I am an Assistant 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).
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.
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:
 and . 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. Show more