Results 91 to 100 of about 536,139 (245)

RNA-Seq Data: A Complexity Journey

Computational and Structural Biotechnology Journal, 2014
A paragraph from the highlights of "Transcriptomics: Throwing light on dark matter" by L. Flintoft (Nature Reviews Genetics 11, 455, 2010), says: "Reports over the past few years of extensive transcription throughout eukaryotic genomes have led to considerable excitement.
openaire   +4 more sources

The impact of quality filter for RNA-Seq

Gene, 2015
With the emergence of large-scale sequencing platforms since 2005, there has been a great revolution regarding methods for decoding DNA sequences, which have also affected quantitative and qualitative gene expression analyses through the RNA-Sequencing technique.
de Sá, Pablo H.C.G., Veras, Adonney A.O., Carneiro, Adriana R., Pinheiro, Kenny C., Pinto, Anne C., Soares, Siomar C., Schneider, Maria P.C., Azevedo, Vasco, Silva, Artur, Ramos, Rommel T.J.   +9 more
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Barcode, UMI, Set format and BUStools [PDF]

, 2019
We introduce the Barcode-UMI-Set format (BUS) for representing pseudoalignments of reads from single-cell RNA-seq experiments. The format can be used with all single-cell RNA-seq technologies, and we show that BUS files can be efficiently generated ...
Melsted, Páll, Ntranos, Vasilis, Pachter, Lior   +2 more
core   +1 more source

Optimizing Splicing Junction Detection in Next Generation Sequencing Data on a Virtual-GRID Infrastructure [PDF]

, 2012
The new protocol for sequencing the messenger RNA in a cell, named RNA-seq produce millions of short sequence fragments. Next Generation Sequencing technology allows more accurate analysis but increase needs in term of computational resources. This paper
Abate, Francesco, Acquaviva, Andrea, Ficarra, Elisa, Mossucca, L., Provenzano, R., Terzo, Olivier   +5 more
core  

Utilizing RNA-Seq Data for Cancer Network Inference

, 2012
An important challenge in cancer systems biology is to uncover the complex network of interactions between genes (tumor suppressor genes and oncogenes) implicated in cancer. Next generation sequencing provides unparalleled ability to probe the expression
Atwal, Gurinder S., Cai, Ying, Fendler, Bernard   +2 more
core   +1 more source

Case study: Targeted RNA-sequencing of aged formalin-fixed paraffin-embedded samples for understanding chemical mode of action

Toxicology Reports, 2022
Formalin-fixed paraffin-embedded (FFPE) samples are the only remaining biological archive for many toxicological and clinical studies, yet their use in genomics has been limited due to nucleic acid damage from formalin fixation.
Michael D. Cannizzo, Charles E. Wood, Susan D. Hester, Leah C. Wehmas   +3 more
doaj  

DREAMSeq: An Improved Method for Analyzing Differentially Expressed Genes in RNA-seq Data

Frontiers in Genetics, 2018
RNA sequencing (RNA-seq) has become a widely used technology for analyzing global gene-expression changes during certain biological processes. It is generally acknowledged that RNA-seq data displays equidispersion and overdispersion characteristics ...
Zhihua Gao, Zhihua Gao, Zhiying Zhao, Wenqiang Tang   +3 more
doaj   +1 more source

Gene ontology analysis for RNA-seq: accounting for selection bias [PDF]

, 2010
Matthew D. Young, Matthew J. Wakefield, Gordon K. Smyth, Alicia Oshlack   +3 more
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Pan‐Cancer Single‐Nucleus Total RNA Sequencing Using snHH‐Seq

Advanced Science
Tumor heterogeneity and its drivers impair tumor progression and cancer therapy. Single‐cell RNA sequencing is used to investigate the heterogeneity of tumor ecosystems. However, most methods of scRNA‐seq amplify the termini of polyadenylated transcripts,
Haide Chen, Xiunan Fang, Jikai Shao, Qi Zhang, Liwei Xu, Jiaye Chen, Yuqing Mei, Mengmeng Jiang, Yuting Wang, Zhouyang Li, Zihang Chen, Yang Chen, Chengxuan Yu, Lifeng Ma, Peijing Zhang, Tianyu Zhang, Yuan Liao, Yuexiao Lv, Xueyi Wang, Lei Yang, Yuting Fu, Daobao Chen, Liming Jiang, Feng Yan, Wei Lu, Gao Chen, Huahao Shen, Jingjing Wang, Changchun Wang, Tingbo Liang, Xiaoping Han, Yongcheng Wang, Guoji Guo   +32 more
doaj   +1 more source

Tracing the Derivation of Embryonic Stem Cells from the Inner Cell Mass by Single-Cell RNA-Seq Analysis [PDF]

, 2010
Fuchou Tang, Cátálin Bárbácioru, Siqin Bao, Caroline Lee, Ellen Nordman, Xiaohui Wang, Kaiqin Lao, M. Azim Surani   +7 more
openalex   +1 more source