Sequence analysis of GerM and SpoVS, uncharacterized bacterial "sporulation" proteins with widespread phylogenetic distribution. - Daniel J. Rigden; Michael Y. Galperin (Bioinform., 2008)

Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of Glycoside Hydrolase. - Daniel J. Rigden; Ruth Y. Eberhardt; Harry J. Gilbert; Qingping Xu; Yuanyuan Chang; Adam Godzik (BMC Bioinform., 2014)

Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase. - Anna Sheydina; Ruth Y. Eberhardt; Daniel J. Rigden; Yuanyuan Chang; Zhanwen Li; Christian M. Zmasek; Herbert L. Axelrod; Adam Godzik (BMC Bioinform., 2014)

The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection. - Xosé M. Fernández-Suárez; Daniel J. Rigden; Michael Y. Galperin (Nucleic Acids Res., 2014)

The 2015 Nucleic Acids Research Database Issue and Molecular Biology Database Collection. - Michael Y. Galperin; Daniel J. Rigden; Xosé M. Fernández-Suárez (Nucleic Acids Res., 2015)

The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection. - Daniel J. Rigden; Xosé M. Fernández-Suárez; Michael Y. Galperin (Nucleic Acids Res., 2016)

ConKit: a python interface to contact predictions. - Felix Simkovic; Jens M. H. Thomas; Daniel J. Rigden (Bioinform., 2017)

The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. - Michael Y. Galperin; Xosé M. Fernández-Suárez; Daniel J. Rigden (Nucleic Acids Res., 2017)

The 2018 Nucleic Acids Research database issue and the online molecular biology database collection. - Daniel J. Rigden; Xosé M. Fernández-Suárez (Nucleic Acids Res., 2018)

The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection. - Daniel J. Rigden; Xosé M. Fernández-Suárez (Nucleic Acids Res., 2019)

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)

The 27th annual Nucleic Acids Research database issue and molecular biology database collection. - Daniel J. Rigden; Xosé M. Fernández (Nucleic Acids Res., 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)

ConPlot: web-based application for the visualization of protein contact maps integrated with other data. - Filomeno Sánchez Rodríguez; Shahram Mesdaghi; Adam J. Simpkin; J. Javier Burgos-Mármol; David L. Murphy; Ville Uski; Ronan M. Keegan; Daniel J. Rigden (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)

The 2021 Nucleic Acids Research database issue and the online molecular biology database collection. - Daniel J. Rigden; Xosé M. Fernández (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)

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)

The 2022 Nucleic Acids Research database issue and the online molecular biology database collection. - Daniel J. Rigden; Xosé M. Fernández (Nucleic Acids Res., 2022)

The 2023 Nucleic Acids Research Database Issue and the online molecular biology database collection. - Daniel J. Rigden; Xosé M. Fernández (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)