Zobrazeno 1 - 10
of 24
pro vyhledávání: '"Caleb M. Radens"'
Autor:
Jorge Vaquero-Garcia, Joseph K. Aicher, San Jewell, Matthew R. Gazzara, Caleb M. Radens, Anupama Jha, Scott S. Norton, Nicholas F. Lahens, Gregory R. Grant, Yoseph Barash
Publikováno v:
Nature Communications, Vol 14, Iss 1, Pp 1-20 (2023)
Here the authors develop MAJIQ v2 to address challenges in detection, quantification, and visualization of RNA splicing variations from large heterogeneous RNA-Seq datasets. They then apply it to analyze 2,335 samples from 13 brain subregions.
Externí odkaz:
https://doaj.org/article/659b8c90e4764e15b37366776268b331
Publikováno v:
eLife, Vol 11 (2022)
Alternative splicing occurs in the vast majority of human genes, giving rise to distinct mRNA and protein isoforms. We, and others, have previously identified hundreds of genes that change their isoform expression upon T cell activation via alternati
Externí odkaz:
https://doaj.org/article/75407e14fee84819bfd252426750416b
Autor:
Barry Slaff, Caleb M. Radens, Paul Jewell, Anupama Jha, Nicholas F. Lahens, Gregory R. Grant, Andrei Thomas-Tikhonenko, Kristen W. Lynch, Yoseph Barash
Publikováno v:
Nature Communications, Vol 12, Iss 1, Pp 1-9 (2021)
Confounding factors on gene expression analysis can be analyzed by several existing tools. Here the authors develop an algorithm called MOCCASIN to correct the effect of known and unknown confounders on RNA splicing quantification.
Externí odkaz:
https://doaj.org/article/b8ed04d2aafd4e4a8c327a67fed001a0
Autor:
Lauren K Brady, Hejia Wang, Caleb M Radens, Yue Bi, Milan Radovich, Amit Maity, Cristina Ivan, Mircea Ivan, Yoseph Barash, Constantinos Koumenis
Publikováno v:
PLoS Biology, Vol 15, Iss 9, p e2002623 (2017)
Cells adjust to hypoxic stress within the tumor microenvironment by downregulating energy-consuming processes including translation. To delineate mechanisms of cellular adaptation to hypoxia, we performed RNA-Seq of normoxic and hypoxic head and neck
Externí odkaz:
https://doaj.org/article/7d5cefc4d03f454db2cedc98127d6412
Publikováno v:
RNA
Human CD4+ T cells are often subdivided into distinct subtypes, including Th1, Th2, Th17, and Treg cells, that are thought to carry out distinct functions in the body. Typically, these T-cell subpopulations are defined by the expression of distinct g
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::511dd4b220dc549c42fd64683dd02206
https://doi.org/10.1261/rna.075929.120
https://doi.org/10.1261/rna.075929.120
Autor:
Caleb M. Radens, Yoseph Barash, Joseph K. Aicher, Gregory R. Grant, Christopher J Green, Matthew R. Gazzara, Scott Norton, Anupama Jha, Jorge Vaquero-Garcia, Nicholas F. Lahens, Paul Jewell
The ubiquity of RNA-seq has led to many methods that use RNA-seq data to analyze variations in RNA splicing. However, available methods are not well suited for handling heterogeneous and large datasets. Such datasets scale to thousands of samples acr
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::62d590ec49055db5a2707ff0f893bcc3
https://doi.org/10.1101/2021.11.03.467086
https://doi.org/10.1101/2021.11.03.467086
Autor:
Anupama Jha, Caleb M. Radens, Yoseph Barash, Gregory R. Grant, Kristen W. Lynch, Barry Slaff, Nicholas F. Lahens, Paul Jewell, Andrei Thomas-Tikhonenko
Publikováno v:
Nature Communications
Nature Communications, Vol 12, Iss 1, Pp 1-9 (2021)
Nature Communications, Vol 12, Iss 1, Pp 1-9 (2021)
The effects of confounding factors on gene expression analysis have been extensively studied following the introduction of high-throughput microarrays and subsequently RNA sequencing. In contrast, there is a lack of equivalent analysis and tools for
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2e29c8bb7af9e854af7bc28ba3dfe904
https://doi.org/10.1038/s41467-021-23608-9
https://doi.org/10.1038/s41467-021-23608-9
Autor:
Simone Sidoli, Matthew R. Gazzara, Josue Baeza, Kristen W. Lynch, Benjamin A. Garcia, Laura M. Agosto, Caleb M. Radens
Publikováno v:
Genome Res
Alternative pre-mRNA splicing has long been proposed to contribute greatly to proteome complexity. However, the extent to which mature mRNA isoforms are successfully translated into protein remains controversial. Here, we used high-throughput RNA seq
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ab416390193ab26586aa9757a5c4b222
https://doi.org/10.1101/gr.248435.119
https://doi.org/10.1101/gr.248435.119
SummaryDistinct T cell subtypes are typically defined by the expression of distinct gene repertoires. However, there is variability between studies regarding the markers used to define each T cell subtype. Moreover, previous analysis of gene expressi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f0269bc5e803f5729a0078cb41fd1a1e