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Page 1
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.
Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G, Behera AK, Gonzalez Martinez JM, Hunt T, Lagarde J, Liang CE, Li H, Meade MJ, Moraga Amador DA, Prjibelski AD, Birol I, Bostan H, Brooks AM, Çelik MH, Chen Y, Du MRM, Felton C, Göke J, Hafezqorani S, Herwig R, Kawaji H, Lee J, Li JL, Lienhard M, Mikheenko A, Mulligan D, Nip KM, Pertea M, Ritchie ME, Sim AD, Tang AD, Wan YK, Wang C, Wong BY, Yang C, Barnes I, Berry AE, Capella-Gutierrez S, Cousineau A, Dhillon N, Fernandez-Gonzalez JM, Ferrández-Peral L, Garcia-Reyero N, Götz S, Hernández-Ferrer C, Kondratova L, Liu T, Martinez-Martin A, Menor C, Mestre-Tomás J, Mudge JM, Panayotova NG, Paniagua A, Repchevsky D, Ren X, Rouchka E, Saint-John B, Sapena E, Sheynkman L, Smith ML, Suner MM, Takahashi H, Youngworth IA, Carninci P, Denslow ND, Guigó R, Hunter ME, Maehr R, Shen Y, Tilgner HU, Wold BJ, Vollmers C, Frankish A, Au KF, Sheynkman GM, Mortazavi A, Conesa A, Brooks AN. Pardo-Palacios FJ, et al. Among authors: prjibelski ad. Nat Methods. 2024 Jul;21(7):1349-1363. doi: 10.1038/s41592-024-02298-3. Epub 2024 Jun 7. Nat Methods. 2024. PMID: 38849569 Free PMC article.
Non-Small Cell Lung Cancer Testing on Reference Specimens: An Italian Multicenter Experience.
Pepe F, Russo G, Venuta A, Scimone C, Nacchio M, Pisapia P, Goteri G, Barbisan F, Chiappetta C, Pernazza A, Campagna D, Giordano M, Perrone G, Sabarese G, Altimari A, de Biase D, Tallini G, Calistri D, Chiadini E, Capelli L, Santinelli A, Gulini AE, Pierpaoli E, Badiali M, Murru S, Murgia R, Guerini Rocco E, Venetis K, Fusco N, Morotti D, Gianatti A, Furlan D, Rossi G, Melocchi L, Russo M, De Luca C, Palumbo L, Simonelli S, Maffè A, Francia di Celle P, Venesio T, Scatolini M, Grosso E, Orecchia S, Fassan M, Balistreri M, Zulato E, Reghellin D, Lazzari E, Santacatterina M, Piredda ML, Riccardi M, Laurino L, Roz E, Longo D, Romeo DP, Fazzari C, Moreno-Manuel A, Puglia GD, Prjibelski AD, Shafranskaya D, Righi L, Listì A, Vitale D, Iaccarino A, Malapelle U, Troncone G. Pepe F, et al. Among authors: prjibelski ad. Oncol Ther. 2024 Mar;12(1):73-95. doi: 10.1007/s40487-023-00252-5. Epub 2024 Jan 11. Oncol Ther. 2024. PMID: 38200361 Free PMC article.
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.
Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G, Behera AK, Gonzalez JM, Hunt T, Lagarde J, Liang CE, Li H, Jerryd Meade M, Moraga Amador DA, Prjibelski AD, Birol I, Bostan H, Brooks AM, Hasan Çelik M, Chen Y, Du MRM, Felton C, Göke J, Hafezqorani S, Herwig R, Kawaji H, Lee J, Liang Li J, Lienhard M, Mikheenko A, Mulligan D, Ming Nip K, Pertea M, Ritchie ME, Sim AD, Tang AD, Kei Wan Y, Wang C, Wong BY, Yang C, Barnes I, Berry A, Capella S, Dhillon N, Fernandez-Gonzalez JM, Ferrández-Peral L, Garcia-Reyero N, Goetz S, Hernández-Ferrer C, Kondratova L, Liu T, Martinez-Martin A, Menor C, Mestre-Tomás J, Mudge JM, Panayotova NG, Paniagua A, Repchevsky D, Rouchka E, Saint-John B, Sapena E, Sheynkman L, Laird Smith M, Suner MM, Takahashi H, Youngworth IA, Carninci P, Denslow ND, Guigó R, Hunter ME, Tilgner HU, Wold BJ, Vollmers C, Frankish A, Fai Au K, Sheynkman GM, Mortazavi A, Conesa A, Brooks AN. Pardo-Palacios FJ, et al. Among authors: prjibelski ad. bioRxiv [Preprint]. 2023 Jul 27:2023.07.25.550582. doi: 10.1101/2023.07.25.550582. bioRxiv. 2023. Update in: Nat Methods. 2024 Jul;21(7):1349-1363. doi: 10.1038/s41592-024-02298-3 PMID: 37546854 Free PMC article. Updated. Preprint.
Modulation of Notch Signaling at Early Stages of Differentiation of Human Induced Pluripotent Stem Cells to Dopaminergic Neurons.
Katolikova NV, Khudiakov AA, Shafranskaya DD, Prjibelski AD, Masharskiy AE, Mor MS, Golovkin AS, Zaytseva AK, Neganova IE, Efimova EV, Gainetdinov RR, Malashicheva AB. Katolikova NV, et al. Among authors: prjibelski ad. Int J Mol Sci. 2023 Jan 11;24(2):1429. doi: 10.3390/ijms24021429. Int J Mol Sci. 2023. PMID: 36674941 Free PMC article.
Pericentromeric satellite lncRNAs are induced in cancer-associated fibroblasts and regulate their functions in lung tumorigenesis.
Enukashvily NI, Ponomartsev NV, Ketkar A, Suezov R, Chubar AV, Prjibelski AD, Shafranskaya DD, Elmshäuser S, Keber CU, Stefanova VN, Akopov AL, Klingmüller U, Pfefferle PI, Stiewe T, Lauth M, Brichkina AI. Enukashvily NI, et al. Among authors: prjibelski ad. Cell Death Dis. 2023 Jan 12;14(1):19. doi: 10.1038/s41419-023-05553-1. Cell Death Dis. 2023. PMID: 36635266 Free PMC article.
Accurate isoform discovery with IsoQuant using long reads.
Prjibelski AD, Mikheenko A, Joglekar A, Smetanin A, Jarroux J, Lapidus AL, Tilgner HU. Prjibelski AD, et al. Nat Biotechnol. 2023 Jul;41(7):915-918. doi: 10.1038/s41587-022-01565-y. Epub 2023 Jan 2. Nat Biotechnol. 2023. PMID: 36593406 Free PMC article.
Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue.
Hardwick SA, Hu W, Joglekar A, Fan L, Collier PG, Foord C, Balacco J, Lanjewar S, Sampson MM, Koopmans F, Prjibelski AD, Mikheenko A, Belchikov N, Jarroux J, Lucas AB, Palkovits M, Luo W, Milner TA, Ndhlovu LC, Smit AB, Trojanowski JQ, Lee VMY, Fedrigo O, Sloan SA, Tombácz D, Ross ME, Jarvis E, Boldogkői Z, Gan L, Tilgner HU. Hardwick SA, et al. Among authors: prjibelski ad. Nat Biotechnol. 2022 Jul;40(7):1082-1092. doi: 10.1038/s41587-022-01231-3. Epub 2022 Mar 7. Nat Biotechnol. 2022. PMID: 35256815 Free PMC article.
24 results