Computational Biology Research Laboratory

Spotlights

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.

September 2020: Paper on TreeFix-TP, a phylogenetic error correction framework for disease transmission network inference, accepted to PSB 2021.

July 2020: Abhijit’s paper on using machine learning to distinguish between additive and replacing horizontal gene transfers accepted to ACM-BCB 2020.

May 2020: Undergraduate researchers Emily Maciejewski, Taylor Wade, and Samson Weiner will all be graduating this spring. Emily will be starting her PhD in computer science at UCLA in Fall. Taylor Wade will be joining a PostBaccalaureate research program at The Jackson Laboratory. Samson will be continuing in the lab as a PhD student starting Fall. Congratulations Emily, Taylor, and Samson!

April 2020: Paper evaluating performance of gene tree rooting methods to appear in PLOS One.

April 2020: Paper on phylogenetic tree comparison and optimal tree completion appears in Algorithms for Molecular Biology.

March 2020: Undergraduate researcher Keegan Yao wins UConn SURF award to support his summer research in the lab.

March 2020: Saurav’s paper on Phylogeny-Based Inference of Disease Transmission Networks accepted to ISBRA 2020.

January 2020: Misagh’s paper on TreeSolve, a new method for rapid error-correction of microbial gene trees, accepted to AlCoB 2020.

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: Paper on DTRL reconciliation for distinguishing between additive and replacing horizontal transfers accepted to ACM-BCB 2019.

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!

April 2019: Invited talk and tutorial on genome-scale phylogenetics at Trees in the Desert Workshop.

March 2019: Misagh Kordi successfully defended his PhD and will soon be starting a postdoc 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.

August 2018: Three new PhD students Abhijit Mondal, Saurav Dhar, and Sumaira Zaman join the research group.

August 2018: Soumya Kundu successfully defended his MS thesis and graduated. Soumya will start his PhD studies in computer science at Stanford in Fall and we wish him all the best!

July 2018: Paper on computing RF(+) distances and optimal phylogenetic tree completions accepted to RECOMB-CG 2018.

June 2018: Lei’s paper on an exact integer linear programming solution for Domain-Gene-Species reconciliation accepted to ACM-BCB 2018.

May 2018: Paper describing the new RecPhyoXML format for reconciled gene trees accepted to Bioinformatics.

April 2018: Paper describing RANGER-DTL 2.0 accepted to Bioinformatics.

December 2017: Soumya’s paper on the uncertainty of gene tree rooting and its impact accepted to BMC Bioinformatics.

October 2017: Lei’s paper on integrated analysis of domain, gene, and species level evolution accepted to APBC 2018 and to IEEE/ACM TCBB.

August 2017: Software for simultaneous analysis of domain, gene, and species level evolution, SEADOG 1.0, is now available.

July 2017: Two new PhD students Lina Kloub and Farzaneh Rastegari join the lab.

May 2017: Workshop on Biogeochemical Dating in Deep Time to be held on May 11-12, 2017, at UConn. This NSF-funded workshop is hosted jointly by Mukul Bansal and Greg Fournier.

May 2017: Paper on exact algorithms for DTL-reconciliation with non-binary gene trees accepted to IEEE/ACM TCBB.

April 2017: Software for DTL reconciliation, RANGER-DTL 2.0, officially released.

March 2017: Undergraduate lab member Soumya Kundu’s research paper on the impact of uncertain gene tree rooting on DTL reconciliation accepted to ISBRA 2017.

December 2016: Undergraduate lab member Soumya Kundu selected to UConn’s University Scholar Program in support of his research on gene tree rooting.

October 2016: Invited plenary talk at the IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) in Atlanta, USA. Slides from the talk are available here.