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For: Jürges C, Dölken L, Erhard F. Dissecting newly transcribed and old RNA using GRAND-SLAM. Bioinformatics 2019;34:i218-i226. [PMID: 29949974 PMCID: PMC6037110 DOI: 10.1093/bioinformatics/bty256] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]  Open
Number Cited by Other Article(s)
51
Uhlitz F, Bischoff P, Peidli S, Sieber A, Trinks A, Lüthen M, Obermayer B, Blanc E, Ruchiy Y, Sell T, Mamlouk S, Arsie R, Wei T, Klotz‐Noack K, Schwarz RF, Sawitzki B, Kamphues C, Beule D, Landthaler M, Sers C, Horst D, Blüthgen N, Morkel M. Mitogen-activated protein kinase activity drives cell trajectories in colorectal cancer. EMBO Mol Med 2021;13:e14123. [PMID: 34409732 PMCID: PMC8495451 DOI: 10.15252/emmm.202114123] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 07/27/2021] [Accepted: 07/30/2021] [Indexed: 01/07/2023]  Open
52
Furlan M, de Pretis S, Pelizzola M. Dynamics of transcriptional and post-transcriptional regulation. Brief Bioinform 2021;22:bbaa389. [PMID: 33348360 PMCID: PMC8294512 DOI: 10.1093/bib/bbaa389] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/12/2020] [Accepted: 11/27/2020] [Indexed: 02/07/2023]  Open
53
Boileau E, Altmüller J, Naarmann-de Vries IS, Dieterich C. A comparison of metabolic labeling and statistical methods to infer genome-wide dynamics of RNA turnover. Brief Bioinform 2021;22:6315814. [PMID: 34228787 PMCID: PMC8574959 DOI: 10.1093/bib/bbab219] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/18/2021] [Accepted: 05/21/2021] [Indexed: 12/27/2022]  Open
54
Narain A, Bhandare P, Adhikari B, Backes S, Eilers M, Dölken L, Schlosser A, Erhard F, Baluapuri A, Wolf E. Targeted protein degradation reveals a direct role of SPT6 in RNAPII elongation and termination. Mol Cell 2021;81:3110-3127.e14. [PMID: 34233157 PMCID: PMC8354102 DOI: 10.1016/j.molcel.2021.06.016] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 04/24/2021] [Accepted: 06/11/2021] [Indexed: 01/22/2023]
55
Rodermund L, Coker H, Oldenkamp R, Wei G, Bowness J, Rajkumar B, Nesterova T, Susano Pinto DM, Schermelleh L, Brockdorff N. Time-resolved structured illumination microscopy reveals key principles of Xist RNA spreading. Science 2021;372:372/6547/eabe7500. [PMID: 34112668 DOI: 10.1126/science.abe7500] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 05/07/2021] [Indexed: 01/23/2023]
56
Finkel Y, Gluck A, Nachshon A, Winkler R, Fisher T, Rozman B, Mizrahi O, Lubelsky Y, Zuckerman B, Slobodin B, Yahalom-Ronen Y, Tamir H, Ulitsky I, Israely T, Paran N, Schwartz M, Stern-Ginossar N. SARS-CoV-2 uses a multipronged strategy to impede host protein synthesis. Nature 2021;594:240-245. [PMID: 33979833 DOI: 10.1038/s41586-021-03610-3] [Citation(s) in RCA: 174] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/04/2021] [Indexed: 02/07/2023]
57
The Zinc Finger Antiviral Protein ZAP Restricts Human Cytomegalovirus and Selectively Binds and Destabilizes Viral UL4/UL5 Transcripts. mBio 2021;12:mBio.02683-20. [PMID: 33947766 PMCID: PMC8263000 DOI: 10.1128/mbio.02683-20] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
58
Goettsch W, Beerenwinkel N, Deng L, Dölken L, Dutilh BE, Erhard F, Kaderali L, von Kleist M, Marquet R, Matthijnssens J, McCallin S, McMahon D, Rattei T, Van Rij RP, Robertson DL, Schwemmle M, Stern-Ginossar N, Marz M. ITN-VIROINF: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics. Viruses 2021;13:v13050766. [PMID: 33925452 PMCID: PMC8145447 DOI: 10.3390/v13050766] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/15/2021] [Accepted: 04/22/2021] [Indexed: 11/16/2022]  Open
59
Meisig J, Dreser N, Kapitza M, Henry M, Rotshteyn T, Rahnenführer J, Hengstler J, Sachinidis A, Waldmann T, Leist M, Blüthgen N. Kinetic modeling of stem cell transcriptome dynamics to identify regulatory modules of normal and disturbed neuroectodermal differentiation. Nucleic Acids Res 2020;48:12577-12592. [PMID: 33245762 PMCID: PMC7736781 DOI: 10.1093/nar/gkaa1089] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 10/21/2020] [Accepted: 10/27/2020] [Indexed: 12/22/2022]  Open
60
Furlan M, Galeota E, Gaudio ND, Dassi E, Caselle M, de Pretis S, Pelizzola M. Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling. Genome Res 2020;30:1492-1507. [PMID: 32978246 PMCID: PMC7605262 DOI: 10.1101/gr.260984.120] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 08/21/2020] [Indexed: 12/13/2022]
61
Qiu Q, Hu P, Qiu X, Govek KW, Cámara PG, Wu H. Massively parallel and time-resolved RNA sequencing in single cells with scNT-seq. Nat Methods 2020;17:991-1001. [PMID: 32868927 PMCID: PMC8103797 DOI: 10.1038/s41592-020-0935-4] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 07/22/2020] [Indexed: 12/31/2022]
62
Erhard F, Dölken L, Schilling B, Schlosser A. Identification of the Cryptic HLA-I Immunopeptidome. Cancer Immunol Res 2020;8:1018-1026. [PMID: 32561536 DOI: 10.1158/2326-6066.cir-19-0886] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/11/2020] [Accepted: 06/10/2020] [Indexed: 11/16/2022]
63
Gene Architecture and Sequence Composition Underpin Selective Dependency of Nuclear Export of Long RNAs on NXF1 and the TREX Complex. Mol Cell 2020;79:251-267.e6. [PMID: 32504555 DOI: 10.1016/j.molcel.2020.05.013] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 03/23/2020] [Accepted: 05/11/2020] [Indexed: 12/14/2022]
64
Wissink EM, Vihervaara A, Tippens ND, Lis JT. Nascent RNA analyses: tracking transcription and its regulation. Nat Rev Genet 2019;20:705-723. [PMID: 31399713 PMCID: PMC6858503 DOI: 10.1038/s41576-019-0159-6] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2019] [Indexed: 12/19/2022]
65
Muthmann N, Hartstock K, Rentmeister A. Chemo-enzymatic treatment of RNA to facilitate analyses. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019;11:e1561. [PMID: 31392842 DOI: 10.1002/wrna.1561] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/17/2019] [Accepted: 07/04/2019] [Indexed: 12/11/2022]
66
On the optimal design of metabolic RNA labeling experiments. PLoS Comput Biol 2019;15:e1007252. [PMID: 31390362 PMCID: PMC6699717 DOI: 10.1371/journal.pcbi.1007252] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 08/19/2019] [Accepted: 07/08/2019] [Indexed: 01/16/2023]  Open
67
Stark R, Grzelak M, Hadfield J. RNA sequencing: the teenage years. Nat Rev Genet 2019;20:631-656. [DOI: 10.1038/s41576-019-0150-2] [Citation(s) in RCA: 1085] [Impact Index Per Article: 180.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2019] [Indexed: 12/12/2022]
68
Hendriks GJ, Jung LA, Larsson AJM, Lidschreiber M, Andersson Forsman O, Lidschreiber K, Cramer P, Sandberg R. NASC-seq monitors RNA synthesis in single cells. Nat Commun 2019;10:3138. [PMID: 31316066 PMCID: PMC6637240 DOI: 10.1038/s41467-019-11028-9] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 06/12/2019] [Indexed: 12/14/2022]  Open
69
scSLAM-seq reveals core features of transcription dynamics in single cells. Nature 2019;571:419-423. [DOI: 10.1038/s41586-019-1369-y] [Citation(s) in RCA: 146] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 06/10/2019] [Indexed: 11/08/2022]
70
Neumann T, Herzog VA, Muhar M, von Haeseler A, Zuber J, Ameres SL, Rescheneder P. Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets. BMC Bioinformatics 2019;20:258. [PMID: 31109287 PMCID: PMC6528199 DOI: 10.1186/s12859-019-2849-7] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 04/25/2019] [Indexed: 11/15/2022]  Open
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