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Reconstruction Set Test (RESET): A computationally efficient method for single sample gene set testing based on randomized reduced rank reconstruction error

PLoS computational biology, 2024-04, Vol.20 (4), p.e1012084-e1012084

2024

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Tissue-adjusted pathway analysis of cancer (TPAC): A novel approach for quantifying tumor-specific gene set dysregulation relative to normal tissue

PLoS computational biology, 2024-01, Vol.20 (1), p.e1011717

2024

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Analyzing cancer gene expression data through the lens of normal tissue-specificity

PLoS computational biology, 2021-06, Vol.17 (6), p.e1009085-e1009085

2021

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CAraCAl: CAMML with the integration of chromatin accessibility

BMC bioinformatics, 2024-06, Vol.25 (1), p.212-16

2024

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Eigenvectors from Eigenvalues Sparse Principal Component Analysis

Journal of computational and graphical statistics, 2022-04, Vol.31 (2), p.486-501

Robert Frost, H.

2022

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A generalized eigenvector centrality for multilayer networks with inter-layer constraints on adjacent node importance

Applied network science, 2024-12, Vol.9 (1), p.14-20, Article 14

Frost, H. Robert

2024

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Transcriptomic Differences between Primary Colorectal Adenocarcinomas and Distant Metastases Reveal Metastatic Colorectal Cancer Subtypes

Cancer research (Chicago, Ill.), 2019-08, Vol.79 (16), p.4227-4241

2019

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CBEA: Competitive balances for taxonomic enrichment analysis

PLoS computational biology, 2022-05, Vol.18 (5), p.e1010091-e1010091

2022

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A multi-omics approach for identifying important pathways and genes in human cancer

BMC bioinformatics, 2018-12, Vol.19 (1), p.479-479, Article 479

2018

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Comparison of pathway and gene-level models for cancer prognosis prediction

BMC bioinformatics, 2020-02, Vol.21 (1), p.76-17, Article 76

2020

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Cancer prognosis prediction using somatic point mutation and copy number variation data: a comparison of gene-level and pathway-based models

BMC bioinformatics, 2020-10, Vol.21 (1), p.467-467, Article 467

2020

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Zbtb20 Restrains CD8 T Cell Immunometabolism and Restricts Memory Differentiation and Antitumor Immunity

The Journal of immunology (1950), 2020-11, Vol.205 (10), p.2649-2666

2020

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Pan-cancer evaluation of gene expression and somatic alteration data for cancer prognosis prediction

BMC cancer, 2021-09, Vol.21 (1), p.1053-1053, Article 1053

2021

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A dietary-wide association study (DWAS) of environmental metal exposure in US children and adults

PloS one, 2014-09, Vol.9 (9), p.e104768

2014

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Associations between the gut microbiome and metabolome in early life

BMC microbiology, 2021-08, Vol.21 (1), p.238-19, Article 238

2021

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Predictors of disease aggressiveness influence outcome from immunotherapy treatment in renal clear cell carcinoma

Oncoimmunology, 2019-01, Vol.8 (1), p.e1500106-e1500106

2019

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CAMML with the Integration of Marker Proteins (ChIMP)

Bioinformatics (Oxford, England), 2022-11, Vol.38 (23), p.5206-5213

2022

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Computation and application of tissue-specific gene set weights

Bioinformatics, 2018-09, Vol.34 (17), p.2957-2964

2018

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Tumor immune infiltration estimated from gene expression profiles predicts colorectal cancer relapse

Oncoimmunology, 2021-01, Vol.10 (1), p.1862529

2021

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Gene set selection via LASSO penalized regression (SLPR)

Nucleic acids research, 2017-07, Vol.45 (12), p.e114-e114

2017

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SPECK: an unsupervised learning approach for cell surface receptor abundance estimation for single-cell RNA-sequencing data

Bioinformatics advances, 2023, Vol.3 (1), p.vbad073

2023

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CAMML: Multi-Label Immune Cell-Typing and Stemness Analysis for Single-Cell RNA-sequencing

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2022, Vol.27, p.199

2022

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Superkine IL-2 and IL-33 Armored CAR T Cells Reshape the Tumor Microenvironment and Reduce Growth of Multiple Solid Tumors

Cancer immunology research, 2022-08, Vol.10 (8), p.962-977

2022

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Cell type-specific interaction analysis using doublets in scRNA-seq

Bioinformatics advances, 2023, Vol.3 (1), p.vbad120

2023

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Unsupervised gene set testing based on random matrix theory

BMC bioinformatics, 2016-11, Vol.17 (1), p.442-442, Article 442

2016

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Reconstruction Set Test (RESET): A computationally efficient method for single sample gene set testing based on randomized reduced rank reconstruction error

Tissue-adjusted pathway analysis of cancer (TPAC): A novel approach for quantifying tumor-specific gene set dysregulation relative to normal tissue

Analyzing cancer gene expression data through the lens of normal tissue-specificity

CAraCAl: CAMML with the integration of chromatin accessibility

Eigenvectors from Eigenvalues Sparse Principal Component Analysis

A generalized eigenvector centrality for multilayer networks with inter-layer constraints on adjacent node importance

Transcriptomic Differences between Primary Colorectal Adenocarcinomas and Distant Metastases Reveal Metastatic Colorectal Cancer Subtypes

CBEA: Competitive balances for taxonomic enrichment analysis

A multi-omics approach for identifying important pathways and genes in human cancer

Comparison of pathway and gene-level models for cancer prognosis prediction

Cancer prognosis prediction using somatic point mutation and copy number variation data: a comparison of gene-level and pathway-based models

Zbtb20 Restrains CD8 T Cell Immunometabolism and Restricts Memory Differentiation and Antitumor Immunity

Pan-cancer evaluation of gene expression and somatic alteration data for cancer prognosis prediction

A dietary-wide association study (DWAS) of environmental metal exposure in US children and adults

Associations between the gut microbiome and metabolome in early life

Predictors of disease aggressiveness influence outcome from immunotherapy treatment in renal clear cell carcinoma

CAMML with the Integration of Marker Proteins (ChIMP)

Computation and application of tissue-specific gene set weights

Tumor immune infiltration estimated from gene expression profiles predicts colorectal cancer relapse

Gene set selection via LASSO penalized regression (SLPR)

SPECK: an unsupervised learning approach for cell surface receptor abundance estimation for single-cell RNA-sequencing data

CAMML: Multi-Label Immune Cell-Typing and Stemness Analysis for Single-Cell RNA-sequencing

Superkine IL-2 and IL-33 Armored CAR T Cells Reshape the Tumor Microenvironment and Reduce Growth of Multiple Solid Tumors

Cell type-specific interaction analysis using doublets in scRNA-seq

Unsupervised gene set testing based on random matrix theory

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