Results 111 to 120 of about 2,190,860 (309)
Parametric analysis of RNA folding [PDF]
arXiv, 2009 We extend recent methods for parametric sequence alignment to the parameter space for scoring RNA folds. This involves the construction of an RNA polytope. A vertex of this polytope corresponds to RNA secondary structures with common branching. We use this polytope and its normal fan to study the effect of varying three parameters in the free energy ...
arxiv
sRNAnalyzer-a flexible and customizable small RNA sequencing data analysis pipeline. [PDF]
, 2017 Although many tools have been developed to analyze small RNA sequencing (sRNA-Seq) data, it remains challenging to accurately analyze the small RNA population, mainly due to multiple sequence ID assignment caused by short read length.
Baxter, David +8 more
core +2 more sources
Molecular Oncology, EarlyView.Cancer‐associated fibroblasts (CAFs) promote cancer growth, invasion (metastasis), and drug resistance. Here, we identified functional and diverse circulating CAFs (cCAFs) in patients with metastatic prostate cancer (mPCa). cCAFs were found in higher numbers and were functional and diverse in mPCa patients versus healthy individuals, suggesting their ...
Richell Booijink +6 more
wiley +1 more source
Egyptian Informatics Journal, 2023 In an attempt to improve the analysis DNA sequence, a new intelligent deep analysis algorithm called reduce frequency bast on fast frequency graph mining (RF-FFGM) is established; This algorithm at the beginning converts the DNA sequence into RNA ...
Zena A. Kadhuim, Samaher Al-Janabi
doaj
RNAome sequencing delineates the complete RNA landscape
Genomics Data, 2015 Standard RNA expression profiling methods rely on enrichment steps for specific RNA classes, thereby not detecting all RNA species. For example, small and large RNAs from the same sample cannot be sequenced in a single sequence run.
Kasper W.J. Derks, Joris Pothof
doaj +1 more source
Inverse folding of RNA pseudoknot structures [PDF]
arXiv, 2009 Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These interactions are called pseudoknots and are observed across the whole spectrum of RNA functionalities.
arxiv
Sequence–structure relationships in RNA loops: establishing the basis for loop homology modeling [PDF]
, 2010 The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules.
Abraham +41 more
core +2 more sources
Surfaceome: a new era in the discovery of immune evasion mechanisms of circulating tumor cells
Molecular Oncology, EarlyView.In the era of immunotherapies, many patients either do not respond or eventually develop resistance. We propose to pave the way for proteomic analysis of surface‐expressed proteins called surfaceome, of circulating tumor cells. This approach seeks to identify immune evasion mechanisms and discover potential therapeutic targets. Circulating tumor cells (
Doryan Masmoudi +3 more
wiley +1 more source
RNA sequence analysis data of Peronospora destructor maintained on onions
Data in Brief, 2019 Peronospora destructor (Berk.) is an important biotrophic oomycete that causes downy mildew on onion (Allium Cepa L.) worldwide, especially in humid and temperate regions.
Kazuki Fujiwara +4 more
doaj
Finding RNA structure in the unstructured RBPome
BMC Genomics, 2018 Background RNA-binding proteins (RBPs) play vital roles in many processes in the cell. Different RBPs bind RNA with different sequence and structure specificities.
Yaron Orenstein +2 more
doaj +1 more source