Xinxian Deng

Cavebear improves pseudotime inference by using reference species time-series data to guide ordering of cells in query species or conditions without time labels.

The paper develops a high-throughput Visual Cell Sorting workflow to link nuclear compartment morphology to single-nucleus transcriptomes, identifying a conserved transcriptional signature of nucleolar size linked to proteostasis.

The paper investigates how sex chromosome aneuploidy affects gene expression and DNA methylation in different cell types, revealing cell-type specific dosage compensation mechanisms.

The paper introduces Icebear, a neural network framework for cross-species imputation and comparison of single-cell transcriptomic profiles, revealing evolutionary adaptations of X-chromosome upregulation in mammals.

This paper introduces Sunbear, a framework for integrating multi-condition and multi-modal single-cell profiles across time to infer temporal profiles and predict dynamic relationships in mouse embryonic development.

12.4 million single-nucleus transcriptomes from 83 staged mouse embryos (E8 to P0) yield 190 cell types, a zygote-to-pup cell-type tree, and rapid postnatal transcriptional shifts.

The paper introduces Sceptic, a supervised pseudotime analysis model that improves prediction accuracy over existing methods for scRNA-seq and single-nucleus image data.

This study shows that KDM6A is required for Xist upregulation during X inactivation initiation in mouse ES cells, as its knockout impairs Xist RNA coating and leads to aberrant Xi gene expression.

The paper investigates how CTCF-mediated chromatin insulation and structure regulate escape from X chromosome inactivation in mouse cells, showing that CTCF binding and domain organization are critical for maintaining XCI.

The paper introduces O-MAP, a method for discovering RNA-interacting proteins, transcripts, and genomic loci in situ with high precision and without genetic manipulation.

The paper integrates single-cell RNA-seq, ATAC-seq, and Hi-C data to study nuclear configuration and gene expression changes during stem cell differentiation and X inactivation, revealing discrete structural changes and delayed chromatin compaction.

This study shows that Firre RNA has trans-acting effects on the inactive X chromosome, affecting histone modifications, PRC2 complex components, and chromatin structure.

This study identifies a deletion of FUNDC2 and CMC4 on Xq28 as sufficient to cause hypergonadotropic hypogonadism in men by disrupting apoptosis, inflammation, and FSH regulation.

This paper applies and extends MMD-MA to align single-cell transcriptome and chromatin accessibility data from ~2000 cells, demonstrating its scalability and accuracy.

Sci-Hi-C is a single-cell Hi-C method that maps 3D genome organization in large numbers of single cells, enabling analysis of chromatin interactions and cellular variability.

The paper shows Dxz4 orientation controls long-range contacts on the inactive X chromosome, maintaining its bipartite structure through CTCF motif direction.

This paper introduces DNase Hi-C and targeted DNase Hi-C methods for high-resolution mapping of chromatin interactions, overcoming limitations of traditional Hi-C techniques.

This paper introduces combinatorial single cell Hi-C, a method for measuring chromosome conformation in single cells, and shows its ability to distinguish cell types and reveal chromosomal heterogeneity.