Xingcheng Lin
North Carolina State University, NC·Biophysics·Early-career
Nearly every step in reading out genetic information depends on proteins binding to DNA or RNA, and on how DNA is folded inside the cell nucleus. Both affect which genes turn on.
- Fields
Biophysics
Chemistry
Computer Science
- Topics
protein–nucleic acid interactions
protein-DNA binding
protein-RNA binding
- Grants
- 2 known grants, through May 2031
What they work on
- Develop a physics-informed AI model that predicts how strongly proteins bind specific DNA or RNA sequences, combining sequence, structure and dynamics so it stays accurate when experimental training data are sparse.
- Use the binding models to design oligonucleotide aptamers, short DNA or RNA strands that latch onto selected target proteins, and test predictions with partner labs studying DNA mismatch recognition and aptamer selection.
- Release the validated models as a publicly accessible computational platform for rapid prediction of protein–nucleic acid binding affinities and high-affinity sequence motifs.
- Build a residue-level simulation of hundreds of nucleosomes to test how histone acetylation, ubiquitylation and methylation, together with regulatory proteins, reshape higher-order chromatin structure and gene regulation.
- Simulate how epigenetic tags drive chromatin phase separation into condensates in the crowded nucleus, and how this crowded environment in turn alters biomolecular interactions and genome compartmentalization.
More about the research
The lab combines artificial intelligence (AI) with physics-based computer modeling to predict these molecular interactions. One project predicts how strongly proteins grip specific DNA or RNA sequences. The other simulates how chemical tags on DNA's packaging proteins reshape the folded genome.
Why it matters
Errors in epigenetic regulation have been linked to many human diseases, and mapping how specific histone tags organize the genome could guide therapies that target this dysregulation. Fast, accurate prediction of protein–DNA and protein–RNA binding could speed discovery of therapeutic and diagnostic oligonucleotide aptamers, and support biotechnology efforts to tune gene expression, such as improving responses to stress and environmental conditions.
Known grants
From NIH and NSF research grants. Labs often have other funding we can't see.
Closest labs
Bruce Armitage
Carnegie Mellon University, PA·Chemistry
Design fluorescent peptide nucleic acid (PNA) probes that bind unmodified C9orf72 repeat RNAs, so these RNAs can be seen in biomolecular condensates by microscopy.
Priya R. Banerjee
University at Buffalo, NY·Biophysics·Early-career
Test whether pioneer transcription factors, proteins that can bind DNA packed into closed chromatin, act by forming liquid-like droplets on DNA that concentrate RNA polymerases and nucleosome-remodeling complexes to switch genes on.
Yong Wang
Pennsylvania State University, PA·Biomedical Engineering
Develop a one-step, three-dimensional method to select aptamers, short DNA or RNA strands that bind targets tightly, inside a non-fouling macroporous hydrogel that resists unwanted sticking.
The school
North Carolina State University: 40 labs on PI Pages, $717M a year on research, 603 research doctorates a year.
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