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Groza, T., Wu, H. , Dinger, M. E., Danis, D., Hilton, C., Bagley, A., Davids, J. R., Luo, L., Lu, Z. and Robinson, P. N. (2023) Term-BLAST-like alignment tool for concept recognition in noisy clinical texts. Bioinformatics, 39(12), btad716. (doi: 10.1093/bioinformatics/btad716) (PMID:38001031) (PMCID:PMC10710372)
McBride, R., Wandy, J. , Weidt, S., Rogers, S. , Davies, V. , Daly, R. and Bryson, K. (2023) TopNEXt: automatic DDA exclusion framework for multi-sample mass spectrometry experiments. Bioinformatics, 39(7), btad406. (doi: 10.1093/bioinformatics/btad406) (PMID:37364005)
Haese-Hill, W. , Crouch, K. and Otto, T. D. (2023) peaks2utr: a robust Python tool for the annotation of 3’ UTRs. Bioinformatics, 39(3), btad112. (doi: 10.1093/bioinformatics/btad112) (PMID:36864613) (PMCID:PMC10008064)
Martin, S., Ayling, M., Patrono, L., Caccamo, M., Murcia, P. and Leggett, R. M. (2023) Capturing variation in metagenomic assembly graphs with MetaCortex. Bioinformatics, 39(1), btad020. (doi: 10.1093/bioinformatics/btad020) (PMID:36722204) (PMCID:PMC9889960)
Meng, Z. et al. (2022) BioCaster in 2021: automatic disease outbreaks detection from global news media. Bioinformatics, 38(18), pp. 4446-4448. (doi: 10.1093/bioinformatics/btac497) (PMID:35900173) (PMCID:PMC9477518)
Viñas, R., Andrés-Terré, H., Liò, P. and Bryson, K. (2022) Adversarial generation of gene expression data. Bioinformatics, 38(3), pp. 730-737. (doi: 10.1093/bioinformatics/btab035) (PMID:33471074) (PMCID:PMC8756177)
Danial, J. S. H., Shalaby, R., Cosentino, K., Mahmoud, M. M. , Medhat, F., Klenerman, D. and Garcia Saez, A. J. (2021) DeepSinse: deep learning-based detection of single molecules. Bioinformatics, 37(21), pp. 3998-4000. (doi: 10.1093/bioinformatics/btab352) (PMID:33964131)
Senf, A., Davies, R., Haziza, F., Marshall, J. , Troncoso-Pastoriza, J., Hofmann, O. and Keane, T. M. (2021) Crypt4GH: a file format standard enabling native access to encrypted data. Bioinformatics, 37(17), pp. 2753-2754. (doi: 10.1093/bioinformatics/btab087) (PMID:33543751) (PMCID:PMC8522443)
Bach, E., Rogers, S. , Williamson, J. and Rousu, J. (2021) Probabilistic framework for integration of mass spectrum and retention time information in small molecule identification. Bioinformatics, 37(12), pp. 1724-1731. (doi: 10.1093/bioinformatics/btaa998) (PMID:33244585)
Allesøe, R. L., Lemvigh, C. K., Phan, M. V.T., Clausen, P. T. L.C., Florensa, A. F., Koopmans, M. P.G., Lund, O. and Cotten, M. (2021) Automated download and clean-up of family-specific databases for kmer-based virus identification. Bioinformatics, 37(5), pp. 705-710. (doi: 10.1093/bioinformatics/btaa857) (PMID:33031509) (PMCID:PMC8097684)
Kamat, M. A., Blackshaw, J. A., Young, R. , Surendran, P., Burgess, S., Danesh, J., Butterworth, A. S. and Staley, J. R. (2019) PhenoScanner V2: an expanded tool for searching human genotype-phenotype associations. Bioinformatics, 35(22), pp. 4851-4853. (doi: 10.1093/bioinformatics/btz469) (PMID:31233103) (PMCID:PMC6853652)
Whitehead, M. J., McCanney, G., Willison, H. J. and Barnett, S. C. (2019) MyelinJ: an ImageJ macro for high throughput analysis of myelinating cultures. Bioinformatics, 35(21), pp. 4528-4530. (doi: 10.1093/bioinformatics/btz403) (PMID:31095292) (PMCID:PMC6821319)
Barbaian, A., Thompson, I. R., Lever, J. , Gagnier, L., Karimi, M. M. and Mager, D. L. (2019) LIONS: analysis suite for detecting and quantifying transposable element initiated transcription from RNA-seq. Bioinformatics, 35(19), pp. 3839-3841. (doi: 10.1093/bioinformatics/btz130) (PMID:30793157)
Kelleher, J. et al. (2019) htsget: a protocol for securely streaming genomic data. Bioinformatics, 35(1), pp. 119-121. (doi: 10.1093/bioinformatics/bty492) (PMID:29931085) (PMCID:PMC6298043)
Kim, C. S., Mohan, S., Ayub, M., Rothwell, D. G., Dive, C., Brady, G. and Miller, C. (2018) In silico error correction improves cfDNA mutation calling. Bioinformatics, 35(14), pp. 2380-2385. (doi: 10.1093/bioinformatics/bty1004) (PMID:30520956) (PMCID:PMC6612818)
Heal, J. W., Bartlett, G. J., Wood, C. W., Thomson, A. R. and Woolfson, D. N. (2018) Applying graph theory to protein structures: an atlas of coiled coils. Bioinformatics, 34(19), pp. 3316-3323. (doi: 10.1093/bioinformatics/bty347) (PMID:29722888)
Megalios, A., Daly, R. and Burgess, K. (2018) MetaboCraft: building a Minecraft plugin for metabolomics. Bioinformatics, 34(15), pp. 2693-2694. (doi: 10.1093/bioinformatics/bty102) (PMID:29608638) (PMCID:PMC6061834)
Modha, S. , Thanki, A., Cotmore, S. F., Davison, A. J. and Hughes, J. (2018) ViCTree: an automated framework for taxonomic classification from protein sequences. Bioinformatics, 34(13), pp. 2195-2200. (doi: 10.1093/bioinformatics/bty099) (PMID:29474519) (PMCID:PMC6022645)
Wandy, J. , Niu, M., Giurghita, D., Daly, R. , Rogers, S. and Husmeier, D. (2018) ShinyKGode: an interactive application for ODE parameter inference using gradient matching. Bioinformatics, 34(13), pp. 2314-2315. (doi: 10.1093/bioinformatics/bty089) (PMID:29490021) (PMCID:PMC6022662)
Lever, J. , Gakkhar, S., Gottlieb, M., Rashnavadi, T., Lin, S., Siu, C., Smith, M., Jones, M. R., Krzywinski, M. and Jones, S. J.M. (2018) A collaborative filtering-based approach to biomedical knowledge discovery. Bioinformatics, 34(4), pp. 652-659. (doi: 10.1093/bioinformatics/btx613) (PMID:29028901)
Chazalviel, M., Frainay, C., Poupin, N., Vinson, F., Merlet, B., Gloaguen, Y. , Cottret, L. and Jourdan, F. (2018) MetExploreViz: web component for interactive metabolic network visualization. Bioinformatics, 34(2), pp. 312-313. (doi: 10.1093/bioinformatics/btx588) (PMID:28968733) (PMCID:PMC5860210)
Wandy, J. , Zhu, Y., van der Hooft, J. J.J. , Daly, R. , Barrett, M. P. and Rogers, S. (2018) Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry. Bioinformatics, 34(2), pp. 317-318. (doi: 10.1093/bioinformatics/btx582) (PMID:28968802) (PMCID:PMC5860206)
Elliott, A. , Leicht, E., Whitmore, A., Reinert, G. and Reed-Tsochas, F. (2018) A nonparametric significance test for sampled networks. Bioinformatics, 34(1), pp. 64-71. (doi: 10.1093/bioinformatics/btx419) (PMID:29036452) (PMCID:PMC5870844)
Gloaguen, Y. , Morton, F. , Daly, R. , Gurden, R., Rogers, S. , Wandy, J. , Wilson, D., Barrett, M. and Burgess, K. (2017) PiMP my metabolome: An integrated, web-based tool for LC-MS metabolomics data. Bioinformatics, 33(24), pp. 4007-4009. (doi: 10.1093/bioinformatics/btx499) (PMID:28961954) (PMCID:PMC5860087)
Wood, C. W., Heal, J. W., Thomson, A. R. , Bartlett, G. J., Ibarra, A. A., Brady, R. L., Sessions, R. B. and Woolfson, D. N. (2017) ISAMBARD: an open-source computational environment for biomolecular analysis, modelling and design. Bioinformatics, 33(19), pp. 3043-3050. (doi: 10.1093/bioinformatics/btx352) (PMID:28582565) (PMCID:PMC5870769)
Chiu, A., Ayub, M., Dive, C., Brady, G., Miller, C. J. and Hancock, J. (2017) twoddpcr: an R/Bioconductor package and Shiny app for Droplet Digital PCR analysis. Bioinformatics, 33(17), pp. 2743-2745. (doi: 10.1093/bioinformatics/btx308) (PMID:28475662) (PMCID:PMC5860069)
Staley, J. R. et al. (2016) PhenoScanner: a database of human genotype-phenotype associations. Bioinformatics, 32(20), pp. 3207-3209. (doi: 10.1093/bioinformatics/btw373) (PMID:27318201) (PMCID:PMC5048068)
Illingworth, C.J.R. (2016) SAMFIRE: multi-locus variant calling for time-resolved sequence data. Bioinformatics, 32(14), pp. 2208-2209. (doi: 10.1093/bioinformatics/btw205) (PMID:27153641) (PMCID:PMC4937198)
Hunt, M., Gall, A., Ong, S. H., Brener, J., Ferns, B., Goulder, P., Nastouli, E., Keane, J. A., Kellam, P. and Otto, T. D. (2015) IVA: accurate de novo assembly of RNA virus genomes. Bioinformatics, 31(14), pp. 2374-2376. (doi: 10.1093/bioinformatics/btv120) (PMID:25725497) (PMCID:PMC4495290)
Burton, P. R. et al. (2015) Data safe havens in health research and healthcare. Bioinformatics, 31(20), pp. 3241-3248. (doi: 10.1093/bioinformatics/btv279) (PMID:26112289) (PMCID:PMC4595892)
Wandy, J., Daly, R. , Breitling, R. and Rogers, S. (2015) Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets. Bioinformatics, 31(12), pp. 1999-2006. (doi: 10.1093/bioinformatics/btv072) (PMID:25649621) (PMCID:PMC4760236)
Sela-Culang, I., Ashkenazi, S. , Peters, B. and Ofran, Y. (2015) PEASE: predicting B-cell epitopes utilizing antibody sequence. Bioinformatics, 31(8), pp. 1313-1315. (doi: 10.1093/bioinformatics/btu790) (PMID:25432167)
Oyeyemi, O. J., Davies, O., Robertson, D. L. and Schwartz, J.-M. (2015) A logical model of HIV-1 interactions with the T-cell activation signalling pathway. Bioinformatics, 31(7), pp. 1075-1083. (doi: 10.1093/bioinformatics/btu787) (PMID:25431332)
Olejnik, M., Steuwer, M. , Gorlatch, S. and Heider, D. (2014) gCUP: rapid GPU-based HIV-1 co-receptor usage prediction for next-generation sequencing. Bioinformatics, 30(22), pp. 3272-3273. (doi: 10.1093/bioinformatics/btu535) (PMID:25123901)
Wood, C. W., Bruning, M., Ibarra, A. Á., Bartlett, G. J., Thomson, A. R. , Sessions, R. B., Brady, R. L. and Woolfson, D. N. (2014) CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies. Bioinformatics, 30(21), pp. 3029-3035. (doi: 10.1093/bioinformatics/btu502) (PMID:25064570) (PMCID:PMC4201159)
Daly, R. , Rogers, S. , Wandy, J., Jankevics, A., Burgess, K. E.V. and Breitling, R. (2014) MetAssign: probabilistic annotation of metabolites from LC–MS data using a Bayesian clustering approach. Bioinformatics, 30(19), pp. 2764-2771. (doi: 10.1093/bioinformatics/btu370) (PMID:24916385) (PMCID:PMC4173012)
Duck, G., Nenadic, G., Brass, A., Robertson, D. L. and Stevens, R. (2014) Extracting patterns of database and software usage from the bioinformatics literature. Bioinformatics, 30(17), i601-i608. (doi: 10.1093/bioinformatics/btu471) (PMID:25161253) (PMCID:PMC4147923)
Suvitaival, T., Rogers, S. and Kaski, S. (2014) Stronger findings for metabolomics through Bayesian modeling of multiple peaks and compound correlations. Bioinformatics, 30(17), i461-i467. (doi: 10.1093/bioinformatics/btu455) (PMID:25161234) (PMCID:PMC4147908)
Watson, M., Schnettler, E. and Kohl, A. (2013) viRome: an R package for the visualization and analysis of viral small RNA sequence datasets. Bioinformatics, 29(15), pp. 1902-1903. (doi: 10.1093/bioinformatics/btt297) (PMID:23709497) (PMCID:PMC3712215)
Medlar, A., Głowacka, D., Stanescu, H., Bryson, K. and Kleta, R. (2013) SwiftLink: parallel MCMC linkage analysis using multicore CPU and GPU. Bioinformatics, 29(4), pp. 413-419. (doi: 10.1093/bioinformatics/bts704) (PMID:23239673)
Illingworth, C. J.R. and Mustonen, V. (2013) A method to infer positive selection from marker dynamics in an asexual population. Bioinformatics, 28(6), pp. 831-837. (doi: 10.1093/bioinformatics/btr722) (PMID:22223745) (PMCID:PMC3307107)
Chokkathukalam, A., Jankevics, A., Creek, D.J., Achcar, F., Barrett, M.P. and Breitling, R. (2013) mzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data. Bioinformatics, 29(2), pp. 281-283. (doi: 10.1093/bioinformatics/bts674) (PMID:23162054) (PMCID:PMC3546800)
Ashkenazi, S. , Snir, R. and Ofran, Y. (2012) Assessing the relationship between conservation of function and conservation of sequence using photosynthetic proteins. Bioinformatics, 28(24), pp. 3203-3210. (doi: 10.1093/bioinformatics/bts608) (PMID:23080118)
Creek, D.J., Jankevics, A., Burgess, K.E.V., Breitling, R. and Barrett, M.P. (2012) IDEOM: an excel interface for analysis of LC-MS based metabolomics data. Bioinformatics, 28(7), pp. 1048-1049. (doi: 10.1093/bioinformatics/bts069) (PMID:22308147)
Liu, W. and Niranjan, M. (2012) Gaussian process modelling for bicoid mRNA regulation in spatio-temporal Bicoid profile. Bioinformatics, 28(3), pp. 366-372. (doi: 10.1093/bioinformatics/btr658) (PMID:22130592)
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. and Knight, R. (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27(16), pp. 2194-2200. (doi: 10.1093/bioinformatics/btr381)
Chignola, R., Vyshemirsky, V. , Farina, M., Del Fabbro, A. and Milotti, E. (2011) Modular model of TNFα cytotoxicity. Bioinformatics, 27(13), pp. 1754-1757. (doi: 10.1093/bioinformatics/btr297) (PMID:21561921)
Mar, J.C., Wells, C.A. and Quackenbush, J. (2011) Defining an informativeness metric for clustering gene expression data. Bioinformatics, 27(8), pp. 1094-100. (doi: 10.1093/bioinformatics/btr074)
Grzegorczyk, M. and Husmeier, D. (2011) Improvements in the reconstruction of time-varying gene regulatory networks: dynamic programming and regularization by information sharing among genes. Bioinformatics, 27(5), pp. 693-699. (doi: 10.1093/bioinformatics/btq711)
Khelashvili, G. et al. (2010) GPCR-OKB: the G protein coupled receptor oligomer knowledge base. Bioinformatics, 26(14), pp. 1804-1805. (doi: 10.1093/bioinformatics/btq264)
Otto, T. D. , Sanders, M., Berriman, M. and Newbold, C. (2010) Iterative correction of reference nucleotides (iCORN) using second generation sequencing technology. Bioinformatics, 26(14), pp. 1704-1707. (doi: 10.1093/bioinformatics/btq269) (PMID:20562415) (PMCID:PMC2894513)
Otto, T. D. et al. (2010) ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes. Bioinformatics, 26(5), pp. 705-707. (doi: 10.1093/bioinformatics/btq011) (PMID:20089515) (PMCID:PMC2828119)
Carver, T., Bohme, U., Otto, T. D. , Parkhill, J. and Berriman, M. (2010) BamView: viewing mapped read alignment data in the context of the reference sequence. Bioinformatics, 26(5), pp. 676-677. (doi: 10.1093/bioinformatics/btq010) (PMID:20071372) (PMCID:PMC2828118)
Assefa, S., Keane, T. M., Otto, T. D. , Newbold, C. and Berriman, M. (2009) ABACAS: algorithm-based automatic contiguation of assembled sequences. Bioinformatics, 25(15), pp. 1968-1969. (doi: 10.1093/bioinformatics/btp347) (PMID:19497936) (PMCID:PMC2712343)
Rogers, S., Scheltema, R. A., Girolami, M. and Breitling, R. (2009) Probabilistic assignment of formulas to mass peaks in metabolomics experiments. Bioinformatics, 25(4), pp. 512-518. (doi: 10.1093/bioinformatics/btn642)
Milne, I., Lindner, D., Bayer, M., Husmeier, D. , McGuire, G., Marshall, D. and Wright, F. (2009) TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. Bioinformatics, 25(1), pp. 126-127. (doi: 10.1093/bioinformatics/btn575)
Cheng, F., Hartmann, S., Gupta, M. , Ibrahim, J.G. and Vision, T.J. (2009) A hierarchical model for incomplete alignments in phylogenetic inference. Bioinformatics, 25(5), pp. 592-598. (doi: 10.1093/bioinformatics/btp015)
Rogers, S., Girolami, M., Kolch, W., Waters, K. M., Liu, T., Thrall, B. and Wiley, H. S. (2008) Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models. Bioinformatics, 24(24), pp. 2894-2900. (doi: 10.1093/bioinformatics/btn553)
Grzegorczyk, M., Husmeier, D. , Edwards, K.D., Ghazal, P. and Millar, A.J. (2008) Modelling non-stationary gene regulatory processes with a non-homogeneous Bayesian network and the allocation sampler. Bioinformatics, 24(18), pp. 2071-2078. (doi: 10.1093/bioinformatics/btn367)
Vyshemirsky, V. and Girolami, M. (2008) BioBayes: a software package for Bayesian inference in systems biology. Bioinformatics, 24(17), pp. 1933-1934. (doi: 10.1093/bioinformatics/btn338) (PMID:18632751)
Evers, L. and Messow, C.-M. (2008) Sparse kernel methods for high-dimensional survival data. Bioinformatics, 24(14), pp. 1632-1638. (doi: 10.1093/bioinformatics/btn253)
Damoulas, T. and Girolami, M. (2008) Probabilistic multi-class multi-kernel learning: on protein fold recognition and remote homology detection. Bioinformatics, 24(10), pp. 1264-1270. (doi: 10.1093/bioinformatics/btn112)
Kim, J., Heslop-Harrison, P., Postlethwaite, I., Bates, D.G. and Cho, K. (2008) Linear time-varying models can reveal non-linear interactions of biomolecular regulatory networks using multiple time-series data. Bioinformatics, 24(10), pp. 1286-1292. (doi: 10.1093/bioinformatics/btn107)
Vyshemirsky, V. and Girolami, M. A. (2008) Bayesian ranking of biochemical system models. Bioinformatics, 24(6), pp. 833-839. (doi: 10.1093/bioinformatics/btm607)
Hong, F. and Breitling, R. (2008) A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments. Bioinformatics, 24(3), pp. 374-382. (doi: 10.1093/bioinformatics/btm620)
Lama, N. and Girolami, M. (2008) vbmp: variational bayesian multinomial probit regression for multi-class classification in R. Bioinformatics, 24(1), pp. 135-136. (doi: 10.1093/bioinformatics/btm535)
Jourdan, F., Breitling, R., Barrett, M.P. and Gilbert, D. (2008) MetaNetter: inference and visualization of high-resolution metabolomic networks. Bioinformatics, 24(1), pp. 143-145. (doi: 10.1093/bioinformatics/btm536)
Archer, J. and Robertson, D. L. (2007) CTree: comparison of clusters between phylogenetic trees made easy. Bioinformatics, 23(21), pp. 2952-2953. (doi: 10.1093/bioinformatics/btm410) (PMID:17717036)
Tian, T., Xu, S., Gao, J. and Burrage, K. (2007) Simulated maximum likelihood method for estimating kinetic rates in gene expression. Bioinformatics, 23(1), pp. 84-91. (doi: 10.1093/bioinformatics/btl552)
Viksna, J. and Gilbert, D. (2007) Assessment of the probabilities for evolutionary structural changes in protein folds. Bioinformatics, 23, pp. 832-841. (doi: 10.1093/bioinformatics/bfm022)
Jakubowska, J., Hunt, E., Chalmers, M., McBride, M. and Dominiczak, A. F. (2007) VisGenome: visualization of single and comparative genome representations. Bioinformatics, 23(19), pp. 2641-2642. (doi: 10.1093/bioinformatics/btm394)
Werhli, A.V., Grzegorczyk, M. and Husmeier, D. (2006) Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical Gaussian models and Bayesian networks. Bioinformatics, 22(20), pp. 2523-2531. (doi: 10.1093/bioinformatics/btl391)
Mueller, M., Goel, A., Thimma, M., Dickens, N.J. , Aitman, T.J. and Mangion, J. (2006) eQTL Explorer: integrated mining of combined genetic linkage and expression experiments. Bioinformatics, 22(4), pp. 509-511. (doi: 10.1093/bioinformatics/btk007)
Morrison, J.L., Breitling, R. , Higham, D.J. and Gilbert, D.R. (2006) A lock-and-key model for protein-protein interactions. Bioinformatics, 22, pp. 2012-2019. (doi: 10.1093/bioinformatics/btl338)
Lehrach, W. P., Husmeier, D. and Williams, C. K. I. (2006) A regularized discriminative model for the prediction of protein-peptide interactions. Bioinformatics, 22(5), pp. 532-540. (doi: 10.1093/bioinformatics/bti804)
Rogers, S. and Girolami, M. (2005) A Bayesian regression approach to the inference of regulatory networks from gene expression data. Bioinformatics, 21, pp. 3131-3137. (doi: 10.1093/bioinformatics/bti487)
Husmeier, D. , Wright, F. and Milne, I. (2005) Detecting interspecific recombination with a pruned probabilistic divergence measure. Bioinformatics, 21(9), pp. 1797-1806. (doi: 10.1093/bioinformatics/bti151)
Husmeier, D. (2005) Discriminating between rate heterogeneity and interspecific recombination in DNA sequence alignments with phylogenetic factorial hidden Markov models. Bioinformatics, 21(Suppl), ii166-ii172. (doi: 10.1093/bioinformatics/bti1127)
Vinciotti, V. et al. (2005) An experimental evaluation of a loop versus a reference design for two-channel microarrays. Bioinformatics, 21, pp. 492-501. (doi: 10.1093/bioinformatics/bti022)
Torrance, G., Gilbert, D., Michalopoulos, I. and Westhead, D. (2005) Protein structure topological comparison, discovery and matching service. Bioinformatics, 21, pp. 2537-2538. (doi: 10.1093/bioinformatics/bti331)
Bakewell, D.J. and Wit, E. (2005) Weighted analysis of microarray gene expression using maximum-likelihood. Bioinformatics, 21, pp. 723-729. (doi: 10.1093/bioinformatics/bti051)
Ward, J. J., McGuffin, J. J., Bryson, K. , Buxton, B. F. and Jones, D. T. (2004) The DISOPRED server for the prediction of protein disorder. Bioinformatics, 20(13), pp. 2138-2139. (doi: 10.1093/bioinformatics/bth195) (PMID:15044227)
Milne, I., Wright, F., Rowe, G., Marshall, D.F., Husmeier, D. and McGuire, G. (2004) TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments. Bioinformatics, 20(11), pp. 1806-1807. (doi: 10.1093/bioinformatics/bth155)
Orton, R.J. , Sellers, W.I. and Gerloff, D.L. (2004) YETI: yeast exploration tool integrator. Bioinformatics, 20(2), pp. 284-285. (doi: 10.1093/bioinformatics/btg408)
Girolami, M. (2004) Biologically Valid Linear Factor Models of Gene Expression. Bioinformatics, p. 26.
Leader, D.P. (2004) BugView: a browser for comparing genomes. Bioinformatics, 20, pp. 129-130. (doi: 10.1093/bioinformatics/btg383)
Jones, A., Hunt, E., Wastling, J.M., Pizarro, A. and Stoeckert, C.J. (2004) An object model and database for functional genomics. Bioinformatics, 20, pp. 1583-1590. (doi: 10.1093/bioinformatics/bth130)
Semple, C., Daniel, P., Hordijk, W., Page, R. and Steel, M. (2004) Supertree algorithms for ancestral divergence dates and nested taxa. Bioinformatics, 20, pp. 2355-2360. (doi: 10.1093/bioinformatics/bth246)
Husmeier, D. (2003) Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks. Bioinformatics, 19(17), pp. 2271-2282. (doi: 10.1093/bioinformatics/btg313)
Wit, E. and McClure, J. (2003) Statistical adjustment of signal censoring in gene expression experiments. Bioinformatics, 19, pp. 1055-1060. (doi: 10.1093/bioinformatics/btg003)
Husmeier, D. and McGuire, G. (2002) Detecting recombination with MCMC. Bioinformatics, 18(Sup 1), S345-S353. (doi: 10.1093/bioinformatics/18.suppl_1.S345)
Husmeier, D. and Wright, F. (2002) A Bayesian approach to discriminate between alternative DNA sequence segmentations. Bioinformatics, 18(2), pp. 226-234. (doi: 10.1093/bioinformatics/18.2.226)
Husmeier, D. and Wright, F. (2001) Probabilistic divergence measures for detecting interspecies recombination. Bioinformatics, 17(Sup 1), S123-S131. (doi: 10.1093/bioinformatics/17.suppl_1.S123)
McGuffin, L. J., Bryson, K. and Jones, D. T. (2001) What are the baselines for protein fold recognition? Bioinformatics, 17(1), pp. 63-72. (doi: 10.1093/bioinformatics/17.1.63) (PMID:11222263)
Page, R.D.M. (2000) Circles: automating the comparative analysis of RNA secondary structure. Bioinformatics, 16(11), pp. 1042-1043. (doi: 10.1093/bioinformatics/16.11.1042)
Thorley, J. L. and Page, R. D.M. (2000) RadCon: phylogenetic tree comparison and consensus. Bioinformatics, 16(5), pp. 486-487. (doi: 10.1093/bioinformatics/16.5.486) (PMID:10871273)
McGuffin, L. J., Bryson, K. and Jones, D. T. (2000) The PSIPRED protein structure prediction server. Bioinformatics, 16(4), pp. 404-405. (doi: 10.1093/bioinformatics/16.4.404) (PMID:10869041)
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