25 papers · ranked by Valyu relevance
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…
Kevin Vo, Sharmin Shila, Yashica Sharma, Grace J. Pei + 5 more
'Cinthia Y. Rosales' 'Vinesh Dahiya' 'Patrick E. Fields' 'M. A. Karim Rumi' 'Christiane Branlant'] Most eukaryotic genes express more than one mature mRNA, defined as transcript variants. This complex phenomenon arises from various mechanisms, such as using alternative transcription start sites and alternative…
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…
Yih-Horng Shiao, Daniele Focosi
The heterogeneity of ribosomes, characterized by structural variations, arises from differences in types, numbers, and/or post-translational modifications of participating ribosomal proteins (RPs), ribosomal RNAs (rRNAs) sequence variants plus post-transcriptional modifications, and additional molecules essential for…
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…
Wang Liu-Wei, Wiep van der Toorn, Patrick Bohn, Martin Hölzer + 2 more
Direct RNA sequencing (dRNA-seq) on the Oxford Nanopore Technology platforms has become increasingly popular in recent years, with promising outlook to transform the field of epitranscriptomics. Reads produced from dRNA-seq can cover up to full-length gene transcripts while containing decipherable information about RNA…
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…
Korina Karagianni, Alessia Bibi, Alisia Madé, Shubhra Acharya + 9 more
'Mikko Parkkonen' 'Teodora Barbalata' 'Prashant K. Srivastava' 'David de Gonzalo-Calvo' 'Constanza Emanueli' 'Fabio Martelli' 'Yvan Devaux' 'Dimitra Dafou' 'A. Yaël Nossent' ''] RNA editing, a common and potentially highly functional form of RNA modification, encompasses two different RNA modifications, namely…
Ziyuan Wang, Mei-Juan Tu, Chengcheng Song, Ziyang Liu + 4 more
The nanopore sequencing of short sequences, whose lengths are typically less than 0.3kb therefore comparable with Illumina sequencing techniques, has recently gained wide attention. Here, we design a scheme for training nanopore basecallers that are specialized for short biomolecules. With bioengineered RNA (BioRNA)…
Anthony Bayega, Spyros Oikonomopoulos, Yu Chang Wang, Jiannis Ragoussis
Full-length transcript sequencing remains a main goal of RNA sequencing. However, even the application of long-read sequencing technologies such as Oxford Nanopore Technologies still fail to yield full-length transcript sequencing for a significant portion of sequenced reads. Since these technologies can sequence reads…
Filip Boskovic, Sarah E. Sandler, Simon Brauburger, Yuan Shui + 6 more
Nanostructures Enable Nanopore Profiling of rRNA Processing and rRNA Variants Authors: Filip Boskovic, Sarah E. Sandler, Simon Brauburger, Yuan Shui, Bhavik Kumar, Joana Pereira Dias, Plamena Naydenova, Jinbo Zhu, Stephen Baker, Ulrich F. Keyser Ribosomal RNAs (rRNAs) serve as species-defining markers and undergo…
Filip Boskovic, Sarah Sandler, Simon Brauburger, Yuan Shui + 6 more
Ribosomal RNAs (rRNAs) serve as species-defining markers and undergo processing steps such as excision of intervening sequences (IVSs). Direct analysis of native rRNAs is hampered by amplification-induced biases and by the high conservation of rRNA sequences, which complicates discrimination of closely related…
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…
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
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…
Mohammed Aledhari, Mohamed Rahouti
Future Directions Authors: ['Mohammed Aledhari' 'Mohamed Rahouti'] Abstract—Gene and RNA editing methods, technologies, and applications are emerging as innovative forms of therapy and medicine, offering more efficient implementation compared to traditional pharmaceutical treatments. Current trends emphasize the urgent…
Michael Lanzillotti, Jennifer Brodbelt
Broad interest in nucleic acids – both their therapeutic capabilities and understanding the nuances of their structure and resulting function – has increased in recent years. Post-transcriptional modifications in particular have become an important analysis target, as these covalent modifications to the sugars…
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
The COVID-19 pandemic underscored the global need for rapid, sensitive, and multiplexed diagnostic assays for viral detection. RT-qPCR remains the standard for SARS-CoV-2 RNA detection, while antigen-based protein assays provide faster, though less sensitive, alternatives. Here, we present a novel diagnostic platform…
Can Firtina
My very first questions in life were met with my parents' patient and loving answers, which sparked a curiosity leading to many more—some of which shaped this thesis. With every question that followed, I have been fortunate to have a life partner who shares in my wonder and journey with her love and patience. This…
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…
Mohammed Alser, Joël Lindegger, Can Fırtına, Nour Almadhoun + 4 more
'Haiyu Mao' 'Gagandeep Singh' 'Juan Gómez-Luna' 'Onur Mutlu'] We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently exist major…
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…
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…
Yipeng Yin, Reed Arneson, Yinan Yuan, Shiyue Fang
The longest oligos that can be chemically synthesized using known methods are typically considered to be 200-mers. Here, we report direct synthesis of an 800-mer green fluorescent protein (GFP) gene and a 1,728-mer Φ29 DNA polymerase gene on an automated synthesizer. Key innovations that enabled the breakthrough…