Bacterial droplet-based single-cell RNA-seq reveals antibiotic-associated heterogeneous cellular states

Direct Comparative Analyses of 10X Genomics Chromium and Smart-seq2

(2021) Xiliang Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Genetic determinants facilitating the evolution of resistance to carbapenem antibiotics

(2021) Peijun Ma et al.   eLife

Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing

(2021) Paul Datlinger et al.   NATURE METHODS

Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution

(2021) Daniel Dar et al.   SCIENCE

Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing

(2020) Sydney B. Blattman et al.   Nature Microbiology

Single-cell RNA-sequencing reports growth-condition-specific global transcriptomes of individual bacteria

(2020) Fabian Imdahl et al.   Nature Microbiology

Single cell RNA sequencing of human microglia uncovers a subset associated with Alzheimer’s disease

(2020) Marta Olah et al.   Nature Communications

Single-cell transcriptomic analysis of Alzheimer’s disease

(2019) Hansruedi Mathys et al.   NATURE

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Mechanisms and clinical relevance of bacterial heteroresistance

(2019) Dan I. Andersson et al.   NATURE REVIEWS MICROBIOLOGY

Simulating multiple faceted variability in single cell RNA sequencing

(2019) Xiuwei Zhang et al.   Nature Communications

A single-nuclei RNA sequencing study of Mendelian and sporadic AD in the human brain

(2019) Jorge L. Del-Aguila et al.   Alzheimers Research & Therapy

Non-templated addition and template switching by Moloney murine leukemia virus (MMLV)-based reverse transcriptases co-occur and compete with each other

(2019) Madalee G. Wulf et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Bacterial Heterogeneity and Antibiotic Survival: Understanding and Combatting Persistence and Heteroresistance

(2019) Liselot Dewachter et al.   MOLECULAR CELL

Simultaneous detection of genotype and phenotype enables rapid and accurate antibiotic susceptibility determination

(2019) Roby P. Bhattacharyya et al.   NATURE MEDICINE

Carbapenem resistance caused by high-level expression of OXA-663 β-lactamase in an OmpK36-deficient Klebsiella pneumoniae clinical isolate

(2018) Peijun Ma et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Noncanonical features and modifications on the 5′-end of bacterial sRNAs and mRNAs

(2018) Nikita Vasilyev et al.   Wiley Interdisciplinary Reviews-RNA

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

Scaling single-cell genomics from phenomenology to mechanism

(2017) Amos Tanay et al.   NATURE

Massively parallel single-nucleus RNA-seq with DroNc-seq

(2017) Naomi Habib et al.   NATURE METHODS

Massively parallel digital transcriptional profiling of single cells

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

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

(2016) Karthik Shekhar et al.   CELL

Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing

(2016) Graham Heimberg et al.   Cell Systems

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

Simultaneous generation of many RNA-seq libraries in a single reaction

(2015) Alexander A Shishkin et al.   NATURE METHODS

A functional perspective on phenotypic heterogeneity in microorganisms

(2015) Martin Ackermann   NATURE REVIEWS MICROBIOLOGY

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

Automated Design of Probes for rRNA-Targeted FluorescenceIn SituHybridization Reveals the Advantages of Using Dual Probes for Accurate Identification

(2014) Erik S. Wright et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2014) Alex K. Shalek et al.   NATURE

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex

(2014) Alex A Pollen et al.   NATURE BIOTECHNOLOGY

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

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

(2013) Alex K. Shalek et al.   NATURE

Quantitative assessment of single-cell RNA-sequencing methods

(2013) Angela R Wu et al.   NATURE METHODS

Measuring mRNA copy number in individual Escherichia coli cells using single-molecule fluorescent in situ hybridization

(2013) Samuel O Skinner et al.   Nature Protocols

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

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

(2010) Y. Taniguchi et al.   SCIENCE

Toxins Hha and CspD and small RNA regulator Hfq are involved in persister cell formation through MqsR in Escherichia coli

(2009) Younghoon Kim et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Agar and broth dilution methods to determine the minimal inhibitory concentration (MIC) of antimicrobial substances

(2008) Irith Wiegand et al.   Nature Protocols

A Stochastic Single-Molecule Event Triggers Phenotype Switching of a Bacterial Cell

(2008) P. J. Choi et al.   SCIENCE