Martin J. Aryee

Gene clustering coordinates transcriptional output of disparate biological processes in eukaryotes

The paper identifies conserved and species-specific gene clusters coordinating disparate biological processes across eukaryotes, revealing regulatory proximity as a mechanism for transcriptional coherence.

Integrating Single-Cell Biophysical and Transcriptomic Features to Resolve Functional Heterogeneity in Mantle Cell Lymphoma

This study integrates single-cell biophysical and transcriptomic data to identify clinically relevant phenotypes in mantle cell lymphoma, linking biophysical properties to gene expression and drug response.

Bone Marrow Adipokine Mediates Hematopoietic Regeneration and Stem Cell Fitness

This study identifies BM adipocyte-derived Resistin, regulated by RXR signaling, as critical for HSC self-renewal and hematopoietic regeneration after myeloablation.

Intraductal Papillary Mucinous Neoplasm Cellular Plasticity is linked with Repeat Element Dysregulation

This study uses spatial transcriptomics to show that IPMN subtypes form a molecular continuum originating from gastric-type cells, with repeat element expression linked to disease progression.

High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion dynamics

The paper uses high-resolution CTCF MNase HiChIP data to analyze chromatin loop structures and introduces FactorFinder, finding that fully extruded CTCF-CTCF loops are rare and that chromatin state affects cohesin extrusion dynamics.

Integrative PTEN Enhancer Discovery Reveals a New Model of Enhancer Organization

The paper identifies 10 PTEN enhancers and proposes a new model of enhancer organization that includes spatial separation of functional and structural elements.

Polycomb-lamina antagonism partitions heterochromatin at the nuclear periphery

The paper develops LIMe-Hi-C to study how Polycomb repressive complex 2 and lamina association regulate heterochromatin sub-compartments.

Genome-wide DNA methylation patterns reveal clinically relevant predictive and prognostic subtypes in osteosarcoma.

This study identifies DNA methylation subtypes in osteosarcoma that predict clinical outcomes and response to chemotherapy.

Detection of allele-specific expression in spatial transcriptomics with spASE

The paper introduces spASE, a method to detect spatial patterns in allele-specific expression from spatial transcriptomics data, showing it can identify cell type-specific effects in mouse hippocampus.

Global-scale CRISPR gene editor specificity profiling by ONE-seq identifies population-specific, variant off-target effects

ONE-seq identifies population-specific off-target effects of CRISPR gene editors using global human genome sequence diversity.

Feature Selection and Dimension Reduction for Single Cell RNA-Seq based on a Multinomial Model

The paper introduces multinomial-based methods for feature selection and dimension reduction in scRNA-Seq, improving clustering performance over existing approaches.

CRISPR adenine and cytosine base editors with reduced RNA off-target activities

The paper describes SECURE-ABE and -CBE base editors with reduced RNA off-target activities and improved DNA editing precision.

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of omics data

STREAM is an interactive pipeline for reconstructing and visualizing complex branching trajectories from single-cell transcriptomic and epigenomic data.

Droplet-based combinatorial indexing for massive scale single-cell epigenomics

The paper introduces a droplet-based combinatorial indexing method for high-throughput scATAC-seq, enabling large-scale single-cell chromatin accessibility profiling in mouse and human cells.

Interrogation of human hematopoiesis at single-cell and single-variant resolution

This study fine-maps genetic variants associated with blood cell traits and identifies cell types and causal mechanisms using single-cell chromatin accessibility data from the UK Biobank.

In vivo CRISPR-Cas gene editing with no detectable genome-wide off-target mutations

The paper introduces VIVO, a method to detect off-target mutations from in vivo CRISPR-Cas editing, showing that well-designed gRNAs can edit efficiently without detectable off-targets.

“Global Transcriptional Response to CRISPR/CAS9-AAV6 Based Genome Editing” Matches Transcriptional Response to Specific Small Molecule Perturbations

The paper compares transcriptional responses to CRISPR/Cas9-AAV6 genome editing with small molecule perturbations, finding distinct gene expression patterns associated with different editing methods.

"Unexpected mutations after CRISPR-Cas9 editing in vivo" are most likely pre-existing sequence variants and not nuclease-induced mutations

The paper challenges the claim that CRISPR-Cas9 induces off-target mutations by showing that the observed variants are likely pre-existing genetic differences between treated mice and the control.

hichipper: A preprocessing pipeline for assessing library quality and DNA loops from HiChIP data

The paper introduces hichipper, a preprocessing tool for HiChIP data that includes quality control, bias correction, and DNA loop calling.

diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data

diffloop identifies and analyzes differential DNA loops between samples using ChIA-PET data, linking loop changes to epigenetic and gene expression differences.

Varying-Censoring Aware Matrix Factorization for Single Cell RNA-Sequencing

This paper introduces a matrix factorization method that accounts for censored data in scRNA-Seq to improve clustering accuracy.

The early pregnancy human placenta shares hypomethylation patterns characteristic of solid tumors

The paper identifies hypomethylation patterns in early placenta similar to solid tumors, linking them to genes involved in EMT, immune response, and inflammation.