Shiny app for screening for core promoter occurrences close to expressed transposons TSSs.

The Genomic Variations Explorer (GenVarX) is a toolset that consists of promoter region component and CNV component for users to perform queries, visualize data, and conduct annotations using genotypic and phenotypic differences.

Phylogeny and classification of Azolla filiculoides MYB genes

Python code to reproduce figures in the SPONGE manuscript.

Django-based web application to explore and analyse Human Transcription Factors

Prediction of the binding sites of multiple transcription factors in a whole genome

Data challenge with kernel methods - MVA MSc

ONCOgenic Regulatory Element discovery

Scripts for reproducing the poster: Co-regulation of RKIP and autophagy genes by VEZF1 and ERCC6 in prostate cancer

Code for the BMC Genomics paper (Integrating binding and expression data to predict transcription factors combined function)

Genomic analysis of decreased DNA repair at TF-binding sites.

AI/ML bioinformatics portfolio covering mutation impact, biomarkers, SNP mapping, regulatory genomics, expression modeling, and TF binding

ATAC-Seq Transcription Factor Footprint Discovery and Analysis

Chiang, S., Shinohara, H., Huang, J. H., Tsai, H. K. & Okada, M. Inferring the transcriptional regulatory mechanism of signal-dependent gene expression via an integrative computational approach. FEBS Lett. (2020).

CRAFT: Cellular Reprogramming Analysis with Integrated Framework and Mechanistic Insight

BiasAway will improve TFBS enrichment analyses and the applied analysis of ChIP-Seq data, particularly for the annotation of reliable TFBSs within ChIP-Seq peaks.

Hepatocyte-specific NRF2 activation controls fibrogenesis and carcinogenesis in steatohepatitis

Documenting my progress towards discovering relevant determinants and better understanding the mechanisms and limitations of KLF4 pioneer factor ability as well as establishing familiarity with the nucleosome/histone/chromatin environment.

R package to predict gene feed forward loops using mediation analysis. Analyses integrate observed miRNA and mRNA expression data and database information on gene interactions.