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--- research:publications [2025/02/15 19:06] – mikael
+++ research:publications [2025/04/24 10:03] (current) – mikael
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 ==== Pre-prints of note ====
+  - Chen R et al [[https://doi.org/10.1101/2025.03.12.642937| https://doi.org/10.1101/2025.03.12.642937]]
   - 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]]
   - 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]]
@@ Line 6: / Line 7: @@
 ==== 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]]
+  - 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//. 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]]
+  - 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//. DOI [[https://doi.org/10.1093/bib/bbaf004|10.1093/bib/bbaf004]]
+  - 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]]