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Meng, Z., Liu, S., Liang, S., Jani, B. and Meng, Z. (2024) Heterogeneous biomedical entity representation learning for gene-disease association prediction. Briefings in Bioinformatics, (Accepted for Publication)
Yi, X., Liu, S., Wu, Y., McCloskey, D. and Meng, Z. (2024) BPP: A platform for automatic biochemical pathway prediction. Briefings in Bioinformatics, (Accepted for Publication)
Ruiz, J. L., Reimering, S., Escobar-Prieto, J. D., Brancucci, N. N.M. , Echeverry, D. F., Abdi, A. I., Marti, M. , Gómez-Díaz, E. and Otto, T. D. (2023) From contigs towards chromosomes: automatic improvement of long read assemblies (ILRA). Briefings in Bioinformatics, 24(4), bbad248. (doi: 10.1093/bib/bbad248) (PMID:37406192) (PMCID:PMC10359078)
Prasad, B. , Bjourson, A. J. and Shukla, P. (2022) Data-driven patient stratification of UK Biobank cohort suggests five endotypes of multimorbidity. Briefings in Bioinformatics, 23(6), bbac410. (doi: 10.1093/bib/bbac410) (PMID:36209412)
Shukla, P. et al. (2022) Immuno-informatics analysis predicts B and T cell consensus epitopes for designing peptide vaccine against SARS-CoV-2 with 99.82% global population coverage. Briefings in Bioinformatics, 23(1), bbab496. (doi: 10.1093/bib/bbab496) (PMID:34962259) (PMCID:PMC8769887)
Hufsky, F. et al. (2021) Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Briefings in Bioinformatics, 22(2), pp. 642-663. (doi: 10.1093/bib/bbaa232) (PMID:33147627) (PMCID:PMC7665365)
Zhang, H., Ferguson, A., Robertson, G., Jiang, M., Zhang, T., Sudlow, C., Smith, K., Rannikmae, K. and Wu, H. (2021) Benchmarking network-based gene prioritization methods for cerebral small vessel disease. Briefings in Bioinformatics, 22(5), bbab006. (doi: 10.1093/bib/bbab006) (PMID:33634312) (PMCID:PMC8425308)
Schirmer, M., Sloan, W. T. and Quince, C. (2014) Benchmarking of viral haplotype reconstruction programmes: an overview of the capacities and limitations of currently available programmes. Briefings in Bioinformatics, 15(3), pp. 431-442. (doi: 10.1093/bib/bbs081)
Carver, T., Harris, S. R., Otto, T. D. , Berriman, M., Parkhill, J. and McQuillan, J. A. (2013) BamView: visualizing and interpretation of next-generation sequencing read alignments. Briefings in Bioinformatics, 14(2), pp. 203-12. (PMID:22253280) (PMCID:PMC3603209)
Page, R. (2008) Biodiversity informatics: the challenge of linking data and the role of shared identifiers. Briefings in Bioinformatics, 9(5), pp. 345-354. (doi: 10.1093/bib/bbn022) (PMID:18445641)
Breitling, R., Gilbert, D., Heiner, M. and Orton, R. (2008) A structured approach for the engineering of biochemical network models, illustrated for signalling pathways. Briefings in Bioinformatics, 9(5), pp. 404-421. (doi: 10.1093/bib/bbn026)
Gilbert, D., Fuss, H., Gu, X., Orton, R. , Robinson, S., Vyshemirsky, V., Kurth, M.J., Downes, C.S. and Dubitzky, W. (2006) Computational methodologies for modelling, analysis and simulation of signalling networks. Briefings in Bioinformatics, 7(4), pp. 339-353. (doi: 10.1093/bib/bbl043)
Yates, A., Chan, C. C. W., Callard, R. E., George, A. J. T. and Stark, J. (2001) An approach to modelling in immunology. Briefings in Bioinformatics, 2(3), pp. 245-257. (doi: 10.1093/bib/2.3.245)