Zobrazeno 1 - 10
of 89
pro vyhledávání: '"Shian Su"'
Autor:
Yue You, Luyi Tian, Shian Su, Xueyi Dong, Jafar S. Jabbari, Peter F. Hickey, Matthew E. Ritchie
Publikováno v:
Genome Biology, Vol 22, Iss 1, Pp 1-32 (2021)
Abstract Background Single-cell RNA-sequencing (scRNA-seq) technologies and associated analysis methods have rapidly developed in recent years. This includes preprocessing methods, which assign sequencing reads to genes to create count matrices for d
Externí odkaz:
https://doaj.org/article/52b16953cfe04fc5a8828e3325d5735b
Autor:
Luyi Tian, Jafar S. Jabbari, Rachel Thijssen, Quentin Gouil, Shanika L. Amarasinghe, Oliver Voogd, Hasaru Kariyawasam, Mei R. M. Du, Jakob Schuster, Changqing Wang, Shian Su, Xueyi Dong, Charity W. Law, Alexis Lucattini, Yair David Joseph Prawer, Coralina Collar-Fernández, Jin D. Chung, Timur Naim, Audrey Chan, Chi Hai Ly, Gordon S. Lynch, James G. Ryall, Casey J. A. Anttila, Hongke Peng, Mary Ann Anderson, Christoffer Flensburg, Ian Majewski, Andrew W. Roberts, David C. S. Huang, Michael B. Clark, Matthew E. Ritchie
Publikováno v:
Genome Biology, Vol 22, Iss 1, Pp 1-24 (2021)
Abstract 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
Externí odkaz:
https://doaj.org/article/b1aa5d4188e746cca4e60723f7229ae1
Autor:
Kevin X. Lau, Elizabeth A. Mason, Joshua Kie, David P. De Souza, Joachim Kloehn, Dedreia Tull, Malcolm J. McConville, Andrew Keniry, Tamara Beck, Marnie E. Blewitt, Matthew E. Ritchie, Shalin H. Naik, Daniela Zalcenstein, Othmar Korn, Shian Su, Irene Gallego Romero, Catrina Spruce, Christopher L. Baker, Tracy C. McGarr, Christine A. Wells, Martin F. Pera
Publikováno v:
Nature Communications, Vol 11, Iss 1, Pp 1-18 (2020)
Human pluripotent cells (hPSCs) in standard culture are similar to mouse epiblast cells, but heterogeneity within hPSC cultures complicates comparisons. Here the authors show that a subpopulation of hPSCs enriched for self-renewal capacity have disti
Externí odkaz:
https://doaj.org/article/1f87c566710a45a38bb6a81fc0b27bcc
Publikováno v:
Genome Biology, Vol 21, Iss 1, Pp 1-16 (2020)
Abstract Long-read technologies are overcoming early limitations in accuracy and throughput, broadening their application domains in genomics. Dedicated analysis tools that take into account the characteristics of long-read data are thus required, bu
Externí odkaz:
https://doaj.org/article/79ac667da73342cfbc0213536936419d
Publikováno v:
PLoS Computational Biology, Vol 17, Iss 10 (2021)
A key benefit of long-read nanopore sequencing technology is the ability to detect modified DNA bases, such as 5-methylcytosine. The lack of R/Bioconductor tools for the effective visualization of nanopore methylation profiles between samples from di
Externí odkaz:
https://doaj.org/article/5f17621a4ffd4711b2156b5a8f90d7c0
Publikováno v:
F1000Research, Vol 8 (2019)
Motivation: The Bioconductor project, a large collection of open source software for the comprehension of large-scale biological data, continues to grow with new packages added each week, motivating the development of software tools focused on exposi
Externí odkaz:
https://doaj.org/article/5eff8e928bd84e228745476edcddd508
Autor:
Cyril Seillet, Lisa A. Mielke, Daniela B. Amann-Zalcenstein, Shian Su, Jerry Gao, Francisca F. Almeida, Wei Shi, Matthew E. Ritchie, Shalin H. Naik, Nicholas D. Huntington, Sebastian Carotta, Gabrielle T. Belz
Publikováno v:
Cell Reports, Vol 17, Iss 2, Pp 436-447 (2016)
Innate lymphoid cells (ILCs) are enriched at mucosal surfaces, where they provide immune surveillance. All ILC subsets develop from a common progenitor that gives rise to pre-committed progenitors for each of the ILC lineages. Currently, the temporal
Externí odkaz:
https://doaj.org/article/47142904a3f54a61bc57324661408c07
Autor:
Charity W. Law, Monther Alhamdoosh, Shian Su, Xueyi Dong, Luyi Tian, Gordon K. Smyth, Matthew E. Ritchie
Publikováno v:
F1000Research, Vol 5 (2018)
The ability to easily and efficiently analyse RNA-sequencing data is a key strength of the Bioconductor project. Starting with counts summarised at the gene-level, a typical analysis involves pre-processing, exploratory data analysis, differential ex
Externí odkaz:
https://doaj.org/article/3f1c5ac2a9a54dca83f76f26c352fd04
Autor:
Luyi Tian, Shian Su, Xueyi Dong, Daniela Amann-Zalcenstein, Christine Biben, Azadeh Seidi, Douglas J Hilton, Shalin H Naik, Matthew E Ritchie
Publikováno v:
PLoS Computational Biology, Vol 14, Iss 8, p e1006361 (2018)
Single-cell RNA sequencing (scRNA-seq) technology allows researchers to profile the transcriptomes of thousands of cells simultaneously. Protocols that incorporate both designed and random barcodes have greatly increased the throughput of scRNA-seq,
Externí odkaz:
https://doaj.org/article/816479d2bf604f45a983e4b4c954ccad
Publikováno v:
F1000Research, Vol 5 (2016)
The ability to easily and efficiently analyse RNA-sequencing data is a key strength of the Bioconductor project. Starting with counts summarised at the gene-level, a typical analysis involves pre-processing, exploratory data analysis, differential ex
Externí odkaz:
https://doaj.org/article/99978fb5eb7a448a811084730cc521b9