Early Transcriptional Landscapes of Chlamydia trachomatis-Infected Epithelial Cells at Single Cell Resolution

Single-Cell Analysis of Diverse Pathogen Responses Defines a Molecular Roadmap for Generating Antigen-Specific Immunity

(2019) Ronnie Blecher-Gonen et al.   Cell Systems

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

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DrImpute: imputing dropout events in single cell RNA sequencing data

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Extreme heterogeneity of influenza virus infection in single cells

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Metallothioneins: Emerging Modulators in Immunity and Infection

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

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Metallothionein regulates intracellular zinc signaling during CD4+ T cell activation

(2016) James M. Rice et al.   BMC IMMUNOLOGY

Chlamydia cell biology and pathogenesis

(2016) Cherilyn Elwell et al.   NATURE REVIEWS MICROBIOLOGY

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

(2016) Zhicheng Ji et al.   NUCLEIC ACIDS RESEARCH

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

(2016) I. Tirosh et al.   SCIENCE

Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella

(2016) Antoine-Emmanuel Saliba et al.   Nature Microbiology

Vimentin in Bacterial Infections

(2016) Tim Mak et al.   Cells

Identifying and removing the cell-cycle effect from single-cell RNA-Sequencing data

(2016) Martin Barron et al.   Scientific Reports

Human and Pathogen Factors Associated with Chlamydia trachomatis-Related Infertility in Women

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Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells

(2015) Monika S. Kowalczyk et al.   GENOME RESEARCH

The Technology and Biology of Single-Cell RNA Sequencing

(2015) Aleksandra A. Kolodziejczyk et al.   MOLECULAR CELL

A new approach to estimating trends in chlamydia incidence

(2015) Hammad Ali et al.   SEXUALLY TRANSMITTED INFECTIONS

Microbial Regulation of p53 Tumor Suppressor

(2015) Alexander I. Zaika et al.   PLoS Pathogens

deML: robust demultiplexing of Illumina sequences using a likelihood-based approach

(2014) Gabriel Renaud et al.   BIOINFORMATICS

Transcriptional Profiling of Human Epithelial Cells Infected with Plasmid-Bearing and Plasmid-Deficient Chlamydia trachomatis

(2014) Stephen F. Porcella et al.   INFECTION AND IMMUNITY

Trachoma

(2014) Hugh R Taylor et al.   LANCET

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

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

Single-cell RNA-seq: advances and future challenges

(2014) Antoine-Emmanuel Saliba et al.   NUCLEIC ACIDS RESEARCH

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

(2014) A. P. Patel et al.   SCIENCE

Tumor Suppressor p53 Alters Host Cell Metabolism to Limit Chlamydia trachomatis Infection

(2014) Christine Siegl et al.   Cell Reports

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

(2013) Y. Liao et al.   BIOINFORMATICS

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

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

(2013) Rickard Sandberg   NATURE METHODS

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Simultaneous Transcriptional Profiling of Bacteria and Their Host Cells

(2013) Michael S. Humphrys et al.   PLoS One

Development status and future prospects for a vaccine against Chlamydia trachomatis infection

(2013) Louise M. Hafner et al.   VACCINE

Chlamydial Intracellular Survival Strategies

(2013) R. J. Bastidas et al.   Cold Spring Harbor Perspectives in Medicine

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Lipid acquisition by intracellular Chlamydiae

(2012) Cherilyn A. Elwell et al.   CELLULAR MICROBIOLOGY

Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling

(2011) Paweł P. Łabaj et al.   BIOINFORMATICS

Quantitative proteomics reveals metabolic and pathogenic properties of Chlamydia trachomatis developmental forms

(2011) Hector A. Saka et al.   MOLECULAR MICROBIOLOGY

Chlamydia trachomatis Infection Causes Mitotic Spindle Pole Defects Independently from its Effects on Centrosome Amplification

(2011) Andrea E. Knowlton et al.   TRAFFIC

The transcriptional landscape of Chlamydia pneumoniae

(2011) Marco Albrecht et al.   GENOME BIOLOGY

Developmental expression of non-coding RNAs in Chlamydia trachomatis during normal and persistent growth

(2010) Y. M. AbdelRahman et al.   NUCLEIC ACIDS RESEARCH

Reactome: a database of reactions, pathways and biological processes

(2010) D. Croft et al.   NUCLEIC ACIDS RESEARCH

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Centrosome abnormalities during aChlamydia trachomatisinfection are caused by dysregulation of the normal duplication pathway

(2009) Kirsten A. Johnson et al.   CELLULAR MICROBIOLOGY

Chlamydia trachomatis-Infected Patients Display Variable Antibody Profiles against the Nine-Member Polymorphic Membrane Protein Family

(2009) C. Tan et al.   INFECTION AND IMMUNITY

Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome

(2009) Marco Albrecht et al.   NUCLEIC ACIDS RESEARCH

The Global Burden of Trachoma: A Review

(2009) Matthew J. Burton et al.   PLoS Neglected Tropical Diseases

Chlamydia effector proteins and new insights into chlamydial cellular microbiology

(2008) Raphael H Valdivia   CURRENT OPINION IN MICROBIOLOGY

Cytoplasmic lipid droplets are translocated into the lumen of the Chlamydia trachomatis parasitophorous vacuole

(2008) J. L. Cocchiaro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA