24 papers · ranked by Valyu relevance
Ian Jhemes Oliveira Sousa, Kerolayne de Melo Nogueira, Ester Miranda Pereira
1## Introduction: from morphology to functional precision in oncology Modern oncology has witnessed a paradigm shift, moving from therapeutic approaches based on histopathological and anatomical characteristics to personalized strategies defined as Precision Medicine (1). This evolution is driven by the increasing…
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…
Xianghao Zhan, Jingyu Xu, Yuanning Zheng, Zinaida Good + 1 more
Spatial transcriptomics enables spatial gene expression profiling, motivating computational models that capture spatially conditioned regulatory relationships. We introduce SAGE-FM, a lightweight spatial transcriptomics foundation model based on graph convolutional networks (GCN) trained with a masked-central-spot…
Apostolos Malatras, Ioannis Michalopoulos
Transcriptomics refers to the study of all transcripts of a cell or a tissue, as well as transcript expression quantification. Transcriptomics technologies include microarrays and RNA-Seq. The accumulation of transcriptomics samples freely available in public repositories has enabled the massive re-analysis of those…
Andrew Xue, Bo Cai, Qian Xue, Nianping Liu + 3 more
Single-cell RNA sequencing has transformed our understanding of tissue complexity and heterogeneous cell states, yet provides little information about the subcellular organization of transcriptomes - despite the central role of RNA localization in splicing, translation, and function. Here we introduce single-cell…
Daria Chudakova, Olga Astakhova, Matthew Shkap, Ekaterina Levichkina + 4 more
Traumatic spinal cord injury (SCI) is a severe medical condition, often resulting in permanent disability, with significant impacts on patients’ quality of life and burden on healthcare systems. Current therapeutic approaches for SCI are insufficient, advocating for the development of more effective treatments. As…
Kayleigh Casmey, Maria Zimmermann, Yuxin Xie, Sierra A. Codeluppi-Arrowsmith + 2 more
Single-cell omics technology has advanced rapidly since its inception, offering increasing precision, resolution, and technical diversity to explore cell-specific molecular features in the human brain and neuropsychiatric disorders. While traditional bulk genomic analyses have provided valuable insights into the…
Tanweer Beckett, Uljana Hesse, Alexandra S. Dubrovina
Rooibos (Aspalathus linearis) is one of the few endemic South African plants that has achieved economic importance and international acclaim, mostly as a herbal tea. Plant production, limited to a small mountainous region in South Africa, is at risk as commercial rooibos longevity is in decline, mostly due to low…
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…
Molly Borowiak, Yun William Yu
Eukaryotic genes can encode multiple protein isoforms based on alternative splicing of their transcribed regions. Most modern novel isoform discovery methods function by identifying and assembling exon splice junctions from an RNAseq sample. However, splice junctions can only be accurately annotated with time-intensive…
Jeremy W. Prokop, Stephanie M. Bilinovich, Ember Tokarski, Sangeetha Vishweswaraiah + 27 more
All three of the above studies showed heterogeneous individuals, where we realized the power of studying heterogeneous biology within RNA sequencing. As the heatmap of [F0007] shows, within many of our cohorts, there are unique patients with strong red bands in nearly every category of data mapping, suggesting that…
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…
Shanaka Liyanaarachchi, Chathurya Wijethunga, S. S. Riaz Ahamed, Ali Absar + 1 more
Spatial transcriptomics is an emerging field that enables the identification of functional regions based on the spatial distribution of gene expression. Integrating this functional information present in transcriptomic data with structural data from histopathology images is an active research area with applications in…
Maxfield M.G. Kelsey, Radha L. Kalekar, John M. Sedivy
Cellular senescence drives aging-related tissue dysfunction through the senescence-associated secretory phenotype (SASP), an inflammatory secretome linked to retrotransposable element (RTE) derepression. Transcriptomic and proteomic approaches have extensively characterized the senescence program, but key gaps remain…
Keunho Byeon, Jin Tae Kwak
Spatial transcriptomics offers spatially resolved gene expression profiling within tissue sections, but its cost and limited throughput hinder large-scale deployment. To extend this capability to routine practice, recent computational methods aim to infer spatial gene expression directly from ubiquitous hematoxylin and…
Authors not listed
The WRN helicase has recently emerged as a promising therapeutic target for microsatellite instability (MSI)-high cancers. Here, we report LXW-P1, a potent WRN degrader derived from marine bromotyrosine alkaloids. Its molecular target was identified using an AI-guided, pathway-informed perturbation transcriptomics…
Pritam Dey, Rajarshi Guhaniyogi, Yang Ni, Bani K. Mallick
Spatially resolved transcriptomics is a fast-developing set of technologies that enables the measurement of localized gene expression across spatial locations in a sample. Detecting spatially varying genes is critical for analyzing such data, yet existing methods often fail to account for inter-gene correlations…
Yiyang Zhang, Bokai Zhao, Xiaoru Zhang, Zongchang Du + 2 more
Single-cell-resolution spatial transcriptomics profiles gene expression at cellular locations in native tissues, yet accurate cell-type annotation remains challenging: imaging-based platforms are constrained by targeted gene panels, whereas sequencing-based platforms often suffer from sparse molecular capture and…
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…
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…
Authors not listed
RNA droplets assembled from co-transcriptionally folded nanostructures have recently emerged as a promising platform for constructing protocells and minimal synthetic cell models. In these systems, a custom-designed DNA template encodes an RNA nanostar, which is produced by transcription and self-assembles into…
Authors not listed
RNA molecules fold into complex three-dimensional structures that determine their function. A wide range of mathematical frameworks, such as chord diagrams, fatgraphs, and context-free grammars, have been used to represent these structures; however, these models have largely been developed from mathematical motivations…
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…
Tiziano Vignolini, Olivia Carril, Victor Tobiasson, Joe Georgeson + 8 more
Ribosome composition can vary through differences in associated proteins, post-transcriptional and post-translational modifications. Such heterogeneity enables ribosomes to respond to environmental^1^ or pathological^2,3^ conditions, and modulate localized translation^4^. A long-standing observation has also been the…