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 with interpretable and efficient deep learning.

Hammelman J, Gifford DK.PLoS Comput Biol. 2021 Aug 9;17(8):e1009282. doi: 10.1371/journal.pcbi.1009282. eCollection 2021 Aug.PMID: 34370721 Free PMC article.

An expansion of the non-coding genome and its regulatory potential underlies vertebrate neuronal diversity.

Closser M, Guo Y, Wang P, Patel T, Jang S, Hammelman J, De Nooij JC, Kopunova R, Mazzoni EO, Ruan Y, Gifford DK, Wichterle H.Neuron. 2022 Jan 5;110(1):70-85.e6. doi: 10.1016/j.neuron.2021.10.014. Epub 2021 Nov 1.PMID: 34727520

Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay.

Hammelman J, Krismer K, Banerjee B, Gifford DK, Sherwood RI.Genome Res. 2020 Oct;30(10):1468-1480. doi: 10.1101/gr.263228.120. Epub 2020 Sep 24.PMID: 32973041 Free PMC article.