Mag Lab

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Exterior view of the Bioscience Building

Welcome to the lab wiki of the Integrative Genomics of Ageing Group. We are a highly interdisciplinary and international team, located in the heart of Liverpool (United Kingdom) and using in silico, in vitro as well as in vivo approaches to study the biology and genetics of ageing. The group's PI is Joao Pedro de Magalhaes, hence the name Mag Lab.

About our lab

Scientists

• Research
• Resources
• Puplications
• People
• Vacancies
• Links
• Contact

Useful Links For Prospective Students

Night time lapse of the Bioscience Building

• Introduction to Biogerontology
• The University of Liverpool
• School of Life Sciences
• Undergraduate
• Graduate School
• Finance & Funding
• Postgraduate School
• Postgraduate Handbook

Infos for Students

If you are a member of the University of Liverpool you can get off-campus access to subscription-required journals (such as Science, Nature, [Cell http://www.cell.com/], etc. via ezproxy.

For this purpose insert ".exproxy.liv.ac.uk." right after the top-level domain (for example: .com, .gov, .de, etc.) and login with you username and password (enable cookies in the browser to avoid repeating this).

Bioinformatics/Informatics Tools/Resources

Programming Language

• HAGR (Human Ageing Genomic Resources)
• GeneAge
• GenDR
• AnAge
• Digital Ageing Atlas
• Bio-Linux
• Firefox
• Zotero

People

• Daniel A. Wuttke
• Joao Magalhaes
• Yang Li

Collaborations

• Dr. Brian Merry, University of Liverpool, Functional and Comparative Genomics
• Prof. Dr. Alan Morgan, University of Liverpool, School of Biomedical Sciences
• Fusheng Tang, University of Arkansas, Little Rock
• Prof. Dr. Robert J. Shmookler Reis, University of Arkansas for Medical Sciences

News & Literature

1. Budovsky A, Abramovich A, Cohen R, Chalifa-Caspi V, and Fraifeld V. Longevity network: construction and implications. Mech Ageing Dev. 2007 Jan;128(1):117-24. DOI:10.1016/j.mad.2006.11.018 |

   Creation of a human longevity-associated Network from homologous of different species. The nodes are very interesting.

2. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, and Ecker JR. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 2009 Nov 19;462(7271):315-22. DOI:10.1038/nature08514 |

   First step to understand the methylation pattern of cells and how it alters in time. This is interesting especially for two aspects: The embryonal development and the ageing process

3. Eisenberg T, Knauer H, Schauer A, Büttner S, Ruckenstuhl C, Carmona-Gutierrez D, Ring J, Schroeder S, Magnes C, Antonacci L, Fussi H, Deszcz L, Hartl R, Schraml E, Criollo A, Megalou E, Weiskopf D, Laun P, Heeren G, Breitenbach M, Grubeck-Loebenstein B, Herker E, Fahrenkrog B, Fröhlich KU, Sinner F, Tavernarakis N, Minois N, Kroemer G, and Madeo F. Induction of autophagy by spermidine promotes longevity. Nat Cell Biol. 2009 Nov;11(11):1305-14. DOI:10.1038/ncb1975 |

   Spermidine is a small molecule, just a polyamine with a very simple structure: C7H19N3

4. Zid BM, Rogers AN, Katewa SD, Vargas MA, Kolipinski MC, Lu TA, Benzer S, and Kapahi P. 4E-BP extends lifespan upon dietary restriction by enhancing mitochondrial activity in Drosophila. Cell. 2009 Oct 2;139(1):149-60. DOI:10.1016/j.cell.2009.07.034 |

   Translating Dietary Restriction into Long Life PaperFlick Supporting Documents

5. Veatch JR, McMurray MA, Nelson ZW, and Gottschling DE. Mitochondrial dysfunction leads to nuclear genome instability via an iron-sulfur cluster defect. Cell. 2009 Jun 26;137(7):1247-58. DOI:10.1016/j.cell.2009.04.014 |

   Mitochondrial Links to Genomic Instability in Aging PaperFlick

6. Brunet A. Cancer: When restriction is good. Nature. 2009 Apr 9;458(7239):713-4. DOI:10.1038/458713a |

   Nice essay about connections of cancer, ageing and CR

7. Kalaany NY and Sabatini DM. Tumours with PI3K activation are resistant to dietary restriction. Nature. 2009 Apr 9;458(7239):725-31. DOI:10.1038/nature07782 |

   I think xenografts are a very bad model of cancer formation [DW].

• Nature Web Focus on Ageing
• Nature Podcast on Ageing
• NPG library on Ageing

Publications

1. de Magalhães JP and Toussaint O. GenAge: a genomic and proteomic network map of human ageing. FEBS Lett. 2004 Jul 30;571(1-3):243-7. DOI:10.1016/j.febslet.2004.07.006 |
2. de Magalhães JP, Migeot V, Mainfroid V, de Longueville F, Remacle J, and Toussaint O. No increase in senescence-associated beta-galactosidase activity in Werner syndrome fibroblasts after exposure to H2O2. Ann N Y Acad Sci. 2004 Jun;1019:375-8. DOI:10.1196/annals.1297.066 |
3. de Magalhães JP and Toussaint O. How bioinformatics can help reverse engineer human aging. Ageing Res Rev. 2004 Apr;3(2):125-41. DOI:10.1016/j.arr.2003.08.006 |
4. de Magalhães JP. Is mammalian aging genetically controlled?. Biogerontology. 2003;4(2):119-20. DOI:10.1023/a:1023356005749 |
5. de Magalhães JP and Toussaint O. The evolution of mammalian aging. Exp Gerontol. 2002 Jun;37(6):769-75. DOI:10.1016/s0531-5565(02)00008-6 |
6. de Magalhães JP, Chainiaux F, Remacle J, and Toussaint O. Stress-induced premature senescence in BJ and hTERT-BJ1 human foreskin fibroblasts. FEBS Lett. 2002 Jul 17;523(1-3):157-62. DOI:10.1016/s0014-5793(02)02973-3 |
7. Dumont P, Royer V, Pascal T, Dierick JF, Chainiaux F, Frippiat C, de Magalhaes JP, Eliaers F, Remacle J, and Toussaint O. Growth kinetics rather than stress accelerate telomere shortening in cultures of human diploid fibroblasts in oxidative stress-induced premature senescence. FEBS Lett. 2001 Aug 3;502(3):109-12. DOI:10.1016/s0014-5793(01)02679-5 |
8. Aledo JC, Valverde H, and de Magalhães JP. Mutational bias plays an important role in shaping longevity-related amino acid content in mammalian mtDNA-encoded proteins. J Mol Evol. 2012 Jun;74(5-6):332-41. DOI:10.1007/s00239-012-9510-7 |
9. Wuttke D and de Magalhães JP. Osh6 links yeast vacuolar functions to lifespan extension and TOR. Cell Cycle. 2012 Jul 1;11(13):2419. DOI:10.4161/cc.21069 |
10. Wood SH, Craig T, Li Y, Merry B, and de Magalhães JP. Whole transcriptome sequencing of the aging rat brain reveals dynamic RNA changes in the dark matter of the genome. Age (Dordr). 2013 Jun;35(3):763-76. DOI:10.1007/s11357-012-9410-1 |
11. Plank M, Wuttke D, van Dam S, Clarke SA, and de Magalhães JP. A meta-analysis of caloric restriction gene expression profiles to infer common signatures and regulatory mechanisms. Mol Biosyst. 2012 Apr;8(4):1339-49. DOI:10.1039/c2mb05255e |
12. Li Y and de Magalhães JP. Accelerated protein evolution analysis reveals genes and pathways associated with the evolution of mammalian longevity. Age (Dordr). 2013 Apr;35(2):301-14. DOI:10.1007/s11357-011-9361-y |
13. de Magalhães JP and Matsuda A. Genome-wide patterns of genetic distances reveal candidate Loci contributing to human population-specific traits. Ann Hum Genet. 2012 Mar;76(2):142-58. DOI:10.1111/j.1469-1809.2011.00695.x |
14. de Magalhães JP, Wuttke D, Wood SH, Plank M, and Vora C. Genome-environment interactions that modulate aging: powerful targets for drug discovery. Pharmacol Rev. 2012 Jan;64(1):88-101. DOI:10.1124/pr.110.004499 |
15. Yu C, Li Y, Holmes A, Szafranski K, Faulkes CG, Coen CW, Buffenstein R, Platzer M, de Magalhães JP, and Church GM. RNA sequencing reveals differential expression of mitochondrial and oxidation reduction genes in the long-lived naked mole-rat when compared to mice. PLoS One. 2011;6(11):e26729. DOI:10.1371/journal.pone.0026729 |
16. Silva AS, Wood SH, van Dam S, Berres S, McArdle A, and de Magalhães JP. Gathering insights on disease etiology from gene expression profiles of healthy tissues. Bioinformatics. 2011 Dec 1;27(23):3300-5. DOI:10.1093/bioinformatics/btr559 |
17. Freitas AA and de Magalhães JP. A review and appraisal of the DNA damage theory of ageing. Mutat Res. 2011 Jul-Oct;728(1-2):12-22. DOI:10.1016/j.mrrev.2011.05.001 |
18. de Magalhães JP. A role for Ras signaling in modulating mammalian aging by the GH/IGF1 axis. Aging (Albany NY). 2011 Apr;3(4):336-7. DOI:10.18632/aging.100309 |
19. Freitas AA, Vasieva O, and de Magalhães JP. A data mining approach for classifying DNA repair genes into ageing-related or non-ageing-related. BMC Genomics. 2011 Jan 12;12:27. DOI:10.1186/1471-2164-12-27 |
20. Fuellen G, Adjaye J, de Grey A, Lepperdinger G, de Magalhães JP, Sühnel J, and Wipat A. Bioinformatics in aging research: a workshop report. Rejuvenation Res. 2010 Dec;13(6):763-7. DOI:10.1089/rej.2010.1125 |
21. de Magalhães JP. Paternal genome effects on aging: evidence for a role of Rasgrf1 in longevity determination?. Mech Ageing Dev. 2011 Jan-Feb;132(1-2):72-3. DOI:10.1016/j.mad.2010.11.004 |
22. Aledo JC, Li Y, de Magalhães JP, Ruíz-Camacho M, and Pérez-Claros JA. Mitochondrially encoded methionine is inversely related to longevity in mammals. Aging Cell. 2011 Apr;10(2):198-207. DOI:10.1111/j.1474-9726.2010.00657.x |
23. Nicholas A, de Magalhaes JP, Kraytsberg Y, Richfield EK, Levanon EY, and Khrapko K. Age-related gene-specific changes of A-to-I mRNA editing in the human brain. Mech Ageing Dev. 2010 Jun;131(6):445-7. DOI:10.1016/j.mad.2010.06.001 |
24. Finch CE, Morgan TE, Longo VD, and de Magalhaes JP. Cell resilience in species life spans: a link to inflammation?. Aging Cell. 2010 Aug;9(4):519-26. DOI:10.1111/j.1474-9726.2010.00578.x |
25. 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, and Franceschi C. Systems biology and longevity: an emerging approach to identify innovative anti-aging targets and strategies. Curr Pharm Des. 2010;16(7):802-13. DOI:10.2174/138161210790883660 |
26. de Magalhães JP, Finch CE, and Janssens G. Next-generation sequencing in aging research: emerging applications, problems, pitfalls and possible solutions. Ageing Res Rev. 2010 Jul;9(3):315-23. DOI:10.1016/j.arr.2009.10.006 |
27. de Magalhães JP and Costa J. A database of vertebrate longevity records and their relation to other life-history traits. J Evol Biol. 2009 Aug;22(8):1770-4. DOI:10.1111/j.1420-9101.2009.01783.x |
28. de Magalhães JP. Ageing research in the post-genome era: new technologies for an old problem. SEB Exp Biol Ser. 2009;62:99-115.
29. Maldonado J, Pereira T, and Estudo AMPA. Self-measurement of blood pressure in arterial hypertension--preliminary results from the AMPA study. Rev Port Cardiol. 2009 Jan;28(1):7-21.
30. de Magalhães JP, Curado J, and Church GM. Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics. 2009 Apr 1;25(7):875-81. DOI:10.1093/bioinformatics/btp073 |
31. de Magalhães JP, Budovsky A, Lehmann G, Costa J, Li Y, Fraifeld V, and Church GM. The Human Ageing Genomic Resources: online databases and tools for biogerontologists. Aging Cell. 2009 Feb;8(1):65-72. DOI:10.1111/j.1474-9726.2008.00442.x |
32. de Magalhães JP and Faragher RG. Cell divisions and mammalian aging: integrative biology insights from genes that regulate longevity. Bioessays. 2008 Jun;30(6):567-78. DOI:10.1002/bies.20760 |
33. de Magalhães JP, Sedivy JM, Finch CE, Austad SN, and Church GM. A proposal to sequence genomes of unique interest for research on aging. J Gerontol A Biol Sci Med Sci. 2007 Jun;62(6):583-4. DOI:10.1093/gerona/62.6.583 |
34. de Magalhães JP and Church GM. Analyses of human-chimpanzee orthologous gene pairs to explore evolutionary hypotheses of aging. Mech Ageing Dev. 2007 May-Jun;128(5-6):355-64. DOI:10.1016/j.mad.2007.03.004 |
35. de Magalhães JP, Costa J, and Church GM. An analysis of the relationship between metabolism, developmental schedules, and longevity using phylogenetic independent contrasts. J Gerontol A Biol Sci Med Sci. 2007 Feb;62(2):149-60. DOI:10.1093/gerona/62.2.149 |
36. de Magalhães JP and Church GM. Cells discover fire: employing reactive oxygen species in development and consequences for aging. Exp Gerontol. 2006 Jan;41(1):1-10. DOI:10.1016/j.exger.2005.09.002 |
37. de Magalhães JP. Human disease-associated mitochondrial mutations fixed in nonhuman primates. J Mol Evol. 2005 Oct;61(4):491-7. DOI:10.1007/s00239-004-0258-6 |
38. de Magalhães JP and Church GM. Genomes optimize reproduction: aging as a consequence of the developmental program. Physiology (Bethesda). 2005 Aug;20:252-9. DOI:10.1152/physiol.00010.2005 |
39. de Magalhães JP and Sandberg A. Cognitive aging as an extension of brain development: a model linking learning, brain plasticity, and neurodegeneration. Mech Ageing Dev. 2005 Oct;126(10):1026-33. DOI:10.1016/j.mad.2005.04.004 |
40. de Magalhães JP. Open-minded scepticism: inferring the causal mechanisms of human ageing from genetic perturbations. Ageing Res Rev. 2005 Jan;4(1):1-22. DOI:10.1016/j.arr.2004.05.003 |
41. de Magalhães JP, Costa J, and Toussaint O. HAGR: the Human Ageing Genomic Resources. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D537-43. DOI:10.1093/nar/gki017 |
42. de Magalhães JP, Chainiaux F, de Longueville F, Mainfroid V, Migeot V, Marcq L, Remacle J, Salmon M, and Toussaint O. Gene expression and regulation in H2O2-induced premature senescence of human foreskin fibroblasts expressing or not telomerase. Exp Gerontol. 2004 Sep;39(9):1379-89. DOI:10.1016/j.exger.2004.06.004 |
43. de Magalhães JP, Cabral JA, and Magalhães D. The influence of genes on the aging process of mice: a statistical assessment of the genetics of aging. Genetics. 2005 Jan;169(1):265-74. DOI:10.1534/genetics.104.032292 |
44. de Magalhães JP. From cells to ageing: a review of models and mechanisms of cellular senescence and their impact on human ageing. Exp Cell Res. 2004 Oct 15;300(1):1-10. DOI:10.1016/j.yexcr.2004.07.006 |
45. de Magalhães JP and Toussaint O. Telomeres and telomerase: a modern fountain of youth?. Rejuvenation Res. 2004 Summer;7(2):126-33. DOI:10.1089/1549168041553044 |
46. ISBN:9780415419543
47. ISBN:9780203866740