26 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…
Craig Smail, Stephen B. Montgomery
RNA sequencing (RNA-seq) enables the accurate measurement of multiple transcriptomic phenotypes for modeling the impacts of disease variants. Advances in technologies, experimental protocols, and analysis strategies are rapidly expanding the application of RNA-seq to identify disease biomarkers, tissue- and…
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…
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…
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…
Min Tu, Jian Zeng, Juntao Zhang, Guozhi Fan + 1 more
RNA-seq has become a state-of-the-art technique for transcriptomic studies. Advances in both RNA-seq techniques and the corresponding analysis tools and pipelines have unprecedently shaped our understanding in almost every aspects of plant sciences. Notably, the integration of huge amount of RNA-seq with other omic…
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…
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…
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…
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.…
Kanjana Laosuntisuk, Amaranatha Vennapusa, Impa M. Somayanda, Adam R. Leman + 2 more
RNA-Sequencing is widely used to investigate changes in gene expression at the transcription level in plants. Most plant RNA-Seq analysis pipelines base the normalization approaches on the assumption that total transcript levels do not vary between samples. However, this assumption has not been demonstrated. In fact…
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.…
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…
Gabriel Pérez-Lara, Tomás C. Moyano, Andrea Vega, Luis F. Larrondo + 4 more
To analyze and visualize comprehensive gene expression patterns in the phytopathogenic fungus Botrytis cinerea, we developed BEB — a web-based B. cinerea gene expression browser. This tool and associated databases (DB) contain manually-curated RNA-Seq experiments conducted in B. cinerea. BEB allows easy gene expression…
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…
Irina Khven, Mariana Ribeiro, Sara Crausaz, Simone Picelli
Effective RNase inhibition is critical for single-cell RNA-sequencing, yet commercial recombinant RNase inhibitors (RRIs) require reducing agents for stability and impose substantial costs. Here, we systematically benchmark SEQURNA, a synthetic thermostable RNase inhibitor, against commercial alternatives using…
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…
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…
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…
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…
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
Oligonucleotides offer a powerful class of new therapeutic modalities, which requires the support of robust and sensitive analytical methods. The primary structure of RNA-based therapeutic drugs is considered a critical quality attribute by regulatory agencies, and must be empirically confirmed to ensure quality…
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
The development of RNA-based therapeutics has significantly expanded the landscape of drug discovery by enabling precise modulation of gene expression. These approaches offer the potential to target previously "undruggable" genes, overcoming limitations inherent to traditional small molecule therapies. However, the…