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 tumor evolution and inferring tumor phylogenies.
- Understanding and modeling evolution at the subgene/domain level.
- Reconstructing highly accurate gene trees for evolutionary and functional genomic studies.
- Inferring infectious disease transmission networks.
- Building whole-genome and multi-locus species phylogenies.
Videos describing some of our work are publicly available on YouTube at the following URLs:
ISMB 2012 talk: https://youtu.be/Z30z9xAh8_U
ISMB 2014 talk: https://youtu.be/GoMcy7jhp6s
ISCBacademy Webinar 2021: https://youtu.be/P8P_yDeInN4
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.
August 2023: Sumaira's paper on improving gene family sequence alignments in the presence of domain rearrangement to appear in the proceedings of ISBRA 2023.
July 2023: Samson's paper on improved simulation of single-cell copy number profiles from tumors to appear in the journal Bioinformatics.
July 2023: Abhijit's paper on generalized domain-gene-species reconciliation to appear in IEEE/ACM Transactions on Computational Biology and Bioinformatics.
April 2023: Lab member Sumaira Zaman has successfully defended her PhD dissertation. Congratulations!
April 2023: After almost two years with the lab, undergraduate researcher Rachel Parsons is graduating and will be starting her PhD in computer science at the University of Maryland in Fall 2023. We wish Rachel all the best!
February 2023: Abhijit's paper on phylogenetic dating using relative time constraints to appear in the journal Bioinformatics.
November 2022: Lab member Abhijit Mondal has successfully defended his PhD dissertation! Congratulations!
July 2022: Paper describing virDTL, a new computational protocol for viral recombination analysis, to appear in the Journal of Computational Biology.
March 2022: Sumaira's paper on the impact of partial gene transfer on gene tree reconstruction to appear in the proceedings of RECOMB-CG 2022.
March 2022: Book chapter describing the use of phylogenetic reconciliation to understand microbial evolution to appear in Methods in Molecular Biology book series.
August 2021: Samson's paper on duplication-transfer-loss reconciliation with extinct and unsampled lineages to appear in Algorithms.
July 2021: Saurav's paper on disease transmission network inference at the level of individuals and geographical regions to appear in IEEE/ACM Transactions on Computational Biology and Bioinformatics.
July 2021: Keegan's paper on optimal completion and comparison of incomplete phylogenetic trees wins best student paper award at CPM 2021.
June 2021: An extended version of TNet designed for geographical transmission network inference is now available: TNet-Geo.
June 2021: Lab member Lina Kloub has successfully defended her PhD dissertation. Congratulations!
May 2021: Lab member Saurav Dhar has graduated with his master's degree. We wish Saurav all the best!
May 2021: After over two years with the lab, undergraduate researcher Keegan Yao is graduating and will be starting his PhD in computer science at Duke. We wish Keegan all the best!
April 2021: Keegan's paper on optimal completion and comparison of incomplete phylogenetic trees to appear in the proceedings of CPM 2021.
February 2021: Lina's paper on detection of large-scale horizontal multigene transfer events to appear in Molecular Biology and Evolution.
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; Domain-aware sequence alignment
Tumor evolution and tumor phylogenetics
Viral transmission network inference
Viral recombination analysis
Tree comparison; Optimal tree completion