Indika Rajapakse

The paper develops an agent-based model of fibroblast scratch assays to simulate wound healing, achieving high accuracy in predicting cell behavior across different geometries.

This paper analyzes coronary flow waveforms using SVD to identify temporal patterns correlated with physiological metrics in pigs.

The paper develops a single-cell transcriptomic reference atlas and evaluates a transcription factor recipe for reprogramming fibroblasts into hematopoietic stem cells, revealing intermediate transcriptomic states and transcriptional remodeling.

This paper introduces ARCH3D, a foundation model for global genome architecture that captures spatial structure and interchromosomal interactions using a novel masked locus modeling task.

This paper introduces an automated wound healing assay using robotics and 3D bioprinting to improve reproducibility and throughput in in vitro studies.

The paper maps multi-way chromatin contacts using long reads and identifies cell type-specific transcription clusters by integrating contacts with chromatin accessibility and gene expression.

This study shows that WAPL regulates T cell 3D genome structure, affecting activation, proliferation, and GVHD severity.

The paper investigates allele-specific relationships between gene expression and genome structure in human cells using integrated haplotype-resolved data.

The paper introduces 4DNvestigator, a toolbox for analyzing time series Hi-C and RNA-seq data, with methods to quantify network and tensor entropy and detect significant changes over time.

The paper introduces a dynamic multilayer network approach to analyze the 4D Nucleome, showing improved predictions of form-function relationships in cellular reprogramming.

This study shows that MYOD1-mediated reprogramming of human fibroblasts into muscle cells involves a genome architecture bifurcation point preceding transcriptional changes.

The paper introduces a data-guided algorithm for cellular reprogramming using transcription factors, validated on human fibroblasts and showing potential for tissue regeneration and cancer cell reprogramming.

The paper investigates parental allele-specific genome architecture and transcription dynamics during the cell cycle in lymphoblastoid cells, identifying allele-biased expression and chromatin organization features.