Joshua D. Welch

Inferring gene regulatory networks from single-cell perturbation data by optimizing causal reach of latent mediator dynamics

CausalODE infers gene regulatory networks from single-cell perturbation data by optimizing causal reach, capturing transient dynamics, and modeling latent protein levels, outperforming existing methods on real datasets.

Human and Mouse Models of the Bipolar Disorder-Associated ANK3 p.W1989R Variant Display Altered Somatostatin Interneuron Connectivity and Function

This study investigates the effects of the ANK3 p.W1989R variant in human and mouse models, showing altered somatostatin interneuron connectivity and function linked to bipolar disorder.

Empirical Estimation of Ambient Contamination in Combinatorial Single-Cell Methods Using Multi-Reference Mapping

The paper introduces methods to estimate and remove ambient contamination in scifi-ATAC data, improving the accuracy of chromatin profiles and biological discovery.

Genome-scale perturbation signatures from primary human CD4+ T cells improve genetics-based prioritization of immune drug targets

The paper introduces IGNITE, a framework that combines genetic data with functional genomics to prioritize immune drug targets, showing improved performance over genetic methods alone.

LIGER2: Scalable Single-Cell Integration with On-Disk Datasets

LIGER2 improves single-cell data integration by enhancing scalability and efficiency while preserving biological variation.

CytoSignal Detects Locations and Dynamics of Ligand-Receptor Signaling at Cellular Resolution from Spatial Transcriptomic Data

CytoSignal detects and quantifies ligand-receptor signaling interactions at cellular resolution from spatial transcriptomic data, enabling spatial gradient analysis and temporal dynamics prediction.

Nuclear Speckles Regulate Splicing During Muscle Stem Cell Activation and Aging

The paper investigates how nuclear speckles regulate splicing and stem cell function in muscle stem cells during activation, injury, and aging.

Single-cell multi-omic analysis of mesenchymal cells reveals molecular signatures and putative regulators of lung allograft fibrosis

Reprogramming the Immune Suppressive Tumor Microenvironment in Glioma Enhances the Efficacy of Immune-Mediated Gene Therapy

This study shows that combining CD73 inhibition with immune-stimulatory gene therapy improves treatment efficacy for wtIDH1 gliomas.

Mechanisms of HIV Latency in Hematopoietic Progenitors: GFI1 as a Key Regulator

This study identifies GFI1 as a key regulator of HIV latency in hematopoietic progenitors through transcriptomic analysis and functional assays.

MIF-mediated reprogramming of myeloid lineage within the glioma tumor microenvironment impacts the efficacy of immune stimulatory gene therapy

This study identifies MIF-CD74 axis regulation of myeloid cells in gliomas and shows that MIF inhibition enhances immune therapy efficacy in wtIDH1 gliomas.

HPV integration in head and neck cancer: downstream splicing events and expression ratios linked with poor outcomes

This study examines HPV integration in HNSCC using RNA-seq data to link splicing events and expression ratios to poor clinical outcomes.

VISTA-FISH: Video Imaging with Spatial-Temporal Analysis by Fluorescent In Situ Hybridization

VISTA-FISH links live-cell imaging with gene expression in neurons to study differentiation and cellular activity.

Predicting the Structural Impact of Human Alternative Splicing

The paper predicts the structural impact of human alternative splicing using AlphaFold2 on over 11,000 isoforms and identifies structural changes across multiple metrics.

Mapping Cell Fate Transition in Space and Time

This paper introduces TopoVelo, a method to infer spatial and temporal dynamics of cell fate transitions from spatial transcriptomic data, improving spatial coherence and accuracy in cell differentiation and migration analysis.

PerturbNet predicts single-cell responses to unseen chemical and genetic perturbations

PerturbNet predicts cell state changes from unseen chemical and genetic perturbations using deep learning and perturbation response data.

Evidence for Transcriptomic Conservation Between the Main Cells of the Drosophila Prostate-Like Accessory Gland and Basal Cells of the Mammalian Prostate.

The paper compares transcriptomic profiles of Drosophila accessory gland cells and mammalian prostate basal cells, finding transcriptomic similarity despite structural and developmental differences.

CytoSimplex: Visualizing Single-cell Fates and Transitions on a Simplex

CytoSimplex visualizes cell differentiation trajectories using simplex geometry to represent cell fate commitment and potential in 2D and 3D plots.

Lung CD4+ resident memory T cells use airway secretory cells to stimulate and regulate neutrophilic allergic airways disease.

This study identifies lung CD4+ resident memory T cells and their interaction with airway secretory cells as key regulators of neutrophilic allergic airways disease in mice and humans.

Characterization of bronchovascular-bundle mesenchymal stromal cells regulating antibody-secreting cell niche in rejecting lung allografts

The paper characterizes CXCL12-expressing mesenchymal stromal cells and their role in supporting antibody-secreting cell niches in rejecting lung allografts.

Integrating single-cell multimodal epigenomic data using 1D-convolutional neural networks

The paper introduces ConvNet-VAEs, a framework for integrating single-cell multimodal epigenomic data using 1D-convolutional variational autoencoders, showing improved dimension reduction and batch correction.

LUMIC: Latent diffUsion for Multiplexed Images of Cells

LUMIC generates high-quality cell images using diffusion models and self-supervised learning, outperforming existing methods across cell lines and treatments.

Epigenetic reprogramming of autophagy leads to uncovering a novel therapeutic target for mutant IDH1 astrocytomas

This study identifies autophagy as a critical survival pathway in mIDH1 gliomas and shows that inhibiting autophagy enhances radiosensitivity and tumor regression in preclinical models.

Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation

The paper performs population-scale single-nucleus multi-omic profiling of skeletal muscle to identify genetic regulation across cell types and traits.

MorphNet Predicts Cell Morphology from Single-Cell Gene Expression

MorphNet predicts cell morphology from gene expression using neural networks trained on paired morphology and molecular data, generating realistic morphological images and generalizing across brain regions.

Bayesian Inference of RNA Velocity from Multi-Lineage Single-Cell Data

This paper introduces VeloVAE, a Bayesian model for RNA velocity inference that improves accuracy and captures complex dynamics in multi-lineage single-cell data.

PyLiger: Scalable single-cell multi-omic data integration in Python

PyLiger provides a Python implementation of the LIGER method for integrating single-cell multi-omic data, offering faster performance and new features.

Nonnegative matrix factorization integrates single-cell multi-omic datasets with partially overlapping features

This paper introduces a nonnegative matrix factorization method to integrate single-cell datasets with partially overlapping features, showing improved integration across multiple data types.

Single-cell multi-omic velocity infers dynamic and decoupled gene regulation

The paper introduces MultiVelo, a model that integrates epigenomic and transcriptomic data to infer dynamic gene regulation and cell fate prediction.

An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types

The paper creates a comprehensive atlas of mouse primary motor cortex cell types using integrated transcriptomic and epigenomic data from over 600,000 samples.