Libeskind-Hadas, Wu, HMC Students Publish Bioinformatics Paper

Research related to the evolution of genes and species being conducted at Harvey Mudd College by professors of computer science Ran Libeskind-Hadas and Yi-Chieh “Jessica” Wu and their research students is published in Bioinformatics, a leading journal that focuses on new developments in genome bioinformatics and computational biology.

Santi Santichaivekin ’22, Rose Liu ’22, Qing Yang ’23, Ross Mawhorter ’18, Trenton Wesley ’23 and Justin Jiang ’23 are co-authors of the paper, “eMPRess: A Systematic Cophylogeny Reconciliation Tool,” which details the software tool they have been developing. A number of other HMC students have contributed to this project in recent years.

Darwin wrote that he could imagine how pairs of species, such as flowers and their bee pollinators, might coevolve so that the two species would adapt and specialize to one another. “Co-evolution arises in symbionts, such as plants and their pollinators as well as in hosts and parasites and other pairs of related entities,” Libeskind-Hadas says. “The problem that we’re studying is that of ‘reconciling’ pairs of evolutionary trees to explain how a given pair of taxa may have co-evolved.”

The HMC research group and others have developed several efficient algorithms that determine how to reconcile pairs of trees and analyze these reconciliations. The eMPRess software tool integrates several of these algorithms into a single software tool for use by biologists.

Students are making key contributions. Santichaivekin, who oversaw the software development team that implemented eMPRess, worked with Mawhorter and Libeskind-Hadas to develop several algorithms over the last several years. Mawhorter and Liu also contributed to the implementation of the algorithms. Jiang, Yang and Wesley developed graphical elements of the eMPRess software tool to aid visualization and use.

Empress is freely available.