Coverage-dependent bias creates the appearance of binary splicing in single cells

Autor: Carlos F Buen Abad Najar, Nir Yosef, Liana F Lareau

Publikováno v: eLife, Vol 9 (2020)

Single-cell RNA sequencing provides powerful insight into the factors that determine each cell’s unique identity. Previous studies led to the surprising observation that alternative splicing among single cells is highly variable and follows a bimod

Externí odkaz: https://doaj.org/article/a28e55f95a8249a8af95b8de7a8c349d

Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila.

Autor: Kasper Daniel Hansen, Liana F Lareau, Marco Blanchette, Richard E Green, Qi Meng, Jan Rehwinkel, Fabian L Gallusser, Elisa Izaurralde, Donald C Rio, Sandrine Dudoit, Steven E Brenner

Publikováno v: PLoS Genetics, Vol 5, Iss 6, p e1000525 (2009)

Alternative mRNA splicing adds a layer of regulation to the expression of thousands of genes in Drosophila melanogaster. Not all alternative splicing results in functional protein; it can also yield mRNA isoforms with premature stop codons that are d

Externí odkaz: https://doaj.org/article/e785901ff7654c09996800ee0afee709

choros: correction of sequence-based biases for accurate quantification of ribosome profiling data

Autor: Amanda Mok, Robert Tunney, Gonzalo Benegas, Edward W. J. Wallace, Liana F. Lareau

Publikováno v: bioRxiv

Ribosome profiling quantifies translation genome-wide by sequencing ribosome-protected fragments, or footprints. Its single-codon resolution allows identification of translation regulation, such as ribosome stalls or pauses, on individual genes. Howe

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9c621899cd02eb7d777f1898f7b14b8a
https://doi.org/10.1101/2023.02.21.529452

riboviz 2:A flexible and robust ribosome profiling data analysis and visualization workflow

Autor: Alexander L Cope, Felicity Anderson, John Favate, Michael Jackson, Amanda Mok, Anna Kurowska, Junchen Liu, Emma MacKenzie, Vikram Shivakumar, Peter Tilton, Sophie M Winterbourne, Siyin Xue, Kostas Kavoussanakis, Liana F Lareau, Premal Shah, Edward W J Wallace

Publikováno v: Cope, A L, Anderson, F, Favate, J, Jackson, M, Mok, A, Kurowska, A, Liu, J, MacKenzie, E, Shivakumar, V, Tilton, P, Winterbourne, S, Xue, S, Kavoussanakis, K, Lareau, L F, Shah, P & Wallace, E W J 2022, ' riboviz 2 : A flexible and robust ribosome profiling data analysis and visualization workflow ', Bioinformatics, vol. 38, no. 8, btac093, pp. 2358-2360 . https://doi.org/10.1093/bioinformatics/btac093

Motivation Ribosome profiling, or Ribo-seq, is the state-of-the-art method for quantifying protein synthesis in living cells. Computational analysis of Ribo-seq data remains challenging due to the complexity of the procedure, as well as variations in

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::12ea581844df67dc0b4f6dabcf7a9a48
https://hdl.handle.net/20.500.11820/3eb45cc9-3a67-4b75-9ceb-2f82ef31ddf0

Identifying cell-state associated alternative splicing events and their co-regulation

Autor: Nir Yosef, Prakruthi Burra, Liana F. Lareau, Carlos F. Buen Abad Najar

Alternative splicing shapes the transcriptome and contributes to each cell’s unique identity, but single-cell RNA sequencing has struggled to capture the impact of alternative splicing. We previously showed that low recovery of mRNAs from single ce

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::801ddc986ddc70b0160bbe1f1a76e7ce
https://doi.org/10.1101/2021.07.23.453605