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.

Belyaeva A, Cammarata L, Radhakrishnan A, Squires C, Yang KD, Shivashankar GV, Uhler C.Nat Commun. 2021 Feb 15;12(1):1024. doi: 10.1038/s41467-021-21056-z.PMID: 33589624 Free PMC article.

3. Multi-domain translation between single-cell imaging and sequencing data using autoencoders.

Yang KD, Belyaeva A, Venkatachalapathy S, Damodaran K, Katcoff A, Radhakrishnan A, Shivashankar GV, Uhler C.Nat Commun. 2021 Jan 4;12(1):31. doi: 10.1038/s41467-020-20249-2.PMID: 33397893 Free PMC article.

4. Network analysis identifies chromosome intermingling regions as regulatory hotspots for transcription.

Belyaeva A, Venkatachalapathy S, Nagarajan M, Shivashankar GV, Uhler C.Proc Natl Acad Sci U S A. 2017 Dec 26;114(52):13714-13719. doi: 10.1073/pnas.1708028115. Epub 2017 Dec 11.PMID: 29229825 Free PMC article.