Results 91 to 100 of about 1,742,697 (207)

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

4SALE – A tool for synchronous RNA sequence and secondary structure alignment and editing

BMC Bioinformatics, 2006
Background In sequence analysis the multiple alignment builds the fundament of all proceeding analyses. Errors in an alignment could strongly influence all succeeding analyses and therefore could lead to wrong predictions.
Schultz Jörg, Dandekar Thomas, Müller Tobias, Seibel Philipp N, Wolf Matthias   +4 more
doaj   +1 more source

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, Uwe Ohler, Bonnie Berger   +2 more
doaj   +1 more source

RNA editing by ADAR1 leads to context-dependent transcriptome-wide changes in RNA secondary structure

Nature Communications, 2017
Adenosine deaminase acting on RNA 1 (ADAR1) edits adenosine to inosine. Here the authors, using parallel analysis of RNA secondary structure sequencing, provide evidence that ADAR1 induces sequence-context-dependent RNA secondary structures changes ...
Oz Solomon, Ayelet Di Segni, Karen Cesarkas, Hagit T. Porath, Victoria Marcu-Malina, Orel Mizrahi, Noam Stern-Ginossar, Nitzan Kol, Sarit Farage-Barhom, Efrat Glick-Saar, Yaniv Lerenthal, Erez Y. Levanon, Ninette Amariglio, Ron Unger, Itamar Goldstein, Eran Eyal, Gidi Rechavi   +16 more
doaj   +1 more source

Identifying RNA contacts from SHAPE-MaP by partial correlation analysis [PDF]

, 2014
In a recent paper Siegfried et al. published a new sequence-based structural RNA assay that utilizes mutational profiling to detect base pairing (MaP).
Doudna, Jennifer, Pachter, Lior, Tambe, Akshay   +2 more
core   +3 more sources

The Reverse Transcription Signature of N-\u3csub\u3e1\u3c/sub\u3e-Methyladenosine in RNA-Seq is Sequence Dependent [PDF]

, 2015
The combination of Reverse Transcription (RT) and high-throughput sequencing has emerged as a powerful combination to detect modified nucleotides in RNA via analysis of either abortive RT-products or of the incorporation of mismatched dNTPs into cDNA ...
Alfonzo, Juan, Anderson, James T., Entian, Karl-dieter, Hauenschild, Ralf, Helm, Mark, Hildebrandt, Andreas, Jaschke, Andres, Lafontaine, Denis L.J., Motorin, Yuri, Schmid, Katharina, Sharma, Sunny, Thuring, Kathrin, Tserovski, Lyudmil, Wacheul, Ludvine, Winz, Marie-Luise   +14 more
core   +1 more source

A multi-objective fuzzy model based on enhanced artificial fish Swarm for multiple RNA sequences alignment

Egyptian Informatics Journal
Ribonucleic Acid (RNA) sequence alignment is a fundamental operation in bioinformatics, essential for analyzing the physicochemical and functional characteristics of RNA molecules.
Medhat A. Tawfeek, Ibrahim Alrashdi, Madallah Alruwaili, Gamal Farouk Elhady   +3 more
doaj   +1 more source

Optimal alignment algorithm for context-sensitive hidden Markov models [PDF]

, 2005
The hidden Markov model is well-known for its efficiency in modeling short-term dependencies between adjacent samples. However, it cannot be used for modeling longer-range interactions between symbols that are distant from each other.
Vaidyanathan, P. P., Yoon, Byung-Jun
core   +1 more source

circRNA-associated-ceRNA networks in patients with traumatic tracheal stenosis

Scientific Reports
Traumatic tracheal stenosis (TTS) is one of the most commonly seen iatrogenic airway injuries caused by tracheal intubation or tracheotomy, which can harm the lives of patients in severe cases.
Shujuan Qin, Wentao Li, Jinmei Wei, Yuhui Wei, Yinning Zhou, Pingping Huang, Sen Tan, Guangnan Liu   +7 more
doaj   +1 more source

RNA sequencing analysis of the developing chicken retina

Scientific Data, 2016
AbstractRNA sequencing transcriptome analysis using massively parallel next generation sequencing technology provides the capability to understand global changes in gene expression throughout a range of tissue samples. Development of the vertebrate retina requires complex temporal orchestration of transcriptional activation and repression.
Langouet-Astrie, Christophe J., Meinsen, Annamarie L., Grunwald, Emily R., Turner, Stephen D., Enke, Raymond A.   +4 more
openaire   +2 more sources