CAraCAl: CAMML with the integration of chromatin accessibility.
BMC Bioinform., December, 2024
A generalized eigenvector centrality for multilayer networks with inter-layer constraints on adjacent node importance.
Appl. Netw. Sci., December, 2024
Tissue-adjusted pathway analysis of cancer (TPAC): A novel approach for quantifying tumor-specific gene set dysregulation relative to normal tissue.
PLoS Comput. Biol., January, 2024
Reconstruction Set Test (RESET): A computationally efficient method for single sample gene set testing based on randomized reduced rank reconstruction error.
PLoS Comput. Biol., 2024
Network analysis using Krylov subspace trajectories.
CoRR, 2024
STREAK: A supervised cell surface receptor abundance estimation strategy for single cell RNA-sequencing data using feature selection and thresholded gene set scoring.
PLoS Comput. Biol., 2023
Eigenvector Centrality for Multilayer Networks with Dependent Node Importance.
Proceedings of the Complex Networks & Their Applications XII, 2023
CAMML with the Integration of Marker Proteins (ChIMP).
Bioinform., November, 2022
Eigenvectors from Eigenvalues Sparse Principal Component Analysis.
J. Comput. Graph. Stat., January, 2022
CBEA: Competitive balances for taxonomic enrichment analysis.
PLoS Comput. Biol., 2022
Iterative execution of discrete and inverse discrete Fourier transforms with applications for signal denoising via sparsification.
CoRR, 2022
Analyzing cancer gene expression data through the lens of normal tissue-specificity.
PLoS Comput. Biol., 2021
Cancer prognosis prediction using somatic point mutation and copy number variation data: a comparison of gene-level and pathway-based models.
BMC Bioinform., 2020
Comparison of pathway and gene-level models for cancer prognosis prediction.
BMC Bioinform., 2020
Gene characteristics predicting missense, nonsense and frameshift mutations in tumor samples.
BMC Bioinform., 2018
A multi-omics approach for identifying important pathways and genes in human cancer.
BMC Bioinform., 2018
Computation and application of tissue-specific gene set weights.
Bioinform., 2018
Unsupervised gene set testing based on random matrix theory.
BMC Bioinform., 2016
An Independent Filter for Gene Set Testing Based on Spectral Enrichment.
IEEE ACM Trans. Comput. Biol. Bioinform., 2015
Modeling Neurovascular Coupling from Clustered Parameter Sets for Multimodal EEG-NIRS.
Comput. Math. Methods Medicine, 2015
Spectral gene set enrichment (SGSE).
BMC Bioinform., 2015
Principal component gene set enrichment (PCGSE).
BioData Min., 2015
Modeling the Autism Spectrum Disorder Phenotype.
Neuroinformatics, 2014
Optimization of gene set annotations via entropy minimization over variable clusters (EMVC).
Bioinform., 2014
Markov Chain Ontology Analysis (MCOA).
BMC Bioinform., 2012
Gene ontology analysis of pairwise genetic associations in two genome-wide studies of sporadic ALS.
BioData Min., 2012
A journey to Semantic Web query federation in the life sciences.
BMC Bioinform., 2009
Application of Information Technology: MediClass: A System for Detecting and Classifying Encounter-based Clinical Events in Any Electronic Medical Record.
J. Am. Medical Informatics Assoc., 2005