Research

This lab works on developing algorithms to analyze next-generation sequencing data. Our research addresses various interrelated problems, including RNA transcriptome reconstruction, allele specific isoform expression estimation, gene differential expression and cancer specific variant identification and neo-epitope prediction. Tackling each of these problems requires employing a combination of computational approaches such as machine learning, grammatical modeling, statistical analysis, dynamic programming and expectation maximization algorithms.

Current Projects

Allele Specific Gene Expression Estimation is an interesting computational biology problem that answers the question of whether the paternal, the maternal, or both copies of an inherited gene are expressed (active) in your body and at what level they are expressed. This question is asked by many biologists, but the computational methods to answer it are still not good enough to accurately give an answer. In this research project, we will build software to address this problem by combining ideas in existing research with some new research ideas.


Classifying introns into major (U2) and minor (U12) introns is a traditionally done through modeling their sequences using Position Weight Matrices (PWM). Research has shown that models capable of representing inter-nucleotide dependencies give better prediction results. For example, Artificial Neural Networks give better results in epitope prediction, compared to PWMs. In this research we are proposing using probabilistic formal grammars to model and classify U2 and U12 introns. Our initial results show that our model, coupled with Support Vector Machines, yields very good prediction accuracy.

Open Positions

The Greater New Haven region has a concentration of biotechnology companies that are seeking graduates with bioinformatics experience. If you are interested to learn how to apply your computer science knowledge and skills to solve problems in biosciences, a bioinformatics research experience opportunity would help you achieve this goal.

The lab has available research positions for highly motivated graduate and undergraduate students. If interested to learn more, email your CV to alseesis1 at southernct dot edu

Previous Lab Members

Smith College

  • Sakina Ali

  • Hellen Du

  • Anushree Goswami

  • Tasaday Green

  • Allie Klump

  • Lorraine Lyu

  • Syrine Matoussi

  • Nox Yu


University of Connecticut

  • Madhumita Das

  • Sowmya Kuruganti

  • Tony Phame



Last day at Smith College before campus closed due to the pandemic with Syrine, Nox, and Anushree