Results 21 to 30 of about 4,264,667 (244)

Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-seq and ESTs [PDF]

, 2014
The reference annotations made for a genome sequence provide the framework for all subsequent analyses of the genome. Correct and complete annotation in addition to the underlying genomic sequence is particularly important when interpreting the results ...
Junfang Song, Geoffrey J Barton, Schurch Nicholas J., Brown, Sara J., Gordon G Simpson, Nicholas J Schurch, McLean, W. H. Irwin, Song Junfang, Simpson Gordon G., Sherstnev, Alexander, Brown Sara J., Alexander Sherstnev, Song, Junfang, McLean W. H. Irwin, Duc, Celine, Kate G Storey, Storey, Kate G., Schurch, Nicholas J., Cole Christian, Sherstnev Alexander, Simpson, Gordon G., Céline Duc, W H Irwin McLean, Cole, Christian; id_orcid, Christian Cole, Barton Geoffrey J., Sara J Brown, Duc Céline, Barton, Geoffrey J.; id_orcid, Storey Kate G.   +29 more
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Methods, Challenges and Potentials of Single Cell RNA-seq [PDF]

, 2012
RNA-sequencing (RNA-seq) has become the tool of choice for transcriptomics. Several recent studies demonstrate its successful adaption to single cell analysis. This allows new biological insights into cell differentiation, cell-to-cell variation and gene
Daniel Hebenstreit, Hebenstreit, Daniel
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Nuclear RNA sequencing of the mouse erythroid cell transcriptome [PDF]

, 2012
Copyright @ 2012 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source ...
Umlauf David, Catherine A. Moir (115926), Chakalova, L, Peter Fraser, Eskiw, CH, Mitchell, JA, Fraser, P, Mitchell Jennifer A., Schoenfelder, S, Umlauf, D, Clay Ieuan, Chakalova Lyubomira, David Umlauf (115924), Ieuan Clay, Jennifer A. Mitchell (32136), Schoenfelder Stefan, Chih-Yu Chen, Eskiw Christopher H., Stefan Schoenfelder, Ieuan Clay (115922), Chih-yu Chen (4730856), Fraser Peter, Takashi Nagano, Christopher H. Eskiw (115928), Takashi Nagano (115932), Christopher H Eskiw, Nagano Takashi, Lyubomira Chakalova, Nagano, T, Peter Fraser (32141), Stefan Schoenfelder (115930), Chen, CY, Moir, CA, Lyubomira Chakalova (23035), Chen Chih-yu, Jennifer A Mitchell, Clay, I, David Umlauf, Catherine A Moir, Moir Catherine A.   +39 more
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Formamide significantly enhances the efficiency of chemical adenylation of RNA sequencing ligation adaptors [PDF]

, 2023
Preadenylated single-stranded DNA ligation adaptors are essential reagents in many next generation RNA sequencing library preparation protocols. These oligonucleotides can be adenylated enzymatically or chemically.
Watts, Jonathan K, Hildebrand, Samuel R, Hedger, Adam K, Khvorova, Anastasia, Yamada, Ken   +4 more
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Direct RNA Sequencing Unfolds the Complex Transcriptome of Vibrio parahaemolyticus

mSystems, 2021
Conventional bacterial genome annotation provides information about coding sequences but ignores untranslated regions and operons. However, untranslated regions contain important regulatory elements as well as targets for many regulatory factors, such as
Mohamad Al kadi, Eiji Ishii, Dang Tat Truong, Daisuke Motooka, Shigeaki Matsuda, Tetsuya Iida, Toshio Kodama, Daisuke Okuzaki   +7 more
doaj   +1 more source

On the design and prospects of direct RNA sequencing [PDF]

Briefings in Functional Genomics, 2017
Throughout the past nearly a decade, the application of high-throughput sequencing to RNA molecules in the form of RNA sequencing (RNA-seq) and its many variations has revolutionized transcriptomic studies by enabling researchers to take a simultaneously deep and truly global look into the transcriptome.
openaire   +2 more sources

An informatics approach to distinguish RNA modifications in nanopore direct RNA sequencing

Genomics, 2022
Modifications in RNA can influence their structure, function, and stability and play essential roles in gene expression and regulation. Methods to detect RNA modifications rely on biophysical techniques such as chromatography or mass spectrometry, which are low throughput, or on high throughput short-read sequencing techniques based on selectively ...
Ramasamy, Soundhar, Mishra, Shubham, Sharma, Surbhi, Parimalam, Sangamithirai Subramanian, Vaijayanthi, Thangavel, Fujita, Yoto, Kovi, Basavaraj, Sugiyama, Hiroshi, Pandian, Ganesh N   +8 more
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Next generation sequencing for studying viruses and RNA silencing-based antiviral defense in crop plants [PDF]

, 2014
The main objectives of this work have been to use next generation sequencing (NGS) and develop bioinformatics tools for plant virus diagnostics and genome reconstruction as well as for investigation of RNA silencing-based antiviral defense.
Seguin, Jonathan
core   +1 more source

Direct-TRI: High-throughput RNA-extracting Method for all Stages of Zebrafish Development

Bio-Protocol, 2021
Recent popularization of next-generation sequencing enables conducting easy transcriptome analysis. Nevertheless, substantial RNA isolation work prior to RNA sequencing, as well as the high cost involved, still makes the routine use of large-scale ...
Kota Ujibe, Kanako Nishimura, Makoto Kashima, Hiromi Hirata   +3 more
doaj   +1 more source

Energy directed folding of RNA sequences

Nucleic Acids Research, 1984
A modification of Nussinov's algorithm (1) for (planar) secondary structure generation is described. Our algorithm postpones decisions on matches involving destabiling loops until they prove to be energetically more favourable than more local matches. We present, moreover, an alternative way of representing secondary structures which avoids unwarranted
Paulien Hogeweg, Ben Hesper
openaire   +4 more sources