Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling

Challenges in unsupervised clustering of single-cell RNA-seq data

(2019) Vladimir Yu Kiselev et al.   NATURE REVIEWS GENETICS

SCINA: Semi-Supervised Analysis of Single Cells in Silico

(2019) Zhang et al.   Genes

Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer

(2018) Allen W. Zhang et al.   CELL

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

scmap: projection of single-cell RNA-seq data across data sets

(2018) Vladimir Yu Kiselev et al.   NATURE METHODS

dropClust: efficient clustering of ultra-large scRNA-seq data

(2018) Debajyoti Sinha et al.   NUCLEIC ACIDS RESEARCH

Interpretable dimensionality reduction of single cell transcriptome data with deep generative models

(2018) Jiarui Ding et al.   Nature Communications

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data

(2018) Nils Eling et al.   Cell Systems

Single-cell RNA-Seq of lymphoma cancers reveals malignant B cell types and co-expression of T cell immune checkpoints

(2018) Noemi Andor et al.   BLOOD

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

Identification of grade and origin specific cell populations in serous epithelial ovarian cancer by single cell RNA-seq

(2018) Andrew J. Shih et al.   PLoS One

Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations

(2018) Sonya A. MacParland et al.   Nature Communications

SC3: consensus clustering of single-cell RNA-seq data

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

The Reactome Pathway Knowledgebase

(2017) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

A pathology atlas of the human cancer transcriptome

(2017) Mathias Uhlen et al.   SCIENCE

Estimation of immune cell content in tumour tissue using single-cell RNA-seq data

(2017) Max Schelker et al.   Nature Communications

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Phenotypic Modulation of Smooth Muscle Cells in Atherosclerosis Is Associated With Downregulation ofLMOD1, SYNPO2, PDLIM7, PLN, andSYNMHighlights

(2016) Ljubica Perisic Matic et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

densityCut: an efficient and versatile topological approach for automatic clustering of biological data

(2016) Jiarui Ding et al.   BIOINFORMATICS

pcaReduce: hierarchical clustering of single cell transcriptional profiles

(2016) Justina žurauskienė et al.   BMC BIOINFORMATICS

An atlas of transcriptional, chromatin accessibility, and surface marker changes in human mesoderm development

(2016) Pang Wei Koh et al.   Scientific Data

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

(2015) Jacob H. Levine et al.   CELL

Computational assignment of cell-cycle stage from single-cell transcriptome data

(2015) Antonio Scialdone et al.   METHODS

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Breaking bad in the germinal center: how deregulation of BCL6 contributes to lymphomagenesis

(2014) Katerina Hatzi et al.   TRENDS IN MOLECULAR MEDICINE

CD146 expression on mesenchymal stem cells is associated with their vascular smooth muscle commitment

(2013) Nicolas Espagnolle et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

Regulation of innate CD8+ T-cell activation mediated by cytokines

(2012) B. E. Freeman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The regulation and role of T follicular helper cells in immunity

(2011) Elissa K. Deenick et al.   IMMUNOLOGY

Identification and angiogenic role of the novel tumor endothelial marker CLEC14A

(2011) M Mura et al.   ONCOGENE

Human immunoglobulin allotypes

(2010) Roy Jefferis et al.   mAbs

Expression of chemokine receptors CXCR4, CXCR5 and CCR7 on B and T lymphocytes from patients with primary antibody deficiency

(2009) D. Payne et al.   CLINICAL AND EXPERIMENTAL IMMUNOLOGY

t(14;18)-negative follicular lymphomas are associated with a high frequency of BCL6 rearrangement at the alternative breakpoint region

(2009) Keni Gu et al.   MODERN PATHOLOGY