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research:publications [2025/01/10 21:58] – mikaelresearch: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://www.biorxiv.org/content/10.1101/2024.12.18.629037v1|https://www.biorxiv.org/content/10.1101/2024.12.18.629037v1]]   - Chen R, Foley G and Bodén M. Learning the Language of Phylogeny with MSA Transformer. [[https://www.biorxiv.org/content/10.1101/2024.12.18.629037v1|https://www.biorxiv.org/content/10.1101/2024.12.18.629037v1]]
-  - Shen S et al. An integrated cell barcoding and computational analysis pipeline for scalable analysis of differentiation at single-cell resolution. [[https://doi.org/10.1101/2022.10.12.511862|https://doi.org/10.1101/2022.10.12.511862]]+  - Sinniah E et al. Epigenetic constraint of cellular genomes evolutionarily links genetic variation to function [[https://doi.org/10.1101/2024.10.28.620690|https://doi.org/10.1101/2024.10.28.620690]]
  
 ==== Journal papers ==== ==== Journal papers ====
  
-  - Tule S, Foley G and Bodén M. (2025) Do Protein Language Models Learn Phylogeny? //Briefings in Bioinformatics//. [[https://www.biorxiv.org/content/10.1101/2024.09.23.614642v2|https://www.biorxiv.org/content/10.1101/2024.09.23.614642v2]] +  - Shen S, Werner T, Lukowski SW, Andersen S, Sun Y, Shim WJ, Mizikovsky D, Kobayashi S, Outhwaite J, Chin HS, Chen X, Chapman G, Martin E, Xia D, Pham D, Su Z, Kim D, Yang P, Tan MC, Sinniah E, Zhao Q, Negi S, Redd MA, Powell JE, Dunwoodie SL, Tam P, Bodén M, Ho JWK, Nguyen Q and Palpant NJ. (2025) Atlas of multilineage stem cell differentiation reveals TMEM88 as a developmental regulator of blood pressure. //Nature Communications//. DOI [[https://doi.org/10.1038/s41467-025-56533-2|10.1038/s41467-025-56533-2]] [[https://doi.org/10.1101/2022.10.12.511862|bioRxiv pre-print]] 
-  - 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//. DOI [[https://doi.org/10.1093/bib/bbaf004| 10.1093/bib/bbaf004]]+  - Tule S, Foley G and Bodén M. (2025) Do Protein Language Models Learn Phylogeny? //Briefings in Bioinformatics//. DOI [[https://doi.org/10.1093/bib/bbaf047|10.1093/bib/bbaf047]] [[https://www.biorxiv.org/content/10.1101/2024.09.23.614642v2|bioRxiv pre-print]] 
 +  - 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//. DOI [[https://doi.org/10.1093/bib/bbaf004|10.1093/bib/bbaf004]]
   - 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://doi.org/10.1186/s13073-024-01415-3|10.1186/s13073-024-01415-3]] [[https://rdcu.be/d2uim|Springer Nature SharedIt]]    - 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://doi.org/10.1186/s13073-024-01415-3|10.1186/s13073-024-01415-3]] [[https://rdcu.be/d2uim|Springer Nature SharedIt]] 
   - Joshi P et al. (2024) Phage Anti-Pycsar Proteins Efficiently Degrade β-Lactam Antibiotics. //Applied Biosciences// 3(4). DOI [[https://doi.org/10.3390/applbiosci3040028|10.3390/applbiosci3040028]]   - Joshi P et al. (2024) Phage Anti-Pycsar Proteins Efficiently Degrade β-Lactam Antibiotics. //Applied Biosciences// 3(4). DOI [[https://doi.org/10.3390/applbiosci3040028|10.3390/applbiosci3040028]]
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   - Hawkins J, Mahony D, Maetschke S, Wakabayashi M, Teasdale RD and Bodén M (2007) Identifying novel peroxisomal proteins. //Proteins// 69(3): 606-616.   - Hawkins J, Mahony D, Maetschke S, Wakabayashi M, Teasdale RD and Bodén M (2007) Identifying novel peroxisomal proteins. //Proteins// 69(3): 606-616.
   - Hawkins J, Davis L and Bodén M (2007) //Predicting nuclear localization//. J Proteome Res 6(4): 1402-1409.   - Hawkins J, Davis L and Bodén M (2007) //Predicting nuclear localization//. J Proteome Res 6(4): 1402-1409.
-  - Bauer, D., Bodén M., Thier, R. and Gillam, E. M. STAR: Predicting recombination sites from amino acid sequence. //BMC Bioinformatics//, 7:437, 2006. (Open access.) +  - Bauer D, Bodén M, Thier R and Gillam EM. STAR: Predicting recombination sites from amino acid sequence. //BMC Bioinformatics//, 7:437, 2006. (Open access.) 
-  - Bodén, M. and Bailey, T. L. Identifying sequence regions undergoing conformational change via predicted continuum secondary structure. //Bioinformatics//. 22(15): 1809-1814, 2006. (Open access.) +  - Bodén M and Bailey TL. Identifying sequence regions undergoing conformational change via predicted continuum secondary structure. //Bioinformatics//. 22(15): 1809-1814, 2006. (Open access.) 
-  - Bodén, M., Yuan, Z. and Bailey, T. L. Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures. //BMC Bioinformatics//. 7:68, 2006. (Open access.) +  - Bodén M, Yuan Z and Bailey TL. Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures. //BMC Bioinformatics//. 7:68, 2006. (Open access.) 
-  - Yuan, Z., Zhang, F., Davis, M. J., Bodén  M. and Teasdale, R. D. Predicting the solvent accessibility of transmembrane residues from protein sequence. //Journal of Proteome Research//. 5(5):1063-1070, 2006. +  - Yuan Z, Zhang F, Davis MJ, Bodén M and Teasdale RD. Predicting the solvent accessibility of transmembrane residues from protein sequence. //Journal of Proteome Research//. 5(5):1063-1070, 2006. 
-  - 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. +  - 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. //Bioinformatics//. 21(10):2279-2286, 2005. +  - Bodén M and Hawkins J. Prediction of subcellular localisation using sequence-biased recurrent networks. //Bioinformatics//. 21(10):2279-2286, 2005. 
-  - Hawkins, J. and Bodén  M. The applicability of recurrent neural networks for biological sequence analysis. //IEEE/ACM Transactions on Computational Biology and Bioinformatics//, 2(3): 243-253, 2005. +  - Hawkins J and Bodén M. The applicability of recurrent neural networks for biological sequence analysis. //IEEE/ACM Transactions on Computational Biology and Bioinformatics//, 2(3): 243-253, 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 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. //Generalization by symbolic abstraction in cascaded recurrent networks, Neurocomputing//, 57, pp. 87-104, 2004. +  - Bodén M. //Generalization by symbolic abstraction in cascaded recurrent networks, Neurocomputing//, 57, pp. 87-104, 2004. 
-  - Bodén, M. and Blair, A. Learning the dynamics of embedded clauses, Applied Intelligence: //Special issue on natural language and machine learning//, 19(1/2), pp. 51-63, 2003. +  - Bodén M and Blair A. Learning the dynamics of embedded clauses, Applied Intelligence: //Special issue on natural language and machine learning//, 19(1/2), pp. 51-63, 2003. 
-  - 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, //Connection Science//, 12 (3/4), pp. 197-210, 2000. +  - Bodén M and Wiles J. Context-free and context-sensitive dynamics in recurrent neural networks, //Connection Science//, 12 (3/4), pp. 197-210, 2000. 
-  - Bodén, M. and Niklasson, L., Semantic systematicity and context in connectionist Networks, //Connection Science//, 12 (2), pp. 111-142, 2000.+  - Bodén M and Niklasson L. Semantic systematicity and context in connectionist Networks, //Connection Science//, 12 (2), pp. 111-142, 2000.
  
 ==== Refereed conference papers (since 2000) ==== ==== Refereed conference papers (since 2000) ====
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