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Select item 98585031.

ESPRESSO: Robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data

Yuan Gao, Feng Wang, Robert Wang, Eric Kutschera, Yang Xu, Stephan Xie, Yuanyuan Wang, Kathryn E. Kadash-Edmondson, Lan Lin, Yi Xing

Sci Adv. 2023 Jan; 9(3): eabq5072. Published online 2023 Jan 20. doi: 10.1126/sciadv.abq5072

PMCID:: PMC9858503

Article PDF–2.0M

Select item 63377392.

A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs

Charlotte Soneson, Michael I Love, Rob Patro, Shobbir Hussain, Dheeraj Malhotra, Mark D Robinson

Life Sci Alliance. 2019 Feb; 2(1): e201800175. Published online 2019 Jan 17. doi: 10.26508/lsa.201800175

PMCID:: PMC6337739

Article PDF–2.6M

Select item 106296673.

Merging short and stranded long reads improves transcript assembly

Amoldeep S. Kainth, Gabriela A. Haddad, Johnathon M. Hall, Alexander J. Ruthenburg

PLoS Comput Biol. 2023 Oct; 19(10): e1011576. Published online 2023 Oct 26. doi: 10.1371/journal.pcbi.1011576

PMCID:: PMC10629667

Article PDF–3.4M

Select item 104020944.

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Francisco J. Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark Diekhans, Sílvia Carbonell-Sala, Brian Williams, Jane E. Loveland, Maite De María, Matthew S. Adams, Gabriela Balderrama-Gutierrez, Amit K. Behera, Jose M. Gonzalez, Toby Hunt, Julien Lagarde, Cindy E. Liang, Haoran Li, Marcus Jerryd Meade, David A. Moraga Amador, Andrey D. Prjibelski, Inanc Birol, Hamed Bostan, Ashley M. Brooks, Muhammed Hasan Çelik, Ying Chen, Mei R,M. Du, Colette Felton, Jonathan Göke, Saber Hafezqorani, Ralf Herwig, Hideya Kawaji, Joseph Lee, Jian Liang Li, Matthias Lienhard, Alla Mikheenko, Dennis Mulligan, Ka Ming Nip, Mihaela Pertea, Matthew E. Ritchie, Andre D. Sim, Alison D. Tang, Yuk Kei Wan, Changqing Wang, Brandon Y. Wong, Chen Yang, If Barnes, Andrew Berry, Salvador Capella, Namrita Dhillon, Jose M. Fernandez-Gonzalez, Luis Ferrández-Peral, Natàlia Garcia-Reyero, Stefan Goetz, Carles Hernández-Ferrer, Liudmyla Kondratova, Tianyuan Liu, Alessandra Martinez-Martin, Carlos Menor, Jorge Mestre-Tomás, Jonathan M. Mudge, Nedka G. Panayotova, Alejandro Paniagua, Dmitry Repchevsky, Eric Rouchka, Brandon Saint-John, Enrique Sapena, Leon Sheynkman, Melissa Laird Smith, Marie-Marthe Suner, Hazuki Takahashi, Ingrid Ashley. Youngworth, Piero Carninci, Nancy D. Denslow, Roderic Guigó, Margaret E. Hunter, Hagen U. Tilgner, Barbara J. Wold, Christopher Vollmers, Adam Frankish, Kin Fai Au, Gloria M. Sheynkman, Ali Mortazavi, Ana Conesa, Angela N. Brooks

Version 1. bioRxiv. Preprint. 2023 Jul 27. doi: 10.1101/2023.07.25.550582

PMCID:: PMC10402094

Article PDF–25M

Select item 104489445.

Context-Aware Transcript Quantification from Long Read RNA-Seq data with Bambu

Ying Chen, Andre Sim, Yuk Kei Wan, Keith Yeo, Joseph Jing Xian Lee, Min Hao Ling, Michael I. Love, Jonathan Göke

Nat Methods. Author manuscript; available in PMC 2024 Feb 1.

Published in final edited form as: Nat Methods. 2023 Aug; 20(8): 1187–1195. Published online 2023 Jun 12. doi: 10.1038/s41592-023-01908-w

PMCID:: PMC10448944

Article PDF–1.5M

Select item 98926556.

satuRn: Scalable analysis of differential transcript usage for bulk and single-cell RNA-sequencing applications

Jeroen Gilis, Kristoffer Vitting-Seerup, Koen Van den Berge, Lieven Clement

Version 2. F1000Res. 2021; 10: 374. Published online 2022 Aug 8. doi: 10.12688/f1000research.51749.2

PMCID:: PMC9892655

Article PDF–5.1M

Select item 110399837.

The repertoire and structure of adhesion GPCR transcript variants assembled from publicly available deep-sequenced human samples

Christina Katharina Kuhn, Udo Stenzel, Sandra Berndt, Ines Liebscher, Torsten Schöneberg, Susanne Horn

Nucleic Acids Res. 2024 Apr 24; 52(7): 3823–3836. Published online 2024 Feb 29. doi: 10.1093/nar/gkae145

PMCID:: PMC11039983

Article PDF–1.6M

Select item 97056748.

Possible Contribution of Alternative Transcript Isoforms in Mature Biofilm Growth Phase of Candida glabrata

Khem Raj, Praveen Rishi, Geeta Shukla, Shivaprakash M. Rudramurhty, Dattatray S. Mongad, Amrita Kaur

Indian J Microbiol. 2022 Dec; 62(4): 583–601. Published online 2022 Aug 27. doi: 10.1007/s12088-022-01036-7

PMCID:: PMC9705674

Article PDF–6.7M

Select item 61789129.

Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification

Michael I. Love, Charlotte Soneson, Rob Patro

Version 3. F1000Res. 2018; 7: 952. Published online 2018 Oct 1. doi: 10.12688/f1000research.15398.3

PMCID:: PMC6178912

Article PDF–5.9M

Select item 693826610.

Transcript degradation and codon usage regulate gene expression in a lytic phage

Benjamin R Jack, Daniel R Boutz, Matthew L Paff, Bartram L Smith, Claus O Wilke

Virus Evol. 2019 Jul; 5(2): vez055. Published online 2019 Dec 31. doi: 10.1093/ve/vez055

PMCID:: PMC6938266

Article PDF–1.0M

Select item 1024558311.

The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity

Fairlie Reese, Brian Williams, Gabriela Balderrama-Gutierrez, Dana Wyman, Muhammed Hasan Çelik, Elisabeth Rebboah, Narges Rezaie, Diane Trout, Milad Razavi-Mohseni, Yunzhe Jiang, Beatrice Borsari, Samuel Morabito, Heidi Yahan Liang, Cassandra J. McGill, Sorena Rahmanian, Jasmine Sakr, Shan Jiang, Weihua Zeng, Klebea Carvalho, Annika K. Weimer, Louise A. Dionne, Ariel McShane, Karan Bedi, Shaimae I. Elhajjajy, Sean Upchurch, Jennifer Jou, Ingrid Youngworth, Idan Gabdank, Paul Sud, Otto Jolanki, J. Seth Strattan, Meenakshi S. Kagda, Michael P. Snyder, Ben C. Hitz, Jill E. Moore, Zhiping Weng, David Bennett, Laura Reinholdt, Mats Ljungman, Michael A. Beer, Mark B. Gerstein, Lior Pachter, Roderic Guigó, Barbara J. Wold, Ali Mortazavi

Version 1. bioRxiv. Preprint. 2023 May 16. doi: 10.1101/2023.05.15.540865

PMCID:: PMC10245583

Article PDF–15M

Select item 759699912.

Illuminating the dark side of the human transcriptome with long read transcript sequencing

Richard I. Kuo, Yuanyuan Cheng, Runxuan Zhang, John W. S. Brown, Jacqueline Smith, Alan L. Archibald, David W. Burt

BMC Genomics. 2020; 21: 751. Published online 2020 Oct 30. doi: 10.1186/s12864-020-07123-7

PMCID:: PMC7596999

Article PDF–2.1M

Select item 895174613.

Perplexity: evaluating transcript abundance estimation in the absence of ground truth

Jason Fan, Skylar Chan, Rob Patro

Algorithms Mol Biol. 2022; 17: 6. Published online 2022 Mar 25. doi: 10.1186/s13015-022-00214-y

PMCID:: PMC8951746

Article PDF–7.7M

Select item 964969014.

Systematic characterization of cancer transcriptome at transcript resolution

Wei Hu, Yangjun Wu, Qili Shi, Jingni Wu, Deping Kong, Xiaohua Wu, Xianghuo He, Teng Liu, Shengli Li

Nat Commun. 2022; 13: 6803. Published online 2022 Nov 10. doi: 10.1038/s41467-022-34568-z

PMCID:: PMC9649690

Article PDF–5.1M

Select item 1095446815.

Nucleotide-level distance metrics to quantify alternative splicing implemented in TranD

Adalena Nanni, James Titus-McQuillan, Kinfeosioluwa S Bankole, Francisco Pardo-Palacios, Sarah Signor, Srna Vlaho, Oleksandr Moskalenko, Alison M Morse, Rebekah L Rogers, Ana Conesa, Lauren M McIntyre

Nucleic Acids Res. 2024 Mar 21; 52(5): e28. Published online 2024 Feb 10. doi: 10.1093/nar/gkae056

PMCID:: PMC10954468

Article PDF–2.0M

Select item 954649416.

BaRTv2: a highly resolved barley reference transcriptome for accurate transcript‐specific RNA‐seq quantification

Max Coulter, Juan Carlos Entizne, Wenbin Guo, Micha Bayer, Ronja Wonneberger, Linda Milne, Miriam Schreiber, Allison Haaning, Gary J. Muehlbauer, Nicola McCallum, John Fuller, Craig Simpson, Nils Stein, John W. S. Brown, Robbie Waugh, Runxuan Zhang

Plant J. 2022 Aug; 111(4): 1183–1202. Published online 2022 Jul 19. doi: 10.1111/tpj.15871