The Computational Biology Research Group develops new computational methods, efficient algorithms, and powerful software tools to help answer fundamental biological questions. We are especially interested in problems related to understanding the evolution of genes, genomes, and species. Some of our specific projects include:
- Inferring gene family and genome evolution through gene duplication, horizontal transfer, and loss.
- Understanding evolution at the sub-gene/domain level.
- Reconstructing highly accurate gene trees in both eukaryotes and prokaryotes for evolutionary and functional genomic studies.
- Building whole-genome and multi-locus species phylogenies.
The computer science and engineering department at UConn is one of the best places in the world for doing research in computational biology and bioinformatics (for example, see this metrics-based ranking). The following research positions are available:
PhD positions: Positions are available in the computational biology group for bright and motivated PhD students. Please click here for further details.
Research opportunities for UConn undergraduate students: Positions are also available for qualified UConn undergraduate students who wish to gain research experience by working on exciting research problems. Please click here for further details.
December 2019: Our software for rapid error-correction of large microbial gene trees, TreeSolve, is now available.
October 2019: Our software for accurate inference of disease transmission networks based on intra-host strain diversity, TNet, is now available.
June 2019: Our software for computing RF(+) distances between phylogenetic trees with partially overlapping leaf sets, RF+, is now available.
May 2019: Undergraduate researcher Samuel Sledzieski will be graduating and starting his PhD in computer science at MIT. We wish Sam all the best!
March 2019: Misagh Kordi successfully defended his PhD and will soon be starting a postdoc with Eran Halperin at UCLA. We wish Misagh all the best!
March 2019: Undergraduate researcher Samson Weiner wins UConn SURF award to support his summer research in the lab.
March 2019: Lei Li successfully defended his PhD and will be staring an exciting new job as an algorithms engineer at a startup in China. We wish Lei all the best!
March 2019: Lei's paper on an extension of the Domain-Gene-Species reconciliation model for simultaneous reconciliation of multiple domain trees and multiple gene trees accepted to ISBRA 2019.
January 2019: Paper describing SaGePhy accepted to Bioinformatics.
October 2018: Our software for improved phylogenetic simulation of gene and subgene/domain level evolution, SaGePhy, is now available.
September 2018: Lei's paper on an exact integer linear programming solution for Domain-Gene-Species reconciliation wins best student paper award at ACM-BCB 2018.
Software Quick Links
Phylogenetic reconciliation; Gene family evolution
Protein domain and subgene level evolution
Phylogenetic simulation of gene and subgene evolution
Horizontal gene transfer inference
Phylogenomics; Whole-genome species tree construction
Gene tree reconstruction and error-correction
Transmission network inference
Tree comparison; Optimal tree completion