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research:publications [2025/01/04 08:36] – mikael | research:publications [2025/02/15 19:06] (current) – mikael | ||
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- Chen R, Foley G and Bodén M. Learning the Language of Phylogeny with MSA Transformer. [[https:// | - Chen R, Foley G and Bodén M. Learning the Language of Phylogeny with MSA Transformer. [[https:// | ||
- | - Tule S, Foley G and Bodén M. Do Protein Language Models Learn Phylogeny? [[https:// | + | - Sinniah E et al. Epigenetic constraint |
- | - Shen S et al. An integrated cell barcoding and computational analysis pipeline for scalable analysis | + | |
==== Journal papers ==== | ==== Journal papers ==== | ||
- | - Zhao QY, Shim WJ, Sun Y, Sinniah E, Shen S, Bodén M and Palpant N. (2025) TRIAGE: An R Package for Regulatory Gene Analysis. //Briefings in Bioinformatics// | + | |
+ | - Tule S, Foley G and Bodén M. (2025) Do Protein Language Models Learn Phylogeny? //Briefings in Bioinformatics// | ||
+ | | ||
- Mora A, Schmidt C, Balderson B, Frezza C and Bodén M. (2024) SiRCle (Signature Regulatory Clustering) model integration reveals mechanisms of phenotype regulation in renal cancer. //Genome Medicine// 16(144). DOI [[https:// | - Mora A, Schmidt C, Balderson B, Frezza C and Bodén M. (2024) SiRCle (Signature Regulatory Clustering) model integration reveals mechanisms of phenotype regulation in renal cancer. //Genome Medicine// 16(144). DOI [[https:// | ||
- Joshi P et al. (2024) Phage Anti-Pycsar Proteins Efficiently Degrade β-Lactam Antibiotics. //Applied Biosciences// | - Joshi P et al. (2024) Phage Anti-Pycsar Proteins Efficiently Degrade β-Lactam Antibiotics. //Applied Biosciences// | ||
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- Hawkins J, Mahony D, Maetschke S, Wakabayashi M, Teasdale RD and Bodén M (2007) Identifying novel peroxisomal proteins. // | - Hawkins J, Mahony D, Maetschke S, Wakabayashi M, Teasdale RD and Bodén M (2007) Identifying novel peroxisomal proteins. // | ||
- Hawkins J, Davis L and Bodén M (2007) // | - Hawkins J, Davis L and Bodén M (2007) // | ||
- | - Bauer, D., Bodén M., Thier, R. and Gillam, E. M. STAR: Predicting recombination sites from amino acid sequence. //BMC Bioinformatics//, | + | - Bauer D, Bodén M, Thier R and Gillam |
- | - Bodén, M. and Bailey, T. L. Identifying sequence regions undergoing conformational change via predicted continuum secondary structure. // | + | - Bodén M and Bailey |
- | - Bodén, M., Yuan, Z. and Bailey, T. L. Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures. //BMC Bioinformatics// | + | - Bodén M, Yuan Z and Bailey |
- | - Yuan, Z., Zhang, F., Davis, M. J., Bodén | + | - Yuan Z, Zhang F, Davis MJ, Bodén M and Teasdale |
- | - Hawkins, J. and Bodén | + | - Hawkins J and Bodén M. Detecting and sorting targeting peptides with recurrent networks and support vector machines. //Journal of Bioinformatics and Computational Biology//, 4(1), 2006. |
- | - Bodén, M. and Hawkins, J. Prediction of subcellular localisation using sequence-biased recurrent networks. // | + | - Bodén M and Hawkins J. Prediction of subcellular localisation using sequence-biased recurrent networks. // |
- | - Hawkins, J. and Bodén | + | - Hawkins J and Bodén M. The applicability of recurrent neural networks for biological sequence analysis. //IEEE/ACM Transactions on Computational Biology and Bioinformatics//, |
- | - Bodén, M. and Hawkins, J. Improved access to sequential motifs: A note on the architectural bias of recurrent networks. //IEEE Transactions on Neural Networks//. 16(2), 2005. | + | - Bodén M and Hawkins J. Improved access to sequential motifs: A note on the architectural bias of recurrent networks. //IEEE Transactions on Neural Networks//. 16(2), 2005. |
- | - Bodén, M. // | + | - Bodén M. // |
- | - Bodén, M. and Blair, A. Learning the dynamics of embedded clauses, Applied Intelligence: | + | - Bodén M and Blair A. Learning the dynamics of embedded clauses, Applied Intelligence: |
- | - Bodén, M. and Wiles, J. On learning context free and context sensitive languages, //IEEE Transactions on Neural Networks//. 13(2), pp. 491-493, 2002. | + | - Bodén M and Wiles J. On learning context free and context sensitive languages, //IEEE Transactions on Neural Networks//. 13(2), pp. 491-493, 2002. |
- | - Bodén, M. and Wiles, J., Context-free and context-sensitive dynamics in recurrent neural networks, // | + | - Bodén M and Wiles J. Context-free and context-sensitive dynamics in recurrent neural networks, // |
- | - Bodén, M. and Niklasson, L., Semantic systematicity and context in connectionist Networks, // | + | - Bodén M and Niklasson L. Semantic systematicity and context in connectionist Networks, // |
==== Refereed conference papers (since 2000) ==== | ==== Refereed conference papers (since 2000) ==== |