Results 1 to 10 of about 1,187,055 (266)

RNA-sequence analysis of human B-cells [PDF]

Genome Research, 2011
RNA-sequencing (RNA-seq) allows quantitative measurement of expression levels of genes and their transcripts. In this study, we sequenced complementary DNA fragments of cultured human B-cells and obtained 879 million 50-bp reads comprising 44 Gb of sequence.
Jonathan M, Toung, Michael, Morley, Mingyao, Li, Vivian G, Cheung   +3 more
openaire   +2 more sources

High-throughput detection of RNA processing in bacteria

BMC Genomics, 2018
Background Understanding the RNA processing of an organism’s transcriptome is an essential but challenging step in understanding its biology. Here we investigate with unprecedented detail the transcriptome of Pseudomonas aeruginosa PAO1, a medically ...
Erin E. Gill, Luisa S. Chan, Geoffrey L. Winsor, Neil Dobson, Raymond Lo, Shannan J. Ho Sui, Bhavjinder K. Dhillon, Patrick K. Taylor, Raunak Shrestha, Cory Spencer, Robert E. W. Hancock, Peter J. Unrau, Fiona S. L. Brinkman   +12 more
doaj   +1 more source

TRAPR: R Package for Statistical Analysis and Visualization of RNA-Seq Data [PDF]

Genomics & Informatics, 2017
High-throughput transcriptome sequencing, also known as RNA sequencing (RNA-Seq), is a standard technology for measuring gene expression with unprecedented accuracy.
Jae Hyun Lim, Soo Youn Lee, Ju Han Kim
doaj   +1 more source

Recognizing RNA structural motifs in HT-SELEX data for ribosomal protein S15

BMC Bioinformatics, 2017
Background Proteins recognize many different aspects of RNA ranging from single stranded regions to discrete secondary or tertiary structures. High-throughput sequencing (HTS) of in vitro selected populations offers a large scale method to study RNA ...
Shermin Pei, Betty L. Slinger, Michelle M. Meyer   +2 more
doaj   +1 more source

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

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

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