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Costa, R. L., Gadelha, L., D'arc, M., Ribeiro-Alves, M., Robertson, D. L. , Schwartz, J.-M., Soares, M. A. and Porto, F. (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, E. P., Siria, D. J., Mitton, J., Mshani, I. H., González-Jiménez, M. , Selvarajah, P., Wynne, K. , Baldini, F. , Okumu, F. O. and Babayan, S. A. (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, G., Jensen, R. W., Lavstsen, T. and Otto, T. D. (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, J. and Daly, R. (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, J. J., Faydaci, B. A., Mcguinness, D. , Shaw, R., Maciewicz, R. A., Robertson, N. A. and Goodyear, C. S. (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, J. B., Thomson, E. C. , McLauchlan, J. , Hughes, J. and Gifford, R. J. (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, R. A., Schwartz, J.-M., Robertson, D. L. and Nenadic, G. (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, M., Bachoumis, G., Mimouli, K., Kyriakopoulou, Z., Robertson, D. L. , Markoulatos, P. and Amoutzias, G. 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, E., Delatola, E. I., Nkuipou-Kenfack, E., Spooner, W., Kolch, W., Schanstra, J. P., Mischak, H. and Koeck, T. (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, M., D’Amore, R., Ijaz, U. Z. , Hall, N. and Quince, C. (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, A., Lycett, S. , Doherty, T., Salvador, L. and Kao, R. (2016) Broadwick: a framework for computational epidemiology. BMC Bioinformatics, 17, 65. (doi: 10.1186/s12859-016-0903-2) (PMID:26846686) (PMCID:PMC4743398)
Suvitaival, T., Rogers, S. and Kaski, S. (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. and Husmeier, D. (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, G., Nenadic, G., Brass, A., Robertson, D. L. and Stevens, R. (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, A., Karnik, R. and Grefen, C. (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, D., Buchan, D. W.A., Bryson, K. and Jones, D. 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. , 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. , Herzyk, P. and Davies, R. (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, J., Baillie, G., Watson, S. J., Kellam, P., Rambaut, A. and Robertson, D. L. (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, J. M. G., Hopcroft, L. E. M. , Baresic, A., Orengo, C. A., Martin, A. C. R. and Valencia, A. (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, C., Lanzen, A., Davenport, R. J. and Turnbaugh, P. J. (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics, 12(38), (doi: 10.1186/1471-2105-12-38)
Page, R.D.M. (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. , 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. (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, M., Harris, K., Kalousis, A., Carpentier, S., Kolch, W., Schanstra, J. P., Haubitz, M., Vlahou, A., Mischak, H. and Girolami, M. (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. 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, J. M.G., Baresic, A., McMillan, L. E.M. , Yeats, C., Clegg, A. B., Orengo, C. A., Martin, A. C.R. and Valencia, A. (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, J. I., Pinney, J. W. and Robertson, D. L. (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. 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. 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, T. D. , Guimaraes, A. C. R., Degrave, W. M. and de Miranda, A. 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, L. E.M. and Martin, A. C.R. (2008) Automatically extracting functionally equivalent proteins from SwissProt. BMC Bioinformatics, 9, p. 418. (doi: 10.1186/1471-2105-9-418)
Otto, T. D. , Gomes, L. H.F., Alves-Ferreira, M., de Miranda, A. B. and Degrave, W. 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, J. M., Pinney, J. W., Stevens, R. D. and Robertson, D. L. (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. (2008) Methylation linear discriminant analysis (MLDA) for identifying differentially methylated CpG islands. BMC Bioinformatics, 9(337), (doi: 10.1186/1471-2105-9-337)
Holden, B. J., Pinney, J. W., Lovell, S. C., Amoutzias, G. D. and Robertson, D. L. (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. 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, A. , Chan, C., Strid, J., Moon, S., Callard, R., George, A. J. and Stark, J. (2007) Reconstruction of cell population dynamics using CFSE. BMC Bioinformatics, 8, p. 196. (doi: 10.1186/1471-2105-8-196)
Rogers, S., Khanin, R. and Girolami, M. (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. (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, L. J., Smith, R. T., Bryson, K. , Sørensen, S.-A. and Jones, D. 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, J., Hunt, E., Chalmers, M. , Leader, D. , McBride, M. and Dominiczak, A. F. (2005) System level visualization of eQTLs and pQTLs. BMC Bioinformatics, 6(Sup 3), P15. (doi: 10.1186/1471-2105-6-S3-P15)
Page, R. 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, S., Jirapech-Umpai, T. and Daly, R. (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, R. (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. (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. and Herzyk, P. (2004) Graph-based iterative Group Analysis enhances microarray interpretation. BMC Bioinformatics, 5, (doi: 10.1186/1471-2105-5-100)