LTMG: a novel statistical modeling of transcriptional expression states in single-cell RNA-Seq data

Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data

(2019) Tianyu Wang et al.   BMC BIOINFORMATICS

Two-phase differential expression analysis for single cell RNA-seq

(2018) Zhijin Wu et al.   BIOINFORMATICS

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

(2018) Elham Azizi et al.   CELL

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing

(2018) Xinyi Guo et al.   NATURE MEDICINE

An accurate and robust imputation method scImpute for single-cell RNA-seq data

(2018) Wei Vivian Li et al.   Nature Communications

Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH

(2018) Eduardo Torre et al.   Cell Systems

A molecular atlas of cell types and zonation in the brain vasculature

(2018) Michael Vanlandewijck et al.   NATURE

Single-cell RNA sequencing of mouse brain and lung vascular and vessel-associated cell types

(2018) Liqun He et al.   Scientific Data

Comparative Analysis of Droplet-Based Ultra-High-Throughput Single-Cell RNA-Seq Systems

(2018) Xiannian Zhang et al.   MOLECULAR CELL

Lineage tracking reveals dynamic relationships of T cells in colorectal cancer

(2018) Lei Zhang et al.   NATURE

Genomic encoding of transcriptional burst kinetics

(2018) Anton J. M. Larsson et al.   NATURE

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

APE1/Ref-1 knockdown in pancreatic ductal adenocarcinoma - characterizing gene expression changes and identifying novel pathways using single-cell RNA sequencing

(2017) Fenil Shah et al.   Molecular Oncology

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning

(2017) Bo Wang et al.   NATURE METHODS

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

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

Modeling gene regulation from paired expression and chromatin accessibility data

(2017) Zhana Duren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Massively parallel digital transcriptional profiling of single cells

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

Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data

(2017) Julien Racle et al.   eLife

Beta-Poisson model for single-cell RNA-seq data analyses

(2016) Trung Nghia Vu et al.   BIOINFORMATICS

Regulation of HIF1  under Hypoxia by APE1/Ref-1 Impacts CA9 Expression: Dual Targeting in Patient-Derived 3D Pancreatic Cancer Models

(2016) D. P. Logsdon et al.   MOLECULAR CANCER THERAPEUTICS

In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus

(2016) Sheel Shah et al.   NEURON

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

A Systematic Ensemble Approach to Thermodynamic Modeling of Gene Expression from Sequence Data

(2015) Md. Abul Hassan Samee et al.   Cell Systems

Apurinic/Apyrimidinic Endonuclease/Redox Factor-1 (APE1/Ref-1) Redox Function Negatively Regulates NRF2

(2014) Melissa L. Fishel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

Transcriptional Regulation and Its Misregulation in Disease

(2013) Tong Ihn Lee et al.   CELL

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Transcriptional burst frequency and burst size are equally modulated across the human genome

(2012) R. D. Dar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Mathematical modeling of gene expression: a guide for the perplexed biologist

(2011) Ahmet Ay et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

T cell exhaustion

(2011) E John Wherry   NATURE IMMUNOLOGY

APE1/Ref-1Role in Redox Signaling: Translational Applications of Targeting the Redox Function of the DNA Repair/Redox Protein APE1/Ref-1

(2011) Mark R. Kelley et al.   Current Molecular Pharmacology

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Mechanisms and Evolution of Control Logic in Prokaryotic Transcriptional Regulation

(2009) S. A. F. T. van Hijum et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

QUBIC: a qualitative biclustering algorithm for analyses of gene expression data

(2009) Guojun Li et al.   NUCLEIC ACIDS RESEARCH

Granzyme K degrades the redox/DNA repair enzyme Ape1 to trigger oxidative stress of target cells leading to cytotoxicity

(2008) Yuming Guo et al.   MOLECULAR IMMUNOLOGY

Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses

(2008) S. Jones et al.   SCIENCE