29 papers · ranked by Valyu relevance
Venket Raghavan, Louis Kraft, Fantin Mesny, Linda Rigerte
A transcriptome constructed from short-read RNA sequencing (RNA-seq) is an easily attainable proxy catalog of protein-coding genes when genome assembly is unnecessary, expensive or difficult. In the absence of a sequenced genome to guide the reconstruction process, the transcriptome must be assembled de novo using only…
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…
Farhana Manzoor, Cyruss A. Tsurgeon, Vibhuti Gupta, Kwang Woo Ahn + 1 more
'Yunfeng Wu'] RNA sequencing (RNA-seq) has emerged as a prominent resource for transcriptomic analysis due to its ability to measure gene expression in a highly sensitive and accurate manner. With the increasing availability of RNA-seq data analysis from clinical studies and patient samples, the development of…
Felix Pförtner, Eva Briem, Wolfgang Enard, Daniel Richter
Bulk and single-cell RNA-seq are powerful tools for transcriptomic analysis, providing insights into many aspects of molecular and cellular phenotypes. Costs constrain the amount of biological insight obtainable within a given budget, and as sequencing prices decline, efficient library protocols have become a decisive…
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…
Kamil Antoszewski, Klaudia Chmielewska, Karolina Jagiello, Tomasz Puzyn
RNA sequencing (RNA-seq) has become a cornerstone of modern biotechnology, offering a comprehensive and high-resolution view of gene expression that enables the discovery of novel transcripts across diverse biological systems. Its applications extend beyond basic transcriptomics, providing powerful tools for uncovering…
Charlotte Gustafsson, Julia Hauenstein, Nicolai Frengen, Aleksandra Krstic + 2 more
RNA sequencing has become the mainstay for studies of gene expression. Still, analysis of rare cells with random hexamer priming – to allow analysis of a broader range of transcripts – remains challenging. We here describe a tagmentation-based, rRNA blocked, random hexamer primed RNAseq approach (T-RHEX-RNAseq) for…
Alessandro Scacchetti, Emily J. Shields, Natalie A. Trigg, Jeremy E. Wilusz + 2 more
Despite the numerous sequencing methods available, the vast diversity in size and chemical modifications of RNA molecules makes the capture of the full spectrum of cellular RNAs a difficult task. By combining quasirandom hexamer priming with a custom template switching strategy, we developed a method to construct…
Jianqiang Sun, Moeko Okada, Toshiaki Tameshige, Rie Shimizu-Inatsugi + 4 more
'Reiko Akiyama' 'Atsushi\xa0J Nagano' 'Jun Sese' 'Kentaro\xa0K Shimizu'] Title: Abstract Although allopolyploid species are common among natural and crop species, it is not easy to distinguish duplicated genes, known as homeologs, during their genomic analysis. Yet, cost-efficient RNA sequencing (RNA-seq) is to be…
Shyam Ji Gupta
—This report presents an in-depth exploration of multiple hypothesis testing in the context of Genomics RNA-seq differential expression (DE) analysis, with a primary focus on techniques designed to control the false discovery rate (FDR). While RNA-seq has become a cornerstone in transcriptomic research, accurately…
Abhishek Shastry, Benjamin P. Ott, Alex Paterson, Matt Simpson + 2 more
RNA sequencing (RNA-seq) is used to quantify transcript levels through measurement of nucleotide sequences. To evaluate statistically significant changes in gene expression, transcript counts between samples are compared using differential expression analysis methods. However, three of the most pressing challenges in…
Hyeongseon Jeon, Juan Xie, Yeseul Jeon, Kyeong Joo Jung + 3 more
'Arkobrato Gupta' 'Won Chang' 'Dongjun Chung'] Gene expression profiling technologies have been used in various applications such as cancer biology. The development of gene expression profiling has expanded the scope of target discovery in transcriptomic studies, and each technology produces data with distinct…
Ionut Atanasoai, Sofia Papavasileiou, Natalie Preiß, Claudia Kutter
Over the past decade, thousands of putative human RNA binding proteins (RBPs) have been identified and increased the demand for specifying RNA binding capacities. Here, we developed RNA affinity purification followed by sequencing (RAPseq) that enables in vitro large-scale profiling of RBP binding to native RNAs.…
Brittney N. Keel, Amanda K. Lindholm-Perry
Decreases in the costs of high-throughput sequencing technologies have led to continually increasing numbers of livestock RNA-Seq studies in the last decade. Although the number of studies has increased dramatically, most livestock RNA-Seq experiments are limited by cost to a small number of biological replicates.…
Alexandra Sneddon, Agin Ravindran, Nadine Hein, Nikolay Shirokikh + 1 more
We present the first biochemical-free technology for Real-time In Silico Enrichment of RNA species (RISER). RISER classifies RNA species from direct RNA nanopore signals, without the need for basecalling or a reference, and communicates with the sequencing hardware in real-time to enact in silico targeted RNA…
Racheal N. Upton, Fernando H. Correr, Jared Lile, Gillian L. Reynolds + 3 more
'Gillian L. Reynolds' 'Kira Falaschi' 'Jason P. Cook' 'Jennifer Lachowiec'] Genomics has transformed our understanding of the genetic architecture of traits and the genetic variation present in plants. Here, we present a review of how RNA-seq can be performed to tackle research challenges addressed by plant sciences.…
Juliana Costa-Silva, David Menotti, Fabricio M. Lopes
Motivation: Bulk RNA-Seq is a widely used method for studying gene expression across a variety of contexts. The significance of RNA-Seq studies has grown with the advent of high-throughput sequencing technologies. Computational methods have been developed for each stage of the identification of differentially expressed…
Jens Hör, Jakob Jung, Svetlana Đurica-Mitić, Lars Barquist + 1 more
Ribosome profiling (Ribo-seq) is a powerful method for the transcriptome-wide assessment of protein synthesis rates and the study of translational control mechanisms. Yet, Ribo-seq also has limitations. These include difficulties with detection of low abundance transcripts and analysis of translation-modulating…
Franziska Hoerbst, G. S. Sidhu, Melissa Tomkins, Richard J. Morris
in Gene Expression using Bayes Factors Authors: ['Franziska Hoerbst' 'G. S. Sidhu' 'Melissa Tomkins' 'Richard J. Morris'] Sequencing technologies have revolutionised the field of molecular biology. We now have the ability to routinely capture the complete RNA profile in tissue samples. This wealth of data allows for…
Yuichi Shichino, Mari Mito, Yasuha Kinugasa, Taisei Wakigawa + 4 more
Translation regulation plays a pivotal role in the diversification of gene expression and the response to intra- and extracellular environmental cues. Ribosome profiling (or Ribo-Seq) serves as a sensitive, quantitative, comprehensive, and data-rich technique to survey ribosome traversal across the cellular…
Aviezer Silverman, Sahar Melamed
Bacteria reside in constantly changing environments and require rapid and precise adjustments of gene expression to ensure survival. Small regulatory RNAs (sRNAs) are a crucial element that bacteria utilize to achieve this. sRNAs are short RNA molecules that modulate gene expression usually through basepairing…
Christos Argyropoulos
component based applications using Object Orientation, PDL, Alien, FFI, Inline and OpenMP Authors: ['Christos Argyropoulos'] Component-Based Software Engineering (CBSE) is a methodology that assembles pre-existing, reusable software components into new applications, which is particularly relevant for fast moving…
Janet Sasso, Barbara Ambrose, Rumiana Tenchov, Ruchira Datta + 3 more
In the last decade, there has been a shift in research, clinical development, and commercial activity to exploit the many roles of RNA in physiology for use in medicine. With the rapid success in the development of lipid-RNA nanoparticles for mRNA vaccines against COVID-19 and with several approved RNA-based drugs, RNA…
Michael Lanzillotti, Jennifer Brodbelt
Recent progress in top-down mass spectrometry analysis of progressively larger nucleic acids has enabled in-depth characterization of intact, modified RNA molecules. Development of methods for desalting and MS/MS fragmentation allows rapid acquisition of high-quality top-down MS/MS spectra of nucleic acids up to 100…
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…
Authors not listed
RNA molecules fold into complex three-dimensional structures that determine their function. A wide range of mathematical frameworks, such as chord diagrams, fatgraphs, and context-free grammars, have been used to represent these structures; however, these models have largely been developed from mathematical motivations…
Authors not listed
Targeting RNA with small molecules represents a promising yet relatively unexplored avenue for the design of new drugs. Nevertheless, challenges arise from the lack of computational models and techniques able to accurately model RNA systems, and predict their binding affinities to small molecules. Here, we tackle these…
Hirotake Udono, Minzhi Fan, Yoko Saito, Hirohisa Ohno + 4 more
Programmable droplets, artificial liquid-like condensates of nucleic acids, are intelligent out-of-equilibrium systems that allow the critical aspects of their biological counterparts to be harnessed programmably, such as molecular sensing and phase-state change. While DNA has been central to the previous efforts, less…
Authors not listed
A chemical method suitable for the synthesis of RNAs containing modifications such as N4-acetylcytidine (ac4C) that are unstable under the basic and nucleophilic conditions used by standard RNA synthesis methods is described. The method uses the 4-((t-butyldimethylsilyl)oxy)-2-methoxybutanoyl (SoM) group for the…