scLong is a billion-parameter foundation model that captures long-range gene context in scRNA-seq by modeling all genes and integrating gene knowledge, outperforming existing models in various tasks.

Nature Communications · Feb 5, 2026Peer-reviewedBioinformatics

An integrated view of the structure and function of the human 4D nucleome

Job Dekker, Betül Akgöl Oksuz, Yang Zhang, Ye Wang, Miriam K. Minsk, Shuzhen Kuang, Liyan Yang, Johan Harmen Gibcus, Nils Krietenstein, Oliver J. Rando, Jie Xu, Derek H. Janssens, Steven Henikoff, Alexander Kukalev, Andréa Willemin, , Feng Yue

The paper integrates 4D Nucleome data to analyze 3D genome structure and function in human cells, revealing chromatin domains, loops, and interactions, and showing how genetic variants affect genome folding.

Nature · Dec 17, 2025Peer-reviewedGenomics

GITAR: an Open Source Tool for Analysis and Visualization of Hi-C Data

Riccardo Calandrelli, Qiuyang Wu, Jihong Guan, Sheng Zhong

GITAR provides a software tool for Hi-C data analysis, including preprocessing, normalization, visualization, and TADs analysis, with a library of processed datasets.

Genomics Proteomics & Bioinformatics · Oct 1, 2018Peer-reviewedBioinformatics

Rainbow-seq: combining cell lineage tracking with single-cell RNA sequencing in preimplantation embryos

Fernando H. Biase, Qiuyang Wu, Riccardo Calandrelli, Marcelo Rivas‐Astroza, Shuigeng Zhou, Zhen Chen, Sheng Zhong

Rainbow-seq combines lineage tracing with single-cell RNA-seq to track cell division history and reveal transcriptome differences in mouse embryos.

iScience · Aug 16, 2018Peer-reviewedDevelopmental Biology

GIVE: toward portable genome browsers for personal websites

Xiaoyi Cao, Zhangming Yan, Qiuyang Wu, Alvin Zheng, Sheng Zhong

GIVE provides a library for creating personalized genome browsers on personal websites without needing system administration.

Genome biology · Jul 17, 2018Peer-reviewedBioinformatics