Kaiyu Qiu

This paper simulates protein evolution using programmable fitness objectives derived from modern protein models, showing that combined objectives improve evolutionary realism and molecular plausibility.

TREAD improves repeat annotation by using protein embeddings instead of sequence profiles, outperforming HMMER in low-data and high-divergence scenarios.

The paper identifies a unique cysteine motif in DPY-6 that facilitates dimerization and is involved in cuticle formation in nematodes.

This study characterizes HLp, a bacterial histone that forms tetramers and wraps ~60 base pairs of DNA, revealing a new mode of histone-DNA interaction in bacteria.

The paper introduces pLM-Repeat, a tool using protein language model embeddings to detect repetitive sequences, achieving comparable sensitivity to HHrepID with faster performance.