[1]

Sahraeian SME, Mohiyuddin M, Sebra R, Tilgner H, Afshar PT, et al. 2017. Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis. Nature Communications 8:59

doi: 10.1038/s41467-017-00050-4
[2]

Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, et al. 2016. A survey of best practices for RNA-seq data analysis. Genome Biology 17:13

doi: 10.1186/s13059-016-0881-8
[3]

Hong M, Tao S, Zhang L, Diao LT, Huang X, et al. 2020. RNA sequencing: new technologies and applications in cancer research. Journal of Hematology & Oncology 13:166

doi: 10.1186/s13045-020-01005-x
[4]

Gondane A, Itkonen HM. 2023. Revealing the history and mystery of RNA-seq. Current Issues in Molecular Biology 45:1860−1874

doi: 10.3390/cimb45030120
[5]

Stark R, Grzelak M, Hadfield J. 2019. RNA sequencing: the teenage years. Nature Reviews Genetics 20:631−656

doi: 10.1038/s41576-019-0150-2
[6]

Pust MM, Mohamed AMT, Stražar M, Arias-Rojas A, Cunningham-Oakes E, et al. 2026. Antisense transcription reveals disease-associated adaptations in the human gut microbiome. Nature Microbiology 11:2464–2477

doi: 10.1038/s41564-026-02442-z
[7]

Chen CH, Pan CY, Lin WC. 2019. Overlapping protein-coding genes in human genome and their coincidental expression in tissues. Scientific Reports 9:13377

doi: 10.1038/s41598-019-49802-w
[8]

Zhou T, Hong Y, Li P, Liu X, Zhang J, et al. 2026. Modtector: ultra-fast modification signal mining on mapped sequencing reads. Bioinformatics 42:btag627

doi: 10.1093/bioinformatics/btag627
[9]

Liao Y, Smyth GK, Shi W. 2014. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30:923−930

doi: 10.1093/bioinformatics/btt656
[10]

Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, et al. 2013. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Protocols 8:1494−1512

doi: 10.1038/nprot.2013.084
[11]

Signal B, Kahlke T. 2022. How_are_we_stranded_here: quick determination of RNA-Seq strandedness. BMC Bioinformatics 23:49

doi: 10.1186/s12859-022-04572-7
[12]

Wang L, Wang S, Li W. 2012. RSeQC: quality control of RNA-seq experiments. Bioinformatics 28:2184−2185

doi: 10.1093/bioinformatics/bts356
[13]

Neph S, Kuehn MS, Reynolds AP, Haugen E, Thurman RE, et al. 2012. BEDOPS: high-performance genomic feature operations. Bioinformatics 28:1919−1920

doi: 10.1093/bioinformatics/bts277
[14]

Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, et al. 2011. Integrative genomics viewer. Nature Biotechnology 29:24−26

doi: 10.1038/nbt.1754
[15]

Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods 9:357−359

doi: 10.1038/nmeth.1923
[16]

Shi W, Wang L, Zhou N, Zhang M, Hao Y, et al. 2026. Nanopore sequencing and multiomics reveal predictable non-coding RNA activation in DNA methylation deficient Arabidopsis thaliana. Communications Biology 9:175

doi: 10.1038/s42003-025-09454-1
[17]

Naphade S, Bhatnagar R, Hanson-Smith V, Choi I, Zhang A. 2022. Systematic comparative analysis of strand-specific RNA-seq library preparation methods for low input samples. Scientific Reports 12:1789

doi: 10.1038/s41598-021-04583-z
[18]

Sigurgeirsson B, Emanuelsson O, Lundeberg J. 2014. Analysis of stranded information using an automated procedure for strand specific RNA sequencing. BMC Genomics 15:631

doi: 10.1186/1471-2164-15-631
[19]

Kopylova E, Noé L, Touzet H. 2012. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics 28:3211−3217

doi: 10.1093/bioinformatics/bts611
[20]

Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754−1760

doi: 10.1093/bioinformatics/btp324
[21]

Shen W, Lees JA, Iqbal Z. 2026. Efficient sequence alignment against millions of prokaryotic genomes with LexicMap. Nature Biotechnology 44:1383−1390

doi: 10.1038/s41587-025-02812-8
[22]

Spitale RC, Flynn RA, Zhang QC, Crisalli P, Lee B, et al. 2015. Structural imprints in vivo decode RNA regulatory mechanisms. Nature 519:486−490

doi: 10.1038/nature14263
[23]

Flynn RA, Zhang QC, Spitale RC, Lee B, Mumbach MR, et al. 2016. Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE. Nature Protocols 11:273−290

doi: 10.1038/nprot.2016.011