Publications

Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression

In single-cell RNA-sequencing (scRNA-seq), gene expression is assessed individually for each cell, allowing the investigation of …
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Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression

Medical Food Assessment Using a Smartphone App With Continuous Glucose Monitoring Sensors: Proof-of-Concept Study

Background: Novel wearable biosensors, ubiquitous smartphone ownership, and telemedicine are converging to enable new paradigms of clinical research. A new generation of continuous glucose monitoring (CGM) devices provides access to clinical-grade measurement of interstitial glucose levels.
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Medical Food Assessment Using a Smartphone App With Continuous Glucose Monitoring Sensors: Proof-of-Concept Study

Normalization benchmark of ATAC-seq datasets shows the importance of accounting for GC-content effects

Modern assays have enabled high-throughput studies of epigenetic regulation of gene expression using DNA sequencing. In particular, the …
DOI

Finding All Significant Closed Connected Subgraphs

In many applications, covariates describing the data are structured according to a known graph $\mathcal{G}$. Subgraphs of …
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Finding All Significant Closed Connected Subgraphs

Improving replicability in single-cell RNA-Seq cell type discovery with Dune

Single-cell transcriptome sequencing (scRNA-Seq) has allowed many new types of investigations at unprecedented and unique levels of …
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Improving replicability in single-cell RNA-Seq cell type discovery with Dune

Non-neuronal expression of SARS-CoV-2 entry genes in the olfaory system suggests mechanisms underlying COVID-19-associated anosmia

Altered olfactory function is a common symptom of COVID-19, but its etiology is unknown. A key question is whether SARS-CoV-2 (CoV-2) – …
DOI

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

Single cell transcriptomics has transformed the characterization of brain cell identity by providing quantitative molecular signatures …
DOI

A multimodal cell census and atlas of the mammalian primary motor cortex

We report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex (MOp or M1) as the initial product …
DOI

Trajectory-based differential expression analysis for single-cell sequencing data

Trajectory inference has radically enhanced single-cell RNA-seq research by enabling the study of dynamic changes in gene expression. …
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Trajectory-based differential expression analysis for single-cell sequencing data

Influence of pulsatile blood flow on allometry of aortic wall shear stress

Shear stress plays an important role in the creation and evolution of atherosclerosis. An key element for in-vivo measurements and …
DOI