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Search · four archives
20 papers · ranked by Valyu relevance
Seeun Cha, Jin Kim, Jisan Kim, Doa Kim + 4 more
The brain is a spatially organized tissue where the molecular characteristics of each cell are closely linked to its anatomical location. However, conventional bulk and single-cell RNA sequencing lose this spatial context during the tissue separation process. Spatial transcriptomics (ST) overcomes these limitations by…
Bencong Zhu, Guanyu Hu, Yang Xie, Lin Xu + 2 more
Department of Statistics, The Chinese University of Hong Kong Guanyu Hu Department of Biostatistics and Data Science and Center for Spatial Temporal Modeling for Applications in Population Sciences, The University of Texas Health Science Center at Houston Yang Xie Peter O'Donnell Jr. School of Public Health, The…
José Camacho, Michael Armstrong, Luz García, Caridad Díaz + 1 more
'Carolina Gómez‐Llorente'] Over the past few years, technological advances have allowed for measurement of omics data at the cell level, creating a new type of data generally referred to as single-cell (sc) omics. On the other hand, the so-called spatial omics are a family of techniques that generate biological…
Souvik Seal, Brian Neelon
Advances in spatial omics enable measurement of genes (spatial transcriptomics) and peptides, lipids, or N-glycans (mass spectrometry imaging) across thousands of locations within a tissue. While detecting spatially variable molecules is a well-studied problem, robust methods for identifying spatially varying…
Souvik Seal, Brian Neelon
Advancements in spatial omics technologies have enabled the measurement of expression profiles of different molecules, such as genes (using spatial transcriptomics), and peptides, lipids, or N-glycans (using mass spectrometry imaging), across thousands of spatial locations within a tissue. While identifying molecules…
Dalong Gao, Jin Ning, Gang Liu, Shiquan Sun + 1 more
Recent advances in various single-cell RNA sequencing (scRNA-seq) technologies have enabled profiling the gene expression level with the whole transcriptome at a single-cell resolution. However, it lacks the spatial context of tissues. The image-based transcriptomics in situ studies (e.g., MERFISH and seqFISH) maintain…
Shicheng Zhang, Koichi Saeki, Hiroshi Haeno
Spatial transcriptomics captures neighborhood-dependent gene expression, but existing workflows do not always fully account for measurement scale and often treat space implicitly. We present geneSCOPE, a framework that integrates ecology-inspired statistics with network analysis. Molecules are binned on a grid whose…
Martin Emons, Samuel Gunz, Helena L. Crowell, Izaskun Mallona + 2 more
'Reinhard Furrer' 'Mark D. Robinson'] Spatial omics assays allow for the molecular characterisation of cells in their spatial context. Notably, the two main technological streams, imaging-based and high-throughput sequencingbased, can give rise to very different data modalities. The characteristics of the two data…
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…
Kevin Leempoel, Solange Duruz, Estelle Rochat, Ivo Widmer + 2 more
Geographic Information Systems (GIS) are becoming increasingly popular in the context of molecular ecology and conservation biology thanks to their display options efficiency, flexibility and management of geodata. Indeed, spatial data for wildlife and livestock species is becoming a trend with many researchers…
Bradley T Martin, Zachery D Zbinden, Michael E Douglas, Marlis R Douglas + 2 more
Genetic tools have been widely adopted for provenance determination (or natal location) of plant and animal tissues, with applications particularly prevalent in wildlife forensics () and conservation (). Dimension reduction techniques such as principal components analysis (PCA) have long been the method of choice for…
Sylvie Stucki, Pablo Orozco‐terWengel, Brenna R. Forester, Solange Duruz + 8 more
'Solange Duruz' 'Licia Colli' 'Charles Masembe' 'Riccardo Negrini' 'Erin L. Landguth' 'Matthew R. Jones' 'Michael W. Bruford' 'Pierre Taberlet' 'Stéphane Joost'] Since its introduction, landscape genomics has developed quickly with the increasing availability of both molecular and topo-climatic data. The current…
Lambda Moses, Alik Huseynov, Joseph M Rich, Lior Pachter
SpatialFeatureExperiment is a Bioconductor package that leverages the versatility of Simple Features for spatial data analysis and SpatialExperiment for single-cell -omics to provide an expansive and convenient S4 class for working with spatial -omics data. SpatialFeatureExperiment can be used to store and analyze a…
John Nagorski, Genevera I. Allen, Y-h. Taguchi
Several modern genomic technologies, such as DNA-Methylation arrays, measure spatially registered probes that number in the hundreds of thousands across multiple chromosomes. The measured probes are by themselves less interesting scientifically; instead scientists seek to discover biologically interpretable genomic…
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…
Mary E Dolan, Constance C Holden, M Kate Beard, Carol J Bult
Background Many commonly used genome browsers display sequence annotations and related attributes as horizontal data tracks that can be toggled on and off according to user preferences. Most genome browsers use only simple keyword searches and limit the display of detailed annotations to one chromosomal region of the…
Junhui Qiu, Qi Zhou, Weicai Ye, Qianjun Chen + 1 more
Background The gene-specific sweep is a selection process where an advantageous mutation along with the nearby neutral sites in a gene region increases the frequency in the population. It has been demonstrated to play important roles in ecological differentiation or phenotypic divergence in microbial populations.…
Authors not listed
Extreme weather events increasingly threaten coastal water quality, yet the mechanisms by which tropical cyclones impair microbial conditions remain poorly quantified. We develop a Large Language Model–Assisted Microbial Source Tracking (LAMST) framework to trace the origins of microbial threats—fecal indicator…
Chris D. Lowe, David J. S. Montagnes, Laura E. Martin, Phillip C. Watts + 1 more
'Phillip C. Watts' 'Tilman Alpermann'] Free-living marine protists are often assumed to be broadly distributed and genetically homogeneous on large spatial scales. However, an increasing application of highly polymorphic genetic markers (e.g., microsatellites) has provided evidence for high genetic diversity and…
Zilin Ren, Jiarong Zhang, Yixiang Zhang, Tingting Yang + 6 more
Forensic short-tandem repeats (STR) genetic markers are multi-allelic and widely utilized for individual identification, kinship testing, and cell-line authentication. Nanopore sequencing, known for its portability, is emerging as a promising approach for STR typing, facilitating real-time and in-field testing.…