Dennis E. Shasha

This paper introduces CyclicChamp, a computational pipeline for designing cyclic peptides of 7-24 residues, achieving stable designs validated by molecular dynamics simulations.

Pheniqs 2.0 improves barcode decoding accuracy and confidence estimation for combinatorial indexing in sequencing data.

Pheniqs improves sequence demultiplexing by incorporating quality scores and error probability estimation, achieving higher accuracy and speed.