Accurate and efficient HiChIP interaction detection by modeling restriction enzyme cut site density as biological signal
Weiyue Ding, Yang Zhou, Quanhong Liu, Yiyuan Guo, Chiping Zhang, Shuilin Jin · 2026
Read Accurate and efficient HiChIP interaction detection by modeling restriction enzyme cut site density as biological signal by Weiyue Ding, Yang Zhou, Quanhong Liu, Yiyuan Guo, Chiping Zhang, Shuilin Jin (2026) in the Tower of Babel, a free online library of public-domain works preserved in clean, searchable text. No sign-up. The full text is served as a plain-text file at a predictable URL, where text is present: https://antarctic-labs.com/tower-of-babel/pmc-13245736.txt.
Description
Weiyue Ding and co-authors improve a method for mapping how DNA folds inside the cell. The method, HiChIP, spots loops where far apart DNA stretches touch. Old tools treat the density of enzyme cut sites as noise to scrub away. The team argues that density is real signal: open, active DNA gets cut more.
Their tool, sintHiChIP, models cut density as part of the biology. Smoothing and distance aware math then pick out loops while keeping local detail. Checks on known data show it finds classic loops well, above all near active gene switches. It also forecast the results of gene silencing tests with high accuracy. The tool runs on a normal workstation.
Catalog record
| CREATOR | Weiyue Ding, Yang Zhou, Quanhong Liu, Yiyuan Guo, Chiping Zhang, Shuilin Jin |
|---|---|
| YEAR | 2026 |
| COLLECTION | PAPERS |
| FORMAT | TXT |
| FILE SIZE | 45 KB |
| VERSION | 1.0 |
| LICENSE | CC BY 4.0 |
| RIGHTS | CC BY |
| SOURCE | Europe PMC |