Zicong Zhang

The paper shows cavefish have improved olfaction through physiological adaptations, not expanded chemosensory receptors, and demonstrates reduced flow rate in olfactory pits enhances foraging.

Rosalind, a DNA foundation model, predicts variant-gene regulatory relationships without proximity bias, identifying distal genes as more impactful in osteoporosis.

The paper introduces e2MPRA, a method that simultaneously measures regulatory activity and epigenomic features of CREs using lentivirus-based MPRA and targeted Cut&Tag or ATAC-seq.

This paper improves AlphaFold's self-confidence scoring by modifying its LDDT prediction head to provide more accurate model quality assessments.

The paper investigates the evolutionary diversification of V1R genes in East African cichlids, finding evidence of introgression contributing to their diversity.

NuFold predicts RNA tertiary structures using deep learning with a nucleobase center representation to bridge the gap between sequence data and structural insights.

The paper identifies functional cis-regulatory elements in three human cell types using lentiMPRAs and develops predictive models for CRE function.

The paper refines the annotation of endogenous retrovirus LTRs in primates by identifying new subfamilies and their regulatory roles through phylogenetic analysis and functional validation.

The paper introduces 3D-AF-Surfer, a tool for real-time structure-based search of AlphaFold2 protein models using molecular surface representation and 3D Zernike descriptors.