Research portfolio

(Click titles to navigate to project homepage)

VenomKB (venomkb.org):

VenomKB is a comprehensive knowledge repository for computational toxinology that I designed to facilitate the representation, storage, and retrieval of venom information. VenomKB is designed to be useful for many purposes:

VenomKB includes a REST API for programmatic access to its data. To learn more, visit VenomKB at www.venomkb.org.


Venom Ontology

An ontology is a computer-readable representation of some body of knowledge that facilitates computer analysis. An ontology can be thought of as the high-level entities in that body of knowledge, linked by specific relationships that define the meaning of those concepts.

I designed Venom Ontology to do exactly this for concepts related to venoms and drug discovery from the compounds contained in venoms.


GEXPRO

GEXPRO is a new software library and utility toolset for data-driven analysis of gene expression data. GEXPRO is written in C++ and includes the ability to interface with data analysis plugins written in high-level programming languages such as Python and R.

This software is under active development. For more information, including opportunities to contribute to GEXPRO's development, please see the project's source code repository at github.com/jdromano2/gexpro.


ASAP2

ASAP2 (Automated Simultaneous Analysis Phylogenetics ver. 2) is a computational pipeline for investigating evolutionary relationships among sets of potentially related genes, using phylogenetic simultaneous analysis. I used ASAP2 to explore the evolutionary history of genes related to Alzheimer disease, and created high-resolution Alzheimer phylogenies that could be used for prioritizing model organism researh.

ASAP2 builds upon work by Neil Sarkar et al, as described in Bioinformatics: doi:10.1186/1471-2105-9-103