145 related articles for article (PubMed ID: 33361112)
1. Effects of transcriptional noise on estimates of gene and transcript expression in RNA sequencing experiments.
Varabyou A; Salzberg SL; Pertea M
Genome Res; 2021 Feb; 31(2):301-308. PubMed ID: 33361112
[TBL] [Abstract][Full Text] [Related]
2. Finding the active genes in deep RNA-seq gene expression studies.
Hart T; Komori HK; LaMere S; Podshivalova K; Salomon DR
BMC Genomics; 2013 Nov; 14():778. PubMed ID: 24215113
[TBL] [Abstract][Full Text] [Related]
3. ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data.
Rodríguez-Martín B; Palumbo E; Marco-Sola S; Griebel T; Ribeca P; Alonso G; Rastrojo A; Aguado B; Guigó R; Djebali S
BMC Genomics; 2017 Jan; 18(1):7. PubMed ID: 28049418
[TBL] [Abstract][Full Text] [Related]
4. EASTR: Identifying and eliminating systematic alignment errors in multi-exon genes.
Shinder I; Hu R; Ji HJ; Chao KH; Pertea M
Nat Commun; 2023 Nov; 14(1):7223. PubMed ID: 37940654
[TBL] [Abstract][Full Text] [Related]
5. BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq.
Rapazote-Flores P; Bayer M; Milne L; Mayer CD; Fuller J; Guo W; Hedley PE; Morris J; Halpin C; Kam J; McKim SM; Zwirek M; Casao MC; Barakate A; Schreiber M; Stephen G; Zhang R; Brown JWS; Waugh R; Simpson CG
BMC Genomics; 2019 Dec; 20(1):968. PubMed ID: 31829136
[TBL] [Abstract][Full Text] [Related]
6. RNA sequencing read depth requirement for optimal transcriptome coverage in Hevea brasiliensis.
Chow KS; Ghazali AK; Hoh CC; Mohd-Zainuddin Z
BMC Res Notes; 2014 Feb; 7():69. PubMed ID: 24484543
[TBL] [Abstract][Full Text] [Related]
7. Exome RNA sequencing reveals rare and novel alternative transcripts.
Halvardson J; Zaghlool A; Feuk L
Nucleic Acids Res; 2013 Jan; 41(1):e6. PubMed ID: 22941640
[TBL] [Abstract][Full Text] [Related]
8. Leveraging transcript quantification for fast computation of alternative splicing profiles.
Alamancos GP; Pagès A; Trincado JL; Bellora N; Eyras E
RNA; 2015 Sep; 21(9):1521-31. PubMed ID: 26179515
[TBL] [Abstract][Full Text] [Related]
9. AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana.
Zhang R; Calixto CP; Tzioutziou NA; James AB; Simpson CG; Guo W; Marquez Y; Kalyna M; Patro R; Eyras E; Barta A; Nimmo HG; Brown JW
New Phytol; 2015 Oct; 208(1):96-101. PubMed ID: 26111100
[TBL] [Abstract][Full Text] [Related]
10. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.
Pertea M; Kim D; Pertea GM; Leek JT; Salzberg SL
Nat Protoc; 2016 Sep; 11(9):1650-67. PubMed ID: 27560171
[TBL] [Abstract][Full Text] [Related]
11. A comparative study of RNA-seq analysis strategies.
Jänes J; Hu F; Lewin A; Turro E
Brief Bioinform; 2015 Nov; 16(6):932-40. PubMed ID: 25788326
[TBL] [Abstract][Full Text] [Related]
12. Event Analysis: Using Transcript Events To Improve Estimates of Abundance in RNA-seq Data.
Newman JRB; Concannon P; Tardaguila M; Conesa A; McIntyre LM
G3 (Bethesda); 2018 Aug; 8(9):2923-2940. PubMed ID: 30021829
[TBL] [Abstract][Full Text] [Related]
13. RNA-seq Data: Challenges in and Recommendations for Experimental Design and Analysis.
Williams AG; Thomas S; Wyman SK; Holloway AK
Curr Protoc Hum Genet; 2014 Oct; 83():11.13.1-20. PubMed ID: 25271838
[TBL] [Abstract][Full Text] [Related]
14. Lack of evidence for increased transcriptional noise in aged tissues.
Ibañez-Solé O; Ascensión AM; Araúzo-Bravo MJ; Izeta A
Elife; 2022 Dec; 11():. PubMed ID: 36576247
[TBL] [Abstract][Full Text] [Related]
15. FDM: a graph-based statistical method to detect differential transcription using RNA-seq data.
Singh D; Orellana CF; Hu Y; Jones CD; Liu Y; Chiang DY; Liu J; Prins JF
Bioinformatics; 2011 Oct; 27(19):2633-40. PubMed ID: 21824971
[TBL] [Abstract][Full Text] [Related]
16. A Conceptual Framework for Abundance Estimation of Genomic Targets in the Presence of Ambiguous Short Sequencing Reads.
Górczak K; Claesen J; Burzykowski T
J Comput Biol; 2020 Aug; 27(8):1232-1247. PubMed ID: 31895597
[No Abstract] [Full Text] [Related]
17. Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs. log-ratio transformation-based methods.
Quinn TP; Crowley TM; Richardson MF
BMC Bioinformatics; 2018 Jul; 19(1):274. PubMed ID: 30021534
[TBL] [Abstract][Full Text] [Related]
18. Merging short and stranded long reads improves transcript assembly.
Kainth AS; Haddad GA; Hall JM; Ruthenburg AJ
PLoS Comput Biol; 2023 Oct; 19(10):e1011576. PubMed ID: 37883581
[TBL] [Abstract][Full Text] [Related]
19. Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens.
Liao W; Jordaan G; Nham P; Phan RT; Pelegrini M; Sharma S
BMC Cancer; 2015 Oct; 15():714. PubMed ID: 26474785
[TBL] [Abstract][Full Text] [Related]
20. A novel method to prioritize RNAseq data for post-hoc analysis based on absolute changes in transcript abundance.
McNutt P; Gut I; Hubbard K; Beske P
Stat Appl Genet Mol Biol; 2015 Jun; 14(3):227-41. PubMed ID: 25781714
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
