17 papers · ranked by Valyu relevance
Lukas M. Weber, Arkajyoti Saha, Abhirup Datta, Kasper D. Hansen + 1 more
'Stephanie C. Hicks'] Feature selection to identify spatially variable genes or other biologically informative genes is a key step during analyses of spatially-resolved transcriptomics data. Here, we propose nnSVG, a scalable approach to identify spatially variable genes based on nearest-neighbor Gaussian processes.…
Zhijian Li, Zain M.Patel, Dongyuan Song, Sai Nirmayi Yasa + 4 more
Background Spatially resolved transcriptomics offers unprecedented insight by enabling the profiling of gene expression within the intact spatial context of cells, effectively adding a new and essential dimension to data interpretation. To efficiently detect spatial structure of interest, an essential step in analyzing…
Rui Jiang, Zhen Li, Yuhang Jia, Siyu Li + 2 more
'Sang Woo Kim'] Recent advances in spatial transcriptomics have revolutionized the understanding of tissue organization. The identification of spatially variable genes (SVGs) is an essential step for downstream spatial domain characterization. Although several methods have been proposed for identifying SVGs, inadequate…
Sikta Das Adhikari, Jiaxin Yang, Jianrong Wang, Yuehua Cui
With the emergence of advanced spatial transcriptomic technologies, there has been a surge in research papers dedicated to analyzing spatial transcriptomics data, resulting in significant contributions to our understanding of biology. The initial stage of downstream analysis of spatial transcriptomic data has centered…
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…
Peiying Cai, Mark D Robinson, Simone Tiberi, Anthony Mathelier
Spatially resolved transcriptomics (SRT) technologies allow the spatial characterization of gene expression profiles in a tissue. SRT techniques can be broadly grouped into two categories: sequencing-based methods (e.g. Slide-seq (), Slide-seq-V2 (), 10X Genomics Visium, spatial transcriptomics (), high definition…
Haotian Zhuang, Xinyi Shang, Wenpin Hou, Zhicheng Ji
Spatially variable genes (SVGs) reveal the molecular and functional heterogeneity of cells across different spatial regions of a tissue. We found that sample-wide SVGs, identified by previous methods across the whole sample, largely overlap with cell-type marker genes derived from single-cell gene expression, leaving…
Yuchen Liang, Guowei Shi, Runlin Cai, Yuchen Yuan + 7 more
'Long Yu' 'Yingjian Huang' 'Qian Shi' 'Lizhe Wang' 'Jun Li' 'Zhonghui Tang'] Computational methods have been proposed to leverage spatially resolved transcriptomic data, pinpointing genes with spatial expression patterns and delineating tissue domains. However, existing approaches fall short in uniformly quantifying…
Haohao Su, Yuesong Wu, Bin Chen, Yuehua Cui
One of the major challenges in spatial transcriptomics is to detect spatially variable genes (SVGs), whose expression patterns are non-random across tissue locations. Many SVGs correlate with cell type compositions, introducing the concept of cell type-specific SVGs (ctSVGs). Existing ctSVG detection methods treat cell…
Yijun Li, Stefan Stanojevic, Bing He, Zheng Jing + 3 more
Spatial transcriptomics has allowed researchers to analyze transcriptome data in its tissue sample’s spatial context. Various methods have been developed for detecting spatially variable genes (SV genes), whose gene expression over the tissue space shows strong spatial autocorrelation. Such genes are often used to…
Carissa Chen, Hani Jieun Kim, Pengyi Yang
Background The identification of genes that vary across spatial domains in tissues and cells is an essential step for spatial transcriptomics data analysis. Given the critical role it serves for downstream data interpretations, various methods for detecting spatially variable genes (SVGs) have been proposed. However…
Yijun Li, Stefan Stanojevic, Bing He, Zheng Jing + 4 more
Spatial omics technologies are one of the breakthroughs in science in the last several years (, , , ). Such technologies are able to systematically measure transcriptome information in the tissue space, thereby preserving the spatial context of gene expression. The addition of spatial information allows researchers to…
Ragnhild Laursen, Han Chen, Jack Demaray, Karin Pelka + 1 more
Methods for identifying complex multicellular spatial neighborhoods do not scale to existing spatial transcriptomics data, and often divide tissues into distinct neighborhoods with hard borders. We develop neighborhood NMF (NNMF) that identifies functionally coherent neighborhoods among heterogeneous cells. NNMF scales…
Jinpu Li, Mauminah Raina, Yiqing Wang, Chunhui Xu + 7 more
Emerging spatial omics technologies empower comprehensive exploration of biological systems from multi-omics perspectives in their native tissue location in two and three-dimensional space. However, sparse sequencing capacity and growing spatial resolution in spatial omics present significant computational challenges…
Hamid Reza Razzaghian, Lars A. Forsberg, Kancherla Reddy Prakash, Szymon Przerada + 14 more
'Szymon Przerada' 'Hanna Paprocka' 'Anna Zywicka' 'Maxwell P. Westerman' 'Nancy L. Pedersen' "Terrance P. O'Hanlon" 'Lisa G. Rider' 'Frederick W. Miller' 'Ewa Srutek' 'Michal Jankowski' 'Wojciech Zegarski' 'Arkadiusz Piotrowski' 'Devin Absher' 'Jan P. Dumanski' 'Tatjana Adamovic'] Although historically considered as…
Mara KN Lawniczak, Alisha K Holloway, David J Begun, Corbin D Jones
Analysis of six Drosophila simulans genotypes revealed that genes with greater variation in gene expression between genotypes also have higher levels of sequence polymorphism in many gene features.
Elena V. Ignatieva, Victor G. Levitsky, Nikolay A. Kolchanov
The expression level of each gene is controlled by its regulatory regions, which determine the precise regulation in a tissue-specific manner, according to the developmental stage of the body and the necessity of a response to external stimuli. Nucleotide substitutions in regulatory gene regions may modify the affinity…