MoCha: Molecular Characterization of Unknown Pathways. - Daniel Lobo; Jennifer Hammelman; Michael Levin 001 (J. Comput. Biol., 2016)

Toward Modeling Regeneration via Adaptable Echo State Networks. - Jennifer Hammelman; Hava T. Siegelmann; Santosh Manicka; Michael Levin 001 (From Parallel to Emergent Computing, 2019)

Discovering differential genome sequence activity with interpretable and efficient deep learning. - Jennifer Hammelman; David K. Gifford (PLoS Comput. Biol., 2021)

seqgra: principled selection of neural network architectures for genomics prediction tasks. - Konstantin Krismer; Jennifer Hammelman; David K. Gifford (Bioinform., 2022)