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--- research:publications [2025/02/15 19:06] – mikael
+++ research:publications [2025/11/11 16:29] (current) – mikael
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 ==== Pre-prints of note ====
-  - 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, Palpant N, Foley G, Bodén M. [[https://doi.org/10.1101/2025.03.12.642937| https://doi.org/10.1101/2025.03.12.642937]]
-  - 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]]
+  - Balderson B, Tule S, Okino M-L, Rieger WJF, Corban S, Jaureguy J, Palpant N, Gaulton KJ, Bodén M, McVicker G. Comprehensive molecular impact mapping of common and rare variants at GWAS loci [[https://doi.org/10.1101/2025.06.05.658079|https://doi.org/10.1101/2025.06.05.658079]]
 ==== Journal papers ====
-  - 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]]
+  - Rieger WJF, Bodén M, Arnold FA and Mora A. Squidly: Enzyme Catalytic Residue Prediction Harnessing a Biology-Informed Contrastive Learning Framework. Accepted //eLife//. DOI [[https://doi.org/10.7554/eLife.108186.1|10.7554/eLife.108186.1]]
-  - 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]]
+  - Thompson R et al. Thermostable ancestors enabled evolutionary diversification of promiscuous chemical defence enzymes. Accepted The EMBO Journal.
-  - 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]]
+  - Chen R, Foley G and Bodén M. (2025) Learning the Language of Phylogeny with MSA Transformer. //Cell Systems// 16. DOI [[https://doi.org/10.1016/j.cels.2025.101445|10.1016/j.cels.2025.101445]] [[https://www.biorxiv.org/content/10.1101/2024.12.18.629037v1|bioRxiv]]
+  - Sinniah E et al. Epigenetic constraint of cellular genomes evolutionarily links genetic variation to function. Accepted //Nucleic Acids Research//. [[https://doi.org/10.1101/2024.10.28.620690|https://doi.org/10.1101/2024.10.28.620690]]
+  - Low YS, Roche SG, Aleksandrova NA, Foley G, Low JKK, Box JK, Croll TI, Chassagnon IR, Lott JS, Deplazes E, Bodén M, Hurst MRH, Piper SJ and Landsberg MJ. Complete structures of the YenTc holotoxin prepore and pore reveal the evolutionary basis for chitinase incorporation into ABC toxins. Accepted //Nature Communications//.
+  - 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//. 16(1356). 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]]
+  - Tule S, Foley G and Bodén M. (2025) Do Protein Language Models Learn Phylogeny? //Briefings in Bioinformatics// 26(1). 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// 26(1). 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]]
   - 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]]