Computational and analytical challenges in single-cell transcriptomics

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An integrated encyclopedia of DNA elements in the human genome

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Evaluation of Factors Related to Late Recurrence - Later than 10 Years after the Initial Treatment - in Primary Breast Cancer

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RNA-Seq: a revolutionary tool for transcriptomics

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TopHat: discovering splice junctions with RNA-Seq

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Gene expression profiling predicts clinical outcome of breast cancer

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Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

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A scaling normalization method for differential expression analysis of RNA-seq data

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The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

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Green fluorescent protein as a marker for gene expression

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Global quantification of mammalian gene expression control

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Sparse inverse covariance estimation with the graphical lasso

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The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups

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

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Ki67 expression in breast cancer

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mRNA-Seq whole-transcriptome analysis of a single cell

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RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

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Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

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The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

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Smart-seq2 for sensitive full-length transcriptome profiling in single cells

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Stochasticity in gene expression: from theories to phenotypes

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Normalization of RNA-seq data using factor analysis of control genes or samples

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Imaging individual mRNA molecules using multiple singly labeled probes

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Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis

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Fast and SNP-tolerant detection of complex variants and splicing in short reads

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Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types

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Stochastic mRNA Synthesis in Mammalian Cells

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Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data

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Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

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Detecting differential usage of exons from RNA-seq data

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Transcriptional Amplification in Tumor Cells with Elevated c-Myc

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Analysis and design of RNA sequencing experiments for identifying isoform regulation

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Bayesian approach to single-cell differential expression analysis

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Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells

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Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

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Understanding mechanisms underlying human gene expression variation with RNA sequencing

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Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

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The evolution of gene expression levels in mammalian organs

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CEL-seq: single-cell RNA-seq by multiplexed linear amplification

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Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

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Quantitative single-cell RNA-seq with unique molecular identifiers

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Single-cell sequencing-based technologies will revolutionize whole-organism science

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Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

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

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Immunological Properties of an Antibody Containing a Fluorescent Group.

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Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

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Accounting for technical noise in single-cell RNA-seq experiments

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Highly Multiplexed Subcellular RNA Sequencing in Situ

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Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

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How to infer gene networks from expression profiles

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baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data

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Using Gene Expression Noise to Understand Gene Regulation

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Validation of noise models for single-cell transcriptomics

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From RNA-seq reads to differential expression results

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Quantitative assessment of single-cell RNA-sequencing methods

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Synthetic spike-in standards for RNA-seq experiments

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A High-Resolution Anatomical Atlas of the Transcriptome in the Mouse Embryo

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Revisiting Global Gene Expression Analysis

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Network component analysis: Reconstruction of regulatory signals in biological systems

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Inferring subnetworks from perturbed expression profiles

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Tracing the Derivation of Embryonic Stem Cells from the Inner Cell Mass by Single-Cell RNA-Seq Analysis

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A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies

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Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity

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Kraken: A set of tools for quality control and analysis of high-throughput sequence data

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Regulatory divergence in <i>Drosophila</i> revealed by mRNA-seq

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Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages

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Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue

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Tools for mapping high-throughput sequencing data

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Entering the era of single-cell transcriptomics in biology and medicine

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Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection

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Single-Cell RNA Sequencing Reveals T Helper Cells Synthesizing Steroids De Novo to Contribute to Immune Homeostasis

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Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data

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Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures

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Reconstruction of the Mouse Otocyst and Early Neuroblast Lineage at Single-Cell Resolution

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Comparative RNA sequencing reveals substantial genetic variation in endangered primatesPreprint

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Quantitative analysis of gene expression in a single cell by qPCR

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Characterisation of transcriptional networks in blood stem and progenitor cells using high-throughput single cell gene expression analysis

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Single-Cell Analysis Reveals that Expression of Nanog Is Biallelic and Equally Variable as that of Other Pluripotency Factors in Mouse ESCs

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What do expression dynamics tell us about the mechanism of transcription?

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Asymmetric Localization of Cdx2 mRNA during the First Cell-Fate Decision in Early Mouse Development

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Identifying Cell Types from Spatially Referenced Single-Cell Expression Datasets

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SCANPY: large-scale single-cell gene expression data analysis

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Scenic: single-cell regulatory network inference and clustering.

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DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

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Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression

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