20 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.…
Fei Qin, Xizhi Luo, Bo Cai, Feifei Xiao + 1 more
The emergence of spatial transcriptomic technologies has opened new avenues to investigate gene activities while preserving the spatial context of tissues. Utilizing data generated by such technologies, the identification of spatially variable (SV) genes is an essential step in investigating tissue landscapes and…
Minsheng Hao, Kui Hua, Xuegong Zhang
Recent developments of spatial transcriptomic sequencing technologies provide powerful tools for understanding cells in the physical context of tissue micro-environments. A fundamental task in spatial gene expression analysis is to identify genes with spatially variable expression patterns, or spatially variable genes…
Hanbyul Lee, Haochen Sun, Xuewei Cao, Berke Karaahmet + 10 more
Spatial gene expression patterns underlie tissue organization, development, and disease, yet current methods for detecting spatially variable genes (SVGs) lack the flexibility to capture multi-scale structure, ensure robustness across platforms, and integrate with genetic data to assess disease relevance. We present…
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…
Michael Fatemi, Eric Feng, Cyril Sharma, Zarif Azher + 11 more
'Ojas Ramwala' 'Scott M. Palisoul' 'Rachael E. Barney' 'Laurent Perreard' 'Fred W. Kolling' 'Lucas A. Salas' 'Brock C. Christensen' 'Gregory J. Tsongalis' 'Louis J. Vaickus' 'Joshua J. Levy'] Over 150 000 Americans are diagnosed with colorectal cancer (CRC) every year, and annually over 50 000 individuals will die from…
Catherine Higgins, Jingyi Jessica Li, Michelle Carey
Recent advancements in spatial transcriptomics (ST) technologies allow researchers to simultaneously measure RNA expression levels for hundreds to thousands of genes while preserving spatial information within tissues, providing critical insights into spatial gene expression patterns, tissue organization, and gene…
Catherine Higgins, Jingyi Jessica Li, Michelle Carey
Novel Method for Identifying Spatial Gene Co-Expression Modules Authors: ['Catherine Higgins' 'Jingyi Jessica Li' 'Michelle Carey'] Recent advancements in spatial transcriptomics technologies allow researchers to simultaneously measure RNA expression levels for hundreds to thousands of genes while preserving spatial…
Jian Hu, Xiangjie Li, Kyle Coleman, Amelia Schroeder + 4 more
Recent advances in spatial transcriptomics technologies have enabled comprehensive characterization of gene expression patterns in the context of tissue microenvironment. To elucidate spatial gene expression variation, we present SpaGCN, a graph convolutional network approach that integrates gene expression, spatial…
Michael Dumelle, Matt Higham, Jay M. Ver Hoef, A. K. M. Anisur Rahman
'A. K. M. Anisur Rahman'] spmodel is an R package used to fit, summarize, and predict for a variety spatial statistical models applied to point-referenced or areal (lattice) data. Parameters are estimated using various methods, including likelihood-based optimization and weighted least squares based on variograms.…
Oluyemi A. Okunlola, Mohannad Alobid, Olusanya E. Olubusoye, Kayode Ayinde + 2 more
'Kayode Ayinde' 'Adewale F. Lukman' 'István Szűcs'] In this study, we propose a robust approach to handling geo-referenced data and discuss its statistical analysis. The linear regression model has been found inappropriate in this type of study. This motivates us to redefine its error structure to incorporate the…
Hezhishi Jiang, Li‐Yan Xu, Tianshu Li, Zekun Chen + 3 more
'Hongmou Zhang' 'Yu Liu'] The communications and interrelations between different locations on the Earth's surface have far-reaching implications for both social and natural systems1–11. Effective spatial analytics ideally require a spatial representation12, where geographic principles are succinctly expressed within a…
Harish Doraiswamy, Juliana Freire
Given the massive growth in the volume of spatial data, there is a great need for systems that can efficiently evaluate spatial queries over large data sets. These queries are notoriously expensive using traditional database solutions. While faster response times can be attained through powerful clusters or servers…
Emiko Dupont, Simon N. Wood, Nicole H. Augustin
In spatial regression models, collinearity between covariates and spatial effects can lead to significant bias in effect estimates. This problem, known as spatial confounding, is encountered modeling forestry data to assess the effect of temperature on tree health. Reliable inference is difficult as results depend on…
Zhe Jiang
—With the advancement of GPS and remote sensing technologies, large amounts of geospatial and spatiotemporal data are being collected from various domains, driving the need for effective and efficient prediction methods. Given spatial data samples with explanatory features and targeted responses (categorical or…
Holger Engleitner, Ashwani Jha, Marta Suarez Pinilla, Amy Nelson + 5 more
'Daniel Herron' 'Geraint Rees' 'Karl Friston' 'Martin Rossor' 'Parashkev Nachev'] Title: Summary The characteristics and determinants of health and disease are often organized in space, reflecting our spatially extended nature. Understanding the influence of such factors requires models capable of capturing spatial…
Zhe Jiang
—With advancements in GPS, remote sensing, and computational simulation, an enormous volume of spatiotemporal data is being collected at an increasing speed from various application domains, spanning Earth sciences, agriculture, smart cities, and public safety. Such emerging geospatial and spatiotemporal big data…
Authors not listed
Scope: I introduce a reproducible, closed-surface mapping of the periodic system onto a sphere with a single equatorial ring, yielding a symmetric alternative to 2D layouts. The construction partitions the sphere into belts that match the cardinalities of the s/p/d/f blocks (2/6/10/14), places lanthanoids and actinoids…
Authors not listed
The range of geometric configurations possible for an arbitrary coordination centre ABn, is a key aspect of stereoisomerism and molecular geometry in general. Despite this, much focus within Chemistry concerning ABn geometries has not taken a rigorous and holistic approach. Using a precise definition for configurations…
Mohsen Farshad
Information and force definition has been intertwined with the concept of entropy for many years. The information for displacement of degrees of freedom with Brownian motions at a given temperature in space emerges as an entropic force between species. Here, we use this concept of entropy to understand the underlying…