S
Shanika L. Amarasinghe
Researcher at Walter and Eliza Hall Institute of Medical Research
Publications - 13
Citations - 1334
Shanika L. Amarasinghe is an academic researcher from Walter and Eliza Hall Institute of Medical Research. The author has contributed to research in topics: Biology & Arabidopsis thaliana. The author has an hindex of 3, co-authored 9 publications receiving 510 citations. Previous affiliations of Shanika L. Amarasinghe include University of Colombo & University of Melbourne.
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Journal ArticleDOI
Opportunities and challenges in long-read sequencing data analysis.
Shanika L. Amarasinghe,Shanika L. Amarasinghe,Shian Su,Shian Su,Xueyi Dong,Xueyi Dong,Luke Zappia,Matthew E. Ritchie,Matthew E. Ritchie,Quentin Gouil,Quentin Gouil +10 more
TL;DR: The current landscape of available tools is reviewed, the principles of error correction, base modification detection, and long-read transcriptomics analysis are focused on, and the challenges that remain are highlighted.
Posted ContentDOI
Comprehensive characterization of single cell full-length isoforms in human and mouse with long-read sequencing
Luyi Tian,Luyi Tian,Jafar S. Jabbari,Rachel Thijssen,Rachel Thijssen,Quentin Gouil,Quentin Gouil,Shanika L. Amarasinghe,Shanika L. Amarasinghe,Hasaru Kariyawasam,Shian Su,Shian Su,Xueyi Dong,Xueyi Dong,Charity W. Law,Charity W. Law,Alexis Lucattini,Jin D. Chung,Timur Naim,Audrey S. M. Chan,Chi Hai Ly,Chi Hai Ly,Gordon S. Lynch,James G. Ryall,Casey J. A. Anttila,Hongke Peng,Hongke Peng,Mary Ann Anderson,Mary Ann Anderson,Mary Ann Anderson,Andrew W. Roberts,David C.S. Huang,David C.S. Huang,Michael B. Clark,Matthew E. Ritchie,Matthew E. Ritchie +35 more
TL;DR: This work performed the first comprehensive characterization of the full-length isoform landscape in single cells of different types and species and identified thousands of unannotated isoforms, revealing previously unseen isoform complexity and providing a better framework for multi-omics data integration.
Journal ArticleDOI
Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing.
Luyi Tian,Luyi Tian,Jafar S. Jabbari,Rachel Thijssen,Rachel Thijssen,Quentin Gouil,Quentin Gouil,Shanika L. Amarasinghe,Shanika L. Amarasinghe,Oliver Voogd,Hasaru Kariyawasam,Mei R. M. Du,Jakob Schuster,Changqing Wang,Shian Su,Shian Su,Xueyi Dong,Xueyi Dong,Charity W. Law,Charity W. Law,Alexis Lucattini,Yair David Joseph Prawer,Coralina Collar-Fernández,Jin D. Chung,Timur Naim,Audrey S. M. Chan,Chi Hai Ly,Chi Hai Ly,Gordon S. Lynch,James G. Ryall,Casey J. A. Anttila,Hongke Peng,Hongke Peng,Mary Ann Anderson,Mary Ann Anderson,Mary Ann Anderson,Christoffer Flensburg,Christoffer Flensburg,Ian J. Majewski,Ian J. Majewski,Andrew W. Roberts,David C.S. Huang,David C.S. Huang,Michael B. Clark,Matthew E. Ritchie,Matthew E. Ritchie +45 more
TL;DR: A modified Chromium 10x droplet-based protocol that subsamples cells for both short-read and long-read (nanopore) sequencing together with a new computational pipeline (FLAMES) is developed to enable isoform discovery, splicing analysis, and mutation detection in single cells as mentioned in this paper.
Journal ArticleDOI
long-read-tools.org: an interactive catalogue of analysis methods for long-read sequencing data.
TL;DR: LongSeq2Seq as discussed by the authors is an open-source database of long-read data analysis tools, including base calling, de novo assembly, quality checking/filtering, and isoform detection.
Journal ArticleDOI
The evolutionary origin of CIPK16: A gene involved in enhanced salt tolerance.
TL;DR: It is found that Arabidopsis thaliana CIPK16 contains a core Brassicales specific indel and a putative nuclear localisation signal, which are synapomorphic characters of CIPk16 genes, and a model is presented that proposes the evolution of C IPK16, 5 and 25 clade.