7 papers
MERLIN-SUITE: Probabilistic modular GRN inference from multi-omics data integrating regulatory priors and transcription factor activity
Suvojit Hazra, Marina Kotvanova, Kirstan Gimse +1
Accurately reconstructing gene regulatory networks (GRNs) is essential for understanding transcriptional processes in development and disease. MERLIN-SUITE (https://github.com/Roy-…
scMTNI: Leveraging cellular trajectory and context to infer dynamic GRNs from single-cell multi-omics data
Suvojit Hazra, Chandrani Kumari, Sushmita Roy
Transcriptional gene regulatory networks (GRNs) depict the directed relationships between regulators and target genes, determining gene expression patterns in a cell-type-specific…
Modeling Dynamics, Cell Type Specificity, and Perturbations in Gene Regulatory Networks
Junha Shin, Spencer Halberg-Spencer, Yuda Liu +3
Gene regulatory networks (GRNs) define the regulatory relationships among molecules such as transcription factors, chromatin remodelers, and target genes. GRNs play a critical role…
The Target Polish: A New Approach to Outlier-Resistant Non-Negative Matrix Factorization
Paul Fogel, Christophe Geissler, George Luta
This paper introduces the "Target Polish," a robust and computationally efficient framework for Non-Negative Matrix Factorization (NMF). Although conventional weighted NMF approach…
Bayesian Regression Analysis with the Drift-Diffusion Model
Zekai Jin, Yaakov Stern, Seonjoo Lee
The Drift-Diffusion Model (DDM) is widely used in neuropsychological studies to understand the decision process by incorporating both reaction times and subjects' responses. Variou…
Comparing Lasso and Adaptive Lasso in High-Dimensional Data: A Genetic Survival Analysis in Triple-Negative Breast Cancer
Pilar González-Barquero, Rosa E. Lillo, Ãlvaro Méndez-Civieta
In high-dimensional survival analysis, effective variable selection is crucial for both model interpretation and predictive performance. This paper investigates Cox regression with…