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