Papers and Relevant Publications
The Human Ageing Genomic Resources and its associated resources have been featured in several publications, including official descriptions and a few analyses by HAGR's authors, and numerous publications by other researchers.
Official descriptions of HAGR
The official, academic paper describing the Human Ageing Genomic Resources is:
de Magalhaes, J. P., et al. (2005) "HAGR: the Human Ageing Genomic Resources." Nucleic Acids Res 33(Database Issue):D537-D543.
We prefer, however, that authors using our resources cite a more recent description of HAGR as it not only details numerous recent updates and enhancements but also as a way to credit new contributors not included in our previous description of HAGR:
de Magalhaes, J. P., et al. (2009) "The Human Ageing Genomic Resources: online databases and tools for biogerontologists." Aging Cell 8(1):65-72.
Finally, we ask that authors employing only our AnAge database cite:
de Magalhaes, J. P., and 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.
Analyses of HAGR datasets by its authors
We conducted a number of broad analyses using HAGR databases. Firstly, we obtained a visualization and interpretation of the genomic and proteomic network of ageing using GenAge:
de Magalhaes, J. P., and Toussaint, O. (2004) "GenAge: a genomic and proteomic network map of human ageing." FEBS Lett 571(1-3):243-247.
An analysis of molecular evolution rates of GenAge was done employing human-chimpanzee gene pairs:
de Magalhaes, J. P., and Church, G. M. (2007) "Analyses of human-chimpanzee orthologous gene pairs to explore evolutionary hypotheses of aging." Mech Ageing Dev 128(5-6):355-364.
Finally, we took advantage of the AnAge dataset to evaluate the relationship between metabolic rates, growth rates, developmental timing, and longevity:
de Magalhaes, J. P., et al. (2007) "An analysis of the relationship between metabolism, developmental schedules, and longevity using phylogenetic independent contrasts." J Gerontol A Biol Sci Med Sci 62(2):149-160.
Other citations in academic journals
The Human Ageing Genomic Resources have been highlighted in:
 Nature Reviews Genetics, 5(5):1362 (WEB WATCH) View online |
 Science, 307(5707):187 (NetWatch) View online |
 Science's SAGE KE, 2004(30):nf69 View online |
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 Biomedical Computation Review, 4(2):7-15 View online |
 BioTechniques, 39(1):21 (WebWatch) View online |
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Other works using and/or citing HAGR:
Chung, H. Y., et al. (2004) "Molecular inflammation hypothesis of aging." Kor J Gerontol 14(1):12-19.
de Magalhaes, J. P. (2005) "Open-minded scepticism: inferring the causal mechanisms of human ageing from genetic perturbations." Ageing Res Rev 4(1):1-22.
Morris, B. J. (2005) "A forkhead in the road to longevity: the molecular basis of lifespan becomes clearer." J Hypertens 23(7):1285-1309.
Raghothama, C., et al. (2005) "Bioinformatics and proteomics approaches for aging research." Biogerontology 6(4):227-232.
Karasik, D., et al. (2005) "Disentangling the genetic determinants of human aging: biological age as an alternative to the use of survival measures." J Gerontol A Biol Sci Med Sci 60(5):574-587.
de Magalhaes, J. P. (2005) "Human disease-associated mitochondrial mutations fixed in nonhuman primates." J Mol Evol 61(4):491-497.
Galvin, J. E., and Ginsberg, S. D. (2005) "Expression profiling in the aging brain: a perspective." Ageing Res Rev 4(4):529-547.
Fried, L. P., et al. (2005) "From bedside to bench: research agenda for frailty." Sci Aging Knowledge Environ 2005(31):pe24.
Blalock, E. M., et al. (2005) "Harnessing the power of gene microarrays for the study of brain aging and Alzheimer's disease: statistical reliability and functional correlation." Ageing Res Rev 4(4):481-512.
Ruggiero, C., and Ferrucci, L. (2006) "The endeavor of high maintenance homeostasis: resting metabolic rate and the legacy of longevity." J Gerontol A Biol Sci Med Sci 61(5):466-471.
Rottenberg, H. (2006) "Longevity and the evolution of the mitochondrial DNA-coded proteins in mammals." Mech Ageing Dev 127(9):748-760.
Lehmann, G. et al. (2006) "Mitochondrial genome anatomy and species-specific lifespan." Rejuvenation Res 9(2):223-226.
Khaidakov, M., et al. (2006) "Direct repeats in mitochondrial DNA and mammalian lifespan." Mech Ageing Dev 127(10):808-812.
Kriete, A., et al. (2006) "Systems approaches to the networks of aging." Ageing Res Rev 5(4):434-448.
Swynghedauw, B., et al. (2006) "Biology of cardiac and vascular senescence." [Article in French] Bull Acad Natl Med 190(4-5):783-792.
Murakami, S. (2006) "Stress resistance in long-lived mouse models." Exp Gerontol 41(10):1014-1019.
Harper, J. M., et al. (2007) "Skin-derived fibroblasts from long-lived species are resistant to some, but not all, lethal stresses and to the mitochondrial inhibitor rotenone." Aging Cell 6(1):1-13.
Seluanov, A., et al. (2007) "Telomerase activity coevolves with body mass not lifespan." Aging Cell 6(1):45–52.
Rottenberg, H. (2007) "Coevolution of exceptional longevity, exceptionally high metabolic rates, and mitochondrial DNA-coded proteins in mammals." Exp Gerontol 42(4):364-373.
Rottenberg, H. (2007) "Exceptional longevity in songbirds is associated with high rates of evolution of cytochrome b, suggesting selection for reduced generation of free radicals." J Exp Biol 210(12):2170-2180.
Martin, G. M., et al. (2007) "Genetic determinants of human health span and life span: progress and new opportunities." PLoS Genet 3(7):e125.
Kahn, A. J. (2007) "Epigenetic and mitochondrial mechanisms in aging and longevity: a report of a meeting of the Longevity Consortium, Napa, California, October 25-27, 2006." J Gerontol A Biol Sci Med Sci 62(6):577-582.
Lambert, A. J., et al. (2007) "Low rates of hydrogen peroxide production by isolated heart mitochondria associate with long maximum lifespan in vertebrate homeotherms." Aging Cell 6(5):607-618.
Lunetta, K. L., et al. (2007) "Genetic correlates of longevity and selected age-related phenotypes: a genome-wide association study in the Framingham Study." BMC Med Genet 6(Suppl 1):S13.
Huhne, R., et al. (2007) "A comparative view at comprehensive information resources on three-dimensional structures of biological macro-molecules." Brief Funct Genomic Proteomic 6(3):220-239.
Xue, H., et al. (2007) "A modular network model of aging." Mol Syst Biol 3:147.
Pletcher, S. D., et al. (2007) "Chemical complexity and the genetics of aging." Annu Rev Ecol Evol Syst 38:299-326.
Moosmann, B., and Behl, C. (2008) "Mitochondrially encoded cysteine predicts animal lifespan." Aging Cell 7(1):32-46.
Nabholz, B., et al. (2008) "Determination of mitochondrial genetic diversity in mammals." Genetics 178(1):351-361.
Nabholz, B., et al. (2008) "Strong variations of mitochondrial mutation rate across mammals--the longevity hypothesis." Mol Biol Evol 25(1):120-130.
Georgopoulo, P. G. (2008) "A multiscale approach for assessing the interactions of environmental and biological systems in a holistic health risk assessment framework." Water Air Soil Pollut Focus 8(1):3-21.
Sebastiani, P., et al. (2008) "A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples." BMC Med Genet 9:6.
Chen, D. P., et al. (2008) "Novel integration of hospital electronic medical records and gene expression measurements to identify genetic markers of maturation." Pac Symp Biocomput 243-254.
Buffenstein, R. (2008) "Negligible senescence in the longest living rodent, the naked mole-rat: insights from a successfully aging species." J Comp Physiol [B] 178(4):439-445.
Welch, J. J., et al. (2008) "Correlates of substitution rate variation in mammalian protein-coding sequences." BMC Evol Biol 8:53.
Kleine, L. L., et al. (2008) "Role of bacterial peptidase F inferred by statistical analysis and further experimental validation." HFSP J 2(1):29-41.
Jorge, M. L. S. P. (2008) "Effects of forest fragmentation on two sister genera of Amazonian rodents (Myoprocta acouchy and Dasyprocta leporina)." Biol Conserv 141(3):617-623.
da Fonseca, R. R., et al. (2008) "The adaptive evolution of the mammalian mitochondrial genome." BMC Genomics 9:119.
Asher, R. J., and Lehmann, T. (2008) "Dental eruption in afrotherian mammals." BMC Genomics 6:14.
Lehmann, G., et al. (2008) "Do mitochondrial DNA and metabolic rate complement each other in determination of the mammalian maximum longevity?" Rejuvenation Res 11(2):409-417.
Gielchinsky, Y., et al. (2008) "Gene expression in women conceiving spontaneously over the age of 45 years." Fertil Steril 89(6):1641-1650.
Pang, C. Y., et al. (2008) "MtDNA mutations, functional decline and turnover of mitochondria in aging." Front Biosci 13(6):3661-3675.
Han, L., et al. (2008) "CpG island density and its correlations with genomic features in mammalian genomes." Genome Biol 9(5):R79.
Hardman, M. J., and Ashcroft, G. S. (2008) "Estrogen, not intrinsic aging, is the major regulator of delayed human wound healing in the elderly." Genome Biol 9(5):R80.
de Magalhaes, J. P., and Faragher, R. G. (2008) "Cell divisions and mammalian aging: integrative biology insights from genes that regulate longevity." Bioessays 30(6):567-578.
Furness, L. J., and Speakman, J. R. (2008) "Energetics and longevity in birds." AGE 30(2-3):75-87.
Buffenstein, R., et al. (2008) "The oxidative stress theory of aging: embattled or invincible? Insights from non-traditional model organisms." AGE 30(2-3):99-109.
Seluanov, A., et al. (2008) "Distinct tumor suppressor mechanisms evolve in rodent species that differ in size and lifespan." Aging Cell 7(6):813-823.
Min, X. J., and Hickey, D. A. (2008) "An evolutionary footprint of age-related natural selection in mitochondrial DNA." J Mol Evol 67(4):412-417.
Kitazoe, Y., et al. (2008) "Adaptive threonine increase in transmembrane regions of mitochondrial proteins in higher primates." PLoS ONE 3(10):e3343.
Managbanag, J. R., et al. (2008) "Shortest-path network analysis is a useful approach toward identifying genetic determinants of longevity." PLoS ONE 3(11):e3802.
Mumby, H., and Vinicius, L. (2008) "Primate growth in the slow lane: a study of inter-species variation in the growth constant A." Evol Biol 35(4):287-295.
Robb, E.L., et al. (2009) "Mitochondria, cellular stress resistance, somatic cell depletion and lifespan." Curr Aging Sci 2(1):12-27.
Gorbunova, V., and Seluanov, A. (2009) "Coevolution of telomerase activity and body mass in mammals: from mice to beavers." Mech Ageing Dev 130(1-2):3-9.
Budovsky, A., et al. (2009) "Common gene signature of cancer and longevity." Mech Ageing Dev 130(1-2):33-39.
Rattan, S.I., and Singh, R. (2009) "Progress & prospects: gene therapy in aging." Gene Ther 16(1):3-9.
Austad, S.N. (2009) "Comparative biology of aging." J Gerontol A Biol Sci Med Sci 64(2):199-201.
Buffenstein, R., and Pinto, M. (2009) "Endocrine function in naturally long-living small mammals." Mol Cell Endocrinol 299(1):101-111.
Wolfson, M., et al. (2009) "The signaling hubs at the crossroad of longevity and age-related disease networks." Int J Biochem Cell Biol 41(3):516-520.
Altar, C.A. et al. (2009) "Target identification for CNS diseases by transcriptional profiling." Neuropsychopharmacology 34(1):18-54.
Bonatto, C.C. et al. (2009) "Shape and size of red blood cells from the Pygoscelid penguins of Antarctica using atomic force microscopy." Polar Biol 32(2):287-293.
Nabholz, B. et al. (2009) "The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals." BMC Evol Biol 9:54.
Galtier, N. et al. (2009) "Inverse relationship between longevity and evolutionary rate of mitochondrial proteins in mammals and birds." Mitochondrion 9(1):51-57.
Bostock, C.V. et al. (2009) "Genetic determinants of ageing processes and diseases in later life." Maturitas 62(3):225-229.
Lynch, H.J., and Fagan, W.F. (2009) "Survivorship curves and their impact on the estimation of maximum population growth rates." Ecology 90(4):1116-1124.
Asher, R.J., and Olbricht, G. (2009) "Dental ontogeny in Macroscelides proboscideus (Afrotheria) and Erinaceus europaeus (Lipotyphla)." J Mamm Evol 16(2):99-115.
Estep, P.W. et al. (2009) "Short-term calorie restriction in male mice feminizes gene expression and alters key regulators of conserved aging regulatory pathways." PLoS One 4(4):e5242.
Somel, M. et al. (2009) "Transcriptional neoteny in the human brain." Proc Natl Acad Sci U S A 106(14):5743-5748.
Demetrius, L. et al. (2009) "Evolutionary entropy: a predictor of body size, metabolic rate and maximal life span." Bull Math Biol 71(4):800-818.
Emamian, E.S. et al. (2009) "Peripheral blood gene expression profiling in Sjögren's syndrome." Genes Immun 10(4):285-296.
Rosenstiel, P. et al. (2009) "Evolution and function of innate immune receptors - insights from marine invertebrates." J Innate Immun 1(4):291-300.
Karol, M.H. (2009) "How environmental agents influence the aging process." Biomolecules & Therapeutics 17(2):113-124.
Forero-Medina, G. et al. (2009) "Body size and extinction risk in Brazilian carnivores." Biota Neotrop 9(2).
Halaschek-Wiener, J. et al. (2009) "Genetic variation in healthy oldest-old." PLoS One 4(8):e6641.
Zhang, T. et al. (2009) "The effect of osteoprotegerin gene modification on wear debris-induced osteolysis in a murine model of knee prosthesis failure." Biomaterials 30(30):6102-6108.
Zetterberg, H. et al. (2009) "The szilard hypothesis on the nature of aging revisited." Genetics 182(1):3-9.
Gillis, J., and Pavlidis, P. (2009) "A methodology for the analysis of differential coexpression across the human lifespan." BMC Bioinformatics 10:306.
Wang, J. et al. (2009) "Disease-aging network reveals significant roles of aging genes in connecting genetic diseases." PLoS Comput Biol 5(9):e1000521.
Simko, G.I. et al. (2009) "Network strategies to understand the aging process and help age-related drug design." Genome Med 1(9):90.
Lescai, F. et al. (2009) "Human longevity and 11p15.5: a study in 1321 centenarians." Eur J Hum Genet 17(11):1515-1519.
Sedivy, J.M. (2009) "How to learn new and interesting things from model systems based on "exotic" biological species." Proc Natl Acad Sci U S A 106(46):19207-19208.
Seluanov, A. et al. (2009) "Hypersensitivity to contact inhibition provides a clue to cancer resistance of naked mole-rat." Proc Natl Acad Sci U S A 106(46):19352-19357.
Argmann, C. et al. (2009) "Ppargamma2 is a key driver of longevity in the mouse." PLoS Genet 5(12):e1000752.
Kohler, M., and Moya-Sola, S. (2009) "Physiological and life history strategies of a fossil large mammal in a resource-limited environment." Proc Natl Acad Sci U S A 106(48):20354-20358.
Munshi-South, J., and Wilkinson, G.S. (2010) "Bats and birds: Exceptional longevity despite high metabolic rates." Ageing Res Rev 9(1):12-19.
Philipp, E.E., and Abele D. (2010) "Masters of longevity: lessons from long-lived bivalves--a mini-review." Gerontology 56(1):55-65.
Marques, F.Z. et al. (2010) "The molecular basis of longevity, and clinical implications." Maturitas 65(2):87-91.
Tristan, T. et al. (2010) "The aging raptor." Vet Clin North Am Exot Anim Pract 13(1):51-84.
Fagan, W.F. et al. (2010) "Pitfalls and challenges of estimating population growth rate from empirical data: consequences for allometric scaling relations." Oikos 119(3):455-464.
Page, M.M. et al. (2010) "Antioxidant enzyme activities are not broadly correlated with longevity in 14 vertebrate endotherm species." Age (Dordr) 32(2):255-270.
Kribs-Zaleta, C. et al. (2010) "Estimating contact process saturation in sylvatic transmission of Trypanosoma cruzi in the United States." PLoS Negl Trop Dis 4(4):e656.
Jobson, R.W. et al. (2010) "An evolutionary genome scan for longevity-related natural selection in mammals." Mol Biol Evol 27(4):840-847.
Lambert, A.J.. et al. (2010) "Low complex I content explains the low hydrogen peroxide production rate of heart mitochondria from the long-lived pigeon, Columba livia." Aging Cell 9(1):78-91.
Hackl, M. et al. (2010) "miR-17, miR-19b, miR-20a, and miR-106a are down-regulated in human aging." Aging Cell 9(2):291-296.
Fortney, K. et al. (2010) "Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging." Genome Biol 11(2):R13.
González-Lagos, C. et al. (2010) "Large-brained mammals live longer." J Evol Biol 23(5):1064-1074.
Cevenini, E. et al. (2010) "Systems biology and longevity: an emerging approach to identify innovative anti-aging targets and strategies." Curr Pharm Des 16(7):802-813.
Tacutu, R. et al. (2010) "MicroRNA-regulated protein-protein interaction networks: how could they help in searching for pro-longevity targets?" Rejuvenation Res 13(2-3):373-377.
Muradian, K.K. et al. (2010) "NUMT ("new mighty") hypothesis of longevity." Rejuvenation Res 13(2-3):152-155.
Ricklefs, R.E. et al. (2010) "Life-history connections to rates of aging in terrestrial vertebrates." Proc Natl Acad Sci U S A 107(22):10314-10319.
If you cite HAGR or any of its tools in an academic publication and wish for it to be mentioned in this page please let us know.