Fabris F, Palmer D, Farooq Z, de Magalhães JP, Freitas AA (submitted) "PICKER-HG: a web server using random forests for classifying human genes into categories." Preprint BioRxiv: 10.1101/681460. [Webpage]
Chatsirisupachai K, Palmer D, Ferreira S, de Magalhães JP (submitted) "A human tissue-specific transcriptomic analysis reveals that ageing hinders cancer and boosts cellular senescence." Preprint BioRxiv: 10.1101/595041.
Fabris F, Palmer D, de Magalhães JP, Freitas AA (in press) "Comparing enrichment analysis and machine learning for identifying gene properties that discriminate between gene classes." Briefings in Bioinformatics.
Chen K, Wei Z, Zhang Q, Wu X, Rong R, Lu Z-L, Su J, de Magalhães JP, Rigden DJ, Meng J (2019) "WHISTLE: a high-accuracy map of the human N6-methyladenosine (m6A) epitranscriptome predicted using a machine learning approach." Nucleic Acids Research 26:1627-1640. [Webpage]
Monaco G, Lee B, Xu W, Mustafah S, Hwang YY, Carre C, Burdin N, Visan L, Ceccarelli M, Poidinger M, Zippelius A, de Magalhães JP, Larbi A (2019) "RNA-seq signatures normalized by mRNA abundance allow absolute deconvolution of human immune cell types." Cell Reports 26:1627-1640. [Supplementary material]
Muntané G, Farré X, Rodríguez JA, Pegueroles C, Hughes DA, de Magalhães JP, Gabaldón T, Navarro A (2018) "Biological processes modulating longevity across primates: a phylogenetic genome-phenome analysis." Molecular Biology and Evolution 35:1990-2004.
Fabris F, Doherty A, Palmer D, de Magalhães JP, Freitas AA (2018) "A new approach for interpreting Random Forest models and its application to the biology of ageing." Bioinformatics 34:2449-2456. [Supplementary material]
Chen K, Wei Z, Liu H, de Magalhães JP, Rong R, Lu Z, Meng J (2018) "Enhancing epitranscriptome module detection from m6A-seq data using threshold-based measurement weighting strategy." BioMed Research International 2018:2075173.
Wei Z, Panneerdoss S, Timilsina S, Mohammad T, Rong R, Lu ZL, de Magalhães JP, Chen Y, Huang Y, Rao M, Meng J (2018) "Topological characterization of human and mouse m5C epitranscriptome revealed by bisulfite sequencing." International Journal of Genomics 2018:1351964.
Tong K-L, Mahmood Zuhdi AS, Wan Ahmad WA, Vanhoutte PM, de Magalhaes JP, Mustafa MR, Wong P-F (2018) "Circulating microRNAs in young patients with acute coronary syndrome." International Journal of Molecular Sciences 19:E1467.
de Magalhães JP, Thompson L, de Lima I, Gaskill D, Li X, Thornton D, Yang C, Palmer D (2018) "A reassessment of genes modulating aging in mice using demographic measurements of the rate of aging." Genetics 208:1617-1630. [Supplementary material] [Software]
Zhao Y, Tyshkovskiy A, Muñoz-Espín D, Tian X, Serrano M, de Magalhaes JP, Nevo E, Gladyshev VN, Seluanov A, Gorbunova V (2018) "Naked mole rats can undergo developmental, oncogene-induced and DNA damage-induced cellular senescence." Proceedings of the National Academy of Sciences 115:1801-1806. [Supplementary material]
Cortese F, Klokov D, Osipov A, Stefaniak J, Moskalev A, Schastnaya J, Cantor C, Aliper A, Mamoshina P, Ushakov I, Sapetsky A, Vanhaelen Q, Alchinova I, Karganov M, Kovalchuk O, Wilkins R, Shtemberg A, Moreels M, Baatout S, Izumchenko E, de Magalhaes JP, Artemov AV, Costes SV, Beheshti A, Mao XW, Pecaut MJ, Kaminskiy D, Ozerov IV, Scheibye-Knudsen M, Zhavoronkov A (2018) "Vive la radioresistance!: converging research in radiobiology and biogerontology to enhance human radioresistance for deep space exploration and colonization." Oncotarget 9:14692-14722.
Tacutu R, Thornton D, Johnson E, Budovsky A, Barardo D, Craig T, Diana E, Lehmann G, Toren D, Wang J, Fraifeld VE, de Magalhães JP (2018) "Human Ageing Genomic Resources: new and updated databases." Nucleic Acids Research 46:D1083-D1090. [Webpage]
Barardo D, Thornton D, Thoppil H, Walsh M, Sharifi S, Ferreira S, Anic A, Fernandes M, Monteiro P, Grum T, Cordeiro R, De-Souza EA, Budovsky A, Araujo N, Gruber J, Petrascheck M, Fraifeld VE, Zhavoronkov A, Moskalev A, de Magalhães JP (2017) "The DrugAge database of aging-related drugs." Aging Cell 16:594-597. [Supplementary material] [Webpage]
Fabris F, de Magalhães JP, Freitas AA (2017) "A review of supervised machine learning applied in ageing research." Biogerontology 18:171-188. [Webpage]
Nam K, Lee KW, Chung O, Yim HS, Cha SS, Lee SW, Jun J, Cho YS, Bhak J, de Magalhães JP, Lee JH, Jeong JY (2017) "Analysis of the FGF gene family provides insights into aquatic adaptation in cetaceans." Scientific Reports 7:40233. [Supplementary material]
Fernandes M, Wan C, Tacutu R, Barardo D, Rajput A, Wang J, Thoppil H, Thornton D, Yang C, Freitas A, de Magalhães JP (2016) "Systematic analysis of the gerontome reveals links between aging and age-related diseases." Human Molecular Genetics 25:4804-4818. [Supplementary material]
Doherty A, de Magalhães JP (2016) "Has gene duplication impacted the evolution of Eutherian longevity?" Aging Cell 15:978-980. [Supplementary material]
Strong R, Miller RA, Antebi A, Astle CM, Bogue M, Denzel MS, Fernandez E, Flurkey K, Hamilton KL, Lamming DW, Javors MA, de Magalhães JP, Marinez PA, McCord JM, Miller BF, Müller M, Nelson JF, Ndukum J, Rainger GE, Richardson A, Sabatini DM, Salmon AB, Simpkins JW, Steegenga WT, Nadon NL, Harrison DE (2016) "Longer lifespan in male mice treated with a weakly estrogenic agonist, an antioxidant, an α-glucosidase inhibitor or a Nrf2-inducer." Aging Cell 15:872-884. [Supplementary material]
Monaco G, Chen H, Poidinger M, Chen J, de Magalhães JP, Larbi A (2016) "flowAI: automatic and interactive anomaly discerning tools for flow cytometry data." Bioinformatics 32:2473-2480. [Supplementary material] [Software]
Holmes AP, Wong SQ, Pulix M, Johnson K, Horton NS, Thomas P, de Magalhães JP, Plagge A (2016) "Reductions in hypothalamic Gfap expression, glial cells and α-tanycytes in lean and hypermetabolic Gnasxl-deficient mice." Molecular Brain 9:39.
Calvert S, Tacutu R, Sharifi S, Teixeira R, Ghosh P, de Magalhães JP (2016) "A network pharmacology approach reveals new candidate caloric restriction mimetics in C. elegans." Aging Cell 15:256-266. [Supplementary material]
Wood SH, van Dam S, Craig T, Tacutu R, O'Toole A, Merry BJ, de Magalhães JP (2015) "Transcriptome analysis in calorie-restricted rats implicates epigenetic and post-translational mechanisms in neuroprotection and aging." Genome Biology 16:285. [Supplementary material]
Cordeiro RM, Stirling S, Fahy GM, de Magalhães JP (2015) "Insights on cryoprotectant toxicity from gene expression profiling of endothelial cells exposed to ethylene glycol." Cryobiology 71:405-412. [Supplementary material] [Webpage]
Monaco G, van Dam S, Casal Novo Ribeiro JL, Larbi A, de Magalhães JP (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 15:259. [Supplementary material]
Moskalev A, Chernyagina E, de Magalhães JP, Barardo D, Thoppil H, Shaposhnikov M, Budovsky A, Fraifeld VE, Garazha A, Tsvetkov V, Bronovitsky E, Bogomolov V, Scerbacov A, Kuryan O, Gurinovich R, Jellen LC, Kennedy B, Mamoshina P, Dobrovolskaya E, Aliper A, Kaminsky D, Zhavoronkov A (2015) "Geroprotectors.org: a new, structured and curated database of current therapeutic interventions in aging and age-related disease." AGING 7:616-628. [Webpage]
Wan C, Freitas AA, de Magalhães JP (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 12:262-275. [Supplementary material]
Craig T, Smelick C, Tacutu R, Wuttke D, Wood SH, Stanley H, Janssens G, Savitskaya E, Moskalev A, Arking R, de Magalhães JP (2015) "The Digital Ageing Atlas: integrating the diversity of age-related changes into a unified resource." Nucleic Acids Research 43:D873-D878. [Webpage]
Keane M, Semeiks J, Webb AE, Li YI, Quesada V, Craig T, Madsen LB, van Dam S, Brawand D, Marques PI, Michalak P, Kang L, Bhak J, Yim HS, Grishin NV, Nielsen NH, Heide-Jorgensen MP, Oziolor EM, Matson CW, Church GM, Stuart GW, Patton JC, George JC, Suydam R, Larsen K, Lopez-Otin C, O'Connell MJ, Bickham JW, Thomsen B, de Magalhães JP (2015) "Insights into the evolution of longevity from the bowhead whale genome." Cell Reports 10:112-120. [Supplementary material] [Webpage]
Keane M, 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.