-
1
-
-
84920883696
-
Heterogeneous host-pathogen encounters: Act locally, think globally
-
Bumann, D. Heterogeneous host-pathogen encounters: act locally, think globally. Cell Host Microbe 17, 13-19 (2015).
-
(2015)
Cell Host Microbe
, vol.17
, pp. 13-19
-
-
Bumann, D.1
-
2
-
-
84912114551
-
The macrophage paradox
-
Price, J. V. & Vance, R. E. The macrophage paradox. Immunity 41, 685-693 (2014).
-
(2014)
Immunity
, vol.41
, pp. 685-693
-
-
Price, J.V.1
Vance, R.E.2
-
3
-
-
84941333786
-
Pathogen cell-to-cell variability drives heterogeneity in host immune responses
-
Avraham, R. et al. Pathogen cell-to-cell variability drives heterogeneity in host immune responses. Cell 162, 1309-1321 (2015).
-
(2015)
Cell
, vol.162
, pp. 1309-1321
-
-
Avraham, R.1
-
4
-
-
4444349432
-
Persistent bacterial infections: The interface of the pathogen and the host immune system
-
Monack, D. M., Mueller, A. & Falkow, S. Persistent bacterial infections: the interface of the pathogen and the host immune system. Nat. Rev. Microbiol. 2, 747-765 (2004).
-
(2004)
Nat. Rev. Microbiol.
, vol.2
, pp. 747-765
-
-
Monack, D.M.1
Mueller, A.2
Falkow, S.3
-
5
-
-
84908456444
-
Phenotypic variation of salmonella in host tissues delays eradication by antimicrobial chemotherapy
-
Claudi, B. et al. Phenotypic variation of salmonella in host tissues delays eradication by antimicrobial chemotherapy. Cell 158, 722-733 (2014).
-
(2014)
Cell
, vol.158
, pp. 722-733
-
-
Claudi, B.1
-
6
-
-
84892181925
-
Internalization of Salmonella by macrophages induces formation of nonreplicating persisters
-
Helaine, S. et al. Internalization of Salmonella by macrophages induces formation of nonreplicating persisters. Science 343, 204-208 (2014).
-
(2014)
Science
, vol.343
, pp. 204-208
-
-
Helaine, S.1
-
7
-
-
77649267953
-
Dynamics of intracellular bacterial replication at the single cell level
-
Helaine, S. et al. Dynamics of intracellular bacterial replication at the single cell level. Proc. Natl Acad. Sci. USA 107, 3746-3751 (2010).
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 3746-3751
-
-
Helaine, S.1
-
8
-
-
15944395145
-
Insights into host responses against pathogens from transcriptional profiling
-
Jenner, R. G. & Young, R. A. Insights into host responses against pathogens from transcriptional profiling. Nat. Rev. Microbiol. 3, 281-294 (2005).
-
(2005)
Nat. Rev. Microbiol.
, vol.3
, pp. 281-294
-
-
Jenner, R.G.1
Young, R.A.2
-
9
-
-
84906228597
-
Single-cell RNA-seq: Advances and future challenges
-
Saliba, A. E., Westermann, A. J., Gorski, S. A. & Vogel, J. Single-cell RNA-seq: advances and future challenges. Nucleic Acids Res. 42, 8845-8860 (2014).
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 8845-8860
-
-
Saliba, A.E.1
Westermann, A.J.2
Gorski, S.A.3
Vogel, J.4
-
10
-
-
84903185013
-
Single-cell RNA-seq reveals dynamic paracrine control of cellular variation
-
Shalek, A. K. et al. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. Nature 510, 363-369 (2014).
-
(2014)
Nature
, vol.510
, pp. 363-369
-
-
Shalek, A.K.1
-
11
-
-
84925088944
-
Now you see me, now you don't: The interaction of Salmonella with innate immune receptors
-
Keestra-Gounder, A. M., Tsolis, R. M. & Bäumler, A. J. Now you see me, now you don't: the interaction of Salmonella with innate immune receptors. Nat. Rev. Microbiol. 13, 206-216 (2015).
-
(2015)
Nat. Rev. Microbiol.
, vol.13
, pp. 206-216
-
-
Keestra-Gounder, A.M.1
Tsolis, R.M.2
Bäumler, A.J.3
-
12
-
-
84882413023
-
Salmonella require the fatty acid regulator PPARδ for the establishment of a metabolic environment essential for long-term persistence
-
Eisele, N. A. et al. Salmonella require the fatty acid regulator PPARδ for the establishment of a metabolic environment essential for long-term persistence. Cell Host Microbe 14, 171-182 (2013).
-
(2013)
Cell Host Microbe
, vol.14
, pp. 171-182
-
-
Eisele, N.A.1
-
13
-
-
84934753454
-
Experimental approaches to phenotypic diversity in infection
-
Kreibich, S. & Hardt, W. D. Experimental approaches to phenotypic diversity in infection. Curr. Opin. Microbiol. 27, 25-36 (2015).
-
(2015)
Curr. Opin. Microbiol.
, vol.27
, pp. 25-36
-
-
Kreibich, S.1
Hardt, W.D.2
-
14
-
-
84887101406
-
Smart-seq2 for sensitive full-length transcriptome profiling in single cells
-
Picelli, S. et al. Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat. Methods 10, 1096-1098 (2013).
-
(2013)
Nat. Methods
, vol.10
, pp. 1096-1098
-
-
Picelli, S.1
-
15
-
-
84891442618
-
Metabolic host responses to infection by intracellular bacterial pathogens
-
Eisenreich, W., Heesemann, J., Rudel, T. & Goebel, W. Metabolic host responses to infection by intracellular bacterial pathogens. Front. Cell Infect. Microbiol. 3, 24 (2013).
-
(2013)
Front. Cell Infect. Microbiol.
, vol.3
, pp. 24
-
-
Eisenreich, W.1
Heesemann, J.2
Rudel, T.3
Goebel, W.4
-
16
-
-
80355146399
-
Transcriptional regulation of macrophage polarization: Enabling diversity with identity
-
Lawrence, T. & Natoli, G. Transcriptional regulation of macrophage polarization: enabling diversity with identity. Nat. Rev. Immunol. 11, 750-761 (2011).
-
(2011)
Nat. Rev. Immunol.
, vol.11
, pp. 750-761
-
-
Lawrence, T.1
Natoli, G.2
-
17
-
-
58249104981
-
Role for Spi-C in the development of red pulp macrophages and splenic iron homeostasis
-
Kohyama, M. et al. Role for Spi-C in the development of red pulp macrophages and splenic iron homeostasis. Nature 457, 318-321 (2009).
-
(2009)
Nature
, vol.457
, pp. 318-321
-
-
Kohyama, M.1
-
18
-
-
37849011401
-
Hemophagocytic macrophages harbor Salmonella enterica during persistent infection
-
Nix, R. N., Altschuler, S. E., Henson, P. M. & Detweiler, C. S. Hemophagocytic macrophages harbor Salmonella enterica during persistent infection. PLoS Pathog. 3, e193 (2007).
-
(2007)
PLoS Pathog.
, vol.3
, pp. e193
-
-
Nix, R.N.1
Altschuler, S.E.2
Henson, P.M.3
Detweiler, C.S.4
-
19
-
-
84893657950
-
The function of Fcγ receptors in dendritic cells and macrophages
-
Guilliams, M., Bruhns, P., Saeys, Y., Hammad, H. & Lambrecht, B. N. The function of Fcγ receptors in dendritic cells and macrophages. Nat. Rev. Immunol. 14, 94-108 (2014).
-
(2014)
Nat. Rev. Immunol.
, vol.14
, pp. 94-108
-
-
Guilliams, M.1
Bruhns, P.2
Saeys, Y.3
Hammad, H.4
Lambrecht, B.N.5
-
20
-
-
67650485985
-
Alternative activation of macrophages: An immunologic functional perspective
-
Martinez, F. O., Helming, L. & Gordon, S. Alternative activation of macrophages: an immunologic functional perspective. Annu. Rev. Immunol. 27, 451-483 (2009).
-
(2009)
Annu. Rev. Immunol.
, vol.27
, pp. 451-483
-
-
Martinez, F.O.1
Helming, L.2
Gordon, S.3
-
21
-
-
23444456772
-
Regulation of immune responses by L-arginine metabolism
-
Bronte, V. & Zanovello, P. Regulation of immune responses by L-arginine metabolism. Nat. Rev. Immunol. 5, 641-654 (2005).
-
(2005)
Nat. Rev. Immunol.
, vol.5
, pp. 641-654
-
-
Bronte, V.1
Zanovello, P.2
-
22
-
-
84928923121
-
Expression and function of S100A8/A9 (calprotectin) in human typhoid fever and the murine Salmonella model
-
De Jong, H. K. et al. Expression and function of S100A8/A9 (calprotectin) in human typhoid fever and the murine Salmonella model. PLOS Negl. Trop. Dis. 9, e0003663 (2015).
-
(2015)
PLOS Negl. Trop. Dis.
, vol.9
, pp. e0003663
-
-
De Jong, H.K.1
-
23
-
-
0034603119
-
Eta-1 (osteopontin): An early component of type-1 (cellmediated) immunity
-
Ashkar, S. et al. Eta-1 (osteopontin): an early component of type-1 (cellmediated) immunity. Science 287, 860-864 (2000).
-
(2000)
Science
, vol.287
, pp. 860-864
-
-
Ashkar, S.1
-
24
-
-
56149103896
-
Macrophage polarization in bacterial infections
-
Benoit, M., Desnues, B. & Mege, J. L. Macrophage polarization in bacterial infections. J. Immunol. 181, 3733-3739 (2008).
-
(2008)
J. Immunol.
, vol.181
, pp. 3733-3739
-
-
Benoit, M.1
Desnues, B.2
Mege, J.L.3
-
25
-
-
84867612777
-
Hemophagocytic macrophages in murine typhoid fever have an anti-inflammatory phenotype
-
McCoy, M. W., Moreland, S. M. & Detweiler, C. S. Hemophagocytic macrophages in murine typhoid fever have an anti-inflammatory phenotype. Infect. Immun. 80, 3642-3649 (2012).
-
(2012)
Infect. Immun.
, vol.80
, pp. 3642-3649
-
-
McCoy, M.W.1
Moreland, S.M.2
Detweiler, C.S.3
-
26
-
-
0034095005
-
Salmonella pathogenicity island 2-dependent evasion of the phagocyte NADPH oxidase
-
Vazquez-Torres, A. et al. Salmonella pathogenicity island 2-dependent evasion of the phagocyte NADPH oxidase. Science 287, 1655-1658 (2000).
-
(2000)
Science
, vol.287
, pp. 1655-1658
-
-
Vazquez-Torres, A.1
-
27
-
-
84892604268
-
Disparate impact of oxidative host defenses determines the fate of Salmonella during systemic infection in mice
-
Burton, N. A. et al. Disparate impact of oxidative host defenses determines the fate of Salmonella during systemic infection in mice. Cell Host Microbe 15, 72-83 (2014).
-
(2014)
Cell Host Microbe
, vol.15
, pp. 72-83
-
-
Burton, N.A.1
-
28
-
-
84869153585
-
Salmonella transforms follicle-associated epithelial cells into M cells to promote intestinal invasion
-
Tahoun, A. et al. Salmonella transforms follicle-associated epithelial cells into M cells to promote intestinal invasion. Cell Host Microbe 12, 645-656 (2012).
-
(2012)
Cell Host Microbe
, vol.12
, pp. 645-656
-
-
Tahoun, A.1
-
29
-
-
84872520213
-
Reprogramming adult Schwann cells to stem cell-like cells by leprosy bacilli promotes dissemination of infection
-
Masaki, T. et al. Reprogramming adult Schwann cells to stem cell-like cells by leprosy bacilli promotes dissemination of infection. Cell 152, 51-67 (2013).
-
(2013)
Cell
, vol.152
, pp. 51-67
-
-
Masaki, T.1
-
30
-
-
84964262313
-
Dual RNA-seq unveils noncoding RNA functions in host-pathogen interactions
-
Westermann, A. J. et al. Dual RNA-seq unveils noncoding RNA functions in host-pathogen interactions. Nature 529, 496-501 (2016).
-
(2016)
Nature
, vol.529
, pp. 496-501
-
-
Westermann, A.J.1
-
31
-
-
84880080554
-
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
-
e00065
-
Figueira, R., Watson, K. G., Holden, D. W. & Helaine, S. 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. mBio 4, e00065-13 (2013).
-
(2013)
MBio
, vol.4
, pp. 13
-
-
Figueira, R.1
Watson, K.G.2
Holden, D.W.3
Helaine, S.4
-
32
-
-
84891677425
-
Full-length RNA-seq from single cells using smart-seq2
-
Picelli, S. et al. Full-length RNA-seq from single cells using smart-seq2. Nat. Protoc. 9, 171-181 (2014).
-
(2014)
Nat. Protoc.
, vol.9
, pp. 171-181
-
-
Picelli, S.1
-
33
-
-
77954070555
-
Incorporation of non-natural nucleotides into template-switching oligonucleotides reduces background and improves cDNA synthesis from very small RNA samples
-
Kapteyn, J., He, R., McDowell, E. T. & Gang, D. R. Incorporation of non-natural nucleotides into template-switching oligonucleotides reduces background and improves cDNA synthesis from very small RNA samples. BMC Genomics 11, 413 (2010).
-
(2010)
BMC Genomics
, vol.11
, pp. 413
-
-
Kapteyn, J.1
He, R.2
McDowell, E.T.3
Gang, D.R.4
-
34
-
-
84902668801
-
Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma
-
Patel, A. P. et al. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science 344, 1396-1401 (2014).
-
(2014)
Science
, vol.344
, pp. 1396-1401
-
-
Patel, A.P.1
-
35
-
-
80255127234
-
Cutadapt removes adapter sequences from high-throughput sequencing reads
-
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10-12 (2011).
-
(2011)
EMBnet.journal
, vol.17
, pp. 10-12
-
-
Martin, M.1
-
36
-
-
84859210032
-
Fast gapped-read alignment with bowtie 2
-
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with bowtie 2. Nat. Methods 9, 357-359 (2012).
-
(2012)
Nat. Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
37
-
-
65449136284
-
TopHat: Discovering splice junctions with RNA-seq
-
Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-seq. Bioinformatics 25, 1105-1111 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
38
-
-
84928987900
-
HTSeq-A python framework to work with high-throughput sequencing data
-
Anders, S., Pyl, P. T. & Huber, W. HTSeq-a python framework to work with high-throughput sequencing data. Bioinformatics 31, 166-169 (2015).
-
(2015)
Bioinformatics
, vol.31
, pp. 166-169
-
-
Anders, S.1
Pyl, P.T.2
Huber, W.3
-
39
-
-
84859885816
-
Differential gene and transcript expression analysis of RNAseq experiments with topHat and cufflinks
-
Trapnell, C. et al. Differential gene and transcript expression analysis of RNAseq experiments with topHat and cufflinks. Nat. Protoc. 7, 562-578 (2012).
-
(2012)
Nat. Protoc.
, vol.7
, pp. 562-578
-
-
Trapnell, C.1
-
40
-
-
84924629414
-
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
-
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
-
(2014)
Genome Biol.
, vol.15
, pp. 550
-
-
Love, M.I.1
Huber, W.2
Anders, S.3
-
41
-
-
84887109584
-
Accounting for technical noise in single-cell RNA-seq experiments
-
Brennecke, P. et al. Accounting for technical noise in single-cell RNA-seq experiments. Nat. Methods 10, 1093-1095 (2013).
-
(2013)
Nat. Methods
, vol.10
, pp. 1093-1095
-
-
Brennecke, P.1
-
42
-
-
46749110034
-
Factominer: An R package for multivariate analysis
-
Lê, S., Josse, J. & Husson, F. Factominer: an R package for multivariate analysis. J. Stat. Soft. 25, 1-18 (2008).
-
(2008)
J. Stat. Soft.
, vol.25
, pp. 1-18
-
-
Lê, S.1
Josse, J.2
Husson, F.3
-
43
-
-
84903574951
-
Bayesian approach to singlecell differential expression analysis
-
Kharchenko, P. V., Silberstein, L. & Scadden, D. T. Bayesian approach to singlecell differential expression analysis. Nat. Methods 11, 740-742 (2014).
-
(2014)
Nat. Methods
, vol.11
, pp. 740-742
-
-
Kharchenko, P.V.1
Silberstein, L.2
Scadden, D.T.3
-
44
-
-
84959189722
-
Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis
-
Fan, J. et al. Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis. Nat. Methods 13, 241-244 (2016).
-
(2016)
Nat. Methods
, vol.13
, pp. 241-244
-
-
Fan, J.1
-
45
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545-15550 (2005).
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
-
46
-
-
84941201582
-
Single-cell messenger RNA sequencing reveals rare intestinal cell types
-
Grün, D. et al. Single-cell messenger RNA sequencing reveals rare intestinal cell types. Nature 525, 251-255 (2015).
-
(2015)
Nature
, vol.525
, pp. 251-255
-
-
Grün, D.1
|