Single-nucleus profiling of human dilated and hypertrophic cardiomyopathy

scCODA is a Bayesian model for compositional single-cell data analysis

(2021) M. Büttner et al.   Nature Communications

Single-Cell Transcriptome Atlas of Murine Endothelial Cells

(2020) Joanna Kalucka et al.   CELL

Single-cell reconstruction of the adult human heart during heart failure and recovery reveals the cellular landscape underlying cardiac function

(2020) Li Wang et al.   NATURE CELL BIOLOGY

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

(2020) Koen Van den Berge et al.   Nature Communications

Dynamic Interstitial Cell Response during Myocardial Infarction Predicts Resilience to Rupture in Genetically Diverse Mice

(2020) Elvira Forte et al.   Cell Reports

Transcriptional and Cellular Diversity of the Human Heart

(2020) Nathan R. Tucker et al.   CIRCULATION

High-Resolution Transcriptomic Profiling of the Heart During Chronic Stress Reveals Cellular Drivers of Cardiac Fibrosis and Hypertrophy

(2020) Micheal A. McLellan et al.   CIRCULATION

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Cells of the adult human heart

(2020) Monika Litviňuková et al.   NATURE

A Human Skin Model Recapitulates Systemic Sclerosis Dermal Fibrosis and Identifies COL22A1 as a TGFβ Early Response Gene that Mediates Fibroblast to Myofibroblast Transition

(2019) Tomoya Watanabe et al.   Genes

Determining cell type abundance and expression from bulk tissues with digital cytometry

(2019) Aaron M. Newman et al.   NATURE BIOTECHNOLOGY

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

Long non-coding and coding RNA profiling using strand-specific RNA-seq in human hypertrophic cardiomyopathy

(2019) Xuanyu Liu et al.   Scientific Data

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

(2019) Ilya Korsunsky et al.   NATURE METHODS

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

The human heart contains distinct macrophage subsets with divergent origins and functions

(2018) Geetika Bajpai et al.   NATURE MEDICINE

Suppression of detyrosinated microtubules improves cardiomyocyte function in human heart failure

(2018) Christina Yingxian Chen et al.   NATURE MEDICINE

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Transcriptome analysis of human heart failure reveals dysregulated cell adhesion in dilated cardiomyopathy and activated immune pathways in ischemic heart failure

(2018) Mary E. Sweet et al.   BMC GENOMICS

High-Dimensional Single-Cell Analysis Identifies Organ-Specific Signatures and Conserved NK Cell Subsets in Humans and Mice

(2018) Adeline Crinier et al.   IMMUNITY

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities

(2018) Kendall R. Sanson et al.   Nature Communications

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Redefining the identity of cardiac fibroblasts

(2017) Michelle D. Tallquist et al.   Nature Reviews Cardiology

ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization

(2016) Guangchuang Yu et al.   Molecular BioSystems

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

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

(2016) I. Tirosh et al.   SCIENCE

RNA-Seq identifies novel myocardial gene expression signatures of heart failure

(2015) Yichuan Liu et al.   GENOMICS

Transcription factor TIP27 regulates glucose homeostasis and insulin sensitivity in a PI3-kinase/Akt-dependent manner in mice

(2015) L Yuan et al.   INTERNATIONAL JOURNAL OF OBESITY

Fibroblast activation protein alpha expression identifies activated fibroblasts after myocardial infarction

(2015) Jochen Tillmanns et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

JAZF1 can regulate the expression of lipid metabolic genes and inhibit lipid accumulation in adipocytes

(2014) Guang-feng Ming et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Improved vectors and genome-wide libraries for CRISPR screening

(2014) Neville E Sanjana et al.   NATURE METHODS

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Thrombospondin-4 regulates fibrosis and remodeling of the myocardium in response to pressure overload

(2012) Ella G. Frolova et al.   FASEB JOURNAL

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

The role of JAZF1 on lipid metabolism and related genes in vitro

(2010) Ling Li et al.   METABOLISM-CLINICAL AND EXPERIMENTAL