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Galperin, Michael Y, Rigden, Daniel J ORCID: 0000-0002-7565-8937 and Fernandez-Suarez, Xose M (2015) The 2015 <i>Nucleic Acids Research</i> Database Issue and Molecular Biology Database Collection. NUCLEIC ACIDS RESEARCH, 43 (D1). D1-D5.

Rigden, Daniel J ORCID: 0000-0002-7565-8937 and Fernandez, Xose M (2018) The 2018 <i>Nucleic Acids Research</i> database issue and the online molecular biology database collection. NUCLEIC ACIDS RESEARCH, 46 (D1). D1-D7.

Rigden, Daniel J ORCID: 0000-0002-7565-8937 and Fernandez, Xose M (2021) The 2021 <i>Nucleic Acids Research</i> database issue and the online molecular biology database collection. NUCLEIC ACIDS RESEARCH, 49 (D1). D1-D9.

Rigden, Daniel J ORCID: 0000-0002-7565-8937 and Fernandez, Xose M (2022) The 2022 <i>Nucleic Acids Research</i> database issue and the online molecular biology database collection. NUCLEIC ACIDS RESEARCH, 50 (D1). D1-D10.

Rigden, Daniel J ORCID: 0000-0002-7565-8937 and Fernandez, Xose M (2023) The 2023 <i>Nucleic Acids</i> <i>Research</i> Database Issue and the online molecular biology database collection. NUCLEIC ACIDS RESEARCH, 51 (D1). D1-D8.

Galperin, Michael Y, Fernandez-Suarez, Xose M and Rigden, Daniel J (2017) The 24th annual <i>Nucleic</i> <i>Acids</i> Research database issue: a look back and upcoming changes. NUCLEIC ACIDS RESEARCH, 45 (D1). D1-D11.

Galperin, Michael Y, Fernandez-Suarez, Xose M and Rigden, Daniel J ORCID: 0000-0002-7565-8937 (2017) The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes (vol 45, pg D1, 2017). NUCLEIC ACIDS RESEARCH, 45 (9). p. 5627.

Rigden, Daniel J ORCID: 0000-0002-7565-8937 and Fernandez, Xose M (2019) The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection. NUCLEIC ACIDS RESEARCH, 47 (D1). D1-D7.

Rigden, Daniel J ORCID: 0000-0002-7565-8937 and Fernandez, Xose M (2020) The 27th annual Nucleic Acids Research database issue and molecular biology database collection. NUCLEIC ACIDS RESEARCH, 48 (D1). D1-D8.

Brennand, Ana, Rico, Eva, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Van Der Smissen, Patrick, Courtoy, Pierre J and Michels, Paul AM (2015) ATG24 Represses Autophagy and Differentiation and Is Essential for Homeostasy of the Flagellar Pocket in <i>Trypanosoma brucei</i>. PLOS ONE, 10 (6). e0130365-.

Simkovic, Felix ORCID: 0000-0003-3430-6828, Oychinnikov, Sergey, Baker, David and Rigden, Daniel J ORCID: 0000-0002-7565-8937 (2017) Applications of contact predictions to structural biology. IUCRJ, 4 (Pt 3). pp. 291-300.

Thomas, Jens MH ORCID: 0000-0003-0277-8505, Simkovic, Felix ORCID: 0000-0003-3430-6828, Keegan, Ronan, Mayans, Olga, Zhang, Chengxin, Zhang, Yang and Rigden, Daniel J ORCID: 0000-0002-7565-8937 (2017) Approaches to ab initio molecular replacement of α-helical transmembrane proteins. Acta Crystallographica Section D: Structural Biology, 73 (12). pp. 985-996.

Millan, Claudia, Keegan, Ronan M, Pereira, Joana, Sammito, Massimo D, Simpkin, Adam J, McCoy, Airlie J, Lupas, Andrei N, Hartmann, Marcus D, Rigden, Daniel J ORCID: 0000-0002-7565-8937 and Read, Randy J (2021) Assessing the utility of CASP14 models for molecular replacement. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 89 (12). pp. 1752-1769.

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-.

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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.

Engdahl, Elin, van Schijndel, Maarten DM, Voulgaris, Dimitrios, Di Criscio, Michela, Ramsbottom, Kerry A ORCID: 0000-0002-7432-9293, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Herland, Anna and Ruegg, Joelle (2021) Bisphenol A Inhibits the Transporter Function of the Blood-Brain Barrier by Directly Interacting with the ABC Transporter Breast Cancer Resistance Protein (BCRP). INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 22 (11). 5534-.

Zhou, Tiankun, Fleming, Jennifer R, Franke, Barbara, Bogomolovas, Julius, Barsukov, Igor ORCID: 0000-0003-4406-9803, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Labeit, Siegfried and Mayans, Olga (2016) CARP interacts with titin at a unique helical N2A sequence and at the domain Ig81 to form a structured complex. FEBS LETTERS, 590 (18). pp. 3098-3110.

Ward, Lucy C, McCue, Hannah V, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Kershaw, Neil M, Ashbrook, Chloe, Hatton, Harry, Goulding, Ellie, Johnson, James R and Carnell, Andrew J ORCID: 0000-0002-6353-403X (2022) Carboxyl Methyltransferase Catalysed Formation of Mono- and Dimethyl Esters under Aqueous Conditions: Application in Cascade Biocatalysis. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 61 (14). e202117324-.

Ward, Lucy C, McCue, Hannah V, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Kershaw, Neil M, Ashbrook, Chloe, Hatton, Harry, Goulding, Ellie, Johnson, James R and Carnell, Andrew J ORCID: 0000-0002-6353-403X (2022) Carboxyl Methyltransferase Catalysed Formation of Mono‐ and Dimethyl Esters under Aqueous Conditions: Application in Cascade Biocatalysis. Angewandte Chemie, 134 (14).

Simkovic, Felix ORCID: 0000-0003-3430-6828, Thomas, Jens MH ORCID: 0000-0003-0277-8505 and Rigden, Daniel J ORCID: 0000-0002-7565-8937 (2017) ConKit: a python interface to contact predictions. BIOINFORMATICS, 33 (14). pp. 2209-2211.

Rodriguez, Filomeno Sanchez, Mesdaghi, Shahram, Simpkin, Adam J, Burgos-Marmol, J Javier, Murphy, David L, Uski, Ville, Keegan, Ronan M and Rigden, Daniel J ORCID: 0000-0002-7565-8937 (2021) ConPlot: web-based application for the visualization of protein contact maps integrated with other data. BIOINFORMATICS, 37 (17). 2763 - 2765.

Sánchez Rodríguez, Filomeno, Mesdaghi, Shahram, Simpkin, Adam J, Burgos-Mármol, J Javier, Murphy, David L, Uski, Ville, Keegan, Ronan M and Rigden, Daniel J (2021) ConPlot: web-based application for the visualization of protein contact maps integrated with other data. Bioinformatics (Oxford, England), 37 (17). 2763 - 2765.

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-.

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Weetman, David, Mitchell, Sara N, Wilding, Craig S, Birks, Daniel P, Yawson, Alexander E, Essandoh, John, Mawejje, Henry D, Djogbenou, Luc S, Steen, Keith, Rippon, Emily J et al (show 4 more authors) , Clarkson, Christopher S, Field, Stuart G, Rigden, Daniel J ORCID: 0000-0002-7565-8937 and Donnelly, Martin J (2015) Contemporary evolution of resistance at the major insecticide target site gene <i>Ace-1</i> by mutation and copy number variation in the malaria mosquito <i>Anophelesgambiae</i>. MOLECULAR ECOLOGY, 24 (11). pp. 2656-2672.

Ramsbottom, Kerry A ORCID: 0000-0002-7432-9293, Carr, Daniel F, Jones, Andrew R ORCID: 0000-0001-6118-9327 and Rigden, Daniel J ORCID: 0000-0002-7565-8937 (2018) Critical assessment of approaches for molecular docking to elucidate associations of HLA alleles with adverse drug reactions. MOLECULAR IMMUNOLOGY, 101. pp. 488-499.

Mesdaghi, Shahram, Price, Rebecca M ORCID: 0009-0003-1777-0925, Madine, Jillian ORCID: 0000-0001-9963-5871 and Rigden, Daniel J ORCID: 0000-0002-7565-8937 (2023) Deep Learning-based structure modelling illuminates structure and function in uncharted regions of β-solenoid fold space. Journal of Structural Biology, 215 (3). p. 108010.

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Zhang, Yuxin, Jiang, Jie, Ma, Jiongming, Wei, Zhen, Wang, Yue, Song, Bowen, Meng, Jia ORCID: 0000-0003-3455-205X, Jia, Guifang, de Magalhães, João Pedro ORCID: 0000-0002-6363-2465, Rigden, Daniel J ORCID: 0000-0002-7565-8937 et al (show 2 more authors) , Hang, Daiyun and Chen, Kunqi (2022) DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology. Nucleic acids research, 51 (D1). gkac1061-gkac1061.

Ward, Lucy C, Goulding, Ellie, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Allan, Faye E, Pellis, Alessandro, Hatton, Harry, Guebitz, Georg M, Salcedo-Sora, Jesus Enrique and Carnell, Andrew J ORCID: 0000-0002-6353-403X (2023) Engineering a Carboxyl Methyltransferase for the Formation of a Furan-Based Bioplastic Precursor. CHEMSUSCHEM, 16 (16). e202300516-.

Rigden, Daniel J ORCID: 0000-0002-7565-8937, Thomas, Jens MH ORCID: 0000-0003-0277-8505, Simkovic, Felix ORCID: 0000-0003-3430-6828, Simpkin, Adam ORCID: 0000-0003-1883-9376, Winn, Martyn D, Mayans, Olga and Keegan, Ronan M (2018) Ensembles generated from crystal structures of single distant homologues solve challenging molecular-replacement cases in <i>AMPLE</i>. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 74 (Pt 3). pp. 183-193.

Simpkin, Adam J, Sanchez Rodriguez, Filomeno, Mesdaghi, Shahram, Kryshtafovych, Andriy and Rigden, Daniel J ORCID: 0000-0002-7565-8937 (2021) Evaluation of model refinement in CASP14. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 89 (12). pp. 1852-1869.

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.

Keegan, Ronan M, Bibby, Jaclyn, Thomas, Jens ORCID: 0000-0003-0277-8505, Xu, Dong, Zhang, Yang, Mayans, Olga, Winn, Martyn D and Rigden, Daniel J ORCID: 0000-0002-7565-8937 (2015) Exploring the speed and performance of molecular replacement with <i>AMPLE</i> using <i>QUARK ab initio</i> protein models. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 71 (Pt 2). pp. 338-343.

Thomas, Jens MH ORCID: 0000-0003-0277-8505, Keegan, Ronan M, Rigden, Daniel J ORCID: 0000-0002-7565-8937 and Davies, Owen R (2020) Extending the scope of coiled-coil crystal structure solution by <i>AMPLE</i> through improved <i>ab initio</i> modelling. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 76 (Pt 3). pp. 272-284.

Simpkin, Adam J ORCID: 0000-0003-1883-9376 and Rigden, Daniel J ORCID: 0000-0002-7565-8937 (2016) GP0.4 from bacteriophage T7: in silico characterisation of its structure and interaction with E. coli FtsZ. BMC research notes, 9 (1). 343-.

Isaacs, Alison T, Mawejje, Henry D, Tomlinson, Sean, Rigden, Daniel J ORCID: 0000-0002-7565-8937 and Donnelly, Martin J (2018) Genome-wide transcriptional analyses in Anopheles mosquitoes reveal an unexpected association between salivary gland gene expression and insecticide resistance. BMC GENOMICS, 19 (1). 225-.

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.

Loxley, Grace M, Unsworth, Jennifer, Turton, Michael J, Jebb, Alexandra, Lilley, Kathryn S, Simpson, Deborah M ORCID: 0000-0002-3962-4895, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Hurst, Jane L ORCID: 0000-0002-3728-9624 and Beynon, Robert J ORCID: 0000-0003-0857-495X (2017) Glareosin: a novel sexually dimorphic urinary lipocalin in the bank vole, Myodes glareolus. Open Biology, 7 (9). 170135-.

Sanchez Rodriguez, Filomeno, Simpkin, Adam J, Davies, Owen R, Keegan, Ronan M and Rigden, Daniel J ORCID: 0000-0002-7565-8937 (2020) Helical ensembles outperform ideal helices in molecular replacement. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 76 (Pt 10). pp. 962-970.

Pereira, Joana, Simpkin, Adam J, Hartmann, Marcus D, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Keegan, Ronan M and Lupas, Andrei N (2021) High-accuracy protein structure prediction in CASP14. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 89 (12). pp. 1687-1699.

Mesdaghi, Shahram, Murphy, David L, Sánchez Rodríguez, Filomeno ORCID: 0000-0002-6377-7269, Burgos-Mármol, J Javier ORCID: 0000-0003-1861-2657 and Rigden, Daniel J ORCID: 0000-0002-7565-8937 (2020) In silico prediction of structure and function for a large family of transmembrane proteins that includes human Tmem41b. F1000Research, 9. 1395-.

Ramsbottom, Kerry ORCID: 0000-0002-7432-9293 (2020) Informatics investigations into HLA-mediated adverse drug reactions. PhD thesis, University of Liverpool.

Ramsbottom, Kerry A ORCID: 0000-0002-7432-9293, Carr, Daniel F, Rigden, Daniel J ORCID: 0000-0002-7565-8937 and Jones, Andrew R ORCID: 0000-0001-6118-9327 (2020) Informatics investigations into anti-thyroid drug induced agranulocytosis associated with multiple HLA-B alleles. PLOS ONE, 15 (2). e0220754-.

Saleh, Hadil, Liloglou, Triantafillos ORCID: 0000-0003-0460-1404, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Parsons, Jason L ORCID: 0000-0002-5052-1125 and Grundy, Gabrielle J ORCID: 0000-0003-1506-3664 (2024) KH-like Domains in PARP9/DTX3L and PARP14 Coordinate Protein-Protein Interactions to Promote Cancer Cell Survival. Journal of molecular biology, 436 (4). p. 168434.

Kozic, Mara, Fox, Stephen J, Thomas, Jens M ORCID: 0000-0003-0277-8505, Verma, Chandra S and Rigden, Daniel J ORCID: 0000-0002-7565-8937 (2018) Large scale ab initio modeling of structurally uncharacterized antimicrobial peptides reveals known and novel folds. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 86 (5). pp. 548-565.

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Hewetson, Aveline, Khan, Nazmul H, Dominguez, Matthew J, Do, Hoa Quynh, Kusko, RE, Borcik, Collin G, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Keegan, Ronan M, Sutton, R Bryan, Latham, Michael P et al (show 2 more authors) , Wylie, Benjamin J and Cornwall, Gail A (2020) Maturation of the functional mouse CRES amyloid from globular form. Proceedings of the National Academy of Sciences of the United States of America, 117 (28). pp. 16363-16372.

Glover, Hannah L, Mendes, Marta, Gomes-Neto, Joana, Rusilowicz-Jones, Emma V, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Dittmar, Gunnar, Urbé, Sylvie and Clague, Michael J ORCID: 0000-0003-3355-9479 (2023) Microtubule association of TRIM3 revealed by differential extraction proteomics. Journal of cell science. jcs.261522-jcs.261522.

Simpkin, Adam J, Thomas, Jens MH ORCID: 0000-0003-0277-8505, Simkovic, Felix, Keegan, Ronan M and Rigden, Daniel J ORCID: 0000-0002-7565-8937 (2019) Molecular replacement using structure predictions from databases. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 75 (Pt 12). pp. 1051-1062.

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Moroz, Olga V, Blagova, Elena, Lebedev, Andrey A, Rodriguez, Filomeno Sanchez, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Tams, Jeppe Wegener, Wilting, Reinhard, Vester, Jan Kjolhede, Longhin, Elena, Hansen, Gustav Hammerich et al (show 4 more authors) , Krogh, Kristian Bertel Romer Morkeberg, Pache, Roland A, Davies, Gideon J and Wilson, Keith S (2021) Multitasking in the gut: the X-ray structure of the multidomain BbgIII from Bifidobacterium bifidum offers possible explanations for its alternative functions. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 77 (Pt 12). pp. 1564-1578.

Bengtsson, Rebecca J, Simpkin, Adam J, Pulford, Caisey V, Low, Ross, Rasko, David A, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Hall, Neil, Barry, Eileen M, Tennant, Sharon M and Baker, Kate S ORCID: 0000-0001-5850-1949 (2022) Pathogenomic analyses of Shigella isolates inform factors limiting shigellosis prevention and control across LMICs. NATURE MICROBIOLOGY, 7 (2). 251-+.

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Simpkin, Adam J ORCID: 0000-0003-1883-9376, Caballero, Iracema, McNicholas, Stuart, Stevenson, Kyle, Jimenez, Elisabet, Rodriguez, Filomneno Sanchez, Fando, Maria, Uski, Ville, Ballard, Charles, Chojnowski, Grzegorz et al (show 5 more authors) , Lebedev, Andrey, Krissinel, Eugene, Uson, Isabel, Rigden, Daniel J ORCID: 0000-0002-7565-8937 and Keegan, Ronan M (2023) Predicted models and <i>CCP</i>4. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 79 (Pt 9). pp. 806-819.

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Owen, Sian V, Wenner, Nicolas, Dulberger, Charles L, Rodwell, Ella V, Bowers-Barnard, Arthur, Quinones-Olvera, Natalia, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Rubin, Eric J, Garner, Ethan C, Baym, Michael et al (show 1 more authors) and Hinton, Jay CD ORCID: 0000-0003-2671-6026 (2021) Prophages encode phage-defense systems with cognate self-immunity. CELL HOST & MICROBE, 29 (11). 1620-+.

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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.

Keegan, Ronan M, McNicholas, Stuart J, Thomas, Jens MH ORCID: 0000-0003-0277-8505, Simpkin, Adam J ORCID: 0000-0003-1883-9376, Simkovic, Felix ORCID: 0000-0003-3430-6828, Uski, Ville, Ballard, Charles C, Winn, Martyn D, Wilson, Keith S and Rigden, Daniel J ORCID: 0000-0002-7565-8937 (2018) Recent developments in <i>MrBUMP</i>: better search-model preparation, graphical interaction with search models, and solution improvement and assessment. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 74 (Pt 3). pp. 167-182.

Simpkin, Adam J, Winn, Martyn D, Rigden, Daniel J ORCID: 0000-0002-7565-8937 and Keegan, Ronan M (2021) Redeployment of automated MrBUMP searchmodel identification for map fitting in cryo-EM. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 77 (Pt 11). pp. 1378-1385.

Thomas, Jens MH ORCID: 0000-0003-0277-8505, Keegan, Ronan M, Bibby, Jaclyn, Winn, Martyn D, Mayans, Olga and Rigden, Daniel J ORCID: 0000-0002-7565-8937 (2015) Routine phasing of coiled-coil protein crystal structures with <i>AMPLE</i>. IUCRJ, 2 (Pt 2). pp. 198-206.

Zacharchenko, Thomas, von Castelmur, Eleonore, Rigden, Daniel J ORCID: 0000-0002-7565-8937 and Mayans, Olga (2015) Structural advances on titin: towards an atomic understanding of multi-domain functions in myofilament mechanics and scaffolding. BIOCHEMICAL SOCIETY TRANSACTIONS, 43 (5). pp. 850-855.

Franke, Barbara, Veses-Garcia, Marta, Diederichs, Kay, Allison, Heather ORCID: 0000-0003-0017-7992, Rigden, Daniel J ORCID: 0000-0002-7565-8937 and Mayans, Olga (2020) Structural annotation of the conserved carbohydrate esterase vb_24B_21 from Shiga toxin-encoding bacteriophage Φ24_B. JOURNAL OF STRUCTURAL BIOLOGY, 212 (1). 107596-.

Rojas-Pirela, Maura, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Michels, Paul A, Caceres, Ana J, Concepcion, Juan Luis and Quinones, Wilfredo (2018) Structure and function of Per-ARNT-Sim domains and their possible role in the life-cycle biology of <i>Trypanosoma cruzi</i>. MOLECULAR AND BIOCHEMICAL PARASITOLOGY, 219. pp. 52-66.

Simpkin, Adam J ORCID: 0000-0003-1883-9376, Mesdaghi, Shahram, Rodriguez, Filomeno Sanchez, Elliott, Luc, Murphy, David L, Kryshtafovych, Andriy, Keegan, Ronan M and Rigden, Daniel J ORCID: 0000-0002-7565-8937 (2023) Tertiary structure assessment at CASP15. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 91 (12). pp. 1616-1635.

Veses-Garcia, Marta, Liu, Xuan, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Kenny, John G, McCarthy, Alan J and Allison, Heather E ORCID: 0000-0003-0017-7992 (2015) Transcriptomic Analysis of Shiga-Toxigenic Bacteriophage Carriage Reveals a Profound Regulatory Effect on Acid Resistance in Escherichia coli. Applied and Environmental Microbiology, 81 (23). pp. 8118-8125.

Rodriguez, Filomeno Sanchez, Chojnowski, Grzegorz, Keegan, Ronan M and Rigden, Daniel J ORCID: 0000-0002-7565-8937 (2022) Using deep-learning predictions of inter-residue distances for model validation. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 78 (Pt 12). pp. 1412-1427.

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-.

Guo, Jingxu, Keegan, Ronan M, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Erskine, Peter T, Wood, Steve P, Li, Sheng and Cooper, Jonathan B (2021) The X-ray structure of juvenile hormone diol kinase from the silkworm <i>Bombyx mori</i>. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 77 (Pt 12). pp. 465-472.

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Dusi, Diva MA, Alves, Elizângela R, Cabral, Gláucia B, Mello, Luciane V, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Silveira, Érica D, Alves-Ferreira, Márcio, Guimarães, Larissa A, Gomes, Ana Cristina MM, Rodrigues, Júlio CM et al (show 1 more authors) and Carneiro, Vera TC (2023) An exonuclease V homologue is expressed predominantly during early megasporogenesis in apomictic Brachiaria brizantha. Planta, 258 (1). p. 5.

Chojnowski, Grzegorz, Simpkin, Adam J, Leonardo, Diego A, Seifert-Davila, Wolfram, Vivas-Ruiz, Dan E, Keegan, Ronan M and Rigden, Daniel J ORCID: 0000-0002-7565-8937 (2022) findMySequence: a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM. IUCrJ, 9 (1). pp. 86-97.

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Nunes, Quentin M ORCID: 0000-0002-7513-8595, Su, Dunhao, Brownridge, Philip J, Simpson, Deborah M ORCID: 0000-0002-3962-4895, Sun, Changye, Li, Yong, Bui, Thao P, Zhang, Xiaoying, Huang, Wei, Rigden, Daniel J ORCID: 0000-0002-7565-8937 et al (show 3 more authors) , Beynon, Robert J ORCID: 0000-0003-0857-495X, Sutton, Robert ORCID: 0000-0001-6600-562X and Fernig, David G ORCID: 0000-0003-4875-4293 (2019) The heparin-binding proteome in normal pancreas and murine experimental acute pancreatitis. PLOS ONE, 14 (6). e0217633-.

Midha, Samriti, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Siozios, Stefanos ORCID: 0000-0002-1104-7061, Hurst, Gregory DD ORCID: 0000-0002-7163-7784 and Jackson, Andrew P ORCID: 0000-0002-5704-8596 (2021) <i>Bodo saltans</i> (Kinetoplastida) is dependent on a novel <i>Paracaedibacter</i>-like endosymbiont that possesses multiple putative toxin-antitoxin systems. ISME JOURNAL, 15 (6). pp. 1680-1694.

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Agirre, Jon, Atanasova, Mihaela, Bagdonas, Haroldas, Ballard, Charles B, Basle, Arnaud, Beilsten-Edmands, James, Borges, Rafael J, Brown, David G, Burgos-Marmol, J Javier ORCID: 0000-0003-1861-2657, Berrisford, John M et al (show 84 more authors) , Bond, Paul S, Caballero, Iracema, Catapano, Lucrezia, Chojnowski, Grzegorz, Cook, Atlanta G, Cowtan, Kevin D, Croll, Tristan I, Debreczeni, Judit E, Devenish, Nicholas E, Dodson, Eleanor J, Drevon, Tarik R, Emsley, Paul, Evans, Gwyndaf, Evans, Phil R, Fando, Maria, Foadi, James, Fuentes-Montero, Luis, Garman, Elspeth F, Gerstel, Markus, Gildea, Richard J, Hatti, Kaushik, Hekkelman, Maarten L, Heuser, Philipp, Hoh, Soon Wen, Hough, Michael A, Jenkins, Huw T, Jimenez, Elisabet, Joosten, Robbie P, Keegan, Ronan M, Keep, Nicholas, Krissinel, Eugene B, Kolenko, Petr, Kovalevskiy, Oleg, Lamzin, Victor S, Lawson, David M, Lebedev, Andrey A, Leslie, Andrew GW, Lohkamp, Bernhard, Long, Fei, Maly, Martin, McCoy, Airlie J, McNicholas, Stuart J, Medina, Ana, Millan, Claudia, Murray, James W, Murshudov, Garib N, Nicholls, Robert A, Noble, Martin EM, Oeffner, Robert, Pannu, Navraj S, Parkhurst, James M, Pearce, Nicholas, Pereira, Joana, Perrakis, Anastassis, Powell, Harold R, Read, Randy J, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Rochira, William, Sammito, Massimo, Rodriguez, Filomeno Sanchez, Sheldrick, George M, Shelley, Kathryn L, Simkovic, Felix, Simpkin, Adam J ORCID: 0000-0003-1883-9376, Skubak, Pavol, Sobolev, Egor, Steiner, Roberto A, Stevenson, Kyle, Tews, Ivo, Thomas, Jens MH ORCID: 0000-0003-0277-8505, Thorn, Andrea, Trivino Valls, Josep, Uski, Ville, Uson, Isabel, Vagin, Alexei, Velankar, Sameer, Vollmar, Melanie, Walden, Helen, Waterman, David, Wilson, Keith S, Winn, Martyn D, Winter, Graeme, Wojdyr, Marcin and Yamashita, Keitaro (2023) The <i>CCP4</i> suite: integrative software for macromolecular crystallography. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 79 (Pt 6). pp. 449-461.

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Krissinel, Eugene, Lebedev, Andrey A, Uski, Ville, Ballard, Charles B, Keegan, Ronan M, Kovalevskiy, Oleg, Nicholls, Robert A, Pannu, Navraj S, Skubak, Pavol, Berrisford, John et al (show 23 more authors) , Fando, Maria, Lohkamp, Bernhard, Wojdyr, Marcin, Simpkin, Adam J ORCID: 0000-0003-1883-9376, Thomas, Jens MH ORCID: 0000-0003-0277-8505, Oliver, Christopher, Vonrhein, Clemens, Chojnowski, Grzegorz, Basle, Arnaud, Purkiss, Andrew, Isupov, Michail N, McNicholas, Stuart, Lowe, Edward, Trivino, Josep, Cowtan, Kevin, Agirre, Jon, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Uson, Isabel, Lamzin, Victor, Tews, Ivo, Bricogne, Gerard, Leslie, Andrew GW and Brown, David G (2022) <i>CCP</i>4 Cloud for structure determination and project management in macromolecular crystallograpny. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 78 (Pt 9). pp. 1079-1089.

Simpkin, Adam J ORCID: 0000-0003-1883-9376, Thomas, Jens MH ORCID: 0000-0003-0277-8505, Keegan, Ronan M and Rigden, Daniel J ORCID: 0000-0002-7565-8937 (2022) <i>MrParse:</i> finding homologues in the PDB and the EBI AlphaFold database tor molecular replacement and more. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 78 (Pt 5). pp. 553-559.

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Liang, Zhanmin, Ye, Haokai, Ma, Jiongming, Wei, Zhen, Wang, Yue, Zhang, Yuxin, Huang, Daiyun, Song, Bowen, Meng, Jia ORCID: 0000-0003-3455-205X, Rigden, Daniel J ORCID: 0000-0002-7565-8937 et al (show 1 more authors) and Chen, Kunqi (2023) m(6) A-Atlas v2.0: updated resources for unraveling the N 6-methyladenosine (m(6)A) epitranscriptome among multiple species. NUCLEIC ACIDS RESEARCH, 52 (D1). D194-D202.

Ma, Jiongming, Song, Bowen, Wei, Zhen, Huang, Daiyun, Zhang, Yuxin, Su, Jionglong, de Magalhães, João Pedro ORCID: 0000-0002-6363-2465, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Meng, Jia ORCID: 0000-0003-3455-205X and Chen, Kunqi (2022) m5C-Atlas: a comprehensive database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome. Nucleic acids research, 50 (D1). D196-D203.

Song, Bowen ORCID: 0000-0002-8586-0573, Huang, Daiyun ORCID: 0000-0002-3067-7165, Zhang, Yuxin ORCID: 0000-0003-1900-6712, Wei, Zhen, Su, Jionglong ORCID: 0000-0001-5360-6493, Pedro de Magalhães, João, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Meng, Jia ORCID: 0000-0003-3455-205X and Chen, Kunqi ORCID: 0000-0002-6025-8957 (2023) m6A-TSHub: Unveiling the Context-specific m⁶A Methylation and m⁶A-affecting Mutations in 23 Human Tissues. Genomics, proteomics & bioinformatics, 21 (4). pp. 678-694.

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.

Collapse authors list.
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.