Search Results - "Spatial Transcriptomics methods"

Disparities in spatially variable gene calling highlight the need for benchmarking spatial transcriptomics methods by Charitakis, Natalie, Salim, Agus, Piers, Adam T., Watt, Kevin I., Porrello, Enzo R., Elliott, David A., Ramialison, Mirana

“…Identifying spatially variable genes (SVGs) is a key step in the analysis of spatially resolved transcriptomics data. SVGs provide biological insights by…”
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Multiplexed spatial transcriptomics methods and the application of expansion microscopy by Fortner, Andra, Bucur, Octavian

“…While spatial transcriptomics has undeniably revolutionized our ability to study cellular organization, it has driven the development of a great number of…”
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A Comparative Review of Spatial Transcriptomics Methods with Focus on Gastrointestinal Cancer Research by Park, Seon Yeong, Kim, Yun Hak

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Spatial transcriptomics and immunophenotyping uncover chronic inflammation-induced immune adaptations favoring dysplasia development in patients at risk of colitis-associated cancer by Frigerio, Sofía, Khan, Hina N, Amini, Mojtaba, Mol, Bregje, Neefjes-Borst, Andra, Wildenberg, Manon E, Ponsioen, Cyriel Y, D’Haens, Geert R, Vercoulen, Yvonne, Grootjans, Joep

“…Abstract Background and Aims Colitis-associated cancer (CAC) is the most severe complication of inflammatory bowel disease (IBD). We hypothesized that chronic…”
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Integrated spatial morpho-transcriptomics predicts functional traits in pancreatic cancer by Gong, Dennis, Liu, Rachel, Cui, Yi, Rhodes, Michael, Bae, Jung Woo, Beechem, Joseph M., Hwang, William L.

“…Analyses of patient-derived cell lines have greatly enhanced discovery of molecular biomarkers and therapeutic targets. However, characterization of cellular…”
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Disparities in spatially variable gene calling highlight the need for benchmarking spatial transcriptomics methods by Charitakis, Natalie C, Agus Salim, Piers, Adam T, Watt, Kevin I, Porrello, Enzo R C, Elliott, David A, Ramialison, Mirana

“…Identifying spatially variable genes (SVGs) is a key step in the analysis of spatially resolved transcriptomics (SRT) data. SVGs provide biological insights by…”
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Systematic comparison of sequencing-based spatial transcriptomic methods by You, Yue, Fu, Yuting, Li, Lanxiang, Zhang, Zhongmin, Jia, Shikai, Lu, Shihong, Ren, Wenle, Liu, Yifang, Xu, Yang, Liu, Xiaojing, Jiang, Fuqing, Peng, Guangdun, Sampath Kumar, Abhishek, Ritchie, Matthew E., Liu, Xiaodong, Tian, Luyi

“…Recent developments of sequencing-based spatial transcriptomics (sST) have catalyzed important advancements by facilitating transcriptome-scale spatial gene…”
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Spatial transcriptomics and the anatomical pathologist: Molecular meets morphology by Pang, Jia‐Min B, Byrne, David J, Bergin, Alice R T, Caramia, Franco, Loi, Sherene, Gorringe, Kylie L, Fox, Stephen B

“…In recent years anatomical pathology has been revolutionised by the incorporation of molecular findings into routine diagnostic practice, and in some diseases…”
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Boosting multiplexing capabilities for error-robust spatial transcriptomic methods using a set exchange approach by Boström, Johan, Zapaɫa, Michaɫ, Adameyko, Igor

“… of mRNA and protein targets simultaneously. This large increase in scope necessitates methods in either increased specificity or in error correction, such as the Hamming codes used in the imaging-based spatial transcriptomic method MERFISH…”
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Comparison of spatial transcriptomics technologies using tumor cryosections by Rademacher, Anne, Huseynov, Alik, Bortolomeazzi, Michele, Wille, Sina Jasmin, Schumacher, Sabrina, Sant, Pooja, Keitel, Denise, Okonechnikov, Konstantin, Ghasemi, David R., Pajtler, Kristian W., Mallm, Jan-Philipp, Rippe, Karsten

“… their spatial tissue context. The rapid development of spatial transcriptomics methods, each with unique characteristics, makes it challenging to select the most suitable technology for specific research objectives…”
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Multiplexed RNA imaging and in situ profiling in living cells by Mi, Lan, Khajouei, Sima, You, Mingxu

“… While established spatial transcriptomics methods – such as fluorescence in situ hybridization and in situ sequencing…”
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Spatially Resolved Transcriptomes—Next Generation Tools for Tissue Exploration by Asp, Michaela, Bergenstråhle, Joseph, Lundeberg, Joakim

“…Recent advances in spatially resolved transcriptomics have greatly expanded the knowledge of complex multicellular biological systems. The field has quickly…”
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Spatial transcriptomics using combinatorial fluorescence spectral and lifetime encoding, imaging and analysis by Vu, Tam, Vallmitjana, Alexander, Gu, Joshua, La, Kieu, Xu, Qi, Flores, Jesus, Zimak, Jan, Shiu, Jessica, Hosohama, Linzi, Wu, Jie, Douglas, Christopher, Waterman, Marian L., Ganesan, Anand, Hedde, Per Niklas, Gratton, Enrico, Zhao, Weian

“… Unfortunately, existing spatial transcriptomics methods are limited due to either low multiplexing or complexity…”
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Expansion spatial transcriptomics by Fan, Yuhang, Andrusivová, Žaneta, Wu, Yunming, Chai, Chew, Larsson, Ludvig, He, Mengxiao, Luo, Liqun, Lundeberg, Joakim, Wang, Bo

“…Capture array-based spatial transcriptomics methods have been widely used to resolve gene expression in tissues…”
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Single-cell atlases: shared and tissue-specific cell types across human organs by Elmentaite, Rasa, Domínguez Conde, Cecilia, Yang, Lu, Teichmann, Sarah A

“…The development of single-cell and spatial transcriptomics methods was instrumental in the conception of the Human Cell Atlas initiative, which aims to generate an integrated map of all cells across the human body…”
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BARcode DEmixing through Non-negative Spatial Regression (BarDensr) by Chen, Shuonan, Loper, Jackson, Chen, Xiaoyin, Vaughan, Alex, Zador, Anthony M., Paninski, Liam

“…Modern spatial transcriptomics methods can target thousands of different types of RNA transcripts in a single slice of tissue…”
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SpaGE: Spatial Gene Enhancement using scRNA-seq by Abdelaal, Tamim, Mourragui, Soufiane, Mahfouz, Ahmed, Reinders, Marcel J T

“… Novel spatial transcriptomics methods do retain cells spatial information but some methods can only measure tens to hundreds of transcripts…”
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SpaceBar enables single-cell-resolution clone tracing with imaging-based spatial transcriptomics by Kinsler, Grant, Fagan, Caitlin, Li, Haiyin, Kaster, Jessica, Dunne, Maggie, Vander Velde, Robert J, Boe, Ryan H, Shaffer, Sydney, Herlyn, Meenhard, Raj, Arjun, Heyman, Yael

“…Imaging-based spatial transcriptomics methods allow for the measurement of spatial determinants of cellular phenotypes but are incompatible with random barcode-based clone-tracing methods, preventing…”
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Macrophage diversity in human cancers: New insight provided by single-cell resolution and spatial context by Rakina, Militsa, Larionova, Irina, Kzhyshkowska, Julia

“…M1/M2 paradigm of macrophage plasticity has existed for decades. Now it becomes clear that this dichotomy doesn't adequately reflect the diversity of…”
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Rigor and Reproducibility of Spatial Transcriptomics Performed on Clinically Sourced Human Tissues by Smith, Kelly D, MacDonald, James W, Li, Xianwu, Beirne, Emily, Stewart, Galen, Bammler, Theo K, Akilesh, Shreeram

“…Spatial transcriptomic profiling enables precise quantification of gene expression with simultaneous localization of expression profiles onto tissue…”
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