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de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465 (2023) Ageing as a software design flaw. GENOME BIOLOGY, 24 (1). 51-.

Palmer, Daniel, Fabris, Fabio, Doherty, Aoife, Freitas, Alex A and de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465 (2021) Ageing transcriptome meta-analysis reveals similarities and differences between key mammalian tissues. AGING-US, 13 (3). pp. 3313-3341.

Marttila, Saara, Chatsirisupachai, Kasit ORCID: 0000-0001-9446-6714, Palmer, Daniel and de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465 (2020) Ageing-associated changes in the expression of lncRNAs in human tissues reflect a transcriptional modulation in ageing pathways. MECHANISMS OF AGEING AND DEVELOPMENT, 185. 111177-.

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Nam, Kiwoong, Lee, Kyeong Won, Chung, Oksung, Yim, Hyung-Soon, Cha, Sun-Shin, Lee, Sae-Won, Jun, JeHoon, Cho, Yun Sung, Bhak, Jong, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465 et al (show 2 more authors) , Lee, Jung-Hyun and Jeong, Jae-Yeon (2017) Analysis of the FGF gene family provides insights into aquatic adaptation in cetaceans. SCIENTIFIC REPORTS, 7 (1). 40233-.

Song, Zitao, Huang, Daiyun, Song, Bowen, Chen, Kunqi, Song, Yiyou, Liu, Gang, Su, Jionglong, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Rigden, Daniel J ORCID: 0000-0002-7565-8937 and Meng, Jia ORCID: 0000-0003-3455-205X (2021) Attention-based multi-label neural networks for integrated prediction and interpretation of twelve widely occurring RNA modifications. NATURE COMMUNICATIONS, 12 (1). 4011-.

Galkin, Fedor, Mamoshina, Polina, Aliper, Alex, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Gladyshev, Vadim N and Zhavoronkov, Alex (2020) Biohorology and biomarkers of aging: Current state-of-the-art, challenges and opportunities. AGEING RESEARCH REVIEWS, 60. 101050-.

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Liu, Lian, Song, Bowen, Ma, Jiani, Song, Yi, Zhang, Song-Yao, Tang, Yujiao, Wu, Xiangyu, Wei, Zhen, Chen, Kunqi, Su, Jionglong et al (show 10 more authors) , Rong, Rong, Lu, Zhiliang ORCID: 0000-0002-3442-1415, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Zhang, Lin, Zhang, Shao-Wu, Huang, Yufei, Lei, Xiujuan, Liu, Hui and Meng, Jia ORCID: 0000-0003-3455-205X (2020) Bioinformatics approaches for deciphering the epitranscriptome: Recent progress and emerging topics. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 18. pp. 1587-1604.

Muntane, Gerard, Farre, Xavier, Rodriguez, Juan Antonio, Pegueroles, Cinta, Hughes, David A, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Gabaldon, Toni and Navarro, Arcadi (2018) Biological Processes Modulating Longevity across Primates: A Phylogenetic Genome-Phenome Analysis. Molecular Biology and Evolution, 35 (8). pp. 1990-2004.

de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Stevens, Michael and Thornton, Daniel ORCID: 0000-0002-4994-2942 (2017) The Business of Anti-Aging Science. TRENDS IN BIOTECHNOLOGY, 35 (11). pp. 1062-1073.

Tong, Kind-Leng, Zuhdi, Ahmad Syadi Mahmood, Ahmad, Wan Azman Wan, Vanhoutte, Paul M, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Mustafa, Mohd Rais and Wong, Pooi-Fong (2018) Circulating MicroRNAs in Young Patients with Acute Coronary Syndrome. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 19 (5). E1467-.

Fabris, Fabio, Palmer, Daniel, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465 and Freitas, Alex A (2020) Comparing enrichment analysis and machine learning for identifying gene properties that discriminate between gene classes. BRIEFINGS IN BIOINFORMATICS, 21 (3). pp. 803-814.

Song, Bowen, Chen, Kunqi, Tang, Yujiao, Wei, Zhen, Su, Jionglong, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Rigden, Daniel J ORCID: 0000-0002-7565-8937 and Meng, Jia ORCID: 0000-0003-3455-205X (2021) ConsRM: collection and large-scale prediction of the evolutionarily conserved RNA methylation sites, with implications for the functional epitranscriptome. BRIEFINGS IN BIOINFORMATICS, 22 (6). bbab088-.

Chen, Kunqi, Wei, Zhen, Liu, Hui, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Rong, Rong, Lu, Zhiliang ORCID: 0000-0002-3442-1415 and Meng, Jia ORCID: 0000-0003-3455-205X (2018) Enhancing Epitranscriptome Module Detection from m<SUP>6</SUP>A-Seq Data Using Threshold-Based Measurement Weighting Strategy. BIOMED RESEARCH INTERNATIONAL, 2018. 2075173-.

Edogbanya, Jacob, Tejada-Martinez, Daniela, Jones, Nigel J ORCID: 0000-0003-1801-1456, Jaiswal, Amit, Bell, Sarah, Cordeiro, Rui, van Dam, Sipko, Rigden, Daniel J ORCID: 0000-0002-7565-8937 and de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465 (2021) Evolution, structure and emerging roles of C1ORF112 in DNA replication, DNA damage responses, and cancer. CELLULAR AND MOLECULAR LIFE SCIENCES, 78 (9). pp. 4365-4376.

de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Mueller, Michael, Rainger, G Ed and Steegenga, Wilma (2016) Fish oil supplements, longevity and aging. AGING-US, 8 (8). pp. 1578-1582.

Albuquerque, Thales AF, do Val, Luisa Drummond, Doherty, Aoife and de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465 (2018) From humans to hydra: patterns of cancer across the tree of life. BIOLOGICAL REVIEWS, 93 (3). pp. 1715-1734.

Lopes, Ines, Altab, Gulam, Raina, Priyanka and de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465 (2021) Gene Size Matters: An Analysis of Gene Length in the Human Genome. FRONTIERS IN GENETICS, 12. 559998-.

van Dam, Sipko, Vosa, Urmo, van der Graaf, Adriaan, Franke, Lude and de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465 (2018) Gene co-expression analysis for functional classification and gene-disease predictions. BRIEFINGS IN BIOINFORMATICS, 19 (4). pp. 575-592.

Raina, Priyanka, Guinea, Rodrigo, Chatsirisupachai, Kasit, Lopes, Ines, Farooq, Zoya, Guinea, Cristina, Solyom, Csaba-Attila and de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465 (2022) GeneFriends: gene co-expression databases and tools for humans and model organisms. NUCLEIC ACIDS RESEARCH, 51 (D1). D145-D158.

Huang, Daiyun, Chen, Kunqi, Song, Bowen, Wei, Zhen, Su, Jionglong, Coenen, Frans ORCID: 0000-0003-1026-6649, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Rigden, Daniel J ORCID: 0000-0002-7565-8937 and Meng, Jia ORCID: 0000-0003-3455-205X (2022) Geographic encoding of transcripts enabled high-accuracy and isoform-aware deep learning of RNA methylation. NUCLEIC ACIDS RESEARCH, 50 (18). pp. 10290-10310.

Doherty, Aoife and de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465 (2016) Has gene duplication impacted the evolution of Eutherian longevity? AGING CELL, 15 (5). pp. 978-980.

Doherty, Aoife, Kernogitski, Yelena, Kulminski, Alexander M and de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465 (2017) Identification of polymorphisms in cancer patients that differentially affect survival with age. AGING-US, 9 (10). 2114-+.

Dhirachaikulpanich, Dhanach ORCID: 0000-0003-2234-1837, Lagger, Cyril ORCID: 0000-0003-1701-6896, Chatsirisupachai, Kasit, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465 and Paraoan, Luminita (2022) Intercellular communication analysis of the human retinal pigment epithelial and choroidal cells predicts pathways associated with aging, cellular senescence and age-related macular degeneration. FRONTIERS IN AGING NEUROSCIENCE, 14. 1016293-.

Barardo, Diogo G, Newby, Danielle, Thornton, Daniel ORCID: 0000-0002-4994-2942, Ghafourian, Taravat, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465 and Freitas, Alex A (2017) Machine learning for predicting lifespan-extending chemical compounds. AGING-US, 9 (7). pp. 1721-1737.

Magdaleno, Gustavo Daniel Vega, Bespalov, Vladislav, Zheng, Yalin ORCID: 0000-0002-7873-0922, Freitas, Alex A and de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465 (2022) Machine learning-based predictions of dietary restriction associations across ageing-related genes. BMC BIOINFORMATICS, 23 (1). 10-.

Tejada-Martinez, Daniela, Avelar, Roberto A ORCID: 0000-0003-4997-9953, Lopes, Ines, Zhang, Bruce, Novoa, Guy, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465 and Trizzino, Marco (2022) Positive Selection and Enhancer Evolution Shaped Lifespan and Body Mass in Great Apes. MOLECULAR BIOLOGY AND EVOLUTION, 39 (2). msab369-.

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Song, Bowen, Wang, Xuan, Liang, Zhanmin, Ma, Jiongming, Huang, Daiyun, Wang, Yue, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Meng, Jia ORCID: 0000-0003-3455-205X, Liu, Gang et al (show 2 more authors) , Chen, Kunqi and Wei, Zhen (2023) RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication. NUCLEIC ACIDS RESEARCH, 51 (D1). D1388-D1396.

Chen, Kunqi, Song, Bowen, Tang, Yujiao, Wei, Zhen, Xu, Qingru, Su, Jionglong, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Rigden, Daniel J ORCID: 0000-0002-7565-8937 and Meng, Jia ORCID: 0000-0003-3455-205X (2021) RMDisease: a database of genetic variants that affect RNA modifications, with implications for epitranscriptome pathogenesis. NUCLEIC ACIDS RESEARCH, 49 (D1). D1396-D1404.

Bennett, Dominic F, Goyala, Anita, Statzer, Cyril, Beckett, Charles W, Tyshkovskiy, Alexander, Gladyshev, Vadim N, Ewald, Collin Y and de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465 (2023) Rilmenidine extends lifespan and healthspan in<i> Caenorhabditis</i><i> elegans</i> via a nischarin I1-imidazoline receptor. AGING CELL, 22 (2). e13774-.

de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465 and Passos, Joao F (2018) Stress, cell senescence and organismal ageing. MECHANISMS OF AGEING AND DEVELOPMENT, 170. pp. 2-9.

Borgoni, Simone, Kudryashova, Ksenia S, Burka, Ksenia and de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465 (2021) Targeting immune dysfunction in aging. AGEING RESEARCH REVIEWS, 70. 101410-.

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Calimport, Stuart RG ORCID: 0000-0002-0085-0385, Bentley, Barry L, Stewart, Claire, Pawelec, Graham, Scuteri, Angelo, Vinciguerra, Manlio ORCID: 0000-0002-1768-3894, Slack, Cathy, Chen, Danica, Harries, Lorna W, Marchant, Gary et al (show 15 more authors) , Fleming, G Alexander, Conboy, Michael, Antebi, Adam, Small, Garry W, Gil, Jesus, Lakatta, Edward G, Richardson, Arlan, Rosen, Clifford, Nikolich, Karoly, Wyss-Coray, Tony, Steinman, Lawrence, Montine, Thomas, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Campisi, Judith and Church, George (2019) To help aging populations, classify organismal senescence. SCIENCE, 366 (6465). 576-+.

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Wei, Zhen, Panneerdoss, Subbarayalu, Timilsina, Santosh, Zhu, Jingting, Mohammad, Tabrez A, Lu, Zhi-Liang ORCID: 0000-0002-3442-1415, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Chen, Yidong, Rong, Rong, Huang, Yufei et al (show 2 more authors) , Rao, Manjeet K and Meng, Jia ORCID: 0000-0003-3455-205X (2018) Topological Characterization of Human and Mouse m<SUP>5</SUP>C Epitranscriptome Revealed by Bisulfite Sequencing. INTERNATIONAL JOURNAL OF GENOMICS, 2018. 1351964-.

Fabris, Fabio, Palmer, Daniel, Salama, Khalid M, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465 and Freitas, Alex A (2020) Using deep learning to associate human genes with age-related diseases. BIOINFORMATICS, 36 (7). pp. 2202-2208.

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Pitrez, Patricia R, Estronca, Luis, Monteiro, Luis Miguel, Colell, Guillem, Vazao, Helena, Santinha, Deolinda, Harhouri, Karim, Thornton, Daniel, Navarro, Claire, Egesipe, Anne-Laure et al (show 11 more authors) , Carvalho, Tania, Dos Santos, Rodrigo L, Levy, Nicolas, Smith, James C, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Ori, Alessandro, Bernardo, Andreia, De Sandre-Giovannoli, Annachiara, Nissan, Xavier, Rosell, Anna and Ferreira, Lino (2020) Vulnerability of progeroid smooth muscle cells to biomechanical forces is mediated by MMP13. NATURE COMMUNICATIONS, 11 (1). 4110-.

Liu, Lian, Song, Bowen, Chen, Kunqi, Zhang, Yuxin, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Lei, Xiujuan and Wei, Zhen (2022) WHISTLE server: A high-accuracy genomic coordinate-based machine learning platform for RNA modification prediction. METHODS, 203. pp. 378-382.

Chen, Kunqi, Wei, Zhen, Zhang, Qing, Wu, Xiangyu, Rong, Rong, Lu, Zhiliang ORCID: 0000-0002-3442-1415, Su, Jionglong, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Rigden, Daniel J ORCID: 0000-0002-7565-8937 and Meng, Jia ORCID: 0000-0003-3455-205X (2019) WHISTLE: a high-accuracy map of the human N<SUP>6</SUP>-methyladenosine (m<SUP>6</SUP>A) epitranscriptome predicted using a machine learning approach. NUCLEIC ACIDS RESEARCH, 47 (7). e41-.

Bojic, Sanja, Murray, Alex, Bentley, Barry L, Spindler, Ralf, Pawlik, Piotr, Cordeiro, Jose L, Bauer, Roman and de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465 (2021) Winter is coming: the future of cryopreservation. BMC BIOLOGY, 19 (1). 56-.

de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465 (2016) A direct communication proposal to test the Zoo Hypothesis. SPACE POLICY, 38. pp. 22-26.

Dayoub, Jose Carlos, Cortese, Franco, Anzic, Andreja, Grum, Tjasa and de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465 (2018) The effects of donor age on organ transplants: A review and implications for aging research. EXPERIMENTAL GERONTOLOGY, 110. pp. 230-240.

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Orkin, Joseph D, Montague, Michael J, Tejada-Martinez, Daniela, de Manuel, Marc, del Campo, Javier, Hernandez, Saul Cheves, Di Fiore, Anthony, Fontsere, Claudia, Hodgson, Jason A, Janiak, Mareike C et al (show 13 more authors) , Kuderna, Lukas FK, Lizano, Esther, Martin, Maria Pia, Niimura, Yoshihito, Perry, George H, Valverde, Carmen Soto, Tang, Jia, Warren, Wesley C, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Kawamura, Shoji, Marques-Bonet, Tomas, Krawetz, Roman and Melin, Amanda D (2021) The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 118 (7). e2010632118-.

Chatsirisupachai, Kasit ORCID: 0000-0001-9446-6714, Palmer, Daniel, Ferreira, Susana and de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465 (2019) A human tissue-specific transcriptomic analysis reveals a complex relationship between aging, cancer, and cellular senescence. AGING CELL, 18 (6). e13041-.

Song, Bowen, Tang, Yujiao, Chen, Kunqi, Wei, Zhen, Rong, Rong, Lu, Zhiliang ORCID: 0000-0002-3442-1415, Su, Jionglong, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Rigden, Daniel J ORCID: 0000-0002-7565-8937 and Meng, Jia ORCID: 0000-0003-3455-205X (2020) m7GHub: deciphering the location, regulation and pathogenesis of internal mRNA N7-methylguanosine (m7G) sites in human. Bioinformatics, 36 (11). pp. 3528-3536.

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Tang, Yujiao, Chen, Kunqi, Song, Bowen, Ma, Jiongming, Wu, Xiangyu, Xu, Qingru, Wei, Zhen, Su, Jionglong, Liu, Gang, Rong, Rong et al (show 4 more authors) , Lu, Zhiliang ORCID: 0000-0002-3442-1415, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Rigden, Daniel J ORCID: 0000-0002-7565-8937 and Meng, Jia ORCID: 0000-0003-3455-205X (2021) m<SUP>6</SUP>A-Atlas: a comprehensive knowledgebase for unraveling the <i>N</i><SUP>6</SUP>-methyladenosine (m<SUP>6</SUP>A) epitranscriptome. NUCLEIC ACIDS RESEARCH, 49 (D1). D134-D143.

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Barros-Viegas, Ana Teresa, Carmona, Vitor, Ferreiro, Elisabete, Guedes, Joana, Cardoso, Ana Maria, Cunha, Pedro, de Almeida, Luis Pereira, de Oliveira, Catarina Resende, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Peca, Joao et al (show 1 more authors) and Cardoso, Ana Luisa (2020) miRNA-31 Improves Cognition and Abolishes Amyloid-β Pathology by Targeting APP and BACE1 in an Animal Model of Alzheimer's Disease. MOLECULAR THERAPY-NUCLEIC ACIDS, 19. pp. 1219-1236.

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Avelar, Roberto A ORCID: 0000-0003-4997-9953, Ortega, Javier Gomez, Tacutu, Robi, Tyler, Eleanor J, Bennett, Dominic, Binetti, Paolo, Budovsky, Arie, Chatsirisupachai, Kasit ORCID: 0000-0001-9446-6714, Johnson, Emily, Murray, Alex et al (show 6 more authors) , Shields, Samuel, Tejada-Martinez, Daniela, Thornton, Daniel, Fraifeld, Vadim E, Bishops, Cleo L and de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465 (2020) A multidimensional systems biology analysis of cellular senescence in aging and disease. Genome Biology, 21 (1). 91-.

Fabris, Fabio, Doherty, Aoife, Palmer, Daniel, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465 and Freitas, Alex A (2018) A new approach for interpreting Random Forest models and its application to the biology of ageing. BIOINFORMATICS, 34 (14). pp. 2449-2456.