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Publications

2015

van Dam S, Craig T, de Magalhães JP (in press) "GeneFriends: A human RNAseq-based gene and transcript co-expression database." Nucleic Acids Research. [Webpage]

Craig T, Smelick C, Tacutu R, Wuttke D, Wood SH, Stanley H, Janssens G, Savitskaya E, Moskalev A, Arking R, de Magalhães JP (in press) "The Digital Ageing Atlas: integrating the diversity of age-related changes into a unified resource." Nucleic Acids Research. [Webpage]

Wan C, Freitas AA, de Magalhães JP (in press) "Predicting the pro-longevity or anti-longevity effect of model organism genes with new hierarchical feature selection methods." IEEE IEEE/ACM Transactions on Computational Biology and Bioinformatics.

2014

Keane K, Craig T, Alfoldi J, Berlin AM, Johnson J, Seluanov A, Gorbunova V, Di Palma F, Lindblad-Toh K, Church GM, de Magalhães JP (2014) "The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations." Bioinformatics 30:3558-3360. [Webpage]

de Magalhães JP (2014) "The scientific quest for lasting youth: prospects for curing aging." Rejuvenation Research 17:458-467.

de Magalhães JP (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 13:2671-2673.

2013

Budovsky A, Craig T, Wang J, Tacutu R, Csordas A, Lourenço J, Fraifeld VE, de Magalhães JP (2013) "LongevityMap: A database of human genetic variants associated with longevity." Trends in Genetics 29:559-560. [Webpage]

de Magalhães JP, Keane M (2013) "Endless paces of degeneration-applying comparative genomics to study evolution's moulding of longevity." EMBO Reports 16:661-662.

Holmes AP, Wood SH, Merry BJ, de Magalhães JP (2013) "A-to-I RNA editing does not change with age in the healthy male rat brain." Biogerontology 14:395-400. [Supplementary material]

Avraam D, de Magalhaes JP, Vasiev B (2013) "A mathematical model of mortality dynamics across the lifespan combining heterogeneity and stochastic effects." Experimental Gerontology 48:801-811.

Keane M, de Magalhães JP (2013) "MYCN/LIN28B/Let-7/HMGA2 pathway implicated by meta-analysis of GWAS in suppression of post-natal proliferation thereby potentially contributing to aging." Mechanisms of Ageing and Development 134:346-348.

Wood SH, Craig T, Li Y, Merry B, de Magalhães JP (2013) "Whole transcriptome sequencing of the aging rat brain reveals dynamic RNA changes in the dark matter of the genome." Age (Dordr) 35:763-776. [Supplementary material] [Webpage]

de Magalhães JP (2013) "How ageing processes influence cancer." Nature Reviews Cancer 13:357-365.

Plank M, Hu G, Silva AS, Wood SH, Hesketh EE, Janssens G, Macedo A, de Magalhães JP, Church GM (2013) "An analysis and validation pipeline for large-scale RNAi-based screens." Scientific Reports 3:1076. [Supplementary material]

Li Y, de Magalhães JP (2013) "Accelerated protein evolution analysis reveals genes and pathways associated with the evolution of mammalian longevity." Age (Dordr) 35:301-314. [Supplementary material] [Webpage]

Sethe S, de Magalhães JP (2013) "Ethical Perspectives in Biogerontology." In: Schermer M, Pinxten W (eds.), Ethics, Health Policy and (Anti-) Aging: Mixed Blessings. Springer, Dordrecht, Netherlands, pp. 173-188.

Tacutu R, Craig T, Budovsky A, Wuttke D, Lehmann G, Taranukha D, Costa J, Fraifeld VE, de Magalhães JP (2013) "Human Ageing Genomic Resources: Integrated databases and tools for the biology and genetics of ageing." Nucleic Acids Research 41:D1027–D1033. [Webpage]

2012

de Magalhães JP (2012) "Programmatic features of aging originating in development: aging mechanisms beyond molecular damage?" FASEB Journal 26:4821-4826.

Tacutu R, Shore DE, Budovsky A, de Magalhães JP, Ruvkun G, Fraifeld VE, Curran SP (2012) "Prediction of C. elegans longevity genes by human and worm longevity networks." PLoS ONE 7:e48282.

van Dam S, Cordeiro R, Craig T, van Dam J, Wood SH, de Magalhães JP (2012) "GeneFriends: An online co-expression analysis tool to identify novel gene targets for aging and complex diseases." BMC Genomics 13:535. [Supplementary material] [Webpage]

Johnson AA, Akman K, Calimport SR, Wuttke D, Stolzing A, de Magalhães JP (2012) "The role of DNA methylation in aging, rejuvenation, and age-related disease." Rejuvenation Research 15:483-494.

Wuttke D, Connor R, Vora C, Craig T, Li Y, Wood S, Vasieva O, Shmookler Reis R, Tang F, de Magalhães JP (2012) "Dissecting the gene network of dietary restriction to identify evolutionarily conserved pathways and new functional genes." PLoS Genetics 8:e1002834. [Supplementary material] [Webpage]

Aledo JC, Valverde H, de Magalhães JP (2012) "Mutational bias plays an important role in shaping longevity-related amino acid content in mammalian mtDNA-encoded proteins." Journal of Molecular Evolution 74:332-341.

Wuttke D, de Magalhães JP (2012) "Osh6 links yeast vacuolar functions to lifespan extension and TOR." Cell Cycle 11:2419-2420.

Plank M, Wuttke D, van Dam S, Clarke S, de Magalhães JP (2012) "A meta-analysis of caloric restriction gene expression profiles to infer common signatures and regulatory mechanisms." Molecular BioSystems 8:1339-1349. [Supplementary material] [Webpage]

de Magalhães JP, 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. [Supplementary material] [Webpage]

de Magalhães JP, Wuttke D, Wood SH, Plank M, Vora C (2012) "Genome-environment interactions that modulate aging: powerful targets for drug discovery." Pharmacological Reviews 64:88-101.

2011

Silva AS, Wood SH, van Dam S, Berres S, McArdle A, de Magalhaes JP (2011) "Gathering insights on disease etiology from gene expression profiles of healthy tissues." Bioinformatics 27:3300-3305. [Supplementary data] [Webpage]

Yu C, Li Y, Holmes A, Szafranski K, Faulkes CG, Coen CW, Buffenstein R, Platzer M, de Magalhães JP, Church GM (2011) "RNA sequencing reveals differential expression of mitochondrial and oxidation reduction genes in the long-lived naked mole-rat (Heterocephalus glaber) when compared to mice." PLoS ONE 6:e26729. [Supplementary material] [Webpage]

Freitas AA, de Magalhaes JP (2011) "A review and appraisal of the DNA damage theory of ageing." Mutation Research/Reviews in Mutation Research 728:12-22.

de Magalhães JP (2011) "The Biology of Ageing: A Primer." In: Stuart-Hamilton I (ed.), An Introduction to Gerontology. Cambridge University Press, Cambridge, UK, pp. 21-47.

de Magalhães JP (2011) "A role for Ras signaling in modulating mammalian aging by the GH/IGF1 axis." Aging (Albany NY) 3:336-337.

Aledo JC, Li Y, de Magalhães JP, Ruiz-Camacho M, Perez-Claros JA (2011) "Mitochondrially encoded methionine is inversely related to longevity in mammals." Aging Cell 10:198-207.

Freitas AA, Vasieva O, de Magalhaes JP (2011) "A data mining approach for classifying DNA repair genes into ageing-related or non-ageing-related." BMC Genomics 12:27. [Supplementary material] [Webpage]

de Magalhães JP (2011) "Paternal genome effects on aging: evidence for a role of Rasgrf1 in longevity determination?" Mechanisms of Ageing and Development 132:72-73.

2010

Fuellen G, Adjaye J, de Grey A, Lepperdinger G, de Magalhães JP, Suhnel J, Wipat A (2010) "Bioinformatics in aging research: a workshop report." Rejuvenation Research 13:763-767.

Cohen AA, de Magalhães JP, Gohil K (2010) "Ecological, biomedical and epidemiological approaches to understanding oxidative balance and ageing: what they can teach each other." Functional Ecology 24:997-1006.

Nicholas A, de Magalhaes JP, Kraytsberg Y, Richfield EK, Levanon EY, Khrapko K (2010) "Age-related gene-specific changes of A-to-I mRNA editing in the human brain." Mechanisms of Ageing and Development 131:445-447.

Finch CE, Morgan TE, Longo VD, de Magalhães JP (2010) "Cell resilience in species lifespans: a link to inflammation?" Aging Cell 9:519-526.

de Magalhães JP, Finch CE, Janssens G (2010) "Next-generation sequencing in aging research: emerging applications, problems, pitfalls and possible solutions." Ageing Research Reviews 9:315-323.

Cevenini E, Bellavista E, Tieri P, Castellani G, Lescai F, Francesconi M, Mishto M, Santoro A, Valensin S, Salvioli S, Capri M, Zaikin A, Monti D, de Magalhães JP, Franceschi C (2010) "Systems biology and longevity: an emerging approach to identify innovative anti-aging targets and strategies." Current Pharmaceutical Design 16:802-813.

2009

de Magalhães JP, Costa J (2009) "A database of vertebrate longevity records and their relation to other life-history traits." Journal of Evolutionary Biology 22:1770-1774. [Webpage]

de Magalhães JP, Curado J, Church GM (2009) "Meta-analysis of age-related gene expression profiles identifies common signatures of aging." Bioinformatics 25:875-881. [Supplementary material] [Webpage]

de Magalhães JP (2009) "Aging Research in the Post-Genome Era: New Technologies for an Old Problem." In: Foyer CH, Faragher R, Thornalley PJ (eds.), Redox Metabolism and Longevity Relationships in Animals and Plants. Taylor and Francis, New York, pp. 99-115.

de Magalhães JP, Budovsky A, Lehmann G, Costa J, Li Y, Fraifeld V, Church GM (2009) "The Human Ageing Genomic Resources: online databases and tools for biogerontologists." Aging Cell 8:65-72. [Webpage]

2008

de Magalhães JP, Faragher RGA (2008) "Cell divisions and mammalian aging: integrative biology insights from genes that regulate longevity." BioEssays 30:567-578.

de Magalhães JP, Sedivy JM, Finch CE, Austad SN, Buffenstein R, Church GM (2008) "Proposal to Sequence an Organism of Unique Interest for Research on Aging: Heterocephalus glaber, the Naked Mole-Rat." Submitted to the NIH/NHGRI on March 17, 2008. [Webpage]

2007

de Magalhães JP, Church GM (2007) "Analyses of human-chimpanzee orthologous gene pairs to explore evolutionary hypotheses of aging." Mechanisms of Ageing and Development 128:355-364. [Supplementary material] [Webpage]

de Magalhães JP, Sedivy JM, Finch CE, Austad SN, Church GM (2007) "A proposal to sequence genomes of unique interest for research on aging." Journal of Gerontology: Biological Sciences 62:583-584. [Webpage]

de Magalhães JP, Costa J, Church GM (2007) "An analysis of the relationship between metabolism, developmental schedules, and longevity using phylogenetic independent contrasts." Journal of Gerontology: Biological Sciences 62:149-160.

2006

de Magalhães JP, Church GM (2006) "Cells discover fire: Employing reactive oxygen species in development and consequences for aging." Experimental Gerontology 41:1-10.

de Magalhães JP (2006) "Species Selection in Comparative Studies of Aging and Antiaging Research." In: Conn PM (ed.), Handbook of Models for Human Aging. Elsevier Academic Press, Burlington, MA, pp. 9-20.

2005

de Magalhães JP (2005) "Human disease-associated mitochondrial mutations fixed in nonhuman primates." Journal of Molecular Evolution 61:491-497. [Supplementary material] [Webpage]

de Magalhães JP, Church GM (2005) "Genomes optimize reproduction: aging as a consequence of the developmental program." Physiology 20:252-259.

de Magalhães JP, Sandberg A (2005) "Cognitive aging as an extension of brain development: A model linking learning, brain plasticity, and neurodegeneration." Mechanisms of Ageing and Development 126:1026-1033.

de Magalhães JP, Costa J, Toussaint O (2005) "HAGR: the Human Ageing Genomic Resources." Nucleic Acids Research 33:D537-D543. [Supplementary material] [Webpage]

de Magalhães JP, Cabral JAS, Magalhães D (2005) "The influence of genes on the aging process of mice: a statistical assessment of the genetics of aging." Genetics 169:265-274. [Supplementary material] [Software]

de Magalhães JP (2005) "Open-minded scepticism: inferring the causal mechanisms of human ageing from genetic perturbations." Ageing Research Reviews 4:1-22.

2004

de Magalhães JP (2004) "From cells to ageing: a review of models and mechanisms of cellular senescence and their impact on human ageing." Experimental Cell Research 300:1-10.

de Magalhães JP, Chainiaux F, de Longueville F, Mainfroid V, Migeot V, Marcq L, Remacle J, Salmon M, Toussaint O (2004) "Gene expression and regulation in H2O2-induced premature senescence of human foreskin fibroblasts expressing or not telomerase." Experimental Gerontology 39:1379-1389. [Supplementary material]

de Magalhães JP, Toussaint O (2004) "Telomeres and telomerase: a modern Fountain of Youth?" Rejuvenation Research 7:126-132.

de Magalhães JP, Toussaint O (2004) "GenAge: a genomic and proteomic network map of human ageing." FEBS Letters 571:243-247.

de Magalhães JP, Migeot V, Mainfroid V, de Longueville F, Remacle J, Toussaint O (2004) "No increase in senescence-associated beta-galactosidase activity in Werner syndrome fibroblasts after exposure to H2O2." In: de Grey ADNJ (ed.), Strategies for Engineered Negligible Senescence: Why Genuine Control of Aging May Be Foreseeable. Annals of the New York Academy of Sciences, Vol. 1019, pp. 375-378.

de Magalhães JP, Toussaint O (2004) "How bioinformatics can help reverse engineer human aging." Ageing Research Reviews 3:125-141.

de Magalhães JP (2004) "The Dream of Elixir Vitae." In: Immortality Institute (ed.), The Scientific Conquest of Death: Essays on Infinite Lifespans. Libros En Red, Buenos Aires, pp. 47-62. [Adapted version]

de Magalhães JP (2004) "Modelling human ageing: role of telomeres in stress-induced premature senescence and design of anti-ageing strategies". Doctoral thesis, University of Namur, Department of Biology, Namur, Belgium.

2003

de Magalhães JP (2003) "Winning the war against aging." The Futurist, 37:48-50. [Adapted version]

de Magalhães JP (2003) "Is mammalian aging genetically controlled?" Biogerontology 4:119-120.

2002

de Magalhães JP, Chainiaux F, Remacle J, Toussaint O (2002) "Stress-induced premature senescence in BJ and hTERT-BJ1 human fibroblasts." FEBS Letters 523:157-162.

Chainiaux F, Magalhaes JP, Eliaers F, Remacle J, Toussaint O (2002) "UV-B induced premature senescence of human diploid skin fibroblasts." International Journal of Biochemistry & Cell Biology 34:1331-1339.

de Magalhães JP, Toussaint O (2002) "The evolution of mammalian aging." Experimental Gerontology 37:769-775.

2001

Frippiat C, Chen QM, Zdanov S, Magalhaes JP, Remacle J, Toussaint O (2001) "Subcytotoxic H2O2 stress triggers a release of transforming growth factor-beta 1, which induces biomarkers of cellular senescence of human diploid fibroblasts." Journal of Biological Chemistry 276:2531-2537.