I am an Associate Professor in the Computer Science department, with affiliate appointments in the Electrical & Computer Engineering department, the National Center for Supercomputing Applications (NCSA), the Infection Genomics for One Health theme of the Institute of Genomic Biology (IGB) and the Cancer Center at the University of Illinois at Urbana-Champaign (UIUC).

Our research focuses on tumor phylogenetics in the context of intra-tumor heterogeneity. We develop phylogeny inference algorithms to study the progression of a tumor from its initial stage, where a healthy cell acquires its first somatic mutation, to the final stages, where tumor cells metastasize and invade and colonize distant organs and tissues. In addition, we develop algorithms to reconstruct patterns of spread in disease outbreaks. More broadly, we are interested in the application of combinatorial optimization techniques to answers questions and solve problems in biology.

Please see my CV for more details.

News

• Sep 3, 2024: I presented our paper at WABI 2024 [slides]
• Aug 28, 2024: Congratulations to Leah for her accepted paper at Cell Genomics. This was a wonderful collaboration with the Aly Khan lab.
• Jul 8, 2024: Some exciting updates from the group:
  • Congratulations to Leah for successfully defending her PhD thesis.
  • Congratulations to Yuanyuan for successfully defending his PhD thesis.
  • Congratulations to Yuanyuan for his accepted paper at WABI 2024.
  • Congratulation to Mrinmoy for his accepted paper at JCB.
• Mar 7, 2024: Congratulations to Xinyu and Yuanyuan for our accepted paper at JCB.
• Jan 16, 2024: Congratulations to Leah for our accepted paper at RECOMB 2024.
• Jan 16, 2024: Congratulations to Yuanyuan for our paper at JCB.
• Aug 23, 2023: Congratulations to Xinyu, Yuanyuan and Mrinmoy for our accepted papers at WABI 2023: [1] and [2].
• Mar 10, 2023: Congratulations to Leah and Chuanyi for our accepted paper at RECOMB-CCB 2023.
• Mar 2, 2023: Congratulations to Chuanyi for successfully defending his PhD thesis.
• Jan 9, 2023: Congratulations to Stefan for our accepted paper at RECOMB 2023.
• Oct 25, 2022: My thoughts on: "What are the keys to succeeding as a computational biologist in today’s research climate?"
• Oct 25, 2022: I gave a virtual talk at the CRC Integromics Group at MD Anderson.
• Oct 25, 2022: Congratulations to Zubair and Gillian for our accepted paper at PLOS CB.
• Jun 20, 2022: Congratulations to Chuanyi and Palash for our accepted paper at Molecular Biology and Evolution.
• Jun 20, 2022: Congratulations to Juho for successfully defending his PhD thesis.
• Apr 6, 2022: Congratulations to Zubair and Gillian for their accepted paper at RECOMB-CCB 2022.
• Mar 20, 2022: Congratulations to Palash for two journal papers: [1] and [2].
• Dec 29, 2021: Congratulations to Chuanyi and Palash for their accepted paper at RECOMB 2022.
• Nov 22, 2021: Congratulations to Palash and Chuanyi for our paper on transcript assembly in coronaviruses.
• Jul 22, 2021: Congratulations to Palash for our WABI paper on co-refining clone trees.
• Jul 20, 2021: Our paper on doublet detection in scDNA-seq data is available online.
• Jul 20, 2021: Distinguishing linear from branching tumor evolution given scDNA-seq data, check out our paper.
• Mar 12, 2021: A couple of exciting updates from the group:
  • Congratulations to Leah and Palash for their (conditionally) accepted paper at ISMB/ECCB 2021.
  • Congratulations to Chuanyi for his accepted paper at Nature Communications.
  • Check out our work on evolution and copy-number aware mutation clustering in cancer, accepted at RECOMB 2021.
  • I received an NSF CAREER award.
  • I am co-chairing the PC of WABI 2021, and I am an area co-chair for ISMB/ECCB 2021.
  • Congratulations to Sarah for successfully defending her PhD thesis.
• Oct 14, 2020: Our PhyDOSE paper is available on PLOS CB.
• Sep 13, 2020: Sarah presented RECAP at ECCB 2020, and Leah presented Phyolin at WABI 2020.
• Jul 9, 2020: I gave a talk at MCW (Model Counting Workshop) 2020.
• Jul 6, 2020: Congratulations to Sarah and Juho for their accepted paper at ECCB 2020, and to Leah for her accepted paper at WABI 2020.
• Jun 18, 2020: Leah presented PhyDOSE at RECOMB-CCB 2020.
• May 14, 2020: Our preprint on SARS-CoV-2 within-host diversity is available. This is joint work with the Peng lab.
• Apr 14, 2020: Congratulations to Palash and Jiaqi for their accepted ISMB 2020 papers.
• Jan 10, 2020: Sarah gave a talk on PhySigs at PSB 2020.
• Nov 26, 2019: Our PhySigs paper is available online.
• Oct 17, 2019: I gave a talk at the University of Maryland, College Park.
• Oct 7, 2019: I presented our work on counting and sampling transmission networks at RECOMB-CG 2019.
• Sep 17, 2019: Congratulations to Sarah for our accepted paper at PSB 2020.
• Aug 6, 2019: Congratulations to Palash for our accepted paper at RECOMB-CG 2019.
• Jul 29, 2019: Two talks at ISMB/ECCB 2019.
• May 3, 2019: I presented our work on multiple consensus trees at RECOMB-CCB 2019.
• Apr 9, 2019: Congratulations to Aini and Yuanyuan for our accepted paper at ISMB/ECCB 2019! Sneak peek at RECOMB CCB.
• Mar 21, 2019: I presented some of our work at CISS 2019.
• Oct 14, 2018: I presented our work on non-uniqueness of solutions in phylogeny inference from mixed samples at RECOMB-CG 2018. Paper is available online.
• Sep 14, 2018: I presented SPhyR at ECCB 2018, which is a method for tumor phylogeny estimation from single-cell DNA sequencing data using Dollo parsimony. Paper is out on Bioinformatics.
• Aug 20, 2018: I presented our theoretical work on the Parsimonious Migration History problem at WABI.
• Aug 9, 2018: Our paper on the hardness of the Parsimonious Migration History problem is available online.
• Jul 19, 2018: I attended the AI in Medicine workshop at the Mayo Clinic in Rochester, MN (link for slides and poster).
• Jul 13, 2018: I gave two talks at ISMB 2018.
• May 5, 2018: Our paper on visualizing small graphs together with a collection of node sets in Cytoscape is available online.
• Apr 26, 2018: Our paper on reconstructing migration patterns in metastatic cancers is available online on Nature Genetics.
• Apr 20, 2018: Our poster won the best poster award at RECOMB CCB.
• Apr 19, 2018: I gave a talk at Indiana University Bloomington.