alice's dilemma
de Magalhaes, J. P. (2004). Alice's dilemma. FUTURES, 36(1), 85-89. doi:10.1016/S0016-3287(03)00141-1
How bioinformatics can help reverse engineer human aging
de Magalhaes, J. P., & Toussaint, O. (2004). How bioinformatics can help reverse engineer human aging. AGEING RESEARCH REVIEWS, 3(2), 125-141. doi:10.1016/j.arr.2003.08.006
No increase in senescence-associated β-galactosidase activity in Werner syndrome fibroblasts after exposure to H<sub>2</sub>O<sub>2</sub>
de Magalhaes, J. P., Migeot, V., Mainfroid, V., de Longueville, F., Remacle, J., & Toussaint, O. (2004). No increase in senescence-associated β-galactosidase activity in Werner syndrome fibroblasts after exposure to H<sub>2</sub>O<sub>2</sub>. STRATEGIES FOR ENGINEERED NEGLIGIBLE SENESCENCE: WHY GENUINE CONTROL OF AGING MAY BE FORESEEABLE, 1019, 375-378. doi:10.1196/annals.1297.066
2003
Winning the war against aging
de Magalhaes, J. P. (2003). Winning the war against aging. FUTURIST, 37(2), 48-50. Retrieved from https://www.webofscience.com/
Is mammalian aging genetically controlled?
de Magalhaes, J. P. (2003). Is mammalian aging genetically controlled?. BIOGERONTOLOGY, 4(2), 119-120. doi:10.1023/A:1023356005749
2002
The one-man rule
de Magalhaes, J. P. (2002). The one-man rule. FUTURIST, 36(6), 41-45. Retrieved from https://www.webofscience.com/
From the Hayflick mosaic to the mosaics of ageing. Role of stress-induced premature senescence in human ageing
Toussaint, O., Remacle, J., Dierick, J. F., Pascal, T., Frippiat, C., Zdanov, S., . . . Chainiaux, F. (2002). From the Hayflick mosaic to the mosaics of ageing. Role of stress-induced premature senescence in human ageing. INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY, 34(11), 1415-1429. doi:10.1016/S1357-2725(02)00034-1
UVB-induced premature senescence of human diploid skin fibroblasts
Chainiaux, F., Magalhaes, J. P., Eliaers, F., Remacle, J., & Toussaint, O. (2002). UVB-induced premature senescence of human diploid skin fibroblasts. INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY, 34(11), 1331-1339. doi:10.1016/S1357-2725(02)00022-5
Stress-induced premature senescence in BJ and hTERT-BJ1 human foreskin fibroblasts
de Magalhaes, J. P., Chainiaux, F., Remacle, J., & Toussaint, O. (2002). Stress-induced premature senescence in BJ and hTERT-BJ1 human foreskin fibroblasts. FEBS LETTERS, 523(1-3), 157-162. doi:10.1016/S0014-5793(02)02973-3
The evolution of mammalian aging
de Magalhaes, J. P., & Toussaint, O. (2002). The evolution of mammalian aging. EXPERIMENTAL GERONTOLOGY, 37(6), 769-775. doi:10.1016/S0531-5565(02)00008-6
2001
Growth kinetics rather than stress accelerate telomere shortening in cultures of human diploid fibroblasts in oxidative stress-induced premature senescence
Dumont, P., Royer, V., Pascal, T., Dierick, J. F., Chainiaux, F., Frippiat, C., . . . Toussaint, O. (2001). Growth kinetics rather than stress accelerate telomere shortening in cultures of human diploid fibroblasts in oxidative stress-induced premature senescence. FEBS LETTERS, 502(3), 109-112. doi:10.1016/S0014-5793(01)02679-5
Hormesis: a quest for virtuality?
Toussaint, O., Remacle, J., Dierick, J. F., Pascal, T., Frippiat, C., Magalhaes, J. P., & Chainaux, F. (2001). Hormesis: a quest for virtuality?. HUMAN & EXPERIMENTAL TOXICOLOGY, 20(6), 311-314. doi:10.1191/096032701701547990
Subcytotoxic H<sub>2</sub>O<sub>2</sub> stress triggers a release of transforming growth factor-β1, which induces biomarkers of cellular senescence of human diploid fibroblasts
Frippiat, C., Chen, Q. M., Zdanov, S., Magalhaes, J. P., Remacle, J., & Toussaint, O. (2001). Subcytotoxic H<sub>2</sub>O<sub>2</sub> stress triggers a release of transforming growth factor-β1, which induces biomarkers of cellular senescence of human diploid fibroblasts. JOURNAL OF BIOLOGICAL CHEMISTRY, 276(4), 2531-2537. doi:10.1074/jbc.M006809200
2000
Stress-induced premature senescence as alternative toxicological method for testing the long-term effects of molecules under development in the industry
Toussaint, O., Dumont, P., Dierick, J. F., Pascal, T., Frippiat, C., Chainiaux, F., . . . Remacle, J. (2000). Stress-induced premature senescence as alternative toxicological method for testing the long-term effects of molecules under development in the industry. BIOGERONTOLOGY, 1(2), 179-183. doi:10.1023/A:1010035712199