H. Robert Frost
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View article: Randomized Spatial PCA (RASP): A computationally efficient method for dimensionality reduction of high-resolution spatial transcriptomics data
Randomized Spatial PCA (RASP): A computationally efficient method for dimensionality reduction of high-resolution spatial transcriptomics data Open
Spatial transcriptomics (ST) provides critical insights into the spatial organization of gene expression, enabling researchers to unravel the intricate relationship between cellular environments and biological function. Identifying spatial…
View article: Autoencoder Denoising for Network-Based Spatial Transcriptomics Data with Applications for Cell Signaling Estimation
Autoencoder Denoising for Network-Based Spatial Transcriptomics Data with Applications for Cell Signaling Estimation Open
We propose an autoencoder-based framework for denoising networks estimated from Spatial Transcriptomics (ST) data for cell signaling analysis. Our method consists of an unsupervised encoder-decoder framework for denoising the network adjac…
View article: Feasibility of computer-aided aortic occlusion catheter in non-traumatic cardiac arrest
Feasibility of computer-aided aortic occlusion catheter in non-traumatic cardiac arrest Open
A computer-aided automated aortic occlusion catheter can be safely implanted with a high success rate with regards to procedure time during ongoing cardiopulmonary resuscitation in patients suffering from cardiac arrest of non-traumatic or…
View article: Mouse-Specific Single cell cytokine activity prediction and Estimation (MouSSE)
Mouse-Specific Single cell cytokine activity prediction and Estimation (MouSSE) Open
The accurate cell-level characterization of cytokine activity is important for understanding the signaling processes underpinning a wide range of immune-mediated conditions such as auto-immune disease, cancer and response to infection. We …
View article: Benchmarking sketching methods on spatial transcriptomics data
Benchmarking sketching methods on spatial transcriptomics data Open
High-throughput spatial transcriptomics (ST) now profiles hundreds of thousands of cells or locations per section, creating computational bottlenecks for routine analysis. Sketching, or intelligent sub-sampling, addresses scale by selectin…
View article: Gene set optimization for cancer transcriptomics using sparse principal component analysis
Gene set optimization for cancer transcriptomics using sparse principal component analysis Open
A common approach for exploring pathway dysregulation in cancer involves the gene set or pathway analysis of tumor transcriptomic data. Unfortunately, the effectiveness of cancer gene set testing is limited by the fact that most gene set c…
View article: Randomized Spatial PCA (RASP): a computationally efficient method for dimensionality reduction of high-resolution spatial transcriptomics data
Randomized Spatial PCA (RASP): a computationally efficient method for dimensionality reduction of high-resolution spatial transcriptomics data Open
Spatial transcriptomics (ST) provides critical insights into the spatial organization of gene expression, enabling researchers to unravel the intricate relationship between cellular environments and biological function. Identifying spatial…
View article: Gene Set Optimization for Single Cell Transcriptomics
Gene Set Optimization for Single Cell Transcriptomics Open
View article: Network Analysis Using Krylov Subspace Trajectories
Network Analysis Using Krylov Subspace Trajectories Open
View article: Cell Signaling Characterization for Spatial Transcriptomics (ST) Data Using Network Analysis
Cell Signaling Characterization for Spatial Transcriptomics (ST) Data Using Network Analysis Open
View article: Revealing tissue architecture through the hypercomplex Fourier analysis of spatial transcriptomics data
Revealing tissue architecture through the hypercomplex Fourier analysis of spatial transcriptomics data Open
Motivation We present an approach for analyzing spatial transcriptomics (ST) data using a quaternion-domain discrete Fourier transform. Quaternions are four-dimensional hypercomplex numbers that have been primarily employed to represent ro…
View article: Randomized Spatial PCA (RASP): a computationally efficient method for dimensionality reduction of high-resolution spatial transcriptomics data
Randomized Spatial PCA (RASP): a computationally efficient method for dimensionality reduction of high-resolution spatial transcriptomics data Open
Spatial transcriptomics (ST) provides critical insights into the spatial organization of gene expression, enabling researchers to unravel the intricate relationship between cellular environments and biological function. Identifying spatial…
View article: Leveraging cell type-specificity for gene set analysis of single cell transcriptomics
Leveraging cell type-specificity for gene set analysis of single cell transcriptomics Open
Although single cell RNA-sequencing (scRNA-seq) provides unprecedented insights into the biology of complex tissues, analyzing such data on a gene-by-gene basis is challenging due to the large number of tested hypotheses and consequent low…
View article: CAraCAl: CAMML with the integration of chromatin accessibility
CAraCAl: CAMML with the integration of chromatin accessibility Open
View article: A generalized eigenvector centrality for multilayer networks with inter-layer constraints on adjacent node importance
A generalized eigenvector centrality for multilayer networks with inter-layer constraints on adjacent node importance Open
We present a novel approach for computing a variant of eigenvector centrality for multilayer networks with inter-layer constraints on node importance. Specifically, we consider a multilayer network defined by multiple edge-weighted, potent…
View article: Identifying tumor type and cell type-specific gene expression alterations in pediatric central nervous system tumors
Identifying tumor type and cell type-specific gene expression alterations in pediatric central nervous system tumors Open
View article: Reconstruction Set Test (RESET): A computationally efficient method for single sample gene set testing based on randomized reduced rank reconstruction error
Reconstruction Set Test (RESET): A computationally efficient method for single sample gene set testing based on randomized reduced rank reconstruction error Open
We have developed a new, and analytically novel, single sample gene set testing method called Reconstruction Set Test (RESET). RESET quantifies gene set importance based on the ability of set genes to reconstruct values for all measured ge…
View article: Network analysis using Krylov subspace trajectories
Network analysis using Krylov subspace trajectories Open
We describe a set of network analysis methods based on the rows of the Krylov subspace matrix computed from a network adjacency matrix via power iteration using a non-random initial vector. We refer to these node-specific row vectors as Kr…
View article: A common set of structurally distinct endogenous retroviruses predict survival in multiple human tumor types
A common set of structurally distinct endogenous retroviruses predict survival in multiple human tumor types Open
Accumulating evidence suggests that viral mimicry induction in cancer cells through the expression of human endogenous retroviral elements (ERVs) enhances tumor immunogenicity and improves response to immunotherapy. However, the characteri…
View article: Tissue-adjusted pathway analysis of cancer (TPAC): A novel approach for quantifying tumor-specific gene set dysregulation relative to normal tissue
Tissue-adjusted pathway analysis of cancer (TPAC): A novel approach for quantifying tumor-specific gene set dysregulation relative to normal tissue Open
We describe a novel single sample gene set testing method for cancer transcriptomics data named tissue-adjusted pathway analysis of cancer (TPAC). The TPAC method leverages information about the normal tissue-specificity of human genes to …
View article: Referee report. For: GBS vaccines in the UK: a round table discussion [version 1; peer review: 3 approved]
Referee report. For: GBS vaccines in the UK: a round table discussion [version 1; peer review: 3 approved] Open
View article: Single cell transcriptomics-level Cytokine Activity Prediction and Estimation (SCAPE)
Single cell transcriptomics-level Cytokine Activity Prediction and Estimation (SCAPE) Open
Cytokine interaction activity modeling is a pressing problem since uncontrolled cytokine influx is at fault in a variety of medical conditions, including viral infections like COVID19, and cancer. Accurate knowledge of cytokine activity le…
View article: All Loop Scattering As A Counting Problem
All Loop Scattering As A Counting Problem Open
This is the first in a series of papers presenting a new understanding of scattering amplitudes based on fundamentally combinatorial ideas in the kinematic space of the scattering data. We study the simplest theory of colored scalar partic…
View article: STREAK: A supervised cell surface receptor abundance estimation strategy for single cell RNA-sequencing data using feature selection and thresholded gene set scoring
STREAK: A supervised cell surface receptor abundance estimation strategy for single cell RNA-sequencing data using feature selection and thresholded gene set scoring Open
The accurate estimation of cell surface receptor abundance for single cell transcriptomics data is important for the tasks of cell type and phenotype categorization and cell-cell interaction quantification. We previously developed an unsup…
View article: Table of Contents
Table of Contents Open
View article: Characterizing control of memory CD8 T cell differentiation by BTB-ZF transcription factor Zbtb20
Characterizing control of memory CD8 T cell differentiation by BTB-ZF transcription factor Zbtb20 Open
Members of the BTB-ZF transcription factor family regulate the immune system. Our laboratory identified that family member Zbtb20 contributes to the differentiation, recall responses, and metabolism of CD8 T cells. Here, we report a charac…
View article: Reconstruction Set Test (RESET): a computationally efficient method for single sample gene set testing based on randomized reduced rank reconstruction error
Reconstruction Set Test (RESET): a computationally efficient method for single sample gene set testing based on randomized reduced rank reconstruction error Open
We have developed a new, and analytically novel, single sample gene set testing method called Reconstruction Set Test (RESET). RESET quantifies gene set importance at both the sample-level and for the entire dataset based on the ability of…
View article: Data from Superkine IL-2 and IL-33 Armored CAR T Cells Reshape the Tumor Microenvironment and Reduce Growth of Multiple Solid Tumors
Data from Superkine IL-2 and IL-33 Armored CAR T Cells Reshape the Tumor Microenvironment and Reduce Growth of Multiple Solid Tumors Open
Chimeric-antigen receptor (CAR) T-cell therapy has shown remarkable efficacy against hematologic tumors. Yet, CAR T-cell therapy has had little success against solid tumors due to obstacles presented by the tumor microenvironment (TME) of …
View article: Supplementary Figure from Superkine IL-2 and IL-33 Armored CAR T Cells Reshape the Tumor Microenvironment and Reduce Growth of Multiple Solid Tumors
Supplementary Figure from Superkine IL-2 and IL-33 Armored CAR T Cells Reshape the Tumor Microenvironment and Reduce Growth of Multiple Solid Tumors Open
Supplementary Figure from Superkine IL-2 and IL-33 Armored CAR T Cells Reshape the Tumor Microenvironment and Reduce Growth of Multiple Solid Tumors
View article: Supplementary Figure from Superkine IL-2 and IL-33 Armored CAR T Cells Reshape the Tumor Microenvironment and Reduce Growth of Multiple Solid Tumors
Supplementary Figure from Superkine IL-2 and IL-33 Armored CAR T Cells Reshape the Tumor Microenvironment and Reduce Growth of Multiple Solid Tumors Open
Supplementary Figure from Superkine IL-2 and IL-33 Armored CAR T Cells Reshape the Tumor Microenvironment and Reduce Growth of Multiple Solid Tumors