16 papers · ranked by Valyu relevance
Chit Tong Lio, Tolga Düz, Markus Hoffmann, Lina-Liv Willruth + 3 more
RNA sequencing offers unique insights into transcriptome diversity, and a plethora of tools have been developed to analyze alternative splicing. One important task is to detect changes in the relative transcript abundance in differential transcript usage (DTU) analysis. The choice of the right analysis tool is…
Panagiotis Papastamoulis, Magnus Rattray
Next generation sequencing allows the identification of genes consisting of differentially expressed transcripts, a term which usually refers to changes in the overall expression level. A specific type of differential expression is differential transcript usage (DTU) and targets changes in the relative within gene…
Shuhua Fu, Parker Wilson, Bo Zhang
Cells can transcribe different isoforms of a gene by using distinct Transcriptional Start Regions (TSRs), which are recognized by RNA-Polymerase II and regulated by cell-type-specific expressed transcription factors, eventually forming tissue and cell-type-specific expression during development. However, how the…
Jakob Sponholz, Andreas Weilinghoff, Juliane Schopf
In qualitative research, data transcription is often labor-intensive and time-consuming. To expedite this process, a workflow utilizing artificial intelligence (AI) was developed. This workflow not only enhances transcription speed but also addresses the issue of AI-generated transcripts often lacking compatibility…
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…
Houjun Liu, Brian MacWhinney, Davida Fromm, Alyssa Lanzi
Purpose: A major barrier to the wider use of language sample analysis (LSA) is the fact that transcription is very time intensive. Methods that can reduce the required time and effort could help in promoting the use of LSA for clinical practice and research. Method: This article describes an automated pipeline, called…
Stephen W. Hartley, James C. Mullikin
Although RNA-Seq data provide unprecedented isoform-level expression information, detection of alternative isoform regulation (AIR) remains difficult, particularly when working with an incomplete transcript annotation. We introduce JunctionSeq, a new method that builds on the statistical techniques used by the…
Shachar Mirkin, Michal Jacovi, Tamar Lavee, Hong-Kwang Jeff Kuo + 5 more
'Samuel Thomas' 'Leslie Sager' 'Lili Kotlerman' 'Elad Venezian' 'Noam Slonim'] This paper describes an English audio and textual dataset of debating speeches, a unique resource for the growing research field of computational argumentation and debating technologies. We detail the process of speech recording by…
Joe Nockels, Paul Gooding, Sarah Ames, Melissa Terras
Handwritten Text Recognition (HTR) technology is now a mature machine learning tool, becoming integrated in the digitisation processes of libraries and archives, speeding up the transcription of primary sources and facilitating full text searching and analysis of historic texts at scale. However, research into how HTR…
Mariia Zelenskaia, Yazhini Arangasamy, Milot Mirdita, Johannes Söding + 2 more
Transcriptome annotation is the task of associating biological and functional context to RNA-Seq data. This represents an essential step in rendering the data usable, especially in cases when a reference genome is absent (). The process typically uses protein sequences, translated in silico from pre-assembled…
Tamer Butto, Stefan Pastore, Max Müller, Kaushik Viswanathan Iyer + 6 more
Nanopore technology offers real-time sequencing opportunities, providing rapid access to sequenced data and allowing researchers to manage the sequencing process efficiently, resulting in cost-effective strategies. Here, we present focused case studies demonstrating the versatility of real-time transcriptomics analysis…
Ludong Yang, Xinxin Zhang, Fan Wang, Li Zhang + 2 more
Nanopore direct RNA sequencing (DRS) provides the direct access to native RNA strands with full-length information, shedding light on rich qualitative and quantitative properties of gene expression profiles. Here with NanoTrans, we present an integrated computational framework that comprehensively covers all major…
William C. Hacker, Adrian H. Elcock
Stochastic simulation models have played an important role in efforts to understand the mechanistic basis of prokaryotic transcription and translation. Despite the fundamental linkage of these processes in bacterial cells, however, most simulation models have been limited to representations of either transcription or…
Wenyu Zhang, Mason Guy, Jerrica Yang, Lucy Hao + 5 more
Large Language Models (LLMs) have revolutionized numerous industries as well as accelerated scientific research. However, their application in planning and conducting experimental science, has been limited. In this study, we introduce an adaptable prompt-set with GPT-4, converting literature experimental procedures…
Vighnesh Ghatpande, Uma Paul, MacKenzie A Howard, Can Cenik
In the last decade, an unexpectedly large number of translated regions (translons) have been discovered using ribosome profiling and proteomics. Translons can regulate mRNA translation and encode micropeptides that contribute to multiprotein complex formation, Ca^2+^ regulation in muscle, and signaling during embryonic…
Michael A. DeJesus, Chaitra Ambadipudi, Richard Baker, Christopher Sassetti + 2 more
'Christopher Sassetti' 'Thomas R. Ioerger' 'Paul P Gardner'] TnSeq has become a popular technique for determining the essentiality of genomic regions in bacterial organisms. Several methods have been developed to analyze the wealth of data that has been obtained through TnSeq experiments. We developed a tool for…