Results 91 to 100 of about 567,059 (348)

Evaluation and application of RNA-Seq by MinION [PDF]

DNA Research, 2018
The current RNA-Seq method analyses fragments of mRNAs, from which it is occasionally difficult to reconstruct the entire transcript structure. Here, we performed and evaluated the recent procedure for full-length cDNA sequencing using the Nanopore sequencer MinION.
Martin C. Frith, Martin C. Frith, Eri Katsumata, Masahide Seki, Yutaka Suzuki, Yoshitaka Sakamoto, Sarun Sereewattanawoot, Sumio Sugano, Sumio Sugano, Katsuya Tsuchihara, Takashi Kohno, Ayako Suzuki, Junko Mizushima-Sugano, Junko Mizushima-Sugano   +13 more
openaire   +3 more sources

ITGAV and SMAD4 influence the progression and clinical outcome of pancreatic ductal adenocarcinoma

Molecular Oncology, EarlyView.
In SMAD4‐positive pancreatic ductal adenocarcinoma (PDAC), integrin subunit alpha V (ITGAV) activates latent TGF‐β, which binds to the TGF‐β receptor and phosphorylates SMAD2/3. The activated SMAD2/3 forms a complex with SMAD4, and together they translocate to the nucleus, modulating gene expression to promote proliferation, migration, and invasion. In
Daniel K. C. Lee, Keyue Chen, Ryan Loke, Xiang Li, David Liubart, Golam T. Saffi, Jonathan T. S. Chow, Ché M. P. Melo, Lydia To, Leonardo Salmena   +9 more
wiley   +1 more source

Seq-ing improved gene expression estimates from microarrays using machine learning [PDF]

, 2015
BACKGROUND: Quantifying gene expression by RNA-Seq has several advantages over microarrays, including greater dynamic range and gene expression estimates on an absolute, rather than a relative scale.
Geeleher, Paul, Korir, Paul K., Seoighe, Cathal   +2 more
core   +1 more source

Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM) [PDF]

Bioinformatics, 2011
Abstract Motivation: A critical task in high-throughput sequencing is aligning millions of short reads to a reference genome. Alignment is especially complicated for RNA sequencing (RNA-Seq) because of RNA splicing. A number of RNA-Seq algorithms are available, and claim to align reads with high accuracy and efficiency while detecting ...
John B. Hogenesch, Gregory R. Grant, Angel Pizarro, Eric A. Pierce, Nicholas F. Lahens, Jonathan Schug, Brian P. Brunk, Christian J. Stoeckert, Michael H. Farkas   +8 more
openaire   +3 more sources

The critical role of DNA damage‐inducible transcript 4 (DDIT4) in stemness character of leukemia cells and leukemia initiation

Molecular Oncology, EarlyView.
Stemness properties, including quiescence, self‐renewal, and chemoresistance, are closely associated with leukemia relapse. Here, we demonstrate that DNA damage‐inducible transcript 4 (DDIT4) is induced in the hypoxic bone marrow niche and is essential for maintaining the stemness of AML1‐ETO9a leukemia cells.
Yishuang Li, Zhijie Cao, Haiyan Xing, Zhenya Xue, Wenbing Liu, Jiayuan Chen, Yihan Mei, Runxia Gu, Hui Wei, Shaowei Qiu, Min Wang, Qing Rao, Jianxiang Wang   +12 more
wiley   +1 more source

Comparison of RNA-Seq and Microarray Gene Expression Platforms for the Toxicogenomic Evaluation of Liver From Short-Term Rat Toxicity Studies

Frontiers in Genetics, 2019
Gene expression profiling is a useful tool to predict and interrogate mechanisms of toxicity. RNA-Seq technology has emerged as an attractive alternative to traditional microarray platforms for conducting transcriptional profiling.
Mohan S. Rao, Terry R. Van Vleet, Rita Ciurlionis, Wayne R. Buck, Scott W. Mittelstadt, Eric A. G. Blomme, Michael J. Liguori   +6 more
doaj   +1 more source

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

Informatics for RNA sequencing: A web resource for analysis on the cloud [PDF]

, 2015
Massively parallel RNA sequencing (RNA-seq) has rapidly become the assay of choice for interrogating RNA transcript abundance and diversity. This article provides a detailed introduction to fundamental RNA-seq molecular biology and informatics concepts ...
Ainscough, Benjamin J, Griffith, Malachi, Griffith, Obi L, Spies, Nicholas C, Walker, Jason R   +4 more
core   +3 more sources

Targeting of PTP4A3 overexpression sensitises HGSOC cells towards chemotherapeutic drugs

Molecular Oncology, EarlyView.
In HGSOC with normal KRAS expression, high PTP4A3 expression regulates autophagy activation. Conversely, in HGSOC with high KRAS expression, KRAS dictates autophagy control, and PTP4A3 is not required. When high PTP4A3 expression is inhibited, HGSOC cells are preferentially sensitised towards DNA‐damaging agents.
Ana López‐Garza, David James, Emma Creagh, James T. Murray   +3 more
wiley   +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