Kieran R. Campbell
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View article: Computational design and evaluation of optimal bait sets for scalable proximity proteomics
Computational design and evaluation of optimal bait sets for scalable proximity proteomics Open
The spatial organization of proteins within eukaryotic cells underlies essential biological processes and can be mapped by identifying nearby proteins using proximity-dependent biotinylation approaches such as BioID. When applied systemati…
View article: Rakaia: interactive discovery of spatial biology at scale
Rakaia: interactive discovery of spatial biology at scale Open
Spatial biology data throughput currently outpaces interpretable analysis, limiting large-scale discovery and translation. Here we present Rakaia, a browser-based platform for multiplexed imaging and spatial transcriptomics, empowering cod…
View article: Integrated spatial proteomics of human PDAC uncovers an expanded tumour-immune-stroma spectrum with genomic associations
Integrated spatial proteomics of human PDAC uncovers an expanded tumour-immune-stroma spectrum with genomic associations Open
Distinctively, pancreatic ductal adenocarcinoma (PDAC) consists of sparse tumour lesions intertwined with extensive desmoplastic stroma. The complexity of tumour-microenvironment interactions within this desmoplasia poses a challenge for a…
View article: Supplementary Figure 3 from IL-15 Complex Enhances Agonistic Anti-CD40 + Anti-PDL1 by Correcting the T-bet to Tox Ratio in CD8<sup>+</sup> T cells Infiltrating Pancreatic Ductal Adenocarcinoma
Supplementary Figure 3 from IL-15 Complex Enhances Agonistic Anti-CD40 + Anti-PDL1 by Correcting the T-bet to Tox Ratio in CD8<sup>+</sup> T cells Infiltrating Pancreatic Ductal Adenocarcinoma Open
CD8 T cell differentiation in PDA.
View article: Supplementary Figure 5 from IL-15 Complex Enhances Agonistic Anti-CD40 + Anti-PDL1 by Correcting the T-bet to Tox Ratio in CD8<sup>+</sup> T cells Infiltrating Pancreatic Ductal Adenocarcinoma
Supplementary Figure 5 from IL-15 Complex Enhances Agonistic Anti-CD40 + Anti-PDL1 by Correcting the T-bet to Tox Ratio in CD8<sup>+</sup> T cells Infiltrating Pancreatic Ductal Adenocarcinoma Open
Antigen specificity and functionality of predominant TCRs from tumors from immunotherapy treated mice.
View article: Supplementary Figure 9 from IL-15 Complex Enhances Agonistic Anti-CD40 + Anti-PDL1 by Correcting the T-bet to Tox Ratio in CD8<sup>+</sup> T cells Infiltrating Pancreatic Ductal Adenocarcinoma
Supplementary Figure 9 from IL-15 Complex Enhances Agonistic Anti-CD40 + Anti-PDL1 by Correcting the T-bet to Tox Ratio in CD8<sup>+</sup> T cells Infiltrating Pancreatic Ductal Adenocarcinoma Open
IL15C synergizes with immunotherapy to target poorly immunogenic KPC2 tumors
View article: Data from IL-15 Complex Enhances Agonistic Anti-CD40 + Anti-PDL1 by Correcting the T-bet to Tox Ratio in CD8<sup>+</sup> T cells Infiltrating Pancreatic Ductal Adenocarcinoma
Data from IL-15 Complex Enhances Agonistic Anti-CD40 + Anti-PDL1 by Correcting the T-bet to Tox Ratio in CD8<sup>+</sup> T cells Infiltrating Pancreatic Ductal Adenocarcinoma Open
Agonistic anti-CD40 with anti–PD-1 can elicit objective responses in a small number of patients with pancreatic ductal adenocarcinoma (PDA). Better understanding of their individual effects on the pancreatic tumor microenvironment will hel…
View article: Supplementary Tables from IL-15 Complex Enhances Agonistic Anti-CD40 + Anti-PDL1 by Correcting the T-bet to Tox Ratio in CD8<sup>+</sup> T cells Infiltrating Pancreatic Ductal Adenocarcinoma
Supplementary Tables from IL-15 Complex Enhances Agonistic Anti-CD40 + Anti-PDL1 by Correcting the T-bet to Tox Ratio in CD8<sup>+</sup> T cells Infiltrating Pancreatic Ductal Adenocarcinoma Open
Supplementary Tables 1-5
View article: Supplementary Figure 1 from IL-15 Complex Enhances Agonistic Anti-CD40 + Anti-PDL1 by Correcting the T-bet to Tox Ratio in CD8<sup>+</sup> T cells Infiltrating Pancreatic Ductal Adenocarcinoma
Supplementary Figure 1 from IL-15 Complex Enhances Agonistic Anti-CD40 + Anti-PDL1 by Correcting the T-bet to Tox Ratio in CD8<sup>+</sup> T cells Infiltrating Pancreatic Ductal Adenocarcinoma Open
Single cell transcriptional atlas following anti-PDL1 or agonistic anti-CD40
View article: Supplementary Figure 2 from IL-15 Complex Enhances Agonistic Anti-CD40 + Anti-PDL1 by Correcting the T-bet to Tox Ratio in CD8<sup>+</sup> T cells Infiltrating Pancreatic Ductal Adenocarcinoma
Supplementary Figure 2 from IL-15 Complex Enhances Agonistic Anti-CD40 + Anti-PDL1 by Correcting the T-bet to Tox Ratio in CD8<sup>+</sup> T cells Infiltrating Pancreatic Ductal Adenocarcinoma Open
Agonistic anti-CD40 + anti-PDL1 promotes tumor-specific CD8 T cell differentiation in spleen
View article: Supplementary Figure 7 from IL-15 Complex Enhances Agonistic Anti-CD40 + Anti-PDL1 by Correcting the T-bet to Tox Ratio in CD8<sup>+</sup> T cells Infiltrating Pancreatic Ductal Adenocarcinoma
Supplementary Figure 7 from IL-15 Complex Enhances Agonistic Anti-CD40 + Anti-PDL1 by Correcting the T-bet to Tox Ratio in CD8<sup>+</sup> T cells Infiltrating Pancreatic Ductal Adenocarcinoma Open
A fraction of TSTEM and TEFF are in the vasculature in dLN and tumor
View article: Supplementary Figure 6 from IL-15 Complex Enhances Agonistic Anti-CD40 + Anti-PDL1 by Correcting the T-bet to Tox Ratio in CD8<sup>+</sup> T cells Infiltrating Pancreatic Ductal Adenocarcinoma
Supplementary Figure 6 from IL-15 Complex Enhances Agonistic Anti-CD40 + Anti-PDL1 by Correcting the T-bet to Tox Ratio in CD8<sup>+</sup> T cells Infiltrating Pancreatic Ductal Adenocarcinoma Open
CD4 T cells and tumor antigen are required for anti-CD40 driven TSTEM accumulation in PDA
View article: Supplementary FIgure 8 from IL-15 Complex Enhances Agonistic Anti-CD40 + Anti-PDL1 by Correcting the T-bet to Tox Ratio in CD8<sup>+</sup> T cells Infiltrating Pancreatic Ductal Adenocarcinoma
Supplementary FIgure 8 from IL-15 Complex Enhances Agonistic Anti-CD40 + Anti-PDL1 by Correcting the T-bet to Tox Ratio in CD8<sup>+</sup> T cells Infiltrating Pancreatic Ductal Adenocarcinoma Open
IL-15C promotes the activity of dual therapy by promoting T-bet in tumor-infiltrating T cells
View article: Supplementary Figure 4 from IL-15 Complex Enhances Agonistic Anti-CD40 + Anti-PDL1 by Correcting the T-bet to Tox Ratio in CD8<sup>+</sup> T cells Infiltrating Pancreatic Ductal Adenocarcinoma
Supplementary Figure 4 from IL-15 Complex Enhances Agonistic Anti-CD40 + Anti-PDL1 by Correcting the T-bet to Tox Ratio in CD8<sup>+</sup> T cells Infiltrating Pancreatic Ductal Adenocarcinoma Open
Comparison of human and murine tumor-infiltrating CD8 T cells.
View article: Damage and Misrepair Signatures: Compact Representations of Pan-cancer Mutational Processes
Damage and Misrepair Signatures: Compact Representations of Pan-cancer Mutational Processes Open
Mutational signatures of single-base substitutions (SBSs) characterize somatic mutation processes which contribute to cancer development and progression. However, current mutational signatures do not distinguish the two independent steps t…
View article: Automated registration of spatial expression data scales multimodal integration to large cohorts
Automated registration of spatial expression data scales multimodal integration to large cohorts Open
Recent advances in spatial proteomics enable quantification of the spatial distribution of protein expression across a variety of scales, resolutions, and multiplexing. Registering images from such technologies across modalities is an esse…
View article: Learning copy number dependent variation in single tumour cell transcriptomes with deep generative models
Learning copy number dependent variation in single tumour cell transcriptomes with deep generative models Open
Large-scale copy number aberrations are a hallmark of many cancers, showing widespread associations with tumour cell phenotypes, therapy resistance, and patient outcomes. Several existing methods can infer copy number profiles from single-…
View article: Multi-view deep learning of highly multiplexed imaging data improves association of cell states with clinical outcomes
Multi-view deep learning of highly multiplexed imaging data improves association of cell states with clinical outcomes Open
Highly multiplexed imaging technologies can quantify the expression of 10s-100s of proteins and their modifications at sub-cellular resolution. Applications to tissue specimens across a broad array of pathologies have enabled patient subty…
View article: IL-15 Complex Enhances Agonistic Anti-CD40 + Anti-PDL1 by Correcting the T-bet to Tox Ratio in CD8+ T cells Infiltrating Pancreatic Ductal Adenocarcinoma
IL-15 Complex Enhances Agonistic Anti-CD40 + Anti-PDL1 by Correcting the T-bet to Tox Ratio in CD8+ T cells Infiltrating Pancreatic Ductal Adenocarcinoma Open
Agonistic anti-CD40 with anti–PD-1 can elicit objective responses in a small number of patients with pancreatic ductal adenocarcinoma (PDA). Better understanding of their individual effects on the pancreatic tumor microenvironment will hel…
View article: Multi-Modal Disentanglement of Spatial Transcriptomics and Histopathology Imaging
Multi-Modal Disentanglement of Spatial Transcriptomics and Histopathology Imaging Open
Spatially-resolved expression profiling data has revolutionized biological research with multiple emerging clinical applications. Spatial transcriptomic assays are often jointly measured with histopathology imaging data, which is frequentl…
View article: Interactive design and validation of antibody panels using single-cell RNA-seq atlases
Interactive design and validation of antibody panels using single-cell RNA-seq atlases Open
Single-cell RNA-sequencing holds promise for identifying novel markers of cellular variation for antibody-based technologies. However, antibody panel design is often difficult due to multiple experimental and biological constraints. We int…
View article: Computational design and evaluation of optimal bait sets for scalable proximity proteomics
Computational design and evaluation of optimal bait sets for scalable proximity proteomics Open
The spatial organization of proteins in eukaryotic cells can be explored by identifying nearby proteins using proximity-dependent biotinylation approaches like BioID. BioID defines the localization of thousands of endogenous proteins in hu…
View article: Inferring tumour microenvironment ecosystems from scRNA-seq atlases
Inferring tumour microenvironment ecosystems from scRNA-seq atlases Open
Accurate inference of granular cell states that co-occur within the tumour microenvironment (TME) is central to defining pro– and anti-tumour environments. Here, we describe how ecosystems of cell populations can be robustly inferred from …
View article: Single-cell decoding of drug induced transcriptomic reprogramming in triple negative breast cancers
Single-cell decoding of drug induced transcriptomic reprogramming in triple negative breast cancers Open
Background The encoding of cell intrinsic drug resistance states in breast cancer reflects the contributions of genomic and non-genomic variations and requires accurate estimation of clonal fitness from co-measurement of transcriptomic and…
View article: Spatial proteomic mapping of human nuclear bodies reveals new functional insights into RNA regulation
Spatial proteomic mapping of human nuclear bodies reveals new functional insights into RNA regulation Open
Nuclear bodies are diverse membraneless suborganelles with emerging links to development and disease. Explaining their structure, function, regulation, and implications in human health will require understanding their protein composition; …
View article: Segmentation aware probabilistic phenotyping of single-cell spatial protein expression data
Segmentation aware probabilistic phenotyping of single-cell spatial protein expression data Open
Spatial protein expression technologies can map cellular content and organization by simultaneously quantifying the expression of >40 proteins at subcellular resolution within intact tissue sections and cell lines. However, necessary image…
View article: The impacts of active and self-supervised learning on efficient annotation of single-cell expression data
The impacts of active and self-supervised learning on efficient annotation of single-cell expression data Open
A crucial step in the analysis of single-cell data is annotating cells to cell types and states. While a myriad of approaches has been proposed, manual labeling of cells to create training datasets remains tedious and time-consuming. In th…