28 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…
Bo Li, Colin N Dewey
Background RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms. This issue is particularly important for quantification with de novo transcriptome assemblies in the absence…
Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero + 7 more
'Alejandra Cervera' 'Andrew McPherson' 'Michał Wojciech Szcześniak' 'Daniel J. Gaffney' 'Laura L. Elo' 'Xuegong Zhang' 'Ali Mortazavi'] RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis…
Malachi Griffith, Jason R. Walker, Nicholas C. Spies, Benjamin J. Ainscough + 2 more
'Benjamin J. Ainscough' 'Obi L. Griffith' 'Francis Ouellette'] Massively parallel RNA sequencing (RNA-seq) has rapidly become the assay of choice for interrogating RNA transcript abundance and diversity. This article provides a detailed introduction to fundamental RNA-seq molecular biology and informatics concepts. We…
John H Malone, Brian Oliver
Microarrays first made the analysis of the transcriptome possible, and have produced much important information. Today, however, researchers are increasingly turning to direct high-throughput sequencing - RNA-Seq - which has considerable advantages for examining transcriptome fine structure - for example in the…
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…
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…
Rui Li, Kai Hu, Haibo Liu, Michael R. Green + 1 more
Over the past decade, a large amount of RNA sequencing (RNA-seq) data were deposited in public repositories, and more are being produced at an unprecedented rate. However, there are few open source tools with point-and-click interfaces that are versatile and offer streamlined comprehensive analysis of RNA-seq datasets.…
Daniel R. Garalde, Elizabeth A. Snell, Daniel Jachimowicz, Andrew J. Heron + 19 more
Ribonucleic acid sequencing can allow us to monitor the RNAs present in a sample. This enables us to detect the presence and nucleotide sequence of viruses, or to build a picture of how active transcriptional processes are changing – information that is useful for understanding the status and function of a sample.…
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…
Jennifer F. Hu, Daniel Yim, Sabrina M. Huber, Jo Marie Bacusmo + 6 more
Current next-generation RNA sequencing methods cannot provide accurate quantification of the population of small RNAs within a sample due to strong sequence-dependent biases in capture, ligation, and amplification during library preparation. We report the development of an RNA sequencing method – AQRNA-seq – that…
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…
Khalid Raza, Sabahuddin Ahmad
Next Generation Sequencing (NGS), a recently evolved technology, have served a lot in the research and development sector of our society. This novel approach is a newbie and has critical advantages over the traditional Capillary Electrophoresis (CE) based Sanger Sequencing. The advancement of NGS has led to numerous…
Marie-Ange Palomares, Cyril Dalmasso, Eric Bonnet, Céline Derbois + 5 more
High-throughput RNA-sequencing has become the gold standard method for whole-transcriptome gene expression analysis, and is widely used in numerous applications to study cell and tissue transcriptomes. It is also being increasingly used in a number of clinical applications, including expression profiling for…
Wei Vivian Li, Jingyi Jessica Li
Background: Since the invention of next-generation RNA sequencing (RNA-seq) technologies, they have become a powerful tool to study the presence and quantity of RNA molecules in biological samples and have revolutionized transcriptomic studies. The analysis of RNA-seq data at four different levels (samples, genes…
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…
Kuan-Hao Chao, Yi-Wen Hsiao, Yi-Fang Lee, Chien‐Yueh Lee + 4 more
'Liang‐Chuan Lai' 'Mong‐Hsun Tsai' 'Tzu‐Pin Lu' 'Eric Y. Chuang'] Abstract—RNA-Seq analysis has revolutionized researchers' understanding of the transcriptome in biological research. Assessing the differences in transcriptomic profiles between tissue samples or patient groups enables researchers to explore the…
Nikita Potemkin, Sophie M.F. Cawood, Jackson Treece, Diane Guévremont + 4 more
RNA sequencing offers unprecedented access to the transcriptome. Key to this is the identification and quantification of many different species of RNA from the same sample at the same time. In this study we describe a novel protocol for simultaneous detection of coding and non-coding transcripts using modifications to…
Gabrielle Deschamps-Francoeur, Vincent Boivin, Sherif Abou Elela, Michelle S Scott
Next generation sequencing techniques revolutionized the study of RNA expression by permitting whole transcriptome analysis. However, sequencing reads generated from nested and multi-copy genes are often either misassigned or discarded, which greatly reduces both quantification accuracy and gene coverage. Here we…
Wei Sun, Yufeng Liu, James J. Crowley, Ting‐Huei Chen + 13 more
'Haitao Chu' 'Shun‐Ping Huang' 'Pei Fen Kuan' 'Yuan Li' 'Darla R. Miller' 'Ginger D. Shaw' 'Yichao Wu' 'Vasyl Zhabotynsky' 'Leonard McMillan' 'Fei Zou' 'Patrick F. Sullivan' 'Fernando Pardo‐Manuel de Villena'] We have developed a statistical method named IsoDOT to assess differential isoform expression (DIE) and…
Ferhat Alkan, Joana Silva, Eric Pintó Barberà, William J. Faller
Ribosome profiling (Ribo-seq) has revolutionized the study of RNA translation. The technique provides information on ribosome positions across all translated RNAs with nucleotide-resolution. However, several technical limitations restrict the sequencing depth of such experiments, the most common of which is the…
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…
Hafeez Haniff, Laurent Knerr, Xiaohui Liu, Gogce Crynen + 5 more
Vascular Endothelial Growth Factor A (VEGFA) stimulates angiogenesis in human endothelial cells and increasing its expression is a potential treatment for heart failure, currently accomplished via gene or mRNA therapy. Herein, we describe a designed small molecule (TGP-377) that specifically and potently enhances VEGFA…
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…
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…
Anna Knörlein, Chris Sarnowski, Tebbe de Vries, Moritz Stoltz + 5 more
Understanding structure-function relationships of RNA-binding proteins requires knowledge of how they bind RNAs in vivo. RNA-protein interactions are studied using light-induced cross-linking at “zero-distance”, yielding nucleotide/amino-acid adducts for mass-spectrometry (MS)-based characterization. However…