Quantifying the effect of experimental perturbations at single-cell resolution

Endocrine-Exocrine Signaling Drives Obesity-Associated Pancreatic Ductal Adenocarcinoma

(2020) Katherine Minjee Chung et al.   CELL

A dopamine-induced gene expression signature regulates neuronal function and cocaine response

(2020) Katherine E. Savell et al.   Science Advances

ClusterMap: Compare multiple Single Cell RNA-Seq datasets across different experimental conditions

(2019) Xin Gao et al.   BIOINFORMATICS

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

cellHarmony: cell-level matching and holistic comparison of single-cell transcriptomes

(2019) Erica A K DePasquale et al.   NUCLEIC ACIDS RESEARCH

Visualizing structure and transitions in high-dimensional biological data

(2019) Kevin R. Moon et al.   NATURE BIOTECHNOLOGY

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

Pseudotime Ordering of Single Human β-Cells Reveals States of Insulin Production and Unfolded Protein Response

(2018) Yurong Xin et al.   DIABETES

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

(2018) Jeffrey A. Farrell et al.   SCIENCE

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo

(2018) Daniel E. Wagner et al.   SCIENCE

Transcriptional Heterogeneity of Beta Cells in the Intact Pancreas

(2018) Lydia Farack et al.   DEVELOPMENTAL CELL

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Graph Laplacian Regularization for Image Denoising: Analysis in the Continuous Domain

(2017) Jiahao Pang et al.   IEEE TRANSACTIONS ON IMAGE PROCESSING

Vertex-frequency analysis on graphs

(2016) David I Shuman et al.   APPLIED AND COMPUTATIONAL HARMONIC ANALYSIS

Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

(2016) Diego Adhemar Jaitin et al.   CELL

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

(2016) Karthik Shekhar et al.   CELL

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Identifying and removing the cell-cycle effect from single-cell RNA-Sequencing data

(2016) Martin Barron et al.   Scientific Reports

Identification of cell types from single-cell transcriptomes using a novel clustering method

(2015) Chen Xu et al.   BIOINFORMATICS

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

(2015) Jacob H. Levine et al.   CELL

Human β-Cell Proliferation and Intracellular Signaling: Part 3

(2015) Andrew F. Stewart et al.   DIABETES

Somatic mosaicism and allele complexity induced by CRISPR/Cas9 RNA injections in mouse zygotes

(2014) Shuo-Ting Yen et al.   DEVELOPMENTAL BIOLOGY

Temporal profiling of cytokine-induced genes in pancreatic β-cells by meta-analysis and network inference

(2014) Miguel Lopes et al.   GENOMICS

Progressive Image Denoising Through Hybrid Graph Laplacian Regularization: A Unified Framework

(2014) Xianming Liu et al.   IEEE TRANSACTIONS ON IMAGE PROCESSING

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

The emerging field of signal processing on graphs: Extending high-dimensional data analysis to networks and other irregular domains

(2013) D. I. Shuman et al.   IEEE SIGNAL PROCESSING MAGAZINE

An optimal -nearest neighbor for density estimation

(2012) Yi-Hung Kung et al.   STATISTICS & PROBABILITY LETTERS

A Variance Minimization Criterion to Feature Selection Using Laplacian Regularization

(2011) Xiaofei He et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

A weighted k-nearest neighbor density estimate for geometric inference

(2011) Gérard Biau et al.   Electronic Journal of Statistics

Kernel density estimation via diffusion

(2010) Z. I. Botev et al.   ANNALS OF STATISTICS

Wavelets on graphs via spectral graph theory

(2010) David K. Hammond et al.   APPLIED AND COMPUTATIONAL HARMONIC ANALYSIS

The Interferon Inducible Gene: Viperin

(2010) Katherine A. Fitzgerald   JOURNAL OF INTERFERON AND CYTOKINE RESEARCH