26 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…
Mihaela Pertea
Despite recent technological advances, the study of the human transcriptome is still in its early stages. Here we provide an overview of the complex human transcriptomic landscape, present the bioinformatics challenges posed by the vast quantities of transcriptomic data, and discuss some of the studies that have tried…
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.…
Adam D Hargreaves, John F Mulley
Portable DNA sequencers such as the Oxford Nanopore MinION device have the potential to be truly disruptive technologies, facilitating new approaches and analyses and, in some cases, taking sequencing out of the lab and into the field. However, the capabilities of these technologies are still being revealed. Here we…
Thidathip Wongsurawat, Piroon Jenjaroenpun, Trudy M. Wassenaar, Taylor D Wadley + 6 more
Sequencing of native RNA and corresponding cDNA was performed using Oxford Nanopore Technology. The % Error of Specific Bases (%ESB) was higher for native RNA than for cDNA, which enabled detection of ribonucleotide modification sites. Based on %ESB differences of the two templates, a bioinformatic tool ELIGOS was…
Jonathan S. Abebe, Yasmine Alwie, Erik Fuhrmann, Jonas Leins + 5 more
High-resolution annotations of transcriptomes from all domains of life are essential for many sequencing-based RNA analyses, including Nanopore direct RNA sequencing (DRS), which would otherwise be hindered by misalignments and other analysis artefacts. DRS allows the capture and full-length sequencing of native RNAs…
Timothy R. Fallon, Tereza Čalounová, Martin Mokrejš, Jing-Ke Weng + 1 more
'Tomáš Pluskal'] Background RNA-seq followed by de novo transcriptome assembly has been a transformative technique in biological research of non-model organisms, but the computational processing of RNA-seq data entails many different software tools. The complexity of these de novo transcriptomics workflows therefore…
Yangmei Qin, Zhe Lin, Dan Shi, Mindong Zhong + 6 more
It is a long-term challenge to undertake reliable transcriptomic research under different circumstances of genome availability. Here, we newly developed a genome-free computational method to aid accurate transcriptome assembly, using the amphioxus as the example. Via integrating ten next generation sequencing (NGS)…
Antonin Morillon, Daniel Gautheret
Genetic, transcriptional, and post-transcriptional variations shape the transcriptome of individual cells, rendering establishing an exhaustive set of reference RNAs a complicated matter. Current reference transcriptomes, which are based on carefully curated transcripts, are lagging behind the extensive RNA variation…
Jorge L. Pérez-Moreno, Mihika T. Kozma, Danielle M. DeLeo, Heather D. Bracken-Grissom + 2 more
Transcriptomes from non-traditional model organisms often harbor a wealth of unexplored data. Examining these datasets can lead to clarity and novel insights in traditional systems, as well as to discoveries across a multitude of fields. Despite significant advances in DNA sequencing technologies and in their adoption…
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…
Prachi Jain, Neeraja M. Krishnan, Binay Panda
RNA-seq allows detection and precise quantification of transcripts, provides comprehensive understanding of exon/intron boundaries, aids discovery of alternatively spliced isoforms and fusion transcripts along with measurement of allele-specific expression. Researchers interested in studying and constructing…
Michael G. Sadovsky, Vladislav V. Birukov, Yuliya A. Putintseva, Konstantin V. Krutovsky
'Konstantin V. Krutovsky'] The paper presents a novel approach to infer a structuredness in a set of symbol sequences such as transcriptome nucleotide sequences. A distribution pattern of triplet frequencies in the Siberian larch (Larix sibirica Ledeb.) transcriptome sequences was investigated in the presented study.…
Tin Nguyen, Zhiyu Zhao, Dongxiao Zhu
Transcriptome assembly from RNA-Seq reads is an active area of bioinformatics research. The ever-declining cost and the increasing depth of RNA-Seq have provided unprecedented opportunities to better identify expressed transcripts. However, the nonlinear transcript structures and the ultra-high throughput of RNA-Seq…
Roderic Guigó
Title: Summary Within the next decade, the genomes of 1.8 million eukaryotic species will be sequenced. Identifying genes in these sequences is essential to understand the biology of the species. This is challenging due to the transcriptional complexity of eukaryotic genomes, which encode hundreds of thousands of…
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…
Fairlie Reese, Brian Williams, Gabriela Balderrama-Gutierrez, Dana Wyman + 41 more
The majority of mammalian genes encode multiple transcript isoforms that result from differential promoter use, changes in exonic splicing, and alternative 3’ end choice. Detecting and quantifying transcript isoforms across tissues, cell types, and species has been extremely challenging because transcripts are much…
N. Ogata, Toshinori Kozaki, Takeshi Yokoyama, Tamako Hata + 1 more
'Kikuo Iwabuchi'] Cells must coordinate adjustments in genome expression to accommodate changes in their environment. We hypothesized that the amount of transcriptome change is proportional to the amount of environmental change. To capture the effects of environmental changes on the transcriptome, we compared…
Wend Yam D D Ouedraogo, Aida Ouangraoua
Eukaryotic genes can encode multiple distinct transcripts through the alternative splicing (AS) of genes. Interest in the AS mechanism and its evolution across different species has stimulated numerous studies, leading to several databases that provide information on AS and transcriptome data across multiple eukaryotic…
Panpaki Seekaki, N. Ogata
> Abstract. Cells coordinate adjustments in genome expression to accommodate changes in their environment. A drug in culture media for in vitro preclinical testing sometimes cause drastic regime shifting of genome expression system depending on the concentrations; e.g. primary cultured cells exposed to high…
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…
Alexander Apostle, Yipeng Yin, Komal Chillar, Adikari M. D. N. Eriyagama + 4 more
Like other viruses, SARS-CoV-2 causes different symptoms and different degrees of harmfulness to different individuals. Potential reasons include an individual's viral dose exposure, the affinity of an individual's ACE2 to the spike protein of the virus, and the ability of the individual's induced immune system to…
Authors not listed
One aim of the international Human Proteome Organization (HUPO) Human Proteome Project (HPP) is to obtain high-confidence translation evidence for every human protein-coding gene established in its target list of 19433 entries based on the protein-coding genes from Ensembl-GENCODE. However, 76 are annotated in…
Authors not listed
Molecular mechanisms governing initiation steps of the assembly of thousands of endogenous multi-protein complexes (EMCs) remain incompletely understood. Here, multiple lines of observations are reported reflecting the biological functions-aligned initiation sequence of hybrid assembly pathways (HAPs) of EMCs. HAPs…
Amal Homer, Andrea Knoll, Uschi Gruber, Oliver Seitz
Fluorogenic hybridization probes allow the detection and localization of specific mRNA molecules in living cells without the need for genetic engineering. However, with the fluorescence properties of currently available oligonucleotide probes, detection in live cells is difficult when the mRNA target is expressed at…
Authors not listed
Machine learning holds significant promise for accelerating biomarker discovery in clinical proteomics, yet its real-world impact remains limited by widespread methodological pitfalls and unrealistic expectations. In this perspective, we critically examine the integration of machine learning into clinical proteomics…