HAGR: the Human Ageing Genomic Resources. - João Pedro de Magalhães; Joana Cósta; Olivier Toussaint (Nucleic Acids Res., 2005)

Meta-analysis of age-related gene expression profiles identifies common signatures of aging. - João Pedro de Magalhães; João Curado; George M. Church (Bioinform., 2009)

Gathering insights on disease etiology from gene expression profiles of healthy tissues. - A. Sofia Silva; Shona H. Wood; Sipko van Dam; Sven Berres; Anne McArdle; João Pedro de Magalhães (Bioinform., 2011)

Human Ageing Genomic Resources: Integrated databases and tools for the biology and genetics of ageing. - Robi Tacutu; Thomas Craig; Arie Budovsky; Daniel Wuttke; Gilad Lehmann; Dmitri Taranukha; Joana Cósta; Vadim E. Fraifeld; João Pedro de Magalhães (Nucleic Acids Res., 2013)

The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations. - Michael Keane; Thomas Craig; Jessica Alföldi; Aaron M. Berlin; Jeremy Johnson; Andrei Seluanov; Vera Gorbunova; Federica Di Palma; Kerstin Lindblad-Toh; George M. Church; João Pedro de Magalhães (Bioinform., 2014)

The Digital Ageing Atlas: integrating the diversity of age-related changes into a unified resource. - Thomas Craig; Chris Smelick; Robi Tacutu; Daniel Wuttke; Shona H. Wood; Henry Stanley; Georges Janssens; Ekaterina Savitskaya; Alexey Moskalev; Robert Arking; João Pedro de Magalhães (Nucleic Acids Res., 2015)

GeneFriends: a human RNA-seq-based gene and transcript co-expression database. - Sipko van Dam; Thomas Craig; João Pedro de Magalhães (Nucleic Acids Res., 2015)

Predicting the Pro-Longevity or Anti-Longevity Effect of Model Organism Genes with New Hierarchical Feature Selection Methods. - Cen Wan; Alex Alves Freitas; João Pedro de Magalhães (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

flowAI: automatic and interactive anomaly discerning tools for flow cytometry data. - Gianni Monaco; Hao Chen; Michael Poidinger; Jinmiao Chen; João Pedro de Magalhães; Anis Larbi (Bioinform., 2016)

Gene co-expression analysis for functional classification and gene-disease predictions. - Sipko van Dam; Urmo Võsa; Adriaan van der Graaf; Lude Franke; João Pedro de Magalhães (Briefings Bioinform., 2018)

A new approach for interpreting Random Forest models and its application to the biology of ageing. - Fabio Fabris; Aoife Doherty; Daniel Palmer; João Pedro de Magalhães; Alex Alves Freitas (Bioinform., 2018)

Human Ageing Genomic Resources: new and updated databases. - Robi Tacutu; Daniel Thornton; Emily Johnson 002; Arie Budovsky; Diogo Barardo; Thomas Craig; Eugene Diana; Gilad Lehmann; Dmitri Toren; Jingwei Wang; Vadim E. Fraifeld; João Pedro de Magalhães (Nucleic Acids Res., 2018)

Comparing enrichment analysis and machine learning for identifying gene properties that discriminate between gene classes. - Fabio Fabris; Daniel Palmer; João Pedro de Magalhães; Alex Alves Freitas (Briefings Bioinform., 2020)

Using deep learning to associate human genes with age-related diseases. - Fabio Fabris; Daniel Palmer; Khalid M. Salama; João Pedro de Magalhães; Alex Alves Freitas (Bioinform., 2020)

m7GHub: deciphering the location, regulation and pathogenesis of internal mRNA N7-methylguanosine (m7G) sites in human. - Bowen Song; Yujiao Tang; Kunqi Chen; Zhen Wei; Rong Rong; Zhiliang Lu; Jionglong Su; João Pedro de Magalhães; Daniel J. Rigden; Jia Meng 001 (Bioinform., 2020)

ConsRM: collection and large-scale prediction of the evolutionarily conserved RNA methylation sites, with implications for the functional epitranscriptome. - Bowen Song; Kunqi Chen; Yujiao Tang; Zhen Wei; Jionglong Su; João Pedro de Magalhães; Daniel J. Rigden; Jia Meng 001 (Briefings Bioinform., 2021)

RMDisease: a database of genetic variants that affect RNA modifications, with implications for epitranscriptome pathogenesis. - Kunqi Chen; Bowen Song; Yujiao Tang; Zhen Wei; Qingru Xu; Jionglong Su; João Pedro de Magalhães; Daniel J. Rigden; Jia Meng 001 (Nucleic Acids Res., 2021)

m6A-Atlas: a comprehensive knowledgebase for unraveling the N6-methyladenosine (m6A) epitranscriptome. - Yujiao Tang; Kunqi Chen; Bowen Song; Jiongming Ma; Xiangyu Wu; Qingru Xu; Zhen Wei; Jionglong Su; Gang Liu; Rong Rong; Zhiliang Lu; João Pedro de Magalhães; et al. (Nucleic Acids Res., 2021)

Machine learning-based predictions of dietary restriction associations across ageing-related genes. - Gustavo Daniel Vega Magdaleno; Vladislav Bespalov; Yalin Zheng; Alex Alves Freitas; João Pedro de Magalhães (BMC Bioinform., 2022)

m5C-Atlas: a comprehensive database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome. - Jiongming Ma; Bowen Song; Zhen Wei; Daiyun Huang; Yuxin Zhang; Jionglong Su; João Pedro de Magalhães; Daniel J. Rigden; Jia Meng 001; Kunqi Chen (Nucleic Acids Res., 2022)

Interpretable Ensembles of Classifiers for Uncertain Data With Bioinformatics Applications. - Marcelo Rodrigues de Holanda Maia; Alexandre Plastino 001; Alex Alves Freitas; João Pedro de Magalhães (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

GeneFriends: gene co-expression databases and tools for humans and model organisms. - Priyanka Raina; Rodrigo Guinea; Kasit Chatsirisupachai; Inês Lopes; Zoya Farooq; Cristina Guinea; Csaba-Attila Solyom; João Pedro de Magalhães (Nucleic Acids Res., 2023)

RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication. - Bowen Song; Xuan Wang; Zhanmin Liang; Jiongming Ma; Daiyun Huang; Yue Wang 060; João Pedro de Magalhães; Daniel J. Rigden; Jia Meng 001; Gang Liu; Kunqi Chen; Zhen Wei (Nucleic Acids Res., 2023)

DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology. - Yuxin Zhang; Jie Jiang 020; Jiongming Ma; Zhen Wei; Yue Wang 060; Bowen Song; Jia Meng 001; Guifang Jia; João Pedro de Magalhães; Daniel J. Rigden; Daiyun Hang; Kunqi Chen (Nucleic Acids Res., 2023)

m6A-TSHub: Unveiling the Context-specific m6A Methylation and m6A-affecting Mutations in 23 Human Tissues. - Bowen Song; Daiyun Huang; Yuxin Zhang; Zhen Wei; Jionglong Su; João Pedro de Magalhães; Daniel J. Rigden; Jia Meng 001; Kunqi Chen (Genom. Proteom. Bioinform., 2023)