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Costa, Raquel L, Gadelha, Luiz, D'arc, Mirela, Ribeiro-Alves, Marcelo, Robertson, David L. ORCID: https://orcid.org/0000-0001-6338-0221, Schwartz, Jean-Marc, Soares, Marcelo A and Porto, Fábio (2024) HIHISIV: a database of gene expression in HIV and SIV host immune response. BMC Bioinformatics, 25, 125. (doi: 10.1186/s12859-024-05740-7) (PMID:38519883) (PMCID:PMC10958971)

Mwanga, Emmanuel P., Siria, Doreen J., Mitton, Joshua, Mshani, Issa H., González-Jiménez, Mario ORCID: https://orcid.org/0000-0002-8853-0588, Selvarajah, Prashanth, Wynne, Klaas ORCID: https://orcid.org/0000-0002-5305-5940, Baldini, Francesco ORCID: https://orcid.org/0000-0002-5904-4070, Okumu, Fredros O. ORCID: https://orcid.org/0000-0003-2731-5654 and Babayan, Simon A. ORCID: https://orcid.org/0000-0002-4949-1117 (2023) Using transfer learning and dimensionality reduction techniques to improve generalisability of machine-learning predictions of mosquito ages from mid-infrared spectra. BMC Bioinformatics, 24, 11. (doi: 10.1186/s12859-022-05128-5) (PMID:36624386) (PMCID:PMC9830685)

MacKenzie, Gavin, Jensen, Rasmus W., Lavstsen, Thomas and Otto, Thomas D. ORCID: https://orcid.org/0000-0002-1246-7404 (2022) Varia: a tool for prediction, analysis and visualisation of variable genes. BMC Bioinformatics, 23, 52. (doi: 10.1186/s12859-022-04573-6) (PMID:35073845) (PMCID:PMC8785495)

Wandy, Joe ORCID: https://orcid.org/0000-0002-3068-4664 and Daly, Rónán ORCID: https://orcid.org/0000-0002-1275-6820 (2021) GraphOmics: an interactive platform to explore and integrate multi-omics data. BMC Bioinformatics, 22, 603. (doi: 10.1186/s12859-021-04500-1) (PMID:34922446) (PMCID:PMC8684259)

Cole, John J., Faydaci, Bekir A., Mcguinness, David ORCID: https://orcid.org/0000-0003-2947-2047, Shaw, Robin, Maciewicz, Rose A., Robertson, Neil A. and Goodyear, Carl S. ORCID: https://orcid.org/0000-0001-5926-5941 (2021) Searchlight: automated bulk RNA-seq exploration and visualisation using dynamically generated R scripts. BMC Bioinformatics, 22(1), 411. (doi: 10.1186/s12859-021-04321-2)

Hung, J. et al. (2020) Keras R-CNN: library for cell detection in biological images using deep neural networks. BMC Bioinformatics, 21, 300. (doi: 10.1186/s12859-020-03635-x) (PMID:32652926) (PMCID:PMC7353739)

Singer, Joshua B., Thomson, Emma C. ORCID: https://orcid.org/0000-0003-1482-0889, McLauchlan, John ORCID: https://orcid.org/0000-0003-2217-9948, Hughes, Joseph ORCID: https://orcid.org/0000-0003-2556-2563 and Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 (2018) GLUE: a flexible software system for virus sequence data. BMC Bioinformatics, 19, 532. (doi: 10.1186/s12859-018-2459-9) (PMID:30563445) (PMCID:PMC6299651)

Stoney, Ruth Alexandra, Schwartz, Jean-Marc, Robertson, David L. ORCID: https://orcid.org/0000-0001-6338-0221 and Nenadic, Goran (2018) Using set theory to reduce redundancy in pathway sets. BMC Bioinformatics, 19, 386. (doi: 10.1186/s12859-018-2355-3) (PMID:30340461) (PMCID:PMC6194563)

Tsimpidis, Michail, Bachoumis, Georgios, Mimouli, Kalliopi, Kyriakopoulou, Zaharoula, Robertson, David L. ORCID: https://orcid.org/0000-0001-6338-0221, Markoulatos, Panayotis and Amoutzias, Grigoris D. (2017) T-RECs: rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes. BMC Bioinformatics, 18, 13. (doi: 10.1186/s12859-016-1420-z) (PMID:28056784) (PMCID:PMC5216575)

Stanley, Eleanor, Delatola, Eleni Ioanna, Nkuipou-Kenfack, Esther, Spooner, William, Kolch, Walter, Schanstra, Joost P., Mischak, Harald and Koeck, Thomas (2016) Comparison of different statistical approaches for urinary peptide biomarker detection in the context of coronary artery disease. BMC Bioinformatics, 17, 496. (doi: 10.1186/s12859-016-1390-1) (PMID:27923348) (PMCID:PMC5139137)

Schirmer, Melanie, D’Amore, Rosalinda, Ijaz, Umer Z. ORCID: https://orcid.org/0000-0001-5780-8551, Hall, Neil and Quince, Christopher (2016) Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data. BMC Bioinformatics, 17, 125. (doi: 10.1186/s12859-016-0976-y) (PMID:26968756) (PMCID:PMC4787001)

O'Hare, Anthony, Lycett, Samantha ORCID: https://orcid.org/0000-0003-3159-596X, Doherty, Thomas, Salvador, Liliana ORCID: https://orcid.org/0000-0001-8472-1179 and Kao, Rowland (2016) Broadwick: a framework for computational epidemiology. BMC Bioinformatics, 17, 65. (doi: 10.1186/s12859-016-0903-2) (PMID:26846686) (PMCID:PMC4743398)

Suvitaival, Tommi, Rogers, Simon ORCID: https://orcid.org/0000-0003-3578-4477 and Kaski, Samuel (2014) Stronger findings from mass spectral data through multi-peak modeling. BMC Bioinformatics, 15, p. 208. (doi: 10.1186/1471-2105-15-208) (PMID:24947013) (PMCID:PMC4080774)

Higham, C. ORCID: https://orcid.org/0000-0002-2580-4115 and Husmeier, D. ORCID: https://orcid.org/0000-0003-1673-7413 (2013) A Bayesian approach for parameter estimation in the extended clock gene circuit of Arabidopsis thaliana. BMC Bioinformatics, 14(Sup 10), S3. (doi: 10.1186/1471-2105-14-S10-S3)

Duck, Geraint, Nenadic, Goran, Brass, Andy, Robertson, David L. ORCID: https://orcid.org/0000-0001-6338-0221 and Stevens, Robert (2013) bioNerDS: exploring bioinformatics' database and software use through literature mining. BMC Bioinformatics, 14, 194. (doi: 10.1186/1471-2105-14-194) (PMID:23768135) (PMCID:PMC3693927)

Karnik, Abhijit, Karnik, Rucha ORCID: https://orcid.org/0000-0001-6876-4099 and Grefen, Christopher (2013) SDM-Assist software to design site-directed mutagenesis primers introducing “silent” restriction sites. BMC Bioinformatics, 14, 105. (doi: 10.1186/1471-2105-14-105) (PMID:23522286) (PMCID:PMC3644487)

Cozzetto, Domenico, Buchan, Daniel W.A., Bryson, Kevin ORCID: https://orcid.org/0000-0002-1163-6368 and Jones, David T. (2013) Protein function prediction by massive integration of evolutionary analyses and multiple data sources. BMC Bioinformatics, 14(Sup 3), S1. (doi: 10.1186/1471-2105-14-S3-S1) (PMID:23514099) (PMCID:PMC3584902)

Gelfond, J.A., Ibrahim, J.G., Gupta, M. ORCID: https://orcid.org/0000-0003-1052-6738, Cheng, M.-H. and Cody, J.D. (2013) Differential expression analysis with global network adjustment. BMC Bioinformatics, 14(258), (doi: 10.1186/1471-2105-14-258)

E-komon, T., Burchmore, R. ORCID: https://orcid.org/0000-0003-1663-9004, Herzyk, P. ORCID: https://orcid.org/0000-0002-7439-292X and Davies, R. ORCID: https://orcid.org/0000-0002-6342-2222 (2012) Predicting the outer membrane proteome of Pasteurella multocida based on consensus prediction enhanced by results integration and manual confirmation. BMC Bioinformatics, 13(1), 63. (doi: 10.1186/1471-2105-13-63) (PMID:22540951) (PMCID:PMC3403877)

Archer, John, Baillie, Greg, Watson, Simon J., Kellam, Paul, Rambaut, Andrew and Robertson, David L. ORCID: https://orcid.org/0000-0001-6338-0221 (2012) Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II. BMC Bioinformatics, 13, 47. (doi: 10.1186/1471-2105-13-47) (PMID:22443413) (PMCID:PMC3359224)

Izarzugaza, Jose M G, Hopcroft, Lisa E M ORCID: https://orcid.org/0000-0002-7022-1322, Baresic, Anja, Orengo, Christine A, Martin, Andrew C R and Valencia, Alfonso (2011) Characterization of pathogenic germline mutations in human protein kinases. BMC Bioinformatics, 12(Sup. 4), S1. (doi: 10.1186/1471-2105-12-S4-S1)

Quince, Christopher, Lanzen, Anders, Davenport, Russell J and Turnbaugh, Peter J. (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics, 12(38), (doi: 10.1186/1471-2105-12-38)

Page, R.D.M. ORCID: https://orcid.org/0000-0002-7101-9767 (2011) Extracting scientific articles from a large digital archive: BioStor and the biodiversity heritage library. BMC Bioinformatics, 12, p. 187. (doi: 10.1186/1471-2105-12-187)

Shi, P., Ray, S. ORCID: https://orcid.org/0000-0003-3965-8136, Zhu, Q. and Kon, M.A. (2011) Top scoring pairs for feature selection in machine learning and applications to cancer outcome prediction. BMC Bioinformatics, 12(1), p. 375. (doi: 10.1186/1471-2105-12-375)

Hughes, J. ORCID: https://orcid.org/0000-0003-2556-2563 (2011) TreeRipper web application: towards a fully automated optical tree recognition software. BMC Bioinformatics, 12(1), p. 178. (doi: 10.1186/1471-2105-12-178)

Dakna, Mohammed, Harris, Keith, Kalousis, Alexandros, Carpentier, Sebastien, Kolch, Walter, Schanstra, Joost P., Haubitz, Marion, Vlahou, Antonia, Mischak, Harald and Girolami, Mark (2010) Addressing the Challenge of Defining Valid Proteomic Biomarkers and Classifiers. BMC Bioinformatics, 11(1), p. 594. (doi: 10.1186/1471-2105-11-594)

Tesson, B.M., Breitling, R. ORCID: https://orcid.org/0000-0001-7173-0922 and Jansen, R.C. (2010) DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules. BMC Bioinformatics, 11(1), p. 497. (doi: 10.1186/1471-2105-11-497)

Wang, J. and Tian, T. (2010) Quantitative model for inferring dynamic regulation of the tumour suppressor gene p53. BMC Bioinformatics, 11, p. 36. (doi: 10.1186/1471-2105-11-36)

Izarzugaza, Jose M.G, Baresic, Anja, McMillan, Lisa E.M. ORCID: https://orcid.org/0000-0002-7022-1322, Yeats, Corin, Clegg, Andrew B., Orengo, Christine A., Martin, Andrew C.R. and Valencia, Alfonso (2009) An integrated approach to the interpretation of single amino acid polymorphisms within the framework of CATH and Gene3D. BMC Bioinformatics, 10(Sup. 8), S5. (doi: 10.1186/1471-2105-10-S8-S5)

MacPherson, Jamie I., Pinney, John W. and Robertson, David L. ORCID: https://orcid.org/0000-0001-6338-0221 (2009) JNets: exploring networks by integrating annotation. BMC Bioinformatics, 10, 95. (doi: 10.1186/1471-2105-10-95) (PMID:19323810) (PMCID:PMC2674432)

Leader, D.P. ORCID: https://orcid.org/0000-0002-0635-1843 and Milner-White, E.J. (2009) Motivated proteins: a web application for studying small three-dimensional protein motifs. BMC Bioinformatics, 10(60), (doi: 10.1186/1471-2105-10-60)

Page, R.D.M. (2009) BioGUID: resolving, discovering, and minting identifiers for biodiversity informatics. BMC Bioinformatics, 10(Sup 14), S5. (doi: 10.1186/1471-2105-10-S14-S5)

Li, Y., Swertz, M., Vera, G., Fu, J.Y., Breitling, R. ORCID: https://orcid.org/0000-0001-7173-0922 and Jansen, R. (2009) DesignGG: an R-package and web tool for the optimal design of genetical genomics experiments. BMC Bioinformatics, 10(188), (doi: 10.1186/1471-2105-10-188)

Otto, Thomas D. ORCID: https://orcid.org/0000-0002-1246-7404, Guimaraes, Ana Carolina R., Degrave, Wim M. and de Miranda, Antonio B. (2008) AnEnPi: Identification and annotation of analogous enzymes. BMC Bioinformatics, 9(1), 544. (doi: 10.1186/1471-2105-9-544) (PMID:19091081) (PMCID:PMC2628392)

McMillan, Lisa E.M. ORCID: https://orcid.org/0000-0002-7022-1322 and Martin, Andrew C.R. (2008) Automatically extracting functionally equivalent proteins from SwissProt. BMC Bioinformatics, 9, p. 418. (doi: 10.1186/1471-2105-9-418)

Otto, Thomas D. ORCID: https://orcid.org/0000-0002-1246-7404, Gomes, Leonardo H.F., Alves-Ferreira, Marcelo, de Miranda, Antonio B. and Degrave, Wim M. (2008) ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS). BMC Bioinformatics, 9, 366. (doi: 10.1186/1471-2105-9-366) (PMID:18782453) (PMCID:PMC2559850)

Eales, James M., Pinney, John W., Stevens, Robert D. and Robertson, David L. ORCID: https://orcid.org/0000-0001-6338-0221 (2008) Methodology capture: discriminating between the "best" and the rest of community practice. BMC Bioinformatics, 9, 359. (doi: 10.1186/1471-2105-9-359) (PMID:18761740) (PMCID:PMC2553348)

Dai, W., Teodoridis, J.M., Graham, J., Zeller, C., Huang, T.H.M., Yan, P., Vass, J.K., Brown, R. and Paul, J. ORCID: https://orcid.org/0000-0001-7367-5816 (2008) Methylation linear discriminant analysis (MLDA) for identifying differentially methylated CpG islands. BMC Bioinformatics, 9(337), (doi: 10.1186/1471-2105-9-337)

Holden, Brian J., Pinney, John W., Lovell, Simon C., Amoutzias, Grigoris D. and Robertson, David L. ORCID: https://orcid.org/0000-0001-6338-0221 (2007) An exploration of alternative visualisations of the basic helix-loop-helix protein interaction network. BMC Bioinformatics, 8, 289. (doi: 10.1186/1471-2105-8-289) (PMID:17683601) (PMCID:PMC1963338)

Nebel, J.C., Herzyk, P. ORCID: https://orcid.org/0000-0002-7439-292X and Gilbert, D.R. (2007) Automatic generation of 3D motifs for classification of protein binding sites. BMC Bioinformatics, 8(321), (doi: 10.1186/1471-2105-8-321)

Yates, Andrew ORCID: https://orcid.org/0000-0003-4606-4483, Chan, Cliburn, Strid, Jessica, Moon, Simon, Callard, Robin, George, Andrew JT and Stark, Jaroslav (2007) Reconstruction of cell population dynamics using CFSE. BMC Bioinformatics, 8, p. 196. (doi: 10.1186/1471-2105-8-196)

Rogers, Simon, Khanin, Raya and Girolami, Mark (2007) Bayesian model-based inference of transcription factor activity. BMC Bioinformatics, 8(Suppl), (doi: 10.1186/1471-2105-8-S2-S2)

Skrabanek, L. et al. (2007) Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base. BMC Bioinformatics, 8(177), (doi: 10.1186/1471-2105-8-177)

Page, R.D.M. ORCID: https://orcid.org/0000-0002-7101-9767 (2007) TBMap: a taxonomic perspective on the phylogenetic database TreeBASE. BMC Bioinformatics, 8(158), (doi: 10.1186/1471-2105-8-158)

Kim, J., Bates, D.G., Postlethwaite, I., Heslop-Harrison, P. and Cho, K-H. (2007) Least-squares methods for identifying biochemical regulatory networks from noisy measurements. BMC Bioinformatics, 8(8), (doi: 10.1186/1471-2105-8-8)

McGuffin, Liam J., Smith, Richard T., Bryson, Kevin ORCID: https://orcid.org/0000-0002-1163-6368, Sørensen, Søren-Aksel and Jones, David T. (2006) High throughput profile-profile based fold recognition for the entire human proteome. BMC Bioinformatics, 7, 288. (doi: 10.1186/1471-2105-7-288) (PMID:16759376) (PMCID:PMC1513610)

Jakubowska, Joanna, Hunt, Ela, Chalmers, Matthew ORCID: https://orcid.org/0000-0001-9816-668X, Leader, David ORCID: https://orcid.org/0000-0002-0635-1843, McBride, Martin ORCID: https://orcid.org/0000-0002-6323-124X and Dominiczak, Anna F. ORCID: https://orcid.org/0000-0003-4913-3608 (2005) System level visualization of eQTLs and pQTLs. BMC Bioinformatics, 6(Sup 3), P15. (doi: 10.1186/1471-2105-6-S3-P15)

Page, RDM and Valiente, G (2005) An edit script for taxonomic classifications. BMC Bioinformatics, 6, (doi: 10.1186/1471-2105-6-208)

Morrison, J.L., Breitling, R., Higham, D.J. and Gilbert, D.R. (2005) GeneRank: using search engine technology for the analysis of microarray experiments. BMC Bioinformatics, 6:233, (doi: 10.1186/1471-2105-6-233)

Aitken, Stuart, Jirapech-Umpai, Thanyaluk and Daly, Ronan ORCID: https://orcid.org/0000-0002-1275-6820 (2005) Inferring gene regulatory networks from classified microarray data: Initial results. BMC Bioinformatics, 6(Suppl), S4. (doi: 10.1186/1471-2105-6-S3-S4)

Page, RDM (2005) A taxonomic search engine: Federating taxonomic databases using web services. BMC Bioinformatics, 6, (doi: 10.1186/1471-2105-6-48)

Breitling, R, Armengaud, P and Amtmann, A ORCID: https://orcid.org/0000-0001-8533-121X (2005) Vector analysis as a fast and easy method to compare gene expression responses between different experimental backgrounds. BMC Bioinformatics, 6, (doi: 10.1186/1471-2105-6-181)

Breitling, R., Amtmann, A. and Herzyk, P. (2004) Iterative Group Analysis (iGA): A simple tool to enhance sensitivity and facilitate interpretation of microarray experiments. BMC Bioinformatics, 5(34),

Breitling, R, Amtmann, A ORCID: https://orcid.org/0000-0001-8533-121X and Herzyk, P ORCID: https://orcid.org/0000-0002-7439-292X (2004) Graph-based iterative Group Analysis enhances microarray interpretation. BMC Bioinformatics, 5, (doi: 10.1186/1471-2105-5-100)