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Items: 1 to 50 of 95

1.

WHISTLE: a high-accuracy map of the human N6-methyladenosine (m6A) epitranscriptome predicted using a machine learning approach.

Chen K, Wei Z, Zhang Q, Wu X, Rong R, Lu Z, Su J, de Magalhães JP, Rigden DJ, Meng J.

Nucleic Acids Res. 2019 Apr 23;47(7):e41. doi: 10.1093/nar/gkz074.

2.

Comparing enrichment analysis and machine learning for identifying gene properties that discriminate between gene classes.

Fabris F, Palmer D, de Magalhães JP, Freitas AA.

Brief Bioinform. 2019 Mar 20. pii: bbz028. doi: 10.1093/bib/bbz028. [Epub ahead of print]

PMID:
30895300
3.

Enhancing Epitranscriptome Module Detection from m6A-Seq Data Using Threshold-Based Measurement Weighting Strategy.

Chen K, Wei Z, Liu H, de Magalhães JP, Rong R, Lu Z, Meng J.

Biomed Res Int. 2018 Jun 14;2018:2075173. doi: 10.1155/2018/2075173. eCollection 2018.

4.

Topological Characterization of Human and Mouse m5C Epitranscriptome Revealed by Bisulfite Sequencing.

Wei Z, Panneerdoss S, Timilsina S, Zhu J, Mohammad TA, Lu ZL, de Magalhães JP, Chen Y, Rong R, Huang Y, Rao MK, Meng J.

Int J Genomics. 2018 Jun 13;2018:1351964. doi: 10.1155/2018/1351964. eCollection 2018.

5.

The effects of donor age on organ transplants: A review and implications for aging research.

Dayoub JC, Cortese F, Anžič A, Grum T, de Magalhães JP.

Exp Gerontol. 2018 Sep;110:230-240. doi: 10.1016/j.exger.2018.06.019. Epub 2018 Jun 20. Review.

6.

Biological Processes Modulating Longevity across Primates: A Phylogenetic Genome-Phenome Analysis.

Muntané G, Farré X, Rodríguez JA, Pegueroles C, Hughes DA, de Magalhães JP, Gabaldón T, Navarro A.

Mol Biol Evol. 2018 Aug 1;35(8):1990-2004. doi: 10.1093/molbev/msy105.

7.

Circulating MicroRNAs in Young Patients with Acute Coronary Syndrome.

Tong KL, Mahmood Zuhdi AS, Wan Ahmad WA, Vanhoutte PM, de Magalhaes JP, Mustafa MR, Wong PF.

Int J Mol Sci. 2018 May 15;19(5). pii: E1467. doi: 10.3390/ijms19051467.

8.

From humans to hydra: patterns of cancer across the tree of life.

Albuquerque TAF, Drummond do Val L, Doherty A, de Magalhães JP.

Biol Rev Camb Philos Soc. 2018 Aug;93(3):1715-1734. doi: 10.1111/brv.12415. Epub 2018 Apr 16. Review.

9.

Vive la radiorésistance!: converging research in radiobiology and biogerontology to enhance human radioresistance for deep space exploration and colonization.

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 Magalhães JP, Artemov AV, Costes SV, Beheshti A, Mao XW, Pecaut MJ, Kaminskiy D, Ozerov IV, Scheibye-Knudsen M, Zhavoronkov A.

Oncotarget. 2018 Feb 12;9(18):14692-14722. doi: 10.18632/oncotarget.24461. eCollection 2018 Mar 6. Review.

10.

A new approach for interpreting Random Forest models and its application to the biology of ageing.

Fabris F, Doherty A, Palmer D, de Magalhães JP, Freitas AA.

Bioinformatics. 2018 Jul 15;34(14):2449-2456. doi: 10.1093/bioinformatics/bty087.

11.

Naked mole rats can undergo developmental, oncogene-induced and DNA damage-induced cellular senescence.

Zhao Y, Tyshkovskiy A, Muñoz-Espín D, Tian X, Serrano M, de Magalhaes JP, Nevo E, Gladyshev VN, Seluanov A, Gorbunova V.

Proc Natl Acad Sci U S A. 2018 Feb 20;115(8):1801-1806. doi: 10.1073/pnas.1721160115. Epub 2018 Feb 5.

12.

Human Ageing Genomic Resources: new and updated databases.

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.

Nucleic Acids Res. 2018 Jan 4;46(D1):D1083-D1090. doi: 10.1093/nar/gkx1042.

13.

Machine learning for predicting lifespan-extending chemical compounds.

Barardo DG, Newby D, Thornton D, Ghafourian T, de Magalhães JP, Freitas AA.

Aging (Albany NY). 2017 Jul 18;9(7):1721-1737. doi: 10.18632/aging.101264.

14.

The Business of Anti-Aging Science.

de Magalhães JP, Stevens M, Thornton D.

Trends Biotechnol. 2017 Nov;35(11):1062-1073. doi: 10.1016/j.tibtech.2017.07.004. Epub 2017 Aug 1. Review.

15.

Stress, cell senescence and organismal ageing.

de Magalhães JP, Passos JF.

Mech Ageing Dev. 2018 Mar;170:2-9. doi: 10.1016/j.mad.2017.07.001. Epub 2017 Jul 5. Review.

16.

The DrugAge database of aging-related drugs.

Barardo D, Thornton D, Thoppil H, Walsh M, Sharifi S, Ferreira S, Anžič 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.

Aging Cell. 2017 Jun;16(3):594-597. doi: 10.1111/acel.12585. Epub 2017 Mar 16.

17.

Systematic analysis of the gerontome reveals links between aging and age-related diseases.

Fernandes M, Wan C, Tacutu R, Barardo D, Rajput A, Wang J, Thoppil H, Thornton D, Yang C, Freitas A, de Magalhães JP.

Hum Mol Genet. 2016 Nov 1;25(21):4804-4818. doi: 10.1093/hmg/ddw307.

18.

In memory of Dr. Olivier Toussaint.

Debacq-Chainiaux F, de Magalhães JP.

Biogerontology. 2017 Feb;18(1):1. doi: 10.1007/s10522-017-9679-7. Epub 2017 Jan 23. No abstract available.

PMID:
28116571
19.

Gene co-expression analysis for functional classification and gene-disease predictions.

van Dam S, Võsa U, van der Graaf A, Franke L, de Magalhães JP.

Brief Bioinform. 2018 Jul 20;19(4):575-592. doi: 10.1093/bib/bbw139.

20.

Fish oil supplements, longevity and aging.

de Magalhães JP, Müller M, Rainger GE, Steegenga W.

Aging (Albany NY). 2016 Aug;8(8):1578-82. doi: 10.18632/aging.101021.

21.

Has gene duplication impacted the evolution of Eutherian longevity?

Doherty A, de Magalhães JP.

Aging Cell. 2016 Oct;15(5):978-80. doi: 10.1111/acel.12503. Epub 2016 Jul 4.

22.

Longer lifespan in male mice treated with a weakly estrogenic agonist, an antioxidant, an α-glucosidase inhibitor or a Nrf2-inducer.

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, Martinez 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.

Aging Cell. 2016 Oct;15(5):872-84. doi: 10.1111/acel.12496. Epub 2016 Jun 16.

23.

flowAI: automatic and interactive anomaly discerning tools for flow cytometry data.

Monaco G, Chen H, Poidinger M, Chen J, de Magalhães JP, Larbi A.

Bioinformatics. 2016 Aug 15;32(16):2473-80. doi: 10.1093/bioinformatics/btw191. Epub 2016 Apr 10.

PMID:
27153628
24.

Reductions in hypothalamic Gfap expression, glial cells and α-tanycytes in lean and hypermetabolic Gnasxl-deficient mice.

Holmes AP, Wong SQ, Pulix M, Johnson K, Horton NS, Thomas P, de Magalhães JP, Plagge A.

Mol Brain. 2016 Apr 14;9:39. doi: 10.1186/s13041-016-0219-1.

25.

Transcriptome analysis in calorie-restricted rats implicates epigenetic and post-translational mechanisms in neuroprotection and aging.

Wood SH, van Dam S, Craig T, Tacutu R, O'Toole A, Merry BJ, de Magalhães JP.

Genome Biol. 2015 Dec 22;16:285. doi: 10.1186/s13059-015-0847-2.

26.

A network pharmacology approach reveals new candidate caloric restriction mimetics in C. elegans.

Calvert S, Tacutu R, Sharifi S, Teixeira R, Ghosh P, de Magalhães JP.

Aging Cell. 2016 Apr;15(2):256-66. doi: 10.1111/acel.12432. Epub 2015 Dec 16.

27.

A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels.

Monaco G, van Dam S, Casal Novo Ribeiro JL, Larbi A, de Magalhães JP.

BMC Evol Biol. 2015 Nov 20;15:259. doi: 10.1186/s12862-015-0534-7.

28.

Insights on cryoprotectant toxicity from gene expression profiling of endothelial cells exposed to ethylene glycol.

Cordeiro RM, Stirling S, Fahy GM, de Magalhães JP.

Cryobiology. 2015 Dec;71(3):405-12. doi: 10.1016/j.cryobiol.2015.10.142. Epub 2015 Oct 22.

PMID:
26471925
29.

Predicting the Pro-Longevity or Anti-Longevity Effect of Model Organism Genes with New Hierarchical Feature Selection Methods.

Wan C, Freitas AA, de Magalhães JP.

IEEE/ACM Trans Comput Biol Bioinform. 2015 Mar-Apr;12(2):262-75. doi: 10.1109/TCBB.2014.2355218.

PMID:
26357215
30.

Geroprotectors.org: a new, structured and curated database of current therapeutic interventions in aging and age-related disease.

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.

Aging (Albany NY). 2015 Sep;7(9):616-28.

31.

The big, the bad and the ugly: Extreme animals as inspiration for biomedical research.

de Magalhães JP.

EMBO Rep. 2015 Jul;16(7):771-6. doi: 10.15252/embr.201540606. Epub 2015 Jun 3. No abstract available.

32.

Being cool: how body temperature influences ageing and longevity.

Keil G, Cummings E, de Magalhães JP.

Biogerontology. 2015 Aug;16(4):383-97. doi: 10.1007/s10522-015-9571-2. Epub 2015 Apr 2. Review.

33.

Insights into the evolution of longevity from the bowhead whale genome.

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-Jørgensen MP, Oziolor EM, Matson CW, Church GM, Stuart GW, Patton JC, George JC, Suydam R, Larsen K, López-Otín C, O'Connell MJ, Bickham JW, Thomsen B, de Magalhães JP.

Cell Rep. 2015 Jan 6;10(1):112-22. doi: 10.1016/j.celrep.2014.12.008.

34.
35.

GeneFriends: a human RNA-seq-based gene and transcript co-expression database.

van Dam S, Craig T, de Magalhães JP.

Nucleic Acids Res. 2015 Jan;43(Database issue):D1124-32. doi: 10.1093/nar/gku1042. Epub 2014 Oct 31.

36.

The Digital Ageing Atlas: integrating the diversity of age-related changes into a unified resource.

Craig T, Smelick C, Tacutu R, Wuttke D, Wood SH, Stanley H, Janssens G, Savitskaya E, Moskalev A, Arking R, de Magalhães JP.

Nucleic Acids Res. 2015 Jan;43(Database issue):D873-8. doi: 10.1093/nar/gku843. Epub 2014 Sep 17.

37.

The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations.

Keane M, Craig T, Alföldi J, Berlin AM, Johnson J, Seluanov A, Gorbunova V, Di Palma F, Lindblad-Toh K, Church GM, de Magalhães JP.

Bioinformatics. 2014 Dec 15;30(24):3558-60. doi: 10.1093/bioinformatics/btu579. Epub 2014 Aug 28.

38.

The scientific quest for lasting youth: prospects for curing aging.

de Magalhães JP.

Rejuvenation Res. 2014 Oct;17(5):458-67. doi: 10.1089/rej.2014.1580.

39.

LongevityMap: a database of human genetic variants associated with longevity.

Budovsky A, Craig T, Wang J, Tacutu R, Csordas A, Lourenço J, Fraifeld VE, de Magalhães JP.

Trends Genet. 2013 Oct;29(10):559-60. doi: 10.1016/j.tig.2013.08.003. Epub 2013 Aug 30.

PMID:
23998809
40.

Endless paces of degeneration--applying comparative genomics to study evolution's moulding of longevity.

de Magalhães JP, Kean M.

EMBO Rep. 2013 Aug;14(8):661-2. doi: 10.1038/embor.2013.96. Epub 2013 Jul 12. No abstract available.

41.

A-to-I RNA editing does not change with age in the healthy male rat brain.

Holmes AP, Wood SH, Merry BJ, de Magalhães JP.

Biogerontology. 2013 Aug;14(4):395-400. doi: 10.1007/s10522-013-9433-8. Epub 2013 May 26.

42.

A mathematical model of mortality dynamics across the lifespan combining heterogeneity and stochastic effects.

Avraam D, de Magalhaes JP, Vasiev B.

Exp Gerontol. 2013 Aug;48(8):801-11. doi: 10.1016/j.exger.2013.05.054. Epub 2013 May 23.

PMID:
23707231
43.

MYCN/LIN28B/Let-7/HMGA2 pathway implicated by meta-analysis of GWAS in suppression of post-natal proliferation thereby potentially contributing to aging.

Keane M, de Magalhães JP.

Mech Ageing Dev. 2013 Jul-Aug;134(7-8):346-8. doi: 10.1016/j.mad.2013.04.006. Epub 2013 Apr 29. Review.

PMID:
23639551
44.

How ageing processes influence cancer.

de Magalhães JP.

Nat Rev Cancer. 2013 May;13(5):357-65. doi: 10.1038/nrc3497. Review.

PMID:
23612461
45.

An analysis and validation pipeline for large-scale RNAi-based screens.

Plank M, Hu G, Silva AS, Wood SH, Hesketh EE, Janssens G, Macedo A, de Magalhães JP, Church GM.

Sci Rep. 2013;3:1076. doi: 10.1038/srep01076. Epub 2013 Jan 16.

46.

Human Ageing Genomic Resources: integrated databases and tools for the biology and genetics of ageing.

Tacutu R, Craig T, Budovsky A, Wuttke D, Lehmann G, Taranukha D, Costa J, Fraifeld VE, de Magalhães JP.

Nucleic Acids Res. 2013 Jan;41(Database issue):D1027-33. doi: 10.1093/nar/gks1155. Epub 2012 Nov 27.

47.

Prediction of C. elegans longevity genes by human and worm longevity networks.

Tacutu R, Shore DE, Budovsky A, de Magalhães JP, Ruvkun G, Fraifeld VE, Curran SP.

PLoS One. 2012;7(10):e48282. doi: 10.1371/journal.pone.0048282. Epub 2012 Oct 29.

48.

The role of DNA methylation in aging, rejuvenation, and age-related disease.

Johnson AA, Akman K, Calimport SR, Wuttke D, Stolzing A, de Magalhães JP.

Rejuvenation Res. 2012 Oct;15(5):483-94. doi: 10.1089/rej.2012.1324. Review.

49.

GeneFriends: an online co-expression analysis tool to identify novel gene targets for aging and complex diseases.

van Dam S, Cordeiro R, Craig T, van Dam J, Wood SH, de Magalhães JP.

BMC Genomics. 2012 Oct 6;13:535. doi: 10.1186/1471-2164-13-535.

50.

Programmatic features of aging originating in development: aging mechanisms beyond molecular damage?

de Magalhães JP.

FASEB J. 2012 Dec;26(12):4821-6. doi: 10.1096/fj.12-210872. Epub 2012 Sep 10.

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