Category: methods

December 8, 2023 / Nat Genet

  • Varrone M, Tavernari D, Santamaria-Martínez A, Walsh LA, Ciriello G
Tissues are organized in cellular niches, the composition and interactions of which can be investigated using spatial omics technologies. However, systematic analyses of tissue composition are challenged by the scale…
November 28, 2023 / BMC Genomics

  • Dezem FS, Marção M, Ben-Cheikh B, Nikulina N, Omotoso A, Burnett D, Coelho P, Hurley J, Gomez C, Phan-Everson T, Ong G, Martelotto L, Lewis ZR, George S, Braubach O, Malta TM, Plummer J
Cell annotation is a crucial methodological component to interpreting single cell and spatial omics data. These approaches were developed for single cell analysis but are often biased, manually curated and…
November 11, 2023 / Nucleic Acids Res

  • Liu N, Bhuva DD, Mohamed A, Bokelund M, Kulasinghe A, Tan CW, Davis MJ
To gain a better understanding of the complexity of gene expression in normal and diseased tissues it is important to account for the spatial context and identity of cells in…
October 24, 2023 / Biomedicines

  • Ivanova E, Fayzullin A, Grinin V, Ermilov D, Arutyunyan A, Timashev P, Shekhter A
Renal cell carcinoma is a significant health burden worldwide, necessitating accurate and efficient diagnostic methods to guide treatment decisions. Traditional pathology practices have limitations, including interobserver variability and time-consuming evaluations.…
October 20, 2023 / Diagnostic Molecular Pathology (2nd ed)

  • Church SE, Jessica Perez, Breana Murphy, Hiromi Sato, Sarah E. Warren, Joseph M. Beechem
Spatial biology is emerging as a new field of research as technological advancements allow investigators to characterize high-plex profiles of RNA transcripts and proteins in the tissue isolated from patients…
October 5, 2023 / Brief Bioinform

  • Tang Z, Liu X, Li Z, Zhang T, Yang B, Su J, Song Q
Spatial cellular authors heterogeneity contributes to differential drug responses in a tumor lesion and potential therapeutic resistance. Recent emerging spatial technologies such as CosMx, MERSCOPE and Xenium delineate the spatial…
September 15, 2023 / Oncol Res

  • Xie F, Xi N, Han Z, Luo W, Shen J, Luo J, Tang X, Pang T, Lv Y, Liang J, Liao L, Zhang H, Jiang Y, Li Y, He J
Spatial omics technology integrates the concept of space into omics research and retains the spatial information of tissues or organs while obtaining molecular information. It is characterized by the ability…
September 12, 2023 / Nat Commun

  • Tang Z, Li Z, Hou T, Zhang T, Yang B, Su J, Song Q
Recent advances in high-throughput molecular imaging have pushed spatial transcriptomics technologies to subcellular resolution, which surpasses the limitations of both single-cell RNA-seq and array-based spatial profiling. The multichannel immunohistochemistry images…
September 11, 2023 / Biomed Pharmacother

  • Song G, Plumlee P, Ahn JY, Wong ST, Zhao H
The blood-brain barrier (BBB) plays a critical role in determining the effectiveness of systemic treatments for brain diseases. Over the years, several innovative approaches in BBB opening and drug delivery…
September 4, 2023 / Int J Biol Sci

  • Du J, An ZJ, Huang ZF, Yang YC, Zhang MH, Fu XH, Shi WY, Hou J
Since its first application in 2016, spatial transcriptomics has become a rapidly evolving technology in recent years. Spatial transcriptomics enables transcriptomic data to be acquired from intact tissue sections and…
September 2, 2023 / Bioinformatics

  • Peters Couto BZ, Robertson N, Patrick E, Ghazanfar S
Motivation: Imaging-based spatial transcriptomics (ST) technologies have achieved subcellular resolution, enabling detection of individual molecules in their native tissue context. Data associated with these technologies promise unprecedented opportunity toward understanding…
September 1, 2023 / J Clin Transl Hepatol

  • Chen G, Xu W, Long Z, Chong Y, Lin B, Jie Y
The liver is the largest glandular organ in the body and has a unique distribution of cells and biomolecules. However, the treatment outcome of end-stage liver disease is extremely poor.…