Search · four archives
Search · four archives
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…
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…
Indira Wu, Tuval Ben-Yehezkel
State-of-the-art short-read transcriptome sequencing methods employ unique molecular identifier (UMI) to accurately classify and count mRNA transcripts. A fundamental limitation of UMI-based short-read transcriptome sequencing is that each read typically covers a small fraction of the transcript sequence. Efforts to…
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…
Roberto Vera Alvarez, David Landsman
Multiple next-generation-sequencing (NGS)-based studies are enabled by the availability of a reference genome of the target organism. Unfortunately, several organisms remain unannotated due to the cost and complexity of generating a complete (or close to complete) reference genome. These unannotated organisms, however…
Vuong Tran, Efthymia Papalexi, Sarah Schroeder, Grace Kim + 13 more
Single cell RNA sequencing (scRNA-seq) has become a core tool for researchers to understand biology. As scRNA-seq has become more ubiquitous, many applications demand higher scalability and sensitivity. Split-pool combinatorial barcoding makes it possible to scale projects to hundreds of samples and millions of cells…
Sho Iwama, Daniel Gitterman, Timothy Brendler-Spaeth, Andrew Waters + 6 more
Advances in high-throughput sequencing have associated millions of putative genetic variants with disease. However, scalable experimental methods to establish causal relationships between genetic variants and downstream transcriptional outcomes remain a major challenge. Single-cell methods that integrate genotyping…
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…
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…
Joel Nunes Leite Junior, Helba Cirino, Priscila C. Antonello, Marcelo Marques Zerillo + 2 more
Transcriptome studies have contributed to the understanding of protein coding and non-coding gene expression of several organisms. They also provide knowledge into host responses to pathogen infections. Not common yet is to detect transcripts from multiple interacting organisms present in a given sample. In addition…
Jiayi Wang, Maria Constanza Maldifassi, Anna Bratus-Neuenschwander, Qin Zhang + 3 more
Long-read scRNA-seq has enabled simultaneous, unbiased identification of transcriptomic variants and expression profiling. However, it often suffers from limited read coverage, which constrains its ability to link genotype and phenotype at single-cell resolution. To address this, we evaluated multiple single-cell…
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.…
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…
Heena Satam, Kandarp Joshi, Upasana Mangrolia, Sanober Waghoo + 7 more
'Gulnaz Zaidi' 'Shravani Rawool' 'Ritesh P. Thakare' 'Shahid Banday' 'Alok K. Mishra' 'Gautam Das' 'Sunil K. Malonia'] Simple Summary Next-generation sequencing (NGS) is a powerful tool used in genomics research. NGS can sequence millions of DNA fragments at once, providing detailed information about the structure of…
Vasilios Zachariadis, Huaitao Cheng, Nathanael J Andrews, Martin Enge
Understanding how genetic variation alters gene expression - how genotype affects phenotype - is a central challenge in biology. To address this question in complex cell mixtures, we developed Direct Nuclear Tagmentation and RNA-sequencing (DNTR-seq), which enables whole genome and mRNA sequencing jointly in single…
Valentine Svensson, Roser Vento‐Tormo, Sarah A. Teichmann
The ability to measure the transcriptomes of single cells has only been feasible for a few years, and is becoming an extremely popular assay. While many types of analysis and questions can be answered using single cell RNA-sequencing, a central focus is the ability to survey the diversity of cell types within a sample.…
James Titus‐McQuillan, Adalena V. Nanni, Lauren M. McIntyre, Rebekah L. Rogers
'Rebekah L. Rogers'] Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding complexity and the functional components of the genome is an untapped wealth of knowledge ripe for exploration. With the "remarkable…
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…
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…
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…
Valentina Boeva
| ABSTRACT 4 | | | | | | | | | --- | --- | --- | --- | --- | --- | --- | --- | | RESUMÉ [FRENCH] 5 | | | | | | | | | PREFACE 6 | | | | | | | | | 1 INTRODUCTION 7 | | | | | | | | | 2 PATTERNS IN THE GENOMIC SEQUENCE AND THEIR ROLE IN REGULATION | | | | | | | | | OF GENE EXPRESSION 11 | | | | | | | | | 2.1 detection of…
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…
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…