Gerald Quon

HLiCA: An integrated cell atlas of the healthy human liver

The paper integrates multiple datasets to create a comprehensive human liver cell atlas, identifying new cell types and associations with demographic factors.

Predicting emergent phenotypes from single cell populations using CELLECTION

CELLECTION predicts emergent phenotypes from single-cell populations by associating subgroups with different phenotypes across diverse tasks.

Human-specific gene expansions contribute to brain evolution

The paper identifies human-specific gene expansions linked to brain evolution by analyzing genome sequences and functional models in zebrafish.

A conditional generative model to disentangle morphological variation from batch effects in model organism imaging studies

This paper introduces a conditional latent diffusion model to separate batch effects from morphological features in zebrafish imaging data, enabling accurate genotype classification.

Deciphering the History of ERK Activity from Fixed-Cell Immunofluorescence Measurements

The paper develops a framework to infer ERK signaling dynamics from fixed-cell immunostains by combining machine learning and differential equations, showing that protein levels reflect different activation timescales.

sciLaMA: A Single-Cell Representation Learning Framework to Leverage Prior Knowledge from Large Language Models

sciLaMA integrates gene embeddings from large language models with scRNA-seq data using a paired-VAE architecture, improving downstream tasks like batch correction and clustering while maintaining computational efficiency.

Sex-specific single cell-level transcriptomic signatures of Rett syndrome disease progression

The paper identifies sex-specific transcriptomic changes in a mouse model of Rett syndrome, showing more differentially expressed genes in females and non-cell-autonomous effects.

Cell adhesion molecules play subclass-specific roles in electrophysiological response and Schizophrenia risk

The paper identifies subclass-specific genes associated with electrophysiological features in mouse interneurons and links cell adhesion molecules to schizophrenia risk.

Projecting clumped transcriptomes onto single cell atlases to achieve single cell resolution

scProjection maps multi-modal RNA measurements to scRNA-seq atlases to extract single cell gene expression profiles and improve spatial and multi-modal analysis.

Interpretable deep generative models for genomics

This paper introduces an interpretable variational autoencoder for genomics that identifies gene neighborhoods and hubs, revealing correlations between neuronal differentiation and mitochondrial complex co-expression.

scBFA: modeling detection patterns to mitigate technical noise in large-scale single cell genomics data

scBFA mitigates technical noise in single cell genomics data by analyzing detection patterns instead of quantification measurements, improving cell type identification and trajectory inference.

Conserved cell types with divergent features between human and mouse cortex

The paper compares cell types in human and mouse cortex using single nucleus RNA-sequencing, finding conserved architecture with species-specific differences.

scAlign: a tool for alignment, integration and rare cell identification from scRNA-seq data

scAlign integrates scRNA-seq datasets and identifies rare cell populations, demonstrating its ability to detect a rare cell type associated with malaria transmission.

Predicting trait regulators by identifying co-localization of DNA binding and GWAS variants in regulatory regions

CONVERGE identifies co-localization of GWAS variants with transcription factor binding sites in regulatory regions to find novel trait regulators, outperforming existing methods in validating type 2 diabetes regulators.

Systems-level properties of EGFR/Ras/ERK signalling amplify local signals to generate gene expressionplasticity

The paper shows that EGFR/Ras/ERK signaling in invasive breast cancer cells produces more dynamic and disordered ERK activity, leading to heterogeneous gene expression compared to non-malignant cells.