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

[1]  Konrad U. Förstner,et al.  Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions , 2016, Nature.

[2]  W. Hardt,et al.  Experimental approaches to phenotypic diversity in infection. , 2015, Current opinion in microbiology.

[3]  Joseph L. Herman,et al.  Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis , 2015, Nature Methods.

[4]  Aviv Regev,et al.  Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses , 2015, Cell.

[5]  Hans Clevers,et al.  Single-cell messenger RNA sequencing reveals rare intestinal cell types , 2015, Nature.

[6]  T. van der Poll,et al.  Expression and Function of S100A8/A9 (Calprotectin) in Human Typhoid Fever and the Murine Salmonella Model , 2015, PLoS neglected tropical diseases.

[7]  A. Bäumler,et al.  Now you see me, now you don't: the interaction of Salmonella with innate immune receptors , 2015, Nature Reviews Microbiology.

[8]  D. Bumann Heterogeneous host-pathogen encounters: act locally, think globally. , 2015, Cell host & microbe.

[9]  Jordan V. Price,et al.  The macrophage paradox. , 2014, Immunity.

[10]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[11]  Paul Theodor Pyl,et al.  HTSeq – A Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[12]  D. Bumann,et al.  Phenotypic Variation of Salmonella in Host Tissues Delays Eradication by Antimicrobial Chemotherapy , 2014, Cell.

[13]  A. Saliba,et al.  Single-cell RNA-seq: advances and future challenges , 2014, Nucleic acids research.

[14]  Rona S. Gertner,et al.  Single cell RNA Seq reveals dynamic paracrine control of cellular variation , 2014, Nature.

[15]  Shawn M. Gillespie,et al.  Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma , 2014, Science.

[16]  P. Kharchenko,et al.  Bayesian approach to single-cell differential expression analysis , 2014, Nature Methods.

[17]  Y. Saeys,et al.  The function of Fcγ receptors in dendritic cells and macrophages , 2014, Nature Reviews Immunology.

[18]  D. Bumann,et al.  Disparate impact of oxidative host defenses determines the fate of Salmonella during systemic infection in mice. , 2014, Cell host & microbe.

[19]  David W. Holden,et al.  Internalization of Salmonella by Macrophages Induces Formation of Nonreplicating Persisters , 2014, Science.

[20]  Åsa K. Björklund,et al.  Full-length RNA-seq from single cells using Smart-seq2 , 2014, Nature Protocols.

[21]  Aleksandra A. Kolodziejczyk,et al.  Accounting for technical noise in single-cell RNA-seq experiments , 2013, Nature Methods.

[22]  Åsa K. Björklund,et al.  Smart-seq2 for sensitive full-length transcriptome profiling in single cells , 2013, Nature Methods.

[23]  A. Chawla,et al.  Salmonella require the fatty acid regulator PPARδ for the establishment of a metabolic environment essential for long-term persistence. , 2013, Cell host & microbe.

[24]  W. Eisenreich,et al.  Metabolic host responses to infection by intracellular bacterial pathogens , 2013, Front. Cell. Infect. Microbiol..

[25]  D. Holden,et al.  Identification of Salmonella Pathogenicity Island-2 Type III Secretion System Effectors Involved in Intramacrophage Replication of S. enterica Serovar Typhimurium: Implications for Rational Vaccine Design , 2013, mBio.

[26]  K. Burr,et al.  Reprogramming Adult Schwann Cells to Stem Cell-like Cells by Leprosy Bacilli Promotes Dissemination of Infection , 2013, Cell.

[27]  J. Haas,et al.  Salmonella transforms follicle-associated epithelial cells into M cells to promote intestinal invasion. , 2012, Cell host & microbe.

[28]  C. Detweiler,et al.  Hemophagocytic Macrophages in Murine Typhoid Fever Have an Anti-Inflammatory Phenotype , 2012, Infection and Immunity.

[29]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[30]  David R. Kelley,et al.  Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.

[31]  G. Natoli,et al.  Transcriptional regulation of macrophage polarization: enabling diversity with identity , 2011, Nature Reviews Immunology.

[32]  Marcel Martin Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[33]  D. Gang,et al.  Incorporation of non-natural nucleotides into template-switching oligonucleotides reduces background and improves cDNA synthesis from very small RNA samples , 2010, BMC Genomics.

[34]  Jessica A. Thompson,et al.  Dynamics of intracellular bacterial replication at the single cell level , 2010, Proceedings of the National Academy of Sciences.

[35]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[36]  S. Gordon,et al.  Alternative activation of macrophages: an immunologic functional perspective. , 2009, Annual review of immunology.

[37]  J. Mege,et al.  Macrophage Polarization in Bacterial Infections , 2008, The Journal of Immunology.

[38]  Sébastien Lê,et al.  FactoMineR: An R Package for Multivariate Analysis , 2008 .

[39]  Sarah E. Altschuler,et al.  Hemophagocytic Macrophages Harbor Salmonella enterica during Persistent Infection , 2007, PLoS pathogens.

[40]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[41]  V. Bronte,et al.  Regulation of immune responses by L-arginine metabolism , 2005, Nature Reviews Immunology.

[42]  Richard A. Young,et al.  Insights into host responses against pathogens from transcriptional profiling , 2005, Nature Reviews Microbiology.

[43]  S. Falkow,et al.  Persistent bacterial infections: the interface of the pathogen and the host immune system , 2004, Nature Reviews Microbiology.

[44]  F. Fang,et al.  Salmonella pathogenicity island 2-dependent evasion of the phagocyte NADPH oxidase. , 2000, Science.

[45]  M. Glimcher,et al.  Eta-1 (osteopontin): an early component of type-1 (cell-mediated) immunity. , 2000, Science.

[46]  K. Murphy,et al.  Role for SpiC in the development of red pulp macrophages and splenic iron homeostasis , 2008 .