Joao Pedro Lourenco Rocha De Magalhaes

Research output

Research output per year 2021 2021 2022 2023 2024

• 14 Article
• 7 Review article
• 2 Short survey

Research output per year

Research output per year

Search results

• Ageing as a software design flaw

  de Magalhães, J. P., 28 Mar 2023, In: Genome Biology. 24, 1, 51.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  File

  • Software Design 100%
  • epigenetics 69%
  • Software 52%
  • software 45%
  • Epigenomics 40%
  59 Downloads (Pure)

• An integrative analysis of the age-associated multi-omic landscape across cancers

  Chatsirisupachai, K., Lesluyes, T., Paraoan, L., Van Loo, P. & De Magalhães, J. P., Dec 2021, In: Nature Communications. 12, 1, 17 p., 2345 .

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • cancer 100%
  • Mutation 90%
  • Neoplasms 34%
  • genes 27%
  • mutations 27%
  23 Downloads (Pure)

• Attention-based multi-label neural networks for integrated prediction and interpretation of twelve widely occurring RNA modifications

  Song, Z., Huang, D., Song, B., Chen, K., Song, Y., Liu, G., Su, J., Magalhães, J. P. D., Rigden, D. J. & Meng, J., 1 Dec 2021, In: Nature Communications. 12, 1, 11 p., 4011 .

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • RNA 100%
  • Post Transcriptional RNA Processing 84%
  • Modification 80%
  • predictions 76%
  • Transcriptome 44%
  21 Downloads (Pure)

• Cellular reprogramming and the rise of rejuvenation biotech

  De Magalhães, J. P. & Ocampo, A., Jun 2022, In: Trends in Biotechnology. 40, 6, p. 639-642 4 p.

  Research output: Contribution to journal › Short survey › peer-review

  Open Access

  File

  • Rejuvenation 100%
  • Cellular Reprogramming 97%
  • Clocks 64%
  • Biological Clocks 55%
  • Industry 33%
  228 Downloads (Pure)

• ConsRM: collection and large-scale prediction of the evolutionarily conserved RNA methylation sites, with implications for the functional epitranscriptome

  Song, B., Chen, K., Tang, Y., Wei, Z., Su, J., De Magalhães, J. P., Rigden, D. J. & Meng, J., Nov 2021, In: Briefings in Bioinformatics. 22, 6, 17 p., bbab088.

  Research output: Contribution to journal › Article › peer-review

  • Methylation 100%
  • RNA 74%
  • Conservation 59%
  • N(6)-methyladenosine 49%
  • Diptera 33%

• Every gene can (and possibly will) be associated with cancer

  De Magalhães, J. P., Mar 2022, In: Trends in Genetics. 38, 3, p. 216-217 2 p.

  Research output: Contribution to journal › Short survey › peer-review

  Open Access

  File

  • Genes 100%
  • PubMed 98%
  • Neoplasms 80%
  27 Downloads (Pure)

• Evolution, structure and emerging roles of C1ORF112 in DNA replication, DNA damage responses, and cancer

  Edogbanya, J., Tejada‐martinez, D., Jones, N. J., Jaiswal, A., Bell, S., Cordeiro, R., Van Dam, S., Rigden, D. J. & De Magalhães, J. P., May 2021, In: Cellular and Molecular Life Sciences. 78, 9, p. 4365-4376 12 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  File

  • DNA Replication 100%
  • DNA Damage 86%
  • DNA Repair 46%
  • Fanconi Anemia 33%
  • Neoplasms 32%
  8 Downloads (Pure)

• Longevity pharmacology comes of age

  Lourenco Rocha De Magalhaes, J. P., Jul 2021, In: Drug Discovery Today. 26, 7, p. 1559-1562 4 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  File
  101 Downloads (Pure)

• m7GHub V2.0: an updated database for decoding the N7-methylguanosine (m⁷G) epitranscriptome

  Wang, X., Zhang, Y., Chen, K., Liang, Z., Ma, J., Xia, R., de Magalhães, J. P., Rigden, D. J., Meng, J. & Song, B., 5 Jan 2024, In: Nucleic Acids Research. 52, D1, p. D203-D212 10 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • 8-methylguanosine 100%
  • Nanopores 39%
  • RNA 35%
  • Databases 31%
  • RNA Sequence Analysis 29%

• Machine learning-based predictions of dietary restriction associations across ageing-related genes

  Vega Magdaleno, G. D., Bespalov, V., Zheng, Y., Freitas, A. A. & Lourenco Rocha De Magalhaes, J. P., Dec 2022, In: BMC Bioinformatics. 23, 1, 28 p., 10.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Classifier 100%
  • Machine Learning 82%
  • Gene 71%
  • Genes 69%
  • Prediction 58%
  30 Downloads (Pure)

• Positive selection and enhancer evolution shaped lifespan and body mass in great apes

  Tejada-martinez, D., Avelar, R. A., Lopes, I., Zhang, B., Novoa, G., De Magalhães, J. P., Trizzino, M. & Malik, H. (ed.), Feb 2022, In: Molecular Biology and Evolution. 39, 2, 16 p., msab369.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Hominidae 100%
  • Pongidae 93%
  • body mass 84%
  • primate 81%
  • Longevity 68%
  21 Downloads (Pure)

• Positive selection and gene duplications in tumour suppressor genes reveal clues about how cetaceans resist cancer

  Tejada-martinez, D., De Magalhães, J. P. & Opazo, J. C., 24 Feb 2021, In: Proceedings of the Royal Society B: Biological Sciences. 288, 1945, 9 p., 20202592.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • tumor suppressor genes 100%
  • Gene Duplication 88%
  • cetacean 84%
  • Whales 82%
  • gene duplication 75%
  31 Downloads (Pure)

• scDiffCom: a tool for differential analysis of cell–cell interactions provides a mouse atlas of aging changes in intercellular communication

  Lagger, C., Ursu, E., Equey, A., Avelar, R. A., Pisco, A. O., Tacutu, R. & de Magalhães, J. P., Nov 2023, In: Nature Aging. 3, 11, p. 1446-1461 16 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • topographic maps 100%
  • cell communication 95%
  • mice 47%
  • cells 26%
  • angiogenesis 25%
  23 Downloads (Pure)

• Sex‐specific aging in animals: perspective and future directions

  Bronikowski, A. M., Meisel, R. P., Biga, P. R., Walters, J., Mank, J. E., Larschan, E., Wilkinson, G. S., Valenzuela, N., Conard, A. M., Magalhães, J. P., Duan, J., Elias, A. E., Gamble, T., Graze, R., Gribble, K. E., Kreiling, J. A. & Riddle, N. C., Feb 2022, In: Aging Cell. 21, 2, 25 p., e13542.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  File

  • Sex Characteristics 100%
  • Direction compound 77%
  • Animals 53%
  • Longevity 19%
  • Metagenomics 13%
  246 Downloads (Pure)

• Targeting immune dysfunction in aging

  Borgoni, S., Kudryashova, K. S., Burka, K. & De Magalhães, J. P., Sept 2021, In: Ageing Research Reviews. 70, 16 p., 101410.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  File

  • Immune System 100%
  • Immune System Phenomena 49%
  • Immunosenescence 45%
  • Homeostasis 23%
  • Direction compound 22%
  106 Downloads (Pure)

• The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS

  Orkin, J. D., Montague, M. J., Tejada-martinez, D., De Manuel, M., Del Campo, J., Cheves Hernandez, S., Di Fiore, A., Fontsere, C., Hodgson, J. A., Janiak, M. C., Kuderna, L. F. K., Lizano, E., Martin, M. P., Niimura, Y., Perry, G. H., Valverde, C. S., Tang, J., Warren, W. C., De Magalhães, J. P., Kawamura, S., & 3 othersMarquès-bonet, T., Krawetz, R. & Melin, A. D., 11 Feb 2021, In: Proceedings of the National Academy of Sciences. 118, 7, 12 p., e2010632118.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Cebidae 100%
  • brain 55%
  • genomics 39%
  • monkeys 28%
  • mammals 22%
  16 Downloads (Pure)

• The hoverfly and the wasp: a critique of the hallmarks of aging as a paradigm

  Gems, D. & De Magalhães, J. P., Sept 2021, In: Ageing Research Reviews. 70, 9 p., 101407.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  File

  • paradigm 100%
  • cancer 41%
  • cause 17%
  • pathology 14%
  • drug 10%
  53 Downloads (Pure)

• The longevity bottleneck hypothesis: Could dinosaurs have shaped ageing in present‐day mammals?

  de Magalhães, J. P., 28 Nov 2023, (E-pub ahead of print) In: BioEssays. 5 p., 2300098.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Dinosaurs 100%
  • Longevity 51%
  • Mammals 51%
  • Pressure 33%
  • Reptiles 22%
  98 Downloads (Pure)

• Trans cohort metabolic reprogramming towards glutaminolysis in long-term successfully treated HIV-infection

  Mikaeloff, F., Svensson Akusjärvi, S., Ikomey, G. M., Krishnan, S., Sperk, M., Gupta, S., Magdaleno, G. D. V., Escós, A., Lyonga, E., Okomo, M. C., Tagne, C. T., Babu, H., Lorson, C. L., Végvári, Á., Banerjea, A. C., Kele, J., Hanna, L. E., Singh, K., De Magalhães, J. P., Benfeitas, R., & 1 othersNeogi, U., 1 Dec 2022, In: Communications Biology. 5, 1, 12 p., 27.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • HIV infections 100%
  • Antiretroviral 95%
  • HIV Infections 59%
  • Metabolic 54%
  • HIV 46%
  23 Downloads (Pure)

• Transcriptomic analysis reveals a tissue-specific loss of identity during ageing and cancer

  Dos Santos, G. A., Chatsirisupachai, K., Avelar, R. A. & de Magalhães, J. P., 26 Oct 2023, In: BMC Genomics. 24, 1, 13 p., 644.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Neoplasms 100%
  • Genes 55%
  • Carcinogenesis 52%
  • Down-Regulation 48%
  • Organ Specificity 43%
  1 Downloads (Pure)

• Transcriptomics age acceleration in prolonged treated HIV infection

  Mikaeloff, F., Gelpi, M., Escos, A., Knudsen, A. D., Høgh, J., Benfield, T., de Magalhães, J. P., Nielsen, S. D. & Neogi, U., 7 Aug 2023, (E-pub ahead of print) In: Aging Cell. e13951.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Acceleration 100%
  • HIV Infections 90%
  • Antigen Presentation 74%
  • HIV 70%
  • GS-7340 59%
  37 Downloads (Pure)

• WHISTLE server: a high-accuracy genomic coordinate-based machine learning platform for RNA modification prediction

  Liu, L., Song, B., Chen, K., Zhang, Y., De Magalhães, J. P., Rigden, D. J., Lei, X. & Wei, Z., Jul 2022, In: Methods. 203, p. 378-382 5 p.

  Research output: Contribution to journal › Article › peer-review

  • RNA 100%
  • Machine learning 60%
  • Servers 59%
  • DNA 28%
  • Proteins 25%

• Winter is coming: the future of cryopreservation

  Bojic, S., Murray, A., Bentley, B. L., Spindler, R., Pawlik, P., Cordeiro, J. L., Bauer, R. & De Magalhães, J. P., 1 Dec 2021, In: BMC Biology. 19, 1, 20 p., 56.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  File

  • Cryopreservation 100%
  • organ transplantation 98%
  • cryopreservation 93%
  • Organ Transplantation 71%
  • organ 61%
  44 Downloads (Pure)