27 papers · ranked by Valyu relevance
Valentine Svensson, Sarah A Teichmann, Oliver Stegle
Technological advances have enabled low-input RNA-sequencing, paving the way for assaying transcriptome variation in spatial contexts, including in tissues. While the generation of spatially resolved transcriptome maps is increasingly feasible, computational methods for analysing the resulting data are not established.…
Uthsav Chitra, Brian J. Arnold, Hirak Sarkar, Cong Ma + 3 more
Spatially resolved transcriptomics technologies provide high-throughput measurements of gene expression in a tissue slice, but the sparsity of this data complicates the analysis of spatial gene expression patterns such as gene expression gradients. We address these issues by deriving a topographic map of a tissue…
Yeojin Kim, Abhishek Ojha, Alex Schrader, Juyeon Lee + 7 more
Spatial transcriptomics (ST) technologies have enabled new explorations into the spatial organization of tissues and their functional implications. However, one of the most fundamental analyses – comparative analysis of spatial gene expression across phenotypes – remains a formidable challenge. We introduce…
Shicheng Zhang, Koichi Saeki, Hiroshi Haeno
Spatial transcriptomics captures context-dependent gene expression; however, existing workflows do not consistently account for measurement scale and often rely on a user-defined spatial neighbor graph, making results sensitive to this choice and limiting cross-study comparability. We present geneSCOPE (gene Spatial…
Jade Xiaoqing Wang, Xiang Zhou
Spatial transcriptomic technologies are becoming increasingly high-resolution, enabling precise measurement of gene expression at the subcellular level. Here, we introduce a computational method called subcellular expression localization analysis (ELLA), for modeling the subcellular localization of mRNAs and detecting…
Boxiang Liu, Yanjun Li, Liang Zhang
Human and animal tissues consist of heterogeneous cell types that organize and interact in highly structured manners. Bulk and single-cell sequencing technologies remove cells from their original microenvironments, resulting in a loss of spatial information. Spatial transcriptomics is a recent technological innovation…
David Liska, Zachery Wolfe, Adam Norris, Guoqiang Yu
As an example of the utility of VISTA, we investigated whether we could predict interesting new spatially restricted gene expression patterns simply by visual browsing through genes on VISTA. We focused on transcription factor genes, which have been extensively studied for their cell-specific expression and function…
Ruishan Liu, Marco Mignardi, Robert Jones, Martin Enge + 3 more
Recently high-throughput image-based transcriptomic methods were developed and enabled researchers to spatially resolve gene expression variation at the molecular level for the first time. In this work, we develop a general analysis tool to quantitatively study the spatial correlations of gene expression in fixed…
Matthew N. Bernstein, Zijian Ni, Aman Prasad, Jared Brown + 4 more
'Chitrasen Mohanty' 'Ron Stewart' 'Michael A. Newton' 'Christina Kendziorski'] Title: Summary Recent advances in spatially resolved transcriptomics technologies enable both the measurement of genome-wide gene expression profiles and their mapping to spatial locations within a tissue. A first step in spatial…
Zhiwei Fan, Tiangang Wang, Kexin Huang, Binwu Ying + 1 more
Recent advances in spatial omics technologies have revolutionized our ability to study biological systems with unprecedented resolution. By preserving the spatial context of molecular measurements, these methods enable comprehensive mapping of cellular heterogeneity, tissue architecture, and dynamic biological…
Shan Yu, Wei Vivian Li
Spatially resolved transcriptomics technologies have opened new avenues for understanding gene expression heterogeneity in spatial contexts. However, existing methods for identifying spatially variable genes often focus solely on statistical significance, limiting their ability to capture continuous expression patterns…
Rebecca Hunt-Newbury, Ryan Viveiros, Robert Johnsen, Allan Mah + 22 more
'Dina Anastas' 'Lily Fang' 'Erin Halfnight' 'David Lee' 'John Lin' 'Adam Lorch' 'Sheldon McKay' 'H. Mark Okada' 'Jie Pan' 'Ana K Schulz' 'Domena Tu' 'Kim Wong' 'Z Zhao' 'Andrey Alexeyenko' 'Thomas Burglin' 'Eric Sonnhammer' 'Ralf Schnabel' 'Steven J Jones' 'Marco A Marra' 'David L Baillie' 'Donald G Moerman' 'John…
Chichun Tan, Ying Ma
The rapid advancement of spatially resolved transcriptomics (SRT) technology enables gene expression profiling across tissue locations while preserving spatial context. Gene co-expression analysis in SRT data provides critical insights into how genes function together within the tissue microenvironment. However…
Zhuoyan Xu, Kris Sankaran
Spatially resolved transcriptomics (ST) measures gene expression along with the spatial coordinates of the measurements. The analysis of ST data involves significant computation complexity. In this work, we propose gene expression dimensionality reduction algorithm that retains spatial structure. We combine the wavelet…
James Boyle, Gregory Hamm, Eleanor Williams, Robin JG Hartman + 3 more
'Magnus Soderburg' 'Ian Henry' 'Michael Casey'] 1Data Science and AI, Translational Science & Experimental Medicine, Research and Early Development, Cardiovascular, Renal and Metabolism, Biopharmaceuticals R&D, AstraZeneca, Cambridge, UK 2 Integrated Bioanalysis, Clinical Pharmacology and Safety Sciences…
Qi Liu, Chih-Yuan Hsu, Yu Shyr
The expeditious growth in spatial omics technologies enable profiling genome-wide molecular events at molecular and single-cell resolution, highlighting a need for fast and reliable methods to characterize spatial patterns. We developed SpaGene, a model-free method to discover any spatial patterns rapidly in large…
Natalie Charitakis, Mirana Ramialison, Hieu T. Nim
The technology to generate Spatially Resolved Transcriptomics (SRT) data is rapidly being improved and applied to investigate a variety of biological tissues. The ability to interrogate how spatially localised gene expression can lend new insight to different tissue development is critical, but the appropriate tools to…
Guanao Yan, Shuo Harper Hua, Jingyi Jessica Li
In the analysis of spatially resolved transcriptomics data, detecting spatially variable genes (SVGs) is crucial. Numerous computational methods exist, but varying SVG definitions and methodologies lead to incomparable results. We review 31 state-of-the-art methods, categorizing SVGs into three types: overall…
Manuel Cambón
This work seeks to analyse the transcriptional effects of some biochemical mechanisms proposed in previous literature which attempts to explain the differential spatial expression of Hedgehog target genes involved in Drosophila development. Specifically, the expression of decapentaplegic and patched, genes whose…
Sofie Y. N. Delbare, Andrew G. Clark, Claude Desplan
Most people who tune pianos do not have perfect pitch. In the days before electronic tuners, they would accomplish this feat with amazing precision by listening for the rate at which two notes, struck simultaneously, would “beat” against each other. The contrast of two tones can allow interval tuning with a pitch error…
Siddhartha G. Jena, Archit Verma, Barbara E. Engelhardt
Genomics methods have uncovered patterns in a range of biological systems, but obscure important aspects of cell behavior: the shape, relative locations of, movement of, and interactions between cells in space. Spatial technologies that collect genomic or epigenomic data while preserving spatial information have begun…
Authors not listed
Self-organizing tissues, such as organoids, offer transformative potential beyond healthcare by enabling the sustainable production of advanced materials. Resource scarcity and global warming drive the need for innovative fabrication solutions. This prospective review explores developmental biology as a manufacturing…
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…
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Understanding how plants respond to dynamic and spatially variable stimuli is a key goal in plant sciences. Traditional imaging methods often involve a trade-off between environmental control and spatial resolution, limiting their ability to capture real-time responses in high resolution. Microfluidic technology…
Zahir Ali, Maged Serag, Gozde Demirer, Bruno Torre + 4 more
Efficient delivery of DNA, RNA, and genome engineering machinery to plant cells will enable efforts to genetically modify plants for global food security, sustainable energy production, synthetic biology applications, and climate change resilience. For the delivery of functional genetic units into plant cells, charged…
Spencer Kim, Dylan Gray, Michelle Shanguhyia, Rachel Steinhardt
Recreating the signaling profile a chemical synapse to analyze serotonin receptor activation is a challenge. This is due in part to the kinetics of the synapse, where neurotransmitters are rapidly released and quickly cleared by active reuptake machinery. One strategy to produce a rapid rise in a bio-orthogonally…
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…