2021

Doctoral Thesis Title: Computational Dissection and prediction of cancer immunotherapy response Publications while at MIT: Evolution of delayed resistance to immunotherapy in a melanoma responder. Liu D, Lin JR, Robitschek EJ, Kasumova GG, Heyde A, Shi A, Kraya A, Zhang G, Moll T, Frederick DT, Chen YA, Wang S, Schapiro D, Ho LL, Bi K, Sahu…

Doctoral Thesis Title: Modeling structured biological processes with machine learning Publications while at MIT:   Generating experimentally unrelated target molecule-binding highly functionalized nucleic-acid polymers using machine learning. Chen JC, Chen JP, Shen MW, Wornow M, Bae M, Yeh WH, Hsu A, Liu DR.Nat Commun. 2022 Aug 4;13(1):4541. doi: 10.1038/s41467-022-31955-4.PMID: 35927274 Free PMC article. Reconstruction of evolving gene variants and fitness…

Thesis Title: Chromatin accessibility informs cell identity: studies in silico, in vitro, and in vivo Publications while at MIT: spatzie: an R package for identifying significant transcription factor motif co-enrichment from enhancer-promoter interactions. Hammelman J, Krismer K, Gifford DK.Nucleic Acids Res. 2022 Jan 31:gkac036. doi: 10.1093/nar/gkac036. Online ahead of print.PMID: 35100401 Discovering differential genome sequence activity…

Doctoral Thesis Title: Computational Methods for Analyzing and Modeling Gene Regulation and 3D Genome Organization Publications while at MIT: 1. DCI: Learning Causal Differences between Gene Regulatory Networks. Belyaeva A, Squires C, Uhler C.Bioinformatics. 2021 Mar 11:btab167. doi: 10.1093/bioinformatics/btab167. Online ahead of print.PMID: 33704425 2. Causal network models of SARS-CoV-2 expression and aging to identify candidates for drug repurposing.…