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Gonzalez-Galarza, Faviel F, McCabe, Antony ORCID: 0000-0003-3089-3674, Santos, Eduardo J Melo dos, Jones, James, Takeshita, Louise ORCID: 0000-0003-4288-4388, Ortega-Rivera, Nestor D, Cid-Pavon, Glenda M Del, Ramsbottom, Kerry ORCID: 0000-0002-7432-9293, Ghattaoraya, Gurpreet, Alfirevic, Ana ORCID: 0000-0002-2801-9817 et al (show 2 more authors) , Middleton, Derek and Jones, Andrew R ORCID: 0000-0001-6118-9327 (2020) Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data and new query tools. Nucleic Acids Research, 48 (D1). D783-D788.

Camacho, Oscar M, Ramsbottom, Kerry A ORCID: 0000-0002-7432-9293, Collins, Andrew ORCID: 0000-0003-0507-6912 and Jones, Andrew R ORCID: 0000-0001-6118-9327 (2023) Assessing Multiple Evidence Streams to Decide on Confidence for Identification of Post-Translational Modifications, within and Across Data Sets. JOURNAL OF PROTEOME RESEARCH, 22 (6). pp. 1828-1842.

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Meyer, Bjoern, Chiaravalli, Jeanne, Gellenoncourt, Stacy, Brownridge, Philip, Bryne, Dominic P, Daly, Leonard A ORCID: 0000-0001-9712-9676, Grauslys, Arturas ORCID: 0000-0002-6736-6854, Walter, Marius, Agou, Fabrice, Chakrabarti, Lisa A et al (show 9 more authors) , Craik, Charles S, Eyers, Claire E ORCID: 0000-0002-3223-5926, Eyers, Patrick A ORCID: 0000-0002-9220-2966, Gambin, Yann, Jones, Andrew R ORCID: 0000-0001-6118-9327, Sierecki, Emma, Verdin, Eric, Vignuzzi, Marco and Emmott, Edward ORCID: 0000-0002-3239-8178 (2021) Characterising proteolysis during SARS-CoV-2 infection identifies viral cleavage sites and cellular targets with therapeutic potential. NATURE COMMUNICATIONS, 12 (1). 5553-.

Al-Momani, Shireen, Qi, Da ORCID: 0000-0001-6079-9764, Ren, Zhe and Jones, Andrew R ORCID: 0000-0001-6118-9327 (2018) Comparative qualitative phosphoproteomics analysis identifies shared phosphorylation motifs and associated biological processes in evolutionary divergent plants. JOURNAL OF PROTEOMICS, 181. pp. 152-159.

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.

Daly, Leonard A ORCID: 0000-0001-9712-9676, Byrne, Dominic P, Perkins, Simon, Brownridge, Philip J, McDonnell, Euan, Jones, Andrew R ORCID: 0000-0001-6118-9327, Eyers, Patrick A ORCID: 0000-0002-9220-2966 and Eyers, Claire E ORCID: 0000-0002-3223-5926 (2023) Custom Workflow for the Confident Identification of Sulfotyrosine-Containing Peptides and Their Discrimination from Phosphopeptides. Journal of proteome research, 22 (12). pp. 3754-3772.

Huang, fang, Grauslys, Arturas, Huokko, tuomas, Caamaño Gutiérrez, Eva, Jones, Andrew R ORCID: 0000-0001-6118-9327 and Liu, Luning ORCID: 0000-0002-8884-4819 (2023) Dynamic changes in the thylakoid proteome of cyanobacteria during light-regulated thylakoid membrane development. Plants, 12 (23). 3967-.

Contreras-Moreira, Bruno, Saraf, Shradha, Naamati, Guy, Casas, Ana M, Amberkar, Sandeep S, Flicek, Paul, Jones, Andrew R ORCID: 0000-0001-6118-9327 and Dyer, Sarah (2023) GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation. Genome biology, 24 (1). p. 223.

Jones, Fiona K, Phillips, Alexander M ORCID: 0000-0002-1637-4803, Jones, Andrew R and Pisconti, Addolorata (2022) The INSR/AKT/mTOR pathway regulates the pace of myogenesis in a syndecan-3-dependent manner. MATRIX BIOLOGY, 113. pp. 61-82.

Ren, Zhe, Qi, Da ORCID: 0000-0001-6079-9764, Pugh, Nina, Li, Kai, Wen, Bo, Zhou, Ruo, Xu, Shaohang, Liu, Siqi and Jones, Andrew R ORCID: 0000-0001-6118-9327 (2019) Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets. Molecular and Cellular Proteomics, 18 (1). pp. 86-98.

Ren, Zhe, Qi, Da, Pugh, Nina, Li, Kai, Wen, Bo, Zhou, Ruo, Xu, Shaohang, Liu, Siqi and Jones, Andrew R ORCID: 0000-0001-6118-9327 (2019) Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets. Molecular & cellular proteomics : MCP, 18 (1). 86 - 98.

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-.

Prakash, Ananth, Garcia-Seisdedos, David, Wang, Shengbo, Kundu, Deepti Jaiswal, Collins, Andrew ORCID: 0000-0003-0507-6912, George, Nancy, Moreno, Pablo, Papatheodorou, Irene, Jones, Andrew R ORCID: 0000-0001-6118-9327 and Vizcaino, Juan Antonio (2023) Integrated View of Baseline Protein Expression in Human Tissues. JOURNAL OF PROTEOME RESEARCH, 22 (3). pp. 729-742.

Jones, Andrew R ORCID: 0000-0001-6118-9327, Deutsch, Eric W and Vizcaino, Juan Antonio (2023) Is DIA proteomics data FAIR? Current data sharing practices, available bioinformatics infrastructure and recommendations for the future. PROTEOMICS, 23 (7-8). e2200014-.

Pearngam, Phorutai, Sriswasdi, Sira, Pisitkun, Trairak ORCID: 0000-0001-6677-2271 and Jones, Andrew R ORCID: 0000-0001-6118-9327 (2021) MHCVision: estimation of global and local false discovery rate for MHC class I peptide binding prediction. BIOINFORMATICS, 37 (21). pp. 3830-3838.

Ramsbottom, Kerry A ORCID: 0000-0002-7432-9293, Prakash, Ananth, Riverol, Yasset Perez, Camacho, Oscar Martin, Martin, Maria-Jesus, Vizcaino, Juan Antonio, Deutsch, Eric W and Jones, Andrew R ORCID: 0000-0001-6118-9327 (2022) Method for Independent Estimation of the False Localization Rate for Phosphoproteomics. JOURNAL OF PROTEOME RESEARCH, 21 (7). pp. 1603-1615.

Grosman, Rudi ORCID: 0000-0002-0233-7112 (2019) NMR METABOLIC PROFILING OF MOSQUITO SPECIES TO UNDERSTAND INSECTICIDE RESISTANCE. PhD thesis, University of Liverpool.

Peffers, Mandy ORCID: 0000-0001-6979-0440, Jones, Andrew R ORCID: 0000-0001-6118-9327, McCabe, Antony ORCID: 0000-0003-3089-3674 and Anderson, James ORCID: 0000-0003-0489-7997 (2017) Neopeptide Analyser: A software tool for neopeptide discovery in proteomics data. Wellcome open research, 2. 24-.

Myall, Ashleigh C, Perkins, Simon, Rushton, David, David, Jonathan, Spencer, Phillippa, Jones, Andrew R ORCID: 0000-0001-6118-9327 and Antczak, Philipp ORCID: 0000-0001-9600-7757 (2021) An OMICs-based meta-analysis to support infection state stratification. BIOINFORMATICS, 37 (16). pp. 2347-2355.

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Ashwood, Christopher, Bittremieux, Wout, Deutsch, Eric W, Doncheva, Nadezhda T, Dorfer, Viktoria, Gabriels, Ralf, Gorshkov, Vladimir, Gupta, Surya, Jones, Andrew R ORCID: 0000-0001-6118-9327, Käll, Lukas et al (show 23 more authors) , Kopczynski, Dominik, Lane, Lydie, Lautenbacher, Ludwig, Legeay, Marc, Locard-Paulet, Marie, Mesuere, Bart, Perez-Riverol, Yasset, Netz, Eugen, Pfeuffer, Julianus, Sachsenberg, Timo, Salz, Renee, Samaras, Patroklos, Schiebenhoefer, Henning, Schmidt, Tobias, Schwämmle, Veit, Soggiu, Alessio, Uszkoreit, Julian, Van Den Bossche, Tim, Van Puyvelde, Bart, Van Strien, Joeri, Verschaffelt, Pieter, Webel, Henry and Willems, Sander (2020) Proceedings of the EuBIC-MS 2020 Developers’ Meeting. .

Kalyuzhnyy, Anton, Eyers, Patrick A ORCID: 0000-0002-9220-2966, Eyers, Claire E ORCID: 0000-0002-3223-5926, Bowler-Barnett, Emily, Martin, Maria J, Sun, Zhi, Deutsch, Eric W and Jones, Andrew R ORCID: 0000-0001-6118-9327 (2022) Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation. JOURNAL OF PROTEOME RESEARCH, 21 (6). pp. 1510-1524.

Oyarzun, Patricio, Kashyap, Manju, Fica, Victor, Salas-Burgos, Alexis, Gonzalez-Galarza, Faviel F, McCabe, Antony ORCID: 0000-0003-3089-3674, Jones, Andrew R ORCID: 0000-0001-6118-9327, Middleton, Derek and Kobe, Bostjan (2021) A Proteome-Wide Immunoinformatics Tool to Accelerate T-Cell Epitope Discovery and Vaccine Design in the Context of Emerging Infectious Diseases: An Ethnicity-Oriented Approach. FRONTIERS IN IMMUNOLOGY, 12. 598778-.

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Deutsch, Eric W, Vizcaino, Juan Antonio, Jones, Andrew R ORCID: 0000-0001-6118-9327, Binz, Pierre-Alain, Lam, Henry, Klein, Joshua, Bittremieux, Wout, Perez-Riverol, Yasset, Tabb, David L, Walzer, Mathias et al (show 19 more authors) , Ricard-Blum, Sylvie, Hermjakob, Henning, Neumann, Steffen, Mak, Tytus D, Kawano, Shin, Mendoza, Luis, Van Den Bossche, Tim, Gabriels, Ralf, Bandeira, Nuno, Carver, Jeremy, Pullman, Benjamin, Sun, Zhi, Hoffmann, Nils, Shofstahl, Jim, Zhu, Yunping, Licata, Luana, Quaglia, Federica, Tosatto, Silvio CE and Orchard, Sandra E (2023) Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. JOURNAL OF PROTEOME RESEARCH, 22 (2). pp. 287-301.

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Deutsch, Eric W, Orchard, Sandra, Binz, Pierre-Alain, Bittremieux, Wout, Eisenacher, Martin, Hermjakob, Henning, Kawano, Shin, Lam, Henry, Mayer, Gerhard, Menschaert, Gerben et al (show 7 more authors) , Perez-Riverol, Yasset, Salek, Reza M, Tabb, David L, Tenzer, Stefan, Vizcaino, Juan Antonio, Walzer, Mathias and Jones, Andrew R ORCID: 0000-0001-6118-9327 (2017) Proteomics Standards Initiative: Fifteen Years of Progress and Future Work. JOURNAL OF PROTEOME RESEARCH, 16 (12). pp. 4288-4298.

Boegelein, Thomas, Rao, Ashwin, Jones, Andrew R and Tatlock, Gordon J (2011) Selective Laser Melting of Oxide Dispersion Strengthened Steels. PhD thesis, University of Liverpool.

Campbell, Amy E ORCID: 0000-0001-8390-4360, Franco, Catarina Ferraz, Ling-I, Su, Corbin, Emma K, Perkins, Simon, Kalyuzhnyy, Anton, Jones, Andrew R ORCID: 0000-0001-6118-9327, Brownridge, Philip J, Perkins, Neil D and Eyers, Claire E ORCID: 0000-0002-3223-5926 (2021) Temporal modulation of the NF-kappa B ReIA network in response to different types of DNA damage. Biochemical Journal, 478 (3). pp. 533-551.

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Leitner, Alexander, Bonvin, Alexandre MJJ, Borchers, Christoph H, Chalkley, Robert J, Chamot-Rooke, Julia, Combe, Colin W, Cox, Juergen, Dong, Meng-Qiu, Fischer, Lutz, Gotze, Michael et al (show 26 more authors) , Gozzo, Fabio C, Heck, Albert JR, Hoopmann, Michael R, Huang, Lan, Ishihama, Yasushi, Jones, Andrew R ORCID: 0000-0001-6118-9327, Kalisman, Nir, Kohlbacher, Oliver, Mechtler, Karl, Moritz, Robert L, Netz, Eugen, Novak, Petr, Petrotchenko, Evgeniy, Sali, Andrej, Scheltema, Richard A, Schmidt, Carla, Schriemer, David, Sinz, Andrea, Sobott, Frank, Stengel, Florian, Thalassinos, Konstantinos, Urlaub, Henning, Viner, Rosa, Vizcaino, Juan A, Wilkins, Marc R and Rappsilber, Juri (2020) Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry. STRUCTURE, 28 (11). pp. 1259-1268.

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Shanmugasundram, Achchuthan, Starns, David, Böhme, Ulrike, Amos, Beatrice, Wilkinson, Paul A, Harb, Omar S, Warrenfeltz, Susanne, Kissinger, Jessica C, McDowell, Mary Ann, Roos, David S et al (show 2 more authors) , Crouch, Kathryn and Jones, Andrew R ORCID: 0000-0001-6118-9327 (2023) TriTrypDB: An integrated functional genomics resource for kinetoplastida. PLoS neglected tropical diseases, 17 (1). e0011058-e0011058.

Clark, Lisa, Sue-Ob, Kawinnat, Mukkawar, Vaishnavi, Jones, Andrew R ORCID: 0000-0001-6118-9327 and Sadanandom, Ari (2022) Understanding SUMO-mediated adaptive responses in plants to improve crop productivity. Essays in biochemistry, 66 (2). EBC20210068-EBC20210068.

Byrne, Dominic P, Clarke, Christopher J, Brownridge, Philip J, Kalyuzhnyy, Anton, Perkins, Simon, Campbell, Amy ORCID: 0000-0001-8390-4360, Mason, David, Jones, Andrew R ORCID: 0000-0001-6118-9327, Eyers, Patrick A ORCID: 0000-0002-9220-2966 and Eyers, Claire E ORCID: 0000-0002-3223-5926 (2020) Use of the Polo-like kinase 4 (PLK4) inhibitor centrinone to investigate intracellular signalling networks using SILAC-based phosphoproteomics. The Biochemical journal, 477 (13). 2451 - 2475.

Byrne, Dominic P, Clarke, Christopher J, Brownridge, Philip J, Kalyuzhnyy, Anton, Perkins, Simon, Campbell, Amy ORCID: 0000-0001-8390-4360, Mason, David, Jones, Andrew R ORCID: 0000-0001-6118-9327, Eyers, Patrick A ORCID: 0000-0002-9220-2966 and Eyers, Claire E ORCID: 0000-0002-3223-5926 (2020) Use of the Polo-like kinase 4 (PLK4) inhibitor centrinone to investigate intracellular signalling networks using SILAC-based phosphoproteomics. The Biochemical journal, 477 (13). pp. 2451-2475.

Pereira, Sara Silva, Heap, John, Jones, Andrew R ORCID: 0000-0001-6118-9327 and Jackson, Andrew P ORCID: 0000-0002-5704-8596 (2019) VAPPER: High-throughput variant antigen profiling in African trypanosomes of livestock. GIGASCIENCE, 8 (9). giz091-.

Takeshita, Louise YC ORCID: 0000-0003-4288-4388, Gonzalez-Galarza, Faviel F, dos Santos, Eduardo JM, Maia, Maria Helena T, Rahman, Mushome M, Zain, Syed MS, Middleton, Derek and Jones, Andrew R ORCID: 0000-0001-6118-9327 (2013) A database for curating the associations between killer cell immunoglobulin-like receptors and diseases in worldwide populations. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2013. bat021-.

McCabe, Antony ORCID: 0000-0003-3089-3674 and Jones, Andrew R ORCID: 0000-0001-6118-9327 (2021) lcmsWorld: High-Performance 3D Visualization Software for Mass Spectrometry. Journal of Proteome Research, 20 (4). pp. 1981-1985.

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Vizcaino, Juan Antonio, Mayer, Gerhard, Perkins, Simon, Barsnes, Harald, Vaudel, Marc, Perez-Riverol, Yasset, Ternent, Tobias, Uszkoreit, Julian, Eisenacher, Martin, Fischer, Lutz et al (show 10 more authors) , Rappsilber, Juri, Netz, Eugen, Walzer, Mathias, Kohlbacher, Oliver, Leitner, Alexander, Chalkley, Robert J, Ghali, Fawaz, Martinez-Bartolome, Salvador, Deutsch, Eric W and Jones, Andrew R ORCID: 0000-0001-6118-9327 (2017) The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics. MOLECULAR & CELLULAR PROTEOMICS, 16 (7). pp. 1275-1285.

Bhamber, Ranjeet S, Jankevics, Andris, Deutsch, Eric W, Jones, Andrew R ORCID: 0000-0001-6118-9327 and Dowsey, Andrew W (2021) mzMLb: A Future-Proof Raw Mass Spectrometry Data Format Based on Standards-Compliant mzML and Optimized for Speed and Storage Requirements. JOURNAL OF PROTEOME RESEARCH, 20 (1). pp. 172-183.

Qi, Da ORCID: 0000-0001-6079-9764, Zhang, Huaizhong, Fan, Jun, Perkins, Simon, Pisconti, Addolorata, Simpson, Deborah M ORCID: 0000-0002-3962-4895, Bessant, Conrad, Hubbard, Simon and Jones, Andrew R ORCID: 0000-0001-6118-9327 (2015) The mzqLibrary - An open source Java library supporting the HUPO-PSI quantitative proteomics standard. PROTEOMICS, 15 (18). pp. 3152-3162.

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Schober, Daniel, Jacob, Daniel, Wilson, Michael, Cruz, Joseph A, Marcu, Ana, Grant, Jason R, Moing, Annick, Deborde, Catherine, de Figueiredo, Luis F, Haug, Kenneth et al (show 22 more authors) , Rocca-Serra, Philippe, Easton, John, Ebbels, Timothy MD, Hao, Jie, Ludwig, Christian, Guenther, Ulrich L, Rosato, Antonio, Klein, Matthias S, Lewis, Ian A, Luchinat, Claudio, Jones, Andrew R ORCID: 0000-0001-6118-9327, Grauslys, Arturas, Larralde, Martin, Yokochi, Masashi, Kobayashi, Naohiro, Porzel, Andrea, Griffin, Julian L, Viant, Mark R, Wishart, David S, Steinbeck, Christoph, Salek, Reza M and Neumann, Steffen (2018) nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data. ANALYTICAL CHEMISTRY, 90 (1). pp. 649-656.

Collins, Andrew ORCID: 0000-0003-0507-6912 and Jones, Andrew R ORCID: 0000-0001-6118-9327 (2018) phpMs: A PHP-Based Mass Spectrometry Utilities Library. JOURNAL OF PROTEOME RESEARCH, 17 (3). pp. 1309-1313.

Menschaert, Gerben, Wang, Xiaojing, Jones, Andrew R ORCID: 0000-0001-6118-9327, Ghali, Fawaz, Fenyo, David, Olexiouk, Volodimir, Zhang, Bing, Deutsch, Eric W, Ternent, Tobias and Vizcaino, Juan Antonio (2018) The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data. GENOME BIOLOGY, 19 (1). 12-.

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Russomanno, Giusy ORCID: 0000-0002-3378-5524, Sison-Young, Rowena, Livoti, Lucia A, Coghlan, Hannah, Jenkins, Rosalind E, Kunnen, Steven J, Fisher, Ciarán P, Reddyhoff, Dennis, Gardner, Iain, Rehman, Adeeb H et al (show 11 more authors) , Fenwick, Stephen W, Jones, Andrew R, De Conchard, Guy Vermeil, Simonin, Gilles, Bertheux, Helene, Weaver, Richard J, Liguori, Michael J, Clausznitzer, Diana, Stevens, James L, Goldring, Christopher E and Copple, Ian M ORCID: 0000-0003-4101-1913 (2022) A systems approach reveals species differences in hepatic stress response capacity. [Preprint]

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Russomanno, Giusy ORCID: 0000-0002-3378-5524, Sison-Young, Rowena, Livoti, Lucia A, Coghlan, Hannah, Jenkins, Rosalind E, Kunnen, Steven J, Fisher, Ciaran P, Reddyhoff, Dennis, Gardner, Iain, Rehman, Adeeb H et al (show 12 more authors) , Fenwick, Stephen W, Jones, Andrew R ORCID: 0000-0001-6118-9327, Vermeil De Conchard, Guy, Simonin, Gilles, Bertheux, Helene, Weaver, Richard J, Johnson, Robert L, Liguori, Michael J, Clausznitzer, Diana, Stevens, James L, Goldring, Christopher E and Copple, Ian M ORCID: 0000-0003-4101-1913 (2023) A systems approach reveals species differences in hepatic stress response capacity. TOXICOLOGICAL SCIENCES, 196 (1). pp. 112-125.

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Ghattaoraya, Gurpreet S ORCID: 0000-0003-4809-7342, Dundar, Yenal ORCID: 0000-0002-9847-1622, González-Galarza, Faviel F, Maia, Maria Helena Thomaz, Santos, Eduardo José Melo, da Silva, Andréa Luciana Soares, McCabe, Antony ORCID: 0000-0003-3089-3674, Middleton, Derek, Alfirevic, Ana ORCID: 0000-0002-2801-9817, Dickson, Rumona ORCID: 0000-0003-1416-0913 et al (show 1 more authors) and Jones, Andrew R ORCID: 0000-0001-6118-9327 (2016) A web resource for mining HLA associations with adverse drug reactions: HLA-ADR. Database : the journal of biological databases and curation, 2016. baw069-.