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ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants.
Pampari A, Shcherbina A, Kvon EZ, Kosicki M, Nair S, Kundu S, Kathiria AS, Risca VI, Kuningas K, Alasoo K, Greenleaf WJ, Pennacchio LA, Kundaje A. Pampari A, et al. Among authors: alasoo k. bioRxiv [Preprint]. 2025 Jan 8:2024.12.25.630221. doi: 10.1101/2024.12.25.630221. bioRxiv. 2025. PMID: 39829783 Free PMC article. Preprint.
Predicted mechanistic impacts of human protein missense variants.
Jänes J, Müller M, Selvaraj S, Manoel D, Stephenson J, Gonçalves C, Lafita A, Polacco B, Obernier K, Alasoo K, Lemos MC, Krogan N, Martin M, Saraiva LR, Burke D, Beltrao P. Jänes J, et al. Among authors: alasoo k. bioRxiv [Preprint]. 2024 May 29:2024.05.29.596373. doi: 10.1101/2024.05.29.596373. bioRxiv. 2024. PMID: 38854010 Free PMC article. Preprint.
Genetic determinants of plasma protein levels in the Estonian population.
Kalnapenkis A, Jõeloo M, Lepik K, Kukuškina V, Kals M, Alasoo K; Estonian Biobank Research Team; Mägi R, Esko T, Võsa U. Kalnapenkis A, et al. Among authors: alasoo k. Sci Rep. 2024 Apr 2;14(1):7694. doi: 10.1038/s41598-024-57966-3. Sci Rep. 2024. PMID: 38565889 Free PMC article.
eQTL Catalogue 2023: New datasets, X chromosome QTLs, and improved detection and visualisation of transcript-level QTLs.
Kerimov N, Tambets R, Hayhurst JD, Rahu I, Kolberg P, Raudvere U, Kuzmin I, Chowdhary A, Vija A, Teras HJ, Kanai M, Ulirsch J, Ryten M, Hardy J, Guelfi S, Trabzuni D, Kim-Hellmuth S, Rayner W, Finucane H, Peterson H, Mosaku A, Parkinson H, Alasoo K. Kerimov N, et al. Among authors: alasoo k. PLoS Genet. 2023 Sep 18;19(9):e1010932. doi: 10.1371/journal.pgen.1010932. eCollection 2023 Sep. PLoS Genet. 2023. PMID: 37721944 Free PMC article.
Systematic visualisation of molecular QTLs reveals variant mechanisms at GWAS loci.
Kerimov N, Tambets R, Hayhurst JD, Rahu I, Kolberg P, Raudvere U, Kuzmin I, Chowdhary A, Vija A, Teras HJ, Kanai M, Ulirsch J, Ryten M, Hardy J, Guelfi S, Trabzuni D, Kim-Hellmuth S, Rayner W, Finucane H, Peterson H, Mosaku A, Parkinson H, Alasoo K. Kerimov N, et al. Among authors: alasoo k. bioRxiv [Preprint]. 2023 Apr 7:2023.04.06.535816. doi: 10.1101/2023.04.06.535816. bioRxiv. 2023. Update in: PLoS Genet. 2023 Sep 18;19(9):e1010932. doi: 10.1371/journal.pgen.1010932 PMID: 37066341 Free PMC article. Updated. Preprint.
Optimized whole-genome CRISPR interference screens identify ARID1A-dependent growth regulators in human induced pluripotent stem cells.
Usluer S, Hallast P, Crepaldi L, Zhou Y, Urgo K, Dincer C, Su J, Noell G, Alasoo K, El Garwany O, Gerety SS, Newman B, Dovey OM, Parts L. Usluer S, et al. Among authors: alasoo k. Stem Cell Reports. 2023 May 9;18(5):1061-1074. doi: 10.1016/j.stemcr.2023.03.008. Epub 2023 Apr 6. Stem Cell Reports. 2023. PMID: 37028423 Free PMC article.
Author Correction: FinnGen provides genetic insights from a well-phenotyped isolated population.
Kurki MI, Karjalainen J, Palta P, Sipilä TP, Kristiansson K, Donner KM, Reeve MP, Laivuori H, Aavikko M, Kaunisto MA, Loukola A, Lahtela E, Mattsson H, Laiho P, Della Briotta Parolo P, Lehisto AA, Kanai M, Mars N, Rämö J, Kiiskinen T, Heyne HO, Veerapen K, Rüeger S, Lemmelä S, Zhou W, Ruotsalainen S, Pärn K, Hiekkalinna T, Koskelainen S, Paajanen T, Llorens V, Gracia-Tabuenca J, Siirtola H, Reis K, Elnahas AG, Sun B, Foley CN, Aalto-Setälä K, Alasoo K, Arvas M, Auro K, Biswas S, Bizaki-Vallaskangas A, Carpen O, Chen CY, Dada OA, Ding Z, Ehm MG, Eklund K, Färkkilä M, Finucane H, Ganna A, Ghazal A, Graham RR, Green EM, Hakanen A, Hautalahti M, Hedman ÅK, Hiltunen M, Hinttala R, Hovatta I, Hu X, Huertas-Vazquez A, Huilaja L, Hunkapiller J, Jacob H, Jensen JN, Joensuu H, John S, Julkunen V, Jung M, Junttila J, Kaarniranta K, Kähönen M, Kajanne R, Kallio L, Kälviäinen R, Kaprio J; FinnGen; Kerimov N, Kettunen J, Kilpeläinen E, Kilpi T, Klinger K, Kosma VM, Kuopio T, Kurra V, Laisk T, Laukkanen J, Lawless N, Liu A, Longerich S, Mägi R, Mäkelä J, Mäkitie A, Malarstig A, Mannermaa A, Maranville J, Matakidou A, Meretoja T, Mozaffari SV, Niemi MEK, Niemi M, Niiranen T, O Donnell CJ, … See abstract for full author list ➔ Kurki MI, et al. Among authors: alasoo k. Nature. 2023 Mar;615(7952):E19. doi: 10.1038/s41586-023-05837-8. Nature. 2023. PMID: 36829046 Free PMC article. No abstract available.
31 results