23 papers · ranked by Valyu relevance
Rohan Lowe, Neil Shirley, Mark Bleackley, Stephen Dolan + 1 more
'Thomas Shafee'] Transcriptomics technologies are the techniques used to study an organism’s [transcriptome](), the sum of all of its [RNA transcripts](). The information content of an organism is recorded in the DNA of its [genome]() and [expressed]() through [transcription](). Here, [mRNA]() serves as a transient…
Ashley Byrne, Charles Cole, Roger Volden, Christopher Vollmers
Long-read sequencing holds great potential for transcriptome analysis because it offers researchers an affordable method to annotate the transcriptomes of non-model organisms. This, in turn, will greatly benefit future work on less-researched organisms like unicellular eukaryotes that cannot rely on large consortia to…
Parul Tyagi, Deeksha Singh, Shivangi Mathur, Ayushi Singh + 1 more
'Rajiv Ranjan'] Transcriptome sequencing or RNA-Sequencing is a high-resolution, sensitive and high-throughput next-generation sequencing (NGS) approach used to study non-model plants and other organisms. In other words, it is an assembly of RNA transcripts from individual or whole samples of functional and…
Dhrithi Deshpande, Karishma Chhugani, Yutong Chang, Aaron Karlsberg + 14 more
'Caitlin Loeffler' 'Jinyang Zhang' 'Agata Muszyńska' 'Viorel Munteanu' 'Harry Yang' 'Jeremy Rotman' 'Laura Tao' 'Brunilda Balliu' 'Elizabeth Tseng' 'Eleazar Eskin' 'Fangqing Zhao' 'Pejman Mohammadi' 'Paweł P. Łabaj' 'Serghei Mangul'] RNA sequencing (RNA-seq) has become an exemplary technology in modern biology and…
Adam D Hargreaves, John F Mulley
Portable DNA sequencers such as the Oxford Nanopore MinION device have the potential to be truly disruptive technologies, facilitating new approaches and analyses and, in some cases, taking sequencing out of the lab and into the field. However, the capabilities of these technologies are still being revealed. Here we…
Joanna Moreton, Abril Izquierdo, Richard D. Emes
De novo assembly of a complete transcriptome without the need for a guiding reference genome is attractive, particularly where the cost and complexity of generating a eukaryote genome is prohibitive. The transcriptome should not however be seen as just a quick and cheap alternative to building a complete genome.…
R.E. Rivera-Vicéns, C.A. Garcia-Escudero, N. Conci, M. Eitel + 1 more
The use of RNA-Seq data and the generation of de novo transcriptome assemblies have been pivotal for studies in ecology and evolution. This is distinctly true for non-model organisms, where no genome information is available. Nevertheless, studies of differential gene expression, DNA enrichment baits design, and…
Dhrithi Deshpande, Karishma Chhugani, Yutong Chang, Aaron Karlsberg + 12 more
'Caitlin Loeffler' 'Jinyang Zhang' 'Agata Muszyńska' 'Jeremy Rotman' 'Laura Tao' 'Brunilda Balliu' 'Elizabeth Tseng' 'Eleazar Eskin' 'Fangqing Zhao' 'Pejman Mohammadi' 'Paweł P. Łabaj' 'Serghei Mangul'] Department of Computer Science, University of California, Los Angeles, 404 Westwood Plaza, Los Angeles, CA 90095, USA…
Matthew D. MacManes
Characterizing transcriptomes in non-model organisms has resulted in a massive increase in our understanding of biological phenomena. This boon, largely made possible via high-throughput sequencing, means that studies of functional, evolutionary and population genomics are now being done by hundreds or even thousands…
Klara Eleftheriadi, Marçal Vázquez-Valls, Rosa Fernández
Transcriptome assembly enables the recovery of expressed genes and isoforms, but the optimal strategy for reconstructing transcriptomes from long-read sequencing remains unresolved. In particular, establishing best practices for generating accurate gene models and selecting representative isoforms is essential for…
Jamie J. Alnasir, Hugh P. Shanahan
Given the wide variability in the quality of NGS data submitted to public repositories, it is essential to identify methods that can perform quality control on these datasets when additional quality control data, such as mean tile data, is missing. This is particularly important because such datasets are routinely…
Isiaka Ibrahim Muhammad, Sze Ling Kong, Siti Nor Akmar Abdullah, Umaiyal Munusamy
'Umaiyal Munusamy'] The availability of data produced from various sequencing platforms offer the possibility to answer complex questions in plant research. However, drawbacks can arise when there are gaps in the information generated, and complementary platforms are essential to obtain more comprehensive data sets…
Timothy R. Fallon, Tereza Čalounová, Martin Mokrejš, Jing-Ke Weng + 1 more
'Tomáš Pluskal'] Background RNA-seq followed by de novo transcriptome assembly has been a transformative technique in biological research of non-model organisms, but the computational processing of RNA-seq data entails many different software tools. The complexity of these de novo transcriptomics workflows therefore…
Alexis Black Pyrkosz, Hans H. Cheng, C. Titus Brown
Whole transcriptome sequencing is increasingly being used as a functional genomics tool to study nonmodel organisms. However, when the reference transcriptome used to calculate differential expression is incomplete, significant error in the inferred expression levels can result. In this study, we use simulated reads…
Prachi Jain, Neeraja M. Krishnan, Binay Panda
RNA-seq allows detection and precise quantification of transcripts, provides comprehensive understanding of exon/intron boundaries, aids discovery of alternatively spliced isoforms and fusion transcripts along with measurement of allele-specific expression. Researchers interested in studying and constructing…
Yinlong Xie, Gengxiong Wu, Jingbo Tang, Ruibang Luo + 12 more
'Jordan Patterson' 'Shanlin Liu' 'Weihua Huang' 'Guangzhu He' 'Shengchang Gu' 'Shengkang Li' 'Xin Zhou' 'Tak‐Wah Lam' 'Yingrui Li' 'Xun Xu' 'Gane Ka‐Shu Wong' 'Jun Wang'] Motivation: Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining the sequences for a large number of…
O.G. Akintunde, Trichina Tucker, Valerie J. Carabetta
The genetic information that dictates the structure and function of all life forms is encoded in the DNA. In 1953, Watson and Crick first presented the double helical structure of a DNA molecule. Their findings unearthed the desire to elucidate the exact composition and sequence of DNA molecules. Discoveries and the…
Hanin Omar, Casey A. Cole, Arjang Fahim, Giuliana Gusmaroli + 2 more
'Stephen A. Borgianini' 'Homayoun Valafar'] Abstract – High-throughput cDNA sequencing (RNAseq) is a very powerful technique to quantify gene expression in an unbiased way. The Crustacean family is among the groups of organisms sparsely represented in current genomic databases. Here we present transcriptome data from…
Authors not listed
Large-scale de novo nucleic acid synthesis is a powerful tool enabling researchers to better understand and engineer biological systems. Fields ranging from genomics to nucleic acid therapeutics to synthetic biology make use of high-throughput experimental approaches requiring access to large pools or libraries of DNA…
Md Vasimuddin, Sanchit Misra, Srinivas Aluru
Rapid advances in next-generation sequencing technologies are improving the throughput and cost of sequencing at a rate significantly faster than the Moore’s law. This necessitates equivalent rate of acceleration of NGS secondary analysis that assembles reads into full genomes and identifies variants between genomes.…
Authors not listed
Metaproteomics enables the large-scale characterization of microbial community proteins, offering crucial insights into their taxonomic composition, functional activities, and interactions within their environments. By directly analyzing proteins, metaproteomics offers insights on community phenotypes and the roles…
Amal Homer, Andrea Knoll, Uschi Gruber, Oliver Seitz
Fluorogenic hybridization probes allow the detection and localization of specific mRNA molecules in living cells without the need for genetic engineering. However, with the fluorescence properties of currently available oligonucleotide probes, detection in live cells is difficult when the mRNA target is expressed at…
Michael Lanzillotti, Jennifer Brodbelt
Mass spectrometry has proven to be a highly effective tool for characterization of RNA post-transcriptional modifications. For both synthetic RNAs and ones from biological sources, mass spectrometry can interrogate multiple, co-occurring covalent modifications at the nucleotide level simultaneously. To expand the…