João Pedro de Magalhães

25 papers Journal 25
YearRankTypeTitle / Venue / Authors
2023 J jnl
DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology.
Nucleic Acids Res.
Yuxin Zhang, Jie Jiang, Jiongming Ma, Zhen Wei, Yue Wang, Bowen Song, Jia Meng, Guifang Jia, João Pedro de Magalhães, Daniel J. Rigden, Daiyun Hang, Kunqi Chen
2023 J jnl
GeneFriends: gene co-expression databases and tools for humans and model organisms.
Nucleic Acids Res.
Priyanka Raina, Rodrigo Guinea, Kasit Chatsirisupachai, Inês Lopes, Zoya Farooq, Cristina Guinea, Csaba-Attila Solyom, João Pedro de Magalhães
2023 J jnl
Interpretable Ensembles of Classifiers for Uncertain Data With Bioinformatics Applications.
IEEE ACM Trans. Comput. Biol. Bioinform.
Marcelo Rodrigues de Holanda Maia, Alexandre Plastino, Alex Alves Freitas, João Pedro de Magalhães
2023 J jnl
RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication.
Nucleic Acids Res.
Bowen Song, Xuan Wang, Zhanmin Liang, Jiongming Ma, Daiyun Huang, Yue Wang, João Pedro de Magalhães, Daniel J. Rigden, Jia Meng, Gang Liu, Kunqi Chen, Zhen Wei
2023 J jnl
m6A-TSHub: Unveiling the Context-specific m
Genom. Proteom. Bioinform.
Bowen Song, Daiyun Huang, Yuxin Zhang, Zhen Wei, Jionglong Su, João Pedro de Magalhães, Daniel J. Rigden, Jia Meng, Kunqi Chen
2022 J jnl
Machine learning-based predictions of dietary restriction associations across ageing-related genes.
BMC Bioinform.
Gustavo Daniel Vega Magdaleno, Vladislav Bespalov, Yalin Zheng, Alex Alves Freitas, João Pedro de Magalhães
2022 J jnl
m5C-Atlas: a comprehensive database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome.
Nucleic Acids Res.
Jiongming Ma, Bowen Song, Zhen Wei, Daiyun Huang, Yuxin Zhang, Jionglong Su, João Pedro de Magalhães, Daniel J. Rigden, Jia Meng, Kunqi Chen
2021 J jnl
ConsRM: collection and large-scale prediction of the evolutionarily conserved RNA methylation sites, with implications for the functional epitranscriptome.
Briefings Bioinform.
Bowen Song, Kunqi Chen, Yujiao Tang, Zhen Wei, Jionglong Su, João Pedro de Magalhães, Daniel J. Rigden, Jia Meng
2021 J jnl
RMDisease: a database of genetic variants that affect RNA modifications, with implications for epitranscriptome pathogenesis.
Nucleic Acids Res.
Kunqi Chen, Bowen Song, Yujiao Tang, Zhen Wei, Qingru Xu, Jionglong Su, João Pedro de Magalhães, Daniel J. Rigden, Jia Meng
2021 J jnl
m6A-Atlas: a comprehensive knowledgebase for unraveling the N6-methyladenosine (m6A) epitranscriptome.
Nucleic Acids Res.
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, Daniel J. Rigden, Jia Meng
2020 J jnl
Comparing enrichment analysis and machine learning for identifying gene properties that discriminate between gene classes.
Briefings Bioinform.
Fabio Fabris, Daniel Palmer, João Pedro de Magalhães, Alex Alves Freitas
2020 J jnl
Using deep learning to associate human genes with age-related diseases.
Bioinform.
Fabio Fabris, Daniel Palmer, Khalid M. Salama, João Pedro de Magalhães, Alex Alves Freitas
2020 J jnl
m7GHub: deciphering the location, regulation and pathogenesis of internal mRNA N7-methylguanosine (m7G) sites in human.
Bioinform.
Bowen Song, Yujiao Tang, Kunqi Chen, Zhen Wei, Rong Rong, Zhiliang Lu, Jionglong Su, João Pedro de Magalhães, Daniel J. Rigden, Jia Meng
2018 J jnl
A new approach for interpreting Random Forest models and its application to the biology of ageing.
Bioinform.
Fabio Fabris, Aoife Doherty, Daniel Palmer, João Pedro de Magalhães, Alex Alves Freitas
2018 J jnl
Gene co-expression analysis for functional classification and gene-disease predictions.
Briefings Bioinform.
Sipko van Dam, Urmo Võsa, Adriaan van der Graaf, Lude Franke, João Pedro de Magalhães
2018 J jnl
Human Ageing Genomic Resources: new and updated databases.
Nucleic Acids Res.
Robi Tacutu, Daniel Thornton, Emily Johnson, Arie Budovsky, Diogo Barardo, Thomas Craig, Eugene Diana, Gilad Lehmann, Dmitri Toren, Jingwei Wang, Vadim E. Fraifeld, João Pedro de Magalhães
2016 J jnl
flowAI: automatic and interactive anomaly discerning tools for flow cytometry data.
Bioinform.
Gianni Monaco, Hao Chen, Michael Poidinger, Jinmiao Chen, João Pedro de Magalhães, Anis Larbi
2015 J jnl
GeneFriends: a human RNA-seq-based gene and transcript co-expression database.
Nucleic Acids Res.
Sipko van Dam, Thomas Craig, João Pedro de Magalhães
2015 J jnl
Predicting the Pro-Longevity or Anti-Longevity Effect of Model Organism Genes with New Hierarchical Feature Selection Methods.
IEEE ACM Trans. Comput. Biol. Bioinform.
Cen Wan, Alex Alves Freitas, João Pedro de Magalhães
2015 J jnl
The Digital Ageing Atlas: integrating the diversity of age-related changes into a unified resource.
Nucleic Acids Res.
Thomas Craig, Chris Smelick, Robi Tacutu, Daniel Wuttke, Shona H. Wood, Henry Stanley, Georges Janssens, Ekaterina Savitskaya, Alexey A. Moskalev, Robert Arking, João Pedro de Magalhães
2014 J jnl
The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations.
Bioinform.
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
2013 J jnl
Human Ageing Genomic Resources: Integrated databases and tools for the biology and genetics of ageing.
Nucleic Acids Res.
Robi Tacutu, Thomas Craig, Arie Budovsky, Daniel Wuttke, Gilad Lehmann, Dmitri Taranukha, Joana Cósta, Vadim E. Fraifeld, João Pedro de Magalhães
2011 J jnl
Gathering insights on disease etiology from gene expression profiles of healthy tissues.
Bioinform.
A. Sofia Silva, Shona H. Wood, Sipko van Dam, Sven Berres, Anne McArdle, João Pedro de Magalhães
2009 J jnl
Meta-analysis of age-related gene expression profiles identifies common signatures of aging.
Bioinform.
João Pedro de Magalhães, João Curado, George M. Church
2005 J jnl
HAGR: the Human Ageing Genomic Resources.
Nucleic Acids Res.
João Pedro de Magalhães, Joana Cósta, Olivier Toussaint