Data Analysis ~ Computational biology ~ Bioinformatics ~ Biostatistics
Capabilities

I developed computational pipelines and analyses to map transcription initiation and chromatin structure in non-model organisms. This page presents workflows, results, and code developed for P. infestans.

Working with Phytophthora infestans was both a challenge and an adventure. Unlike current researchers studying humans, who can simply select a ready-made reference genome from a database, I had no such luxury. The reference genome and annotation files I needed weren’t available in the standard repositories used by most bioinformatics tools. This meant I had to dig deeper: reading documentation, examining source code, and piecing together how each package handled genomic data. Step by step, I learned to transform my genome files into the precise data structures those tools required. Only after this groundwork could I begin the analyses themselves. Working with P. infestans strengthened not only my technical skills but also my resilience and creativity, growth that would have been unlikely in more established systems.

5′-prime MACE Sequencing (Chapter 1)

Nucleosome Occupancy Analysis (Chapter 2)

The documents contain the code used to perform the analyses presented in my dissertation. Because my advisor had limited experience in computational research, I developed this work largely independently. On occasion, I sought guidance from package developers through GitHub or from administrators of the high-performance computing cluster.