JADE improves multi-slice spatial transcriptomics analysis by jointly aligning slices and learning shared embeddings, outperforming existing methods on benchmark datasets.

neural information processing systems · Jan 1, 2025Peer-reviewedBioinformatics

A phylogenetic method linking nucleotide substitution rates to rates of continuous trait evolution

Patrick Gemmell, Timothy B. Sackton, Scott V. Edwards, Jun S. Liu

This paper introduces a phylogenetic method to link nucleotide substitution rates to continuous trait evolution, showing associations between conserved sequences and traits like body size and lifespan.

PLoS Computational Biology · Apr 24, 2024Peer-reviewedBioinformatics

SIMPLEs: a single-cell RNA sequencing imputation strategy preserving gene modules and cell clusters variation

Zhirui Hu, Songpeng Zu, Jun S. Liu

SIMPLEs improves scRNA-seq imputation by preserving gene modules and cell clusters, outperforming existing methods and revealing biological insights.

NAR Genomics and Bioinformatics · Sep 28, 2020Peer-reviewedBioinformatics

Determinants of transcription factor regulatory range

Chen-Hao Chen, Rongbin Zheng, Collin J. Tokheim, Xin Dong, Jing‐Yu Fan, Changxin Wan, Qin Tang, Myles A Brown, Jun S. Liu, Clifford A. Meyer, X. Shirley Liu

The paper identifies two classes of transcription factors based on their regulatory range and shows that long-range TFs' activity depends on chromatin state.

Nature Communications · May 18, 2020Peer-reviewedGenomics

Exploring functional variation affecting ceRNA regulation in humans

Mulin Jun Li, Jiexing Wu, Peng Jiang, Wei Li, Yun Zhu, Daniel Fernandez, Russell J. H. Ryan, Yiwen Chen, Junwen Wang, Jun S. Liu, X. Shirley Liu

The paper identifies genetic variations affecting ceRNA regulation by analyzing RNA-seq data and GWAS results, revealing new regulatory mechanisms and disease associations.

bioRxiv · Mar 22, 2015 · PreprintGenetics