Christine M. Distèche

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 paper reconstructs cellular trajectories of mammalian embryogenesis using scRNA-seq data and identifies key transcription factors at branch points.

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

This study shows KDM6A differentially regulates maternal and paternal alleles in mouse genes, with distinct chromatin changes depending on the allele.

The paper shows RNA stabilizes heterochromatin domains by acting as a structural scaffold, using CUT&RUN.RNase to study RNA's role in chromatin organization.

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 develops sci-LIANTI, a single-cell DNA sequencing method, to map meiotic crossovers and chromosome mis-segregation in hybrid mice, finding frequent mitotic segregation during meiosis.

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.