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For: Soneson C, Yao Y, Bratus-Neuenschwander A, Patrignani A, Robinson MD, Hussain S. A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes. Nat Commun 2019;10:3359. [PMID: 31366910 PMCID: PMC6668388 DOI: 10.1038/s41467-019-11272-z] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/04/2019] [Indexed: 11/29/2022]  Open
Number Cited by Other Article(s)
1
Schimmich C, Gondard M, Caignard G, Valle-Casuso JC, Vitour D, Piumi F. Host-pathogen protein interaction studies: quality control of cDNA libraries using nanopore sequencing. PLoS One 2025;20:e0324917. [PMID: 40445964 PMCID: PMC12124543 DOI: 10.1371/journal.pone.0324917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2025] [Accepted: 05/02/2025] [Indexed: 06/02/2025]  Open
2
He J, Ganesamoorthy D, Chang JJY, Zhang J, Trevor SL, Gibbons KS, McPherson SJ, Kling JC, Schlapbach LJ, Blumenthal A, Coin LJM, RAPIDS Study Group. Utilizing Nanopore direct RNA sequencing of blood from patients with sepsis for discovery of co- and post-transcriptional disease biomarkers. BMC Infect Dis 2025;25:692. [PMID: 40355874 PMCID: PMC12070577 DOI: 10.1186/s12879-025-11078-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Collaborators] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2025] [Accepted: 05/02/2025] [Indexed: 05/15/2025]  Open
3
Li Q, Keskus AG, Wagner J, Izydorczyk MB, Timp W, Sedlazeck FJ, Klein AP, Zook JM, Kolmogorov M, Schatz MC. Unraveling the hidden complexity of cancer through long-read sequencing. Genome Res 2025;35:599-620. [PMID: 40113261 PMCID: PMC12047254 DOI: 10.1101/gr.280041.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2025]
4
Monzó C, Frankish A, Conesa A. Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation. Genome Res 2025;35:583-592. [PMID: 40032585 PMCID: PMC12047247 DOI: 10.1101/gr.279865.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Accepted: 01/30/2025] [Indexed: 03/05/2025]
5
Chen Y, Davidson NM, Wan YK, Yao F, Su Y, Gamaarachchi H, Sim A, Patel H, Low HM, Hendra C, Wratten L, Hakkaart C, Sawyer C, Iakovleva V, Lee PL, Xin L, Ng HEV, Loo JM, Ong X, Ng HQA, Wang J, Koh WQC, Poon SYP, Stanojevic D, Tran HD, Lim KHE, Toh SY, Ewels PA, Ng HH, Iyer NG, Thiery A, Chng WJ, Chen L, DasGupta R, Sikic M, Chan YS, Tan BOP, Wan Y, Tam WL, Yu Q, Khor CC, Wüstefeld T, Lezhava A, Pratanwanich PN, Love MI, Goh WSS, Ng SB, Oshlack A, Göke J. A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines. Nat Methods 2025;22:801-812. [PMID: 40082608 PMCID: PMC11978509 DOI: 10.1038/s41592-025-02623-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/04/2025] [Indexed: 03/16/2025]
6
Kovaka S, Hook PW, Jenike KM, Shivakumar V, Morina LB, Razaghi R, Timp W, Schatz MC. Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment. Nat Methods 2025;22:681-691. [PMID: 40155722 PMCID: PMC11978507 DOI: 10.1038/s41592-025-02631-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 02/16/2025] [Indexed: 04/01/2025]
7
Hatzimanolis O, Sykes AM, Cristino AS. Circular RNAs in neurological conditions - computational identification, functional validation, and potential clinical applications. Mol Psychiatry 2025;30:1652-1675. [PMID: 39966624 PMCID: PMC11919710 DOI: 10.1038/s41380-025-02925-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 01/11/2025] [Accepted: 02/10/2025] [Indexed: 02/20/2025]
8
Monzó C, Liu T, Conesa A. Transcriptomics in the era of long-read sequencing. Nat Rev Genet 2025:10.1038/s41576-025-00828-z. [PMID: 40155769 DOI: 10.1038/s41576-025-00828-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2025] [Indexed: 04/01/2025]
9
Song J, Lin LA, Tang C, Chen C, Yang Q, Zhang D, Zhao Y, Wei HC, Linghu K, Xu Z, Chen T, He Z, Liu D, Zhong Y, Zhu W, Zeng W, Chen L, Song G, Chen M, Jiang J, Zhou J, Wang J, Chen B, Ying B, Wang Y, Geng J, Lin JW, Chen L. DEMINERS enables clinical metagenomics and comparative transcriptomic analysis by increasing throughput and accuracy of nanopore direct RNA sequencing. Genome Biol 2025;26:76. [PMID: 40155949 PMCID: PMC11954306 DOI: 10.1186/s13059-025-03536-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Accepted: 03/10/2025] [Indexed: 04/01/2025]  Open
10
Gumińska N, Matylla-Kulińska K, Krawczyk PS, Maj M, Orzeł W, Mackiewicz Z, Brouze A, Mroczek S, Dziembowski A. Direct profiling of non-adenosines in poly(A) tails of endogenous and therapeutic mRNAs with Ninetails. Nat Commun 2025;16:2664. [PMID: 40102414 PMCID: PMC11920217 DOI: 10.1038/s41467-025-57787-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 11/27/2024] [Indexed: 03/20/2025]  Open
11
Min K, Park A. Shape-Shifting Mechanisms: Integrative Multi-Omics Insights Into Candida albicans Morphogenesis. MYCOBIOLOGY 2025;53:250-257. [PMID: 40098942 PMCID: PMC11912286 DOI: 10.1080/12298093.2025.2460304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2024] [Revised: 01/23/2025] [Accepted: 01/25/2025] [Indexed: 03/19/2025]
12
Czarnocka-Cieciura A, Brouze M, Gumińska N, Mroczek S, Gewartowska O, Krawczyk PS, Dziembowski A. Comprehensive analysis of poly(A) tails in mouse testes and ovaries using Nanopore Direct RNA Sequencing. Sci Data 2025;12:43. [PMID: 39794363 PMCID: PMC11724052 DOI: 10.1038/s41597-024-04226-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 12/02/2024] [Indexed: 01/13/2025]  Open
13
Ibrahim F, Mourelatos Z. Defining the True Native Ends of RNAs at Single-Molecule Level with TERA-Seq. Methods Mol Biol 2025;2863:359-372. [PMID: 39535720 PMCID: PMC12013618 DOI: 10.1007/978-1-0716-4176-7_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2024]
14
Schiksnis E, Nicastro I, Pasquinelli A. Full-length direct RNA sequencing reveals extensive remodeling of RNA expression, processing and modification in aging Caenorhabditis elegans. Nucleic Acids Res 2024;52:13896-13913. [PMID: 39558169 PMCID: PMC11662692 DOI: 10.1093/nar/gkae1064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 09/12/2024] [Accepted: 10/22/2024] [Indexed: 11/20/2024]  Open
15
Haile S, Corbett RD, O’Neill K, Xu J, Smailus DE, Pandoh PK, Bayega A, Bala M, Chuah E, Coope RJN, Moore RA, Mungall KL, Zhao Y, Ma Y, Marra MA, Jones SJM, Mungall AJ. Adaptable and comprehensive approaches for long-read nanopore sequencing of polyadenylated and non-polyadenylated RNAs. Front Genet 2024;15:1466338. [PMID: 39687742 PMCID: PMC11647301 DOI: 10.3389/fgene.2024.1466338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Accepted: 11/11/2024] [Indexed: 12/18/2024]  Open
16
Calvo-Roitberg E, Daniels RF, Pai AA. Challenges in identifying mRNA transcript starts and ends from long-read sequencing data. Genome Res 2024;34:1719-1734. [PMID: 39567236 DOI: 10.1101/gr.279559.124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 08/16/2024] [Indexed: 11/22/2024]
17
Zhu XT, Sanz-Jimenez P, Ning XT, Tahir Ul Qamar M, Chen LL. Direct RNA sequencing in plants: Practical applications and future perspectives. PLANT COMMUNICATIONS 2024;5:101064. [PMID: 39155503 PMCID: PMC11589328 DOI: 10.1016/j.xplc.2024.101064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/17/2024] [Accepted: 08/14/2024] [Indexed: 08/20/2024]
18
Lin KN, Volkel K, Cao C, Hook PW, Polak RE, Clark AS, San Miguel A, Timp W, Tuck JM, Velev OD, Keung AJ. A primordial DNA store and compute engine. NATURE NANOTECHNOLOGY 2024;19:1654-1664. [PMID: 39174834 DOI: 10.1038/s41565-024-01771-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 07/19/2024] [Indexed: 08/24/2024]
19
Xu Z, Zheng X, Fan J, Jiao Y, Huang S, Xie Y, Xu S, Lu Y, Liu A, Liu R, Yang Y, Luo GZ, Pan T, Wang X. Microbiome-induced reprogramming in post-transcriptional landscape using nanopore direct RNA sequencing. Cell Rep 2024;43:114798. [PMID: 39365698 DOI: 10.1016/j.celrep.2024.114798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 08/10/2024] [Accepted: 09/10/2024] [Indexed: 10/06/2024]  Open
20
Ren L, Shi L, Zheng Y. Reference Materials for Improving Reliability of Multiomics Profiling. PHENOMICS (CHAM, SWITZERLAND) 2024;4:487-521. [PMID: 39723231 PMCID: PMC11666855 DOI: 10.1007/s43657-023-00153-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/18/2023] [Accepted: 12/22/2023] [Indexed: 12/28/2024]
21
Nagy GÁ, Tombácz D, Prazsák I, Csabai Z, Dörmő Á, Gulyás G, Kemenesi G, Tóth GE, Holoubek J, Růžek D, Kakuk B, Boldogkői Z. Exploring the transcriptomic profile of human monkeypox virus via CAGE and native RNA sequencing approaches. mSphere 2024;9:e0035624. [PMID: 39191390 PMCID: PMC11423596 DOI: 10.1128/msphere.00356-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 07/31/2024] [Indexed: 08/29/2024]  Open
22
Ghavi Hossein-Zadeh N. An overview of recent technological developments in bovine genomics. Vet Anim Sci 2024;25:100382. [PMID: 39166173 PMCID: PMC11334705 DOI: 10.1016/j.vas.2024.100382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2024]  Open
23
Saville L, Wu L, Habtewold J, Cheng Y, Gollen B, Mitchell L, Stuart-Edwards M, Haight T, Mohajerani M, Zovoilis A. NERD-seq: a novel approach of Nanopore direct RNA sequencing that expands representation of non-coding RNAs. Genome Biol 2024;25:233. [PMID: 39198865 PMCID: PMC11351768 DOI: 10.1186/s13059-024-03375-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 08/20/2024] [Indexed: 09/01/2024]  Open
24
Yang Y, Lu Y, Wang Y, Wen X, Qi C, Piao W, Jin H. Current progress in strategies to profile transcriptomic m6A modifications. Front Cell Dev Biol 2024;12:1392159. [PMID: 39055651 PMCID: PMC11269109 DOI: 10.3389/fcell.2024.1392159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/18/2024] [Indexed: 07/27/2024]  Open
25
Schiksnis EC, Nicastro IA, Pasquinelli AE. Full-length direct RNA sequencing reveals extensive remodeling of RNA expression, processing and modification in aging Caenorhabditis elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.18.599640. [PMID: 38948813 PMCID: PMC11213008 DOI: 10.1101/2024.06.18.599640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
26
Relier S, Schiffers S, Beiki H, Oberdoerffer S. Enhanced ac4C detection in RNA via chemical reduction and cDNA synthesis with modified dNTPs. RNA (NEW YORK, N.Y.) 2024;30:938-953. [PMID: 38697668 PMCID: PMC11182010 DOI: 10.1261/rna.079863.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 04/04/2024] [Indexed: 05/05/2024]
27
Grigorev K, Nelson TM, Overbey EG, Houerbi N, Kim J, Najjar D, Damle N, Afshin EE, Ryon KA, Thierry-Mieg J, Thierry-Mieg D, Melnick AM, Mateus J, Mason CE. Direct RNA sequencing of astronaut blood reveals spaceflight-associated m6A increases and hematopoietic transcriptional responses. Nat Commun 2024;15:4950. [PMID: 38862496 PMCID: PMC11166648 DOI: 10.1038/s41467-024-48929-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/17/2024] [Indexed: 06/13/2024]  Open
28
Bošković F, Maffeo C, Patiño-Guillén G, Tivony R, Aksimentiev A, Keyser UF. Nanopore Translocation Reveals Electrophoretic Force on Noncanonical RNA:DNA Double Helix. ACS NANO 2024;18:15013-15024. [PMID: 38822455 PMCID: PMC11171748 DOI: 10.1021/acsnano.4c01466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/13/2024] [Accepted: 05/22/2024] [Indexed: 06/03/2024]
29
Liu-Wei W, van der Toorn W, Bohn P, Hölzer M, Smyth RP, von Kleist M. Sequencing accuracy and systematic errors of nanopore direct RNA sequencing. BMC Genomics 2024;25:528. [PMID: 38807060 PMCID: PMC11134706 DOI: 10.1186/s12864-024-10440-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 05/21/2024] [Indexed: 05/30/2024]  Open
30
Sneddon A, Ravindran A, Shanmuganandam S, Kanchi M, Hein N, Jiang S, Shirokikh N, Eyras E. Biochemical-free enrichment or depletion of RNA classes in real-time during direct RNA sequencing with RISER. Nat Commun 2024;15:4422. [PMID: 38789440 PMCID: PMC11126589 DOI: 10.1038/s41467-024-48673-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024]  Open
31
Nodari R, Arghittu M, Bailo P, Cattaneo C, Creti R, D’Aleo F, Saegeman V, Franceschetti L, Novati S, Fernández-Rodríguez A, Verzeletti A, Farina C, Bandi C. Forensic Microbiology: When, Where and How. Microorganisms 2024;12:988. [PMID: 38792818 PMCID: PMC11123702 DOI: 10.3390/microorganisms12050988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/30/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024]  Open
32
Bošković F, Maffeo C, Patiño-Guillén G, Tivony R, Aksimentiev A, Keyser UF. Nanopore translocation reveals electrophoretic force on non-canonical RNA:DNA double helix. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.12.557357. [PMID: 37745457 PMCID: PMC10515835 DOI: 10.1101/2023.09.12.557357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
33
Pardo-Palacios FJ, Arzalluz-Luque A, Kondratova L, Salguero P, Mestre-Tomás J, Amorín R, Estevan-Morió E, Liu T, Nanni A, McIntyre L, Tseng E, Conesa A. SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms. Nat Methods 2024;21:793-797. [PMID: 38509328 PMCID: PMC11093726 DOI: 10.1038/s41592-024-02229-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 03/01/2024] [Indexed: 03/22/2024]
34
Baek A, Lee GE, Golconda S, Rayhan A, Manganaris AA, Chen S, Tirumuru N, Yu H, Kim S, Kimmel C, Zablocki O, Sullivan MB, Addepalli B, Wu L, Kim S. Single-molecule epitranscriptomic analysis of full-length HIV-1 RNAs reveals functional roles of site-specific m6As. Nat Microbiol 2024;9:1340-1355. [PMID: 38605174 PMCID: PMC11087264 DOI: 10.1038/s41564-024-01638-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 02/15/2024] [Indexed: 04/13/2024]
35
Drury RE, Camara S, Chelysheva I, Bibi S, Sanders K, Felle S, Emary K, Phillips D, Voysey M, Ferreira DM, Klenerman P, Gilbert SC, Lambe T, Pollard AJ, O'Connor D. Multi-omics analysis reveals COVID-19 vaccine induced attenuation of inflammatory responses during breakthrough disease. Nat Commun 2024;15:3402. [PMID: 38649734 PMCID: PMC11035709 DOI: 10.1038/s41467-024-47463-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 04/02/2024] [Indexed: 04/25/2024]  Open
36
Jiang C, Li P, Ma Y, Yoneda N, Kawai K, Uehara S, Ohnishi Y, Suemizu H, Cao H. Comprehensive gene profiling of the metabolic landscape of humanized livers in mice. J Hepatol 2024;80:622-633. [PMID: 38049085 PMCID: PMC10947884 DOI: 10.1016/j.jhep.2023.11.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 10/12/2023] [Accepted: 11/06/2023] [Indexed: 12/06/2023]
37
Koster CC, Kleefeldt AA, van den Broek M, Luttik M, Daran JM, Daran-Lapujade P. Long-read direct RNA sequencing of the mitochondrial transcriptome of Saccharomyces cerevisiae reveals condition-dependent intron abundance. Yeast 2024;41:256-278. [PMID: 37642136 DOI: 10.1002/yea.3893] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/11/2023] [Accepted: 07/18/2023] [Indexed: 08/31/2023]  Open
38
Iturbe P, Martín AS, Hamamoto H, Marcet-Houben M, Galbaldón T, Solano C, Lasa I. Noncontiguous operon atlas for the Staphylococcus aureus genome. MICROLIFE 2024;5:uqae007. [PMID: 38651166 PMCID: PMC11034616 DOI: 10.1093/femsml/uqae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 03/20/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
39
Degalez F, Charles M, Foissac S, Zhou H, Guan D, Fang L, Klopp C, Allain C, Lagoutte L, Lecerf F, Acloque H, Giuffra E, Pitel F, Lagarrigue S. Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues. Sci Rep 2024;14:6588. [PMID: 38504112 PMCID: PMC10951430 DOI: 10.1038/s41598-024-56705-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 03/09/2024] [Indexed: 03/21/2024]  Open
40
Cackett G, Sýkora M, Portugal R, Dulson C, Dixon L, Werner F. Transcription termination and readthrough in African swine fever virus. Front Immunol 2024;15:1350267. [PMID: 38545109 PMCID: PMC10965686 DOI: 10.3389/fimmu.2024.1350267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/30/2024] [Indexed: 04/13/2024]  Open
41
Kovaka S, Hook PW, Jenike KM, Shivakumar V, Morina LB, Razaghi R, Timp W, Schatz MC. Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.05.583511. [PMID: 38496646 PMCID: PMC10942365 DOI: 10.1101/2024.03.05.583511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
42
Beletskiy A, Zolotar A, Fortygina P, Chesnokova E, Uroshlev L, Balaban P, Kolosov P. Downregulation of Ribosomal Protein Genes Is Revealed in a Model of Rat Hippocampal Neuronal Culture Activation with GABA(A)R/GlyRa2 Antagonist Picrotoxin. Cells 2024;13:383. [PMID: 38474347 PMCID: PMC10930765 DOI: 10.3390/cells13050383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024]  Open
43
Zhang Y, Zhao J, Cheng J, Wang X, Wang H, Shao Y, Mao X, He X. Bromine-mediated strategy endows efficient electrochemical oxidation of amine to nitrile. Chem Commun (Camb) 2024;60:2369-2372. [PMID: 38318781 DOI: 10.1039/d3cc05861a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
44
Liharska L, Charney A. Transcriptomics : Approaches to Quantifying Gene Expression and Their Application to Studying the Human Brain. Curr Top Behav Neurosci 2024;68:129-176. [PMID: 38972894 DOI: 10.1007/7854_2024_466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
45
Zong L, Zhu Y, Jiang Y, Xia Y, Liu Q, Wang J, Gao S, Luo B, Yuan Y, Zhou J, Jiang S. An optimized workflow of full-length transcriptome sequencing for accurate fusion transcript identification. RNA Biol 2024;21:122-131. [PMID: 39540613 PMCID: PMC11572239 DOI: 10.1080/15476286.2024.2425527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/23/2024] [Accepted: 10/25/2024] [Indexed: 11/16/2024]  Open
46
Xu R, Prakoso D, Salvador LCM, Rajeev S. Leptospira transcriptome sequencing using long-read technology reveals unannotated transcripts and potential polyadenylation of RNA molecules. Microbiol Spectr 2023;11:e0223423. [PMID: 37861327 PMCID: PMC10715090 DOI: 10.1128/spectrum.02234-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/11/2023] [Indexed: 10/21/2023]  Open
47
Mestre-Tomás J, Liu T, Pardo-Palacios F, Conesa A. SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark. Genome Biol 2023;24:286. [PMID: 38082294 PMCID: PMC10712166 DOI: 10.1186/s13059-023-03127-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023]  Open
48
Wang X, Wei X, van der Zalm MM, Zhang Z, Subramanian N, Demers AM, Walters EG, Hesseling A, Liu C. Quantitation of Circulating Mycobacterium tuberculosis Antigens by Nanopore Biosensing in Children Evaluated for Pulmonary Tuberculosis in South Africa. ACS NANO 2023;17:21093-21104. [PMID: 37643288 PMCID: PMC10668583 DOI: 10.1021/acsnano.3c04420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
49
Teragawa S, Wang L. ConF: A Deep Learning Model Based on BiLSTM, CNN, and Cross Multi-Head Attention Mechanism for Noncoding RNA Family Prediction. Biomolecules 2023;13:1643. [PMID: 38002325 PMCID: PMC10669714 DOI: 10.3390/biom13111643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023]  Open
50
Dong X, Du MRM, Gouil Q, Tian L, Jabbari JS, Bowden R, Baldoni PL, Chen Y, Smyth GK, Amarasinghe SL, Law CW, Ritchie ME. Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures. Nat Methods 2023;20:1810-1821. [PMID: 37783886 DOI: 10.1038/s41592-023-02026-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/25/2023] [Indexed: 10/04/2023]
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