RNomics: a computational search for box C/D snoRNA genes in the D. melanogaster genome. [PDF]
, 2004 Motivation: In eukaryotes, the family of non-coding RNA genes includes a number of genes encoding small nucleolar RNAs (mainly C/D and H/ACA snoRNAs), which act as guides in the maturation or post-transcriptional modifications of target RNA molecules ...
ACCARDO MC +6 more
core
A dynamic programming algorithm for RNA structure prediction including pseudoknots [PDF]
arXiv, 1998 We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of ${\cal O}(N^6)$ in time and ${\cal O}(N^4)$ in storage. The description of the algorithm is complex, which led us to adopt a useful graphical representation (Feynman diagrams) borrowed from ...
arxiv
U17XS8, a small nucleolar RNA with a 12 nt complementarity to 18S rRNA and coded by a sequence repeated in the six introns ofXenopus laevisribosomal protein S8 gene [PDF]
, 1994 Francesco Cecconi +5 more
openalex +1 more source
On an RNA-membrane protogenome [PDF]
arXivSelected ribonucleotide sequences bind well to zwitterionic phospholipid bilayer membranes, though randomized RNAs do not. There are no evident repeated sequences in selected membrane binding RNAs. This implies small and varied motifs responsible for membrane affinity. Such subsequences have been partially defined. Bound RNAs require divalents like Mg2+
arxiv
Autocatalytic Sets and RNA Secondary Structure [PDF]
arXiv, 2016 The dominant paradigm in origin of life research is that of an RNA world. However, despite experimental progress towards the spontaneous formation of RNA, the RNA world hypothesis still has its problems. Here, we introduce a novel computational model of chemical reaction networks based on RNA secondary structure and analyze the existence of ...
arxiv
Journal of Biological Chemistry, 2003 Messenger RNA 3′-end formation is functionally coupled to transcription by RNA polymerase II. By tagging and purifying Ref2, a non-essential protein previously implicated in mRNA cleavage and termination, we isolated a multiprotein complex, holo-CPF ...
Eduard Nedea +9 more
semanticscholar +1 more source
Pleomorphic adenoma and carcinoma ex‐pleomorphic adenoma tumorigenesis: A proteomic analysis
Oral Diseases, Volume 31, Issue 3, Page 865-878, March 2025.Abstract Objectives To conduct a comprehensive proteomic analysis of normal salivary gland tissue, pleomorphic adenoma (PA), and carcinoma ex‐pleomorphic adenoma (CXPA), and validate the proteomic findings using immunohistochemistry. Methods Six normal salivary gland tissues, seven PA and seven CXPA samples underwent laser microdissection followed by ...
Virgílio Gonzales Zanella +13 more
wiley +1 more source
The landscape of small nucleolar RNA expression in multiple myeloma is determined by cytogenetic alterations. [PDF]
Leukemia, 2023 Zhao D +13 more
europepmc +1 more source
The Host Gene for Intronic U17 Small Nucleolar RNAs in Mammals Has No Protein-Coding Potential and Is a Member of the 5′-Terminal Oligopyrimidine Gene Family [PDF]
, 1998 Paweł Pelczar, Witold Filipowicz
openalex +1 more source
Deciphering recent transposition patterns in plants through comparison of 811 genome assemblies
Plant Biotechnology Journal, Volume 23, Issue 4, Page 1121-1132, April 2025.Summary Transposable elements (TEs) are significant drivers of genome evolution, yet their recent dynamics and impacts within and among species, as well as the roles of host genes and non‐coding RNAs in the transposition process, remain elusive. With advancements in large‐scale pan‐genome sequencing and the development of open data sharing, large‐scale
Yan Huang, Sunil Kumar Sahu, Xin Liu
wiley +1 more source