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Article
Open AccessHigh-plex immunofluorescence imaging and traditional histology of the same tissue section for discovering image-based biomarkers
Precision medicine is critically dependent on better methods for diagnosing and staging disease and predicting drug response. Histopathology using hematoxylin and eosin (H&E)-stained tissue (not genomics) rema...
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Article
Open AccessUnMICST: Deep learning with real augmentation for robust segmentation of highly multiplexed images of human tissues
Upcoming technologies enable routine collection of highly multiplexed (20–60 channel), subcellular resolution images of mammalian tissues for research and diagnosis. Extracting single cell data from such image...
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Article
Open AccessMultiplexed and reproducible high content screening of live and fixed cells using Dye Drop
High-throughput measurement of cells perturbed using libraries of small molecules, gene knockouts, or different microenvironmental factors is a key step in functional genomics and pre-clinical drug discovery. ...
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Article
Open AccessA multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses
The phenotype of a cell and its underlying molecular state is strongly influenced by extracellular signals, including growth factors, hormones, and extracellular matrix proteins. While these signals are normal...
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Article
Open AccessSingle cell spatial analysis reveals the topology of immunomodulatory purinergic signaling in glioblastoma
How the glioma immune microenvironment fosters tumorigenesis remains incompletely defined. Here, we use single-cell RNA-sequencing and multiplexed tissue-imaging to characterize the composition, spatial organi...
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Article
Open AccessMCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging
Highly multiplexed tissue imaging makes detailed molecular analysis of single cells possible in a preserved spatial context. However, reproducible analysis of large multichannel images poses a substantial comp...
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Article
MITI minimum information guidelines for highly multiplexed tissue images
The imminent release of tissue atlases combining multichannel microscopy with single-cell sequencing and other omics data from normal and diseased specimens creates an urgent need for data and metadata standar...
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Article
Open AccessAuthor Correction: Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Article
Open AccessImmunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer
Combined PARP and immune checkpoint inhibition has yielded encouraging results in ovarian cancer, but predictive biomarkers are lacking. We performed immunogenomic profiling and highly multiplexed single-cell ...
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Article
HSF1 phase transition mediates stress adaptation and cell fate decisions
Under proteotoxic stress, some cells survive whereas others die. The mechanisms governing this heterogeneity in cell fate remain unknown. Here we report that condensation and phase transition of heat-shock fac...
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Article
Open AccessHighly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer
In this data descriptor, we document a dataset of multiplexed immunofluorescence images and derived single-cell measurements of immune lineage and other markers in formaldehyde-fixed and paraffin-embedded (FFP...
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Article
Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues
Spatial map** of proteins in tissues is hindered by limitations in multiplexing, sensitivity and throughput. Here we report immunostaining with signal amplification by exchange reaction (Immuno-SABER), which...
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Article
Open AccessHighly selective inhibition of histone demethylases by de novo macrocyclic peptides
The JmjC histone demethylases (KDMs) are linked to tumour cell proliferation and are current cancer targets; however, very few highly selective inhibitors for these are available. Here we report cyclic peptide...
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Article
Open AccessAssessing histone demethylase inhibitors in cells: lessons learned
Histone lysine demethylases (KDMs) are of interest as drug targets due to their regulatory roles in chromatin organization and their tight associations with diseases including cancer and mental disorders. The ...
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Article
Open AccessH3K27me3 demethylases regulate in vitro chondrogenesis and chondrocyte activity in osteoarthritis
Epigenetic changes (i.e., chromatin modifications) occur during chondrogenesis and in osteoarthritis (OA). We investigated the effect of H3K27me3 demethylase inhibition on chondrogenesis and assessed its utili...
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Using Fluorescence Recovery After Photobleaching to Study Gap Junctional Communication In Vitro
Fluorescence recovery after photobleaching (FRAP) is a microscopy-based technique to study the movement of fluorescent molecules inside a cell. Although initially developed to investigate intracellular mobilit...
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Article
The Mechanical, Structural, and Compositional Changes of Tendon Exposed to Elastase
The mechanical response of tendon is dependent on the interaction of structural molecules that constitute the extracellular matrix. However, little is known about the role of elastic fibers that are present in...
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Article
Open AccessAssessing cellular efficacy of bromodomain inhibitors using fluorescence recovery after photobleaching
Acetylation of lysine residues in histone tails plays an important role in the regulation of gene transcription. Bromdomains are the readers of acetylated histone marks, and, consequently, bromodomain-containi...
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Chapter
Near Infrared Three-Dimensional Nonlinear Optical Monitoring of Stem Cell Differentiation
Under certain conditions, embryonic stem cells (ESCs) can be induced to differentiate into cartilage cells (chondrocytes), neuronal cells and pancreatic cells to a state suitable for transplantation to treat d...
