Nature Biotechnology, Год журнала: 2025, Номер unknown
Опубликована: Янв. 24, 2025
Язык: Английский
Nature Reviews Genetics, Год журнала: 2023, Номер 24(8), С. 494 - 515
Опубликована: Март 2, 2023
Язык: Английский
Процитировано
647
Cell Reports Methods, Год журнала: 2023, Номер 3(6), С. 100498 - 100498
Опубликована: Июнь 1, 2023
Biological systems are immensely complex, organized into a multi-scale hierarchy of functional units based on tightly regulated interactions between distinct molecules, cells, organs, and organisms. While experimental methods enable transcriptome-wide measurements across millions popular bioinformatic tools do not support systems-level analysis. Here we present hdWGCNA, comprehensive framework for analyzing co-expression networks in high-dimensional transcriptomics data such as single-cell spatial RNA sequencing (RNA-seq). hdWGCNA provides functions network inference, gene module identification, enrichment analysis, statistical tests, visualization. Beyond conventional RNA-seq, is capable performing isoform-level analysis using long-read data. We showcase from autism spectrum disorder Alzheimer's disease brain samples, identifying disease-relevant modules. directly compatible with Seurat, widely used R package demonstrate the scalability by dataset containing nearly 1 million cells.
Язык: Английский
Процитировано
289
Cancer Cell, Год журнала: 2023, Номер 41(3), С. 404 - 420
Опубликована: Фев. 16, 2023
Язык: Английский
Процитировано
222
Nature Medicine, Год журнала: 2022, Номер 28(12), С. 2486 - 2496
Опубликована: Дек. 1, 2022
Язык: Английский
Процитировано
154
Nature Communications, Год журнала: 2023, Номер 14(1)
Опубликована: Июль 26, 2023
Abstract Ulcerative colitis and Crohn’s disease are chronic inflammatory intestinal diseases with perplexing heterogeneity in manifestation response to treatment. While the molecular basis for this remains uncharacterized, single-cell technologies allow us explore transcriptional states within tissues at an unprecedented resolution which could further understanding of these complex diseases. Here, we apply RNA-sequencing human inflamed intestine show that largest differences among patients present myeloid compartment including macrophages neutrophils. Using spatial transcriptomics tissue (CosMx Spatial Molecular Imaging) spatially localize each macrophage neutrophil subsets identified by unravel diversity based on their localization. Finally, combined analysis reveals a strong communication network involving fibroblasts. Our data sheds light cellular complexity points towards stromal compartments as important patient-to-patient heterogeneity.
Язык: Английский
Процитировано
123
Genomics, Год журнала: 2023, Номер 115(5), С. 110671 - 110671
Опубликована: Июнь 21, 2023
The diverse cell types of an organ have a highly structured organization to enable their efficient and correct function. To fully appreciate gene functions in given type, one needs understand how much, when where the is expressed. Classic bulk RNA sequencing popular single destroy structural fail provide spatial information. However, location expression or complex tissue provides key clues comprehend neighboring genes cells cross talk, transduce signals work together as team complete job. functional requirement for content has been driving force rapid development transcriptomics technologies past few years. Here, we present overview current with special focus on commercially available currently being commercialized technologies, highlight applications by category discuss experimental considerations first experiment.
Язык: Английский
Процитировано
89
Journal of Translational Medicine, Год журнала: 2023, Номер 21(1)
Опубликована: Май 18, 2023
Spatial transcriptomics technologies developed in recent years can provide various information including tissue heterogeneity, which is fundamental biological and medical research, have been making significant breakthroughs. Single-cell RNA sequencing (scRNA-seq) cannot spatial information, while allow gene expression to be obtained from intact sections the original physiological context at a resolution. Various insights generated into architecture further elucidation of interaction between cells microenvironment. Thus, we gain general understanding histogenesis processes disease pathogenesis, etc. Furthermore, silico methods involving widely distributed R Python packages for data analysis play essential roles deriving indispensable bioinformation eliminating technological limitations. In this review, summarize available transcriptomics, probe several applications, discuss computational strategies raise future perspectives, highlighting developmental potential.
Язык: Английский
Процитировано
81
Journal of genetics and genomics/Journal of Genetics and Genomics, Год журнала: 2023, Номер 50(9), С. 625 - 640
Опубликована: Март 27, 2023
The ability to explore life kingdoms is largely driven by innovations and breakthroughs in technology, from the invention of microscope 350 years ago recent emergence single-cell sequencing, which scientific community has been able visualize at an unprecedented resolution. Most recently, Spatially Resolved Transcriptomics (SRT) technologies have filled gap probing spatial or even three-dimensional organization molecular foundation behind mysteries life, including origin different cellular populations developed totipotent cells human diseases. In this review, we introduce progress challenges on SRT perspectives bioinformatic tools, as well representative applications. With currently fast-moving promising results early adopted research projects, can foresee bright future such new tools understanding most profound analytical level.
Язык: Английский
Процитировано
78
Nature Methods, Год журнала: 2023, Номер 20(3), С. 387 - 399
Опубликована: Фев. 16, 2023
Язык: Английский
Процитировано
72
Nature Reviews Clinical Oncology, Год журнала: 2023, Номер 20(4), С. 211 - 228
Опубликована: Янв. 31, 2023
Язык: Английский
Процитировано
67