Fast, sensitive and accurate integration of single-cell data with Harmony

A single-cell molecular map of mouse gastrulation and early organogenesis

(2019) Blanca Pijuan-Sala et al.   NATURE

Tubular cell and keratinocyte single-cell transcriptomics applied to lupus nephritis reveal type I IFN and fibrosis relevant pathways

(2019) Evan Der et al.   NATURE IMMUNOLOGY

The immune cell landscape in kidneys of patients with lupus nephritis

(2019) Arnon Arazi et al.   NATURE IMMUNOLOGY

BBKNN: fast batch alignment of single cell transcriptomes

(2019) Krzysztof Polański et al.   BIOINFORMATICS

MafB Is Critical for Glucagon Production and Secretion in Mouse Pancreatic α Cells In Vivo

(2018) Megumi C. Katoh et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Exponential scaling of single-cell RNA-seq in the past decade

(2018) Valentine Svensson et al.   Nature Protocols

Functionally distinct disease-associated fibroblast subsets in rheumatoid arthritis

(2018) Fumitaka Mizoguchi et al.   Nature Communications

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

A test metric for assessing single-cell RNA-seq batch correction

(2018) Maren Büttner et al.   NATURE METHODS

Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region

(2018) Jeffrey R. Moffitt et al.   SCIENCE

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes

(2016) Åsa Segerstolpe et al.   Cell Metabolism

De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

(2016) Dominic Grün et al.   Cell Stem Cell

Single-cell transcriptomes identify human islet cell signatures and reveal cell-type–specific expression changes in type 2 diabetes

(2016) Nathan Lawlor et al.   GENOME RESEARCH

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

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

Expansion of the Gene Ontology knowledgebase and resources

(2016)   NUCLEIC ACIDS RESEARCH

Insm1 cooperates with Neurod1 and Foxa2 to maintain mature pancreatic  -cell function

(2015) S. Jia et al.   EMBO JOURNAL

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Pdx1 Maintains β Cell Identity and Function by Repressing an α Cell Program

(2014) Tao Gao et al.   Cell Metabolism

X-Box Binding Protein 1 Is Essential for Insulin Regulation of Pancreatic  -Cell Function

(2013) M. Akiyama et al.   DIABETES

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Satb1 Is an Activity-Modulated Transcription Factor Required for the Terminal Differentiation and Connectivity of Medial Ganglionic Eminence-Derived Cortical Interneurons

(2012) J. Close et al.   JOURNAL OF NEUROSCIENCE

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

(2012) Oliver Stegle et al.   Nature Protocols

Islet-1 RegulatesArxTranscription during Pancreatic Islet α-Cell Development

(2011) Jingxuan Liu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Pdx1 (MODY4) regulates pancreatic beta cell susceptibility to ER stress

(2009) Mira M. Sachdeva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pancreatic α-cell dysfunction in diabetes

(2008) R. Burcelin et al.   DIABETES & METABOLISM