24 papers · ranked by Valyu relevance
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…
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…
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…
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…
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.…
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…
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…
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.…
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…
Konrad U. Förstner, Jörg Vogel, Cynthia M. Sharma
RNA-Seq has become a potent and widely used method to qualitatively and quantitatively study transcriptomes. In order to draw biological conclusions based on RNA-Seq data, several steps some of which are computationally intensive, have to be taken. Our READemption pipeline takes care of these individual tasks and…
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…
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…
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…
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…
Joël Simoneau, Ryan Gosselin, Michelle S. Scott
RNA-seq is a modular experimental and computational approach that aims in identifying and quantifying RNA molecules. The modularity of the RNA-seq technology enables adaptation of the protocol to develop new ways to explore RNA biology, but this modularity also brings forth the importance of methodological…
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…
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…
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…
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…