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Search · four archives
23 papers · ranked by Valyu relevance
Qingwen Li, Dongxu Li, Chen Sun, Guangtao Song + 2 more
Comprehensive transcriptome profiling is essential for understanding RNA diversity and regulation, yet accurate identification and quantification of full-length transcript isoforms remain challenging with short-read sequencing technologies. Nanopore sequencing enables direct sequencing of long cDNA molecules and thus…
David Wissel, Madison M. Mehlferber, Khue M. Nguyen, Vasilii Pavelko + 3 more
Background The assembly of fragmented RNA-sequencing reads into complete transcripts is error-prone, particularly for genes with complex splicing, resulting in ambiguity in transcript discovery and quantification. PacBio long-read RNA sequencing resolves transcripts with greater clarity than short-read technologies.…
Houlin Yu, Christophe H. Georgescu, Akanksha Khorgade, Ghamdan Al-Eryani + 19 more
Recent advances in long-read transcriptome sequencing enable high-throughput profiling of full-length RNA isoforms in bulk, single-cell, and single-nucleus samples. However, long-read datasets typically contain a mixture of complete and partial transcripts, leading to pervasive ambiguity in read-to-isoform assignment…
Robin Gradin, Johan Andersson, Andy Forreryd, Henrik Johansson + 3 more
Non-animal methods for identification and characterization of skin sensitizers are continuously evolving, advancing towards more effective, accurate, and informational assays. The GARDskin assay is a scientifically and regulatory recognized assay for the assessment of skin sensitizers. It currently relies on targeted…
Arya Jadhav, Zachary J. DeBruine
Single-cell RNA-seq captures both mature (spliced) and nascent (unspliced) transcripts, yet standard preprocessing typically collapses these signals into a single expression matrix, obscuring recoverable transcriptional structure and introducing splicing-dependent artifacts in downstream embeddings in foundation…
Liyong He, Kaitong Dang, Qian Sun, Wenjia Wang + 11 more
The technological advancements in single-cell transcriptome analysis make significant progress in both depth and breadth. However, balancing the cell analysis throughput with full-length transcript coverage remains a persistent challenge. Here, CBTi-seq (Combinational Barcoded Tn5 Transposon Insertion sequencing) is…
Kamil Antoszewski, Klaudia Chmielewska, Karolina Jagiello, Tomasz Puzyn
RNA sequencing (RNA-seq) has become a cornerstone of modern biotechnology, offering a comprehensive and high-resolution view of gene expression that enables the discovery of novel transcripts across diverse biological systems. Its applications extend beyond basic transcriptomics, providing powerful tools for uncovering…
Chia-Ling Chou, Anastasiya Grinko, Li-Tao Guo, Alexander M. Leipold + 4 more
The ability to map messenger RNA (mRNA) molecules from individual cells using next-generation sequencing technologies, known as single-cell RNA-seq (scRNA-seq), is transforming biology by redefining cellular identities with unmatched detail. However, all current protocols depend on copying RNA into complementary DNA…
Shakunthala Natarajan, Claudia Sterling, Nancy Choudhary, Najnin Khatun + 3 more
Rapid developments in sequencing technologies have reduced the costs of transcriptomic experiments and resulted in a plethora of publicly available RNA-seq datasets. This is a valuable resource that can be harnessed to obtain novel biological insights through data upcycling. In this wake, we introduce XpBrew, an…
Ali Hamraoui, Audrey Onfroy, Catherine Sénamaud-Beaufort, Fanny Coulpier + 3 more
Alternative splicing plays a crucial role in transcriptomic complexity, yet remains difficult to resolve at the single-cell level due to the limitations of short-read technologies. Coupling single-cell with long-read sequencing offers full-length transcript coverage, enabling more accurate isoform detection. Diverse…
Zijie Xu, Zhen Zhou, Chao Tang, Yating Zhang + 12 more
The generation of transcript variants via alternative utilisation of transcription start sites (TSSs) is a pivotal regulatory mechanism in physiological and pathological states. Recent advancements in 5’ single-cell RNA sequencing (scRNA-seq) have enabled TSS analysis at the single-cell level. However, RNA degradation…
Latiefa Kamarulzaman, Sooyeon Kim, Takuya Hidaka, Misaki Tsuchida + 1 more
Recent advances in shotgun proteomics and immunoassays have yielded powerful single-cell proteomics technologies. However, current methods lack the sensitivity required to comprehensively quantify protein abundances in individual cells. Here, we present single-cell PAGE-PISA, an ultra-sensitive proteome profiling…
Lorenzo Mauri, Federica Stolf, Amy H. Herring, Cameron Miller + 1 more
Interpreting gene expression data requires methods that can uncover coordinated patterns corresponding to biological pathways. Traditional approaches such as principal component analysis and factor models reduce dimensionality, but latent components may have unclear biological meaning. Current approaches to incorporate…
Y-H Taguchi, Turki Turki
Integrating transcriptome, translatome, and proteome data remains challenging because changes in mRNA, ribosome occupancy, and protein abundance do not always occur simultaneously. To address this, we applied tensor-decomposition-based unsupervised feature extraction to a tri-omics dataset generated under…
Kristian Bodulić, Kristian Vlahoviček
Accurate assessment of transcriptome assembly quality is critical to ensure the reliability of subsequent transcriptomic analyses. Here, we present CATS (Comprehensive Assessment of Transcript Sequences), a tool offering both reference-free (CATS-rf) and reference-based (CATS-rb) transcriptome quality evaluation…
Jiaxin Li, Shanjun Mao
Identifying key driver genes governing biological processes such as development and disease progression remains a challenge. While existing methods can reconstruct cellular trajectories or infer static gene regulatory networks (GRNs), they often fail to quantify time-resolved regulatory effects within specific temporal…
Yuhang Yang, Yonggan Bu, Shengyuan Zhou, Yiming Luo + 1 more
Spatial Transcriptomics (ST) measures gene expression while preserving spatial context, but its high cost and low throughput leave public datasets small. Inferring expression directly from widely available Hematoxylin and Eosin (H&E) stained histology offers a cost-effective alternative. However, existing approaches…
Yu Yajun, Xu Guoping, Jiang, Steve + 6 more
RNA sequencing (RNA-seq) and data-independent acquisition mass spectrometry (DIA-MS) proteomic data were collected from 73 and 46 NSCLC cell lines, respectively. Following preprocessing, 1,605 shared genes were retained for analysis. Feature selection was performed using least absolute shrinkage and selection operator…
Jiabei Cheng, Jingbo Zhou, Jun Xia, Changkai Li + 3 more
Simultaneous measurement of multiple omics modalities in single cells enables researchers to gain a more comprehensive understanding of cellular states and regulatory mechanisms. However, due to high experimental costs, significant noise, and incomplete modality coverage, a variety of computational methods for modality…
Authors not listed
mRNA-based technology has emerged as a new class of medicines with a wide range of applications, including viral vaccines, cancer vaccines, and therapeutics for the treatment of metabolic diseases and cardiovascular conditions. Impurities, including double-stranded RNA (dsRNA), mRNA fragments, and mRNA multimers…
Junha Shin, Spencer Halberg, Yuda Liu, Suvojit Hazra + 2 more
- 1 Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA, 53715 - 2 Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA, 53726 - 3 email: sroy@biostat.wisc.edu - \* These authors contributed equally to this article. - \* This article is…
Philipp Röchner, Clarissa Krämer, Johannes U Mayer, Franz Rothlauf + 2 more
Next-generation sequencing (NGS) is a key technique for studying the DNA and RNA of organisms. However, identifying quality problems in NGS data across different experimental settings remains challenging. To develop automated quality-control tools, researchers require datasets with features that capture the…
Song, Zhengyu
RNA modification represents a series of finely regulated molecular processes that influence RNA metabolism, including splicing, translation, localization, stability, turnover, and interactions with RNA-binding proteins (RBPs) or other RNAs, thereby diversifying genetic information [1]. Over 170 different types of RNA…