Engelfriet ML, Guo Y, Arnold A, Valen E, Ciosk R. Reprograming gene expression in ‘hibernating’ C. elegans involves the IRE-1/XBP-1 pathway. Elife. 2025 May 6;13:RP101186. doi: 10.7554/eLife.101186. PMID: 40326887; PMCID: PMC12055002.
Auxillos J, Stigliani A, Vaagensø CS, Garland W, Niazi AM, Valen E, Jensen TH, Sandelin A. True length of diverse capped RNA sequencing (TLDR-seq): 5′-3′-end sequencing of capped RNAs regardless of 3′-end status. Nucleic Acids Res. 2025 Mar 20;53(6):gkaf240. doi: 10.1093/nar/gkaf240. PMID: 40183637; PMCID: PMC11969664.
Tierney JAS, Świrski MI, Tjeldnes H, Kiran AM, Carancini G, Kiniry SJ, Michel AM, Kufel J, Valen E, Baranov PV. RiboSeq.Org: an integrated suite of resources for ribosome profiling data analysis and visualization. Nucleic Acids Res. 2025 Jan 6;53(D1):D268-D274. doi: 10.1093/nar/gkae1020. PMID: 39540432; PMCID: PMC11701704.
2024
Deutsch EW, Kok LW, Mudge JM, Ruiz-Orera J, Fierro-Monti I, Sun Z, Abelin JG, Alba MM, Aspden JL, Bazzini AA, Bruford EA, Brunet MA, Calviello L, Carr SA, Carvunis AR, Chothani S, Clauwaert J, Dean K, Faridi P, Frankish A, Hubner N, Ingolia NT, Magrane M, Martin MJ, Martinez TF, Menschaert G, Ohler U, Orchard S, Rackham O, Roucou X, Slavoff SA, Valen E, Wacholder A, Weissman JS, Wu W, Xie Z, Choudhary J, Bassani-Sternberg M, Vizcaíno JA, Ternette N, Moritz RL, Prensner JR, van Heesch S. High-quality peptide evidence for annotating non-canonical open reading frames as human proteins. bioRxiv [Preprint]. 2024 Sep 9:2024.09.09.612016. doi: 10.1101/2024.09.09.612016. PMID: 39314370; PMCID: PMC11419116.
Sivertsen A, Mortensen N, Solem U, Valen E, Bullita MF, Wensaas K-A, Litleskare S, Rørtveit G, Grewal HMS, Ulvestad E. Comprehensive contact tracing during an outbreak of alpha-variant SARS-CoV-2 in a rural community reveals less viral genomic diversity and higher household secondary attack rates than expected. mSphere. 2024 Aug 28;9(8):e0011424. doi: 10.1128/msphere.00114-24. Epub 2024 Aug 7. PMID: 39109863; PMCID: PMC11351100.
Kelley LH, Caldas IV, Sullenberger MT, Yongblah KE, Niazi AM, Iyer A, Li Y, Tran PM, Valen E, Ahmed-Braimah YH, Maine EM. Poly(U) polymerase activity in Caenorhabditis elegans regulates abundance and tailing of sRNA and mRNA. Genetics. 2024 Oct 7;228(2):iyae120. doi: 10.1093/genetics/iyae120. PMID: 39067069; PMCID: PMC11457939.
Tierney JAS, Świrski M, Tjeldnes H, Mudge JM, Kufel J, Whiffin N, Valen E, Baranov PV. Ribosome decision graphs for the representation of eukaryotic RNA translation complexity. Genome Res. 2024 May 15;34(4):530-538. doi: 10.1101/gr.278810.123. PMID: 38719470; PMCID: PMC11146595.
2023
Tierney JAS, Świrski M, Tjeldnes H, Mudge JM, Kufel J, Whiffin N, Valen E, Baranov PV. Ribosome Decision Graphs for the Representation of Eukaryotic RNA Translation Complexity. bioRxiv [Preprint]. 2023 Nov 12:2023.11.10.566564. doi: 10.1101/2023.11.10.566564. Update in: Genome Res. 2024 May 15;34(4):530-538. doi: 10.1101/gr.278810.123. PMID: 37986835; PMCID: PMC10659439.
Svalastoga P, Kaci A, Molnes J, Solheim MH, Johansson BB, Krogvold L, Skrivarhaug T, Valen E, Johansson S, Molven A, Sagen JV, Søfteland E, Bjørkhaug L, Tjora E, Aukrust I, Njølstad PR. Characterisation of HNF1A variants in paediatric diabetes in Norway using functional and clinical investigations to unmask phenotype and monogenic diabetes. Diabetologia. 2023 Dec;66(12):2226-2237. doi: 10.1007/s00125-023-06012-4. Epub 2023 Oct 5. PMID: 37798422; PMCID: PMC10627920.
Begik O, Diensthuber G, Liu H, Delgado-Tejedor A, Kontur C, Niazi AM, Valen E, Giraldez AJ, Beaudoin JD, Mattick JS, Novoa EM. Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing. Nat Methods. 2023 Jan;20(1):75-85. doi: 10.1038/s41592-022-01714-w. Epub 2022 Dec 19. PMID: 36536091; PMCID: PMC9834059.
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