Wang Q, Mao Y
Adv Biotechnol (Singap). 2025; 1(4):6.
PMID: 39883220
PMC: 11727582.
DOI: 10.1007/s44307-023-00006-4.
Juzenas S, Goda K, Kiseliovas V, Zvirblyte J, Quintinal-Villalonga A, Siurkus J
Nucleic Acids Res. 2025; 53(2).
PMID: 39797728
PMC: 11724362.
DOI: 10.1093/nar/gkae1312.
Lyu J, Chen C
Int J Mol Sci. 2024; 25(23).
PMID: 39684556
PMC: 11640990.
DOI: 10.3390/ijms252312845.
Calvo-Roitberg E, Daniels R, Pai A
Genome Res. 2024; 34(11):1719-1734.
PMID: 39567236
PMC: 11610588.
DOI: 10.1101/gr.279559.124.
Feng F, Yuen R, Wang Y, Hua A, Kepler T, Wetzler L
iScience. 2024; 27(1):108749.
PMID: 38269092
PMC: 10805652.
DOI: 10.1016/j.isci.2023.108749.
High-throughput mapping of RNA solvent accessibility at the single-nucleotide resolution by RtcB ligation between a fixed 5'-OH-end linker and unique 3'-P-end fragments from hydroxyl radical cleavage.
Solayman M, Litfin T, Zhou Y, Zhan J
RNA Biol. 2022; 19(1):1179-1189.
PMID: 36369947
PMC: 9662193.
DOI: 10.1080/15476286.2022.2145098.
SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells.
Moody J, Kouno T, Chang J, Ando Y, Carninci P, Shin J
Bioinformatics. 2022; 38(22):5126-5128.
PMID: 36173306
PMC: 9665856.
DOI: 10.1093/bioinformatics/btac644.
Bookend: precise transcript reconstruction with end-guided assembly.
Schon M, Lutzmayer S, Hofmann F, Nodine M
Genome Biol. 2022; 23(1):143.
PMID: 35768836
PMC: 9245221.
DOI: 10.1186/s13059-022-02700-3.
Fast and highly sensitive full-length single-cell RNA sequencing using FLASH-seq.
Hahaut V, Pavlinic D, Carbone W, Schuierer S, Balmer P, Quinodoz M
Nat Biotechnol. 2022; 40(10):1447-1451.
PMID: 35637419
PMC: 9546769.
DOI: 10.1038/s41587-022-01312-3.
Reply to Grigoriev et al., "Sequences of SARS-CoV-2 'Hybrids' with the Human Genome: Signs of Non-coding RNA?".
Yan B, Chakravorty S, Mirabelli C, Wang L, Trujillo-Ochoa J, Chauss D
J Virol. 2021; 96(2):e0169021.
PMID: 34705544
PMC: 8791293.
DOI: 10.1128/JVI.01690-21.
Global approaches for profiling transcription initiation.
Policastro R, Zentner G
Cell Rep Methods. 2021; 1(5).
PMID: 34632443
PMC: 8496859.
DOI: 10.1016/j.crmeth.2021.100081.
Single-cell RNA cap and tail sequencing (scRCAT-seq) reveals subtype-specific isoforms differing in transcript demarcation.
Hu Y, Zhong J, Xiao Y, Xing Z, Sheu K, Fan S
Nat Commun. 2020; 11(1):5148.
PMID: 33051455
PMC: 7555861.
DOI: 10.1038/s41467-020-18976-7.
FB5P-seq: FACS-Based 5-Prime End Single-Cell RNA-seq for Integrative Analysis of Transcriptome and Antigen Receptor Repertoire in B and T Cells.
Attaf N, Cervera-Marzal I, Dong C, Gil L, Renand A, Spinelli L
Front Immunol. 2020; 11:216.
PMID: 32194545
PMC: 7062913.
DOI: 10.3389/fimmu.2020.00216.
Machine-driven parameter screen of biochemical reactions.
Poulain S, Arnaud O, Kato S, Chen I, Ishida H, Carninci P
Nucleic Acids Res. 2020; 48(7):e37.
PMID: 32025730
PMC: 7144897.
DOI: 10.1093/nar/gkaa079.
Comprehensive transcriptome analysis of cochlear spiral ganglion neurons at multiple ages.
Li C, Li X, Bi Z, Sugino K, Wang G, Zhu T
Elife. 2020; 9.
PMID: 31913118
PMC: 7299348.
DOI: 10.7554/eLife.50491.
Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods.
Wright C, Rajpurohit A, Burke E, Williams C, Collado-Torres L, Kimos M
BMC Genomics. 2019; 20(1):513.
PMID: 31226924
PMC: 6588940.
DOI: 10.1186/s12864-019-5870-3.
BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing.
Alpern D, Gardeux V, Russeil J, Mangeat B, Meireles-Filho A, Breysse R
Genome Biol. 2019; 20(1):71.
PMID: 30999927
PMC: 6474054.
DOI: 10.1186/s13059-019-1671-x.
C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution.
Kouno T, Moody J, Kwon A, Shibayama Y, Kato S, Huang Y
Nat Commun. 2019; 10(1):360.
PMID: 30664627
PMC: 6341120.
DOI: 10.1038/s41467-018-08126-5.
SMARTcleaner: identify and clean off-target signals in SMART ChIP-seq analysis.
Zhao D, Zheng D
BMC Bioinformatics. 2018; 19(1):544.
PMID: 30587107
PMC: 6307164.
DOI: 10.1186/s12859-018-2577-4.
SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA.
Cvetesic N, Leitch H, Borkowska M, Muller F, Carninci P, Hajkova P
Genome Res. 2018; 28(12):1943-1956.
PMID: 30404778
PMC: 6280763.
DOI: 10.1101/gr.235937.118.