-
1
-
-
81255141781
-
The development of vaccines: how the past led to the future
-
Plotkin S., Plotkin S. The development of vaccines: how the past led to the future. Nature Reviews Microbiology 2011, 9:889.
-
(2011)
Nature Reviews Microbiology
, vol.9
, pp. 889
-
-
Plotkin, S.1
Plotkin, S.2
-
2
-
-
79956079190
-
Immunological mechanisms of vaccination
-
Pulendran B., Ahmed R. Immunological mechanisms of vaccination. Nature Immunology 2011, 12:509.
-
(2011)
Nature Immunology
, vol.12
, pp. 509
-
-
Pulendran, B.1
Ahmed, R.2
-
3
-
-
77958479678
-
Vaccines and the future of human immunology
-
Germain R.N. Vaccines and the future of human immunology. Immunity 2010, 33:441-450.
-
(2010)
Immunity
, vol.33
, pp. 441-450
-
-
Germain, R.N.1
-
4
-
-
79957627493
-
A 2020 vision for vaccines against HIV, tuberculosis and malaria
-
Rappuoli R., Aderem A. A 2020 vision for vaccines against HIV, tuberculosis and malaria. Nature 2011, 473:463-469.
-
(2011)
Nature
, vol.473
, pp. 463-469
-
-
Rappuoli, R.1
Aderem, A.2
-
5
-
-
32944478316
-
Translating innate immunity into immunological memory: implications for vaccine development
-
Pulendran B., Ahmed R. Translating innate immunity into immunological memory: implications for vaccine development. Cell 2006, 124:849-863.
-
(2006)
Cell
, vol.124
, pp. 849-863
-
-
Pulendran, B.1
Ahmed, R.2
-
6
-
-
77954357410
-
Correlates of protection induced by vaccination
-
Plotkin S.A. Correlates of protection induced by vaccination. Clinical and Vaccine Immunology 2010, 17:1055-1065.
-
(2010)
Clinical and Vaccine Immunology
, vol.17
, pp. 1055-1065
-
-
Plotkin, S.A.1
-
7
-
-
70349451542
-
Learning immunology from the yellow fever vaccine: innate immunity to systems vaccinology
-
Pulendran B. Learning immunology from the yellow fever vaccine: innate immunity to systems vaccinology. Nature Reviews Immunology 2009, 9:741-747.
-
(2009)
Nature Reviews Immunology
, vol.9
, pp. 741-747
-
-
Pulendran, B.1
-
9
-
-
79957777939
-
Systems biology approaches to new vaccine development
-
Oberg A.L., Kennedy R.B., Li P., Ovsyannikova I.G., Poland G.A. Systems biology approaches to new vaccine development. Current Opinion in Immunology 2011, 23:436-443.
-
(2011)
Current Opinion in Immunology
, vol.23
, pp. 436-443
-
-
Oberg, A.L.1
Kennedy, R.B.2
Li, P.3
Ovsyannikova, I.G.4
Poland, G.A.5
-
10
-
-
80051966191
-
Solving vaccine mysteries: a systems biology perspective
-
Trautmann L., Sekaly R. Solving vaccine mysteries: a systems biology perspective. Nature Immunology 2011, 12:729.
-
(2011)
Nature Immunology
, vol.12
, pp. 729
-
-
Trautmann, L.1
Sekaly, R.2
-
11
-
-
79953050420
-
Systems biology in immunology-a computational modeling perspective
-
Germain R.N., Meier-Schellersheim M., Nita-Lazar A., Fraser I.D. Systems biology in immunology-a computational modeling perspective. Annual Review of Immunology 2011, 29:527.
-
(2011)
Annual Review of Immunology
, vol.29
, pp. 527
-
-
Germain, R.N.1
Meier-Schellersheim, M.2
Nita-Lazar, A.3
Fraser, I.D.4
-
12
-
-
80051989398
-
Systems biology of vaccination for seasonal influenza in humans
-
Nakaya H.I., Wrammert J., Lee E.K., Racioppi L., Marie-Kunze S., Haining W.N., et al. Systems biology of vaccination for seasonal influenza in humans. Nature Immunology 2011, 12:786-795.
-
(2011)
Nature Immunology
, vol.12
, pp. 786-795
-
-
Nakaya, H.I.1
Wrammert, J.2
Lee, E.K.3
Racioppi, L.4
Marie-Kunze, S.5
Haining, W.N.6
-
13
-
-
84857058237
-
Systems vaccinology: its promise and challenge for HIV vaccine development
-
Nakaya H.I., Pulendran B. Systems vaccinology: its promise and challenge for HIV vaccine development. Current Opinion in HIV and AIDS 2012, 7:24.
-
(2012)
Current Opinion in HIV and AIDS
, vol.7
, pp. 24
-
-
Nakaya, H.I.1
Pulendran, B.2
-
14
-
-
32944455665
-
Yellow fever vaccine YF-17D activates multiple dendritic cell subsets via TLR2, 7, 8, and 9 to stimulate polyvalent immunity
-
Querec T., Bennouna S., Alkan S., Laouar Y., Gorden K., Flavell R., et al. Yellow fever vaccine YF-17D activates multiple dendritic cell subsets via TLR2, 7, 8, and 9 to stimulate polyvalent immunity. The Journal of Experimental Medicine 2006, 203:413-424.
-
(2006)
The Journal of Experimental Medicine
, vol.203
, pp. 413-424
-
-
Querec, T.1
Bennouna, S.2
Alkan, S.3
Laouar, Y.4
Gorden, K.5
Flavell, R.6
-
15
-
-
57849085182
-
Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans
-
Querec T.D., Akondy R.S., Lee E.K., Cao W., Nakaya H.I., Teuwen D., et al. Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans. Nature Immunology 2008, 10:116-125.
-
(2008)
Nature Immunology
, vol.10
, pp. 116-125
-
-
Querec, T.D.1
Akondy, R.S.2
Lee, E.K.3
Cao, W.4
Nakaya, H.I.5
Teuwen, D.6
-
16
-
-
59649129816
-
Yellow fever vaccine induces integrated multilineage and polyfunctional immune responses
-
Gaucher D., Therrien R., Kettaf N., Angermann B.R., Boucher G., Filali-Mouhim A., et al. Yellow fever vaccine induces integrated multilineage and polyfunctional immune responses. The Journal of Experimental Medicine 2008, 205:3119-3131.
-
(2008)
The Journal of Experimental Medicine
, vol.205
, pp. 3119-3131
-
-
Gaucher, D.1
Therrien, R.2
Kettaf, N.3
Angermann, B.R.4
Boucher, G.5
Filali-Mouhim, A.6
-
17
-
-
13444259647
-
Regulation of cap-dependent translation by eIF4E inhibitory proteins
-
Richter J.D., Sonenberg N. Regulation of cap-dependent translation by eIF4E inhibitory proteins. Nature 2005, 433:477-480.
-
(2005)
Nature
, vol.433
, pp. 477-480
-
-
Richter, J.D.1
Sonenberg, N.2
-
18
-
-
34250899722
-
Signal integration in the endoplasmic reticulum unfolded protein response
-
Ron D., Walter P. Signal integration in the endoplasmic reticulum unfolded protein response. Nature Reviews Molecular Cell Biology 2007, 8:519-529.
-
(2007)
Nature Reviews Molecular Cell Biology
, vol.8
, pp. 519-529
-
-
Ron, D.1
Walter, P.2
-
19
-
-
84874433635
-
Merck Ad5/HIV induces broad innate immune activation that predicts CD8+ T-cell responses but is attenuated by preexisting Ad5 immunity
-
E3503-E12
-
Zak D.E., Andersen-Nissen E., Peterson E.R., Sato A., Hamilton M.K., Borgerding J., et al. Merck Ad5/HIV induces broad innate immune activation that predicts CD8+ T-cell responses but is attenuated by preexisting Ad5 immunity. Proceedings of the National Academy of Sciences of the United States of America 2012, 109. E3503-E12.
-
(2012)
Proceedings of the National Academy of Sciences of the United States of America
, vol.109
-
-
Zak, D.E.1
Andersen-Nissen, E.2
Peterson, E.R.3
Sato, A.4
Hamilton, M.K.5
Borgerding, J.6
-
20
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders S., Huber W. Differential expression analysis for sequence count data. Genome Biology 2010, 11:R106.
-
(2010)
Genome Biology
, vol.11
-
-
Anders, S.1
Huber, W.2
-
21
-
-
75249087100
-
EdgeR: a Bioconductor package for differential expression analysis of digital gene expression data
-
Robinson M.D., McCarthy D.J., Smyth G.K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010, 26:139-140.
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
22
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell C., Williams B.A., Pertea G., Mortazavi A., Kwan G., Van Baren M.J., et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology 2010, 28:511-515.
-
(2010)
Nature Biotechnology
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
Van Baren, M.J.6
-
23
-
-
70449713405
-
Data management: it starts at the bench
-
Chaussabel D., Ueno H., Banchereau J., Quinn C. Data management: it starts at the bench. Nature Immunology 2009, 10:1225.
-
(2009)
Nature Immunology
, vol.10
, pp. 1225
-
-
Chaussabel, D.1
Ueno, H.2
Banchereau, J.3
Quinn, C.4
-
24
-
-
77955868506
-
Computational solutions to large-scale data management and analysis
-
Schadt E.E., Linderman M.D., Sorenson J., Lee L., Nolan G.P. Computational solutions to large-scale data management and analysis. Nature Reviews Genetics 2010, 11:647-657.
-
(2010)
Nature Reviews Genetics
, vol.11
, pp. 647-657
-
-
Schadt, E.E.1
Linderman, M.D.2
Sorenson, J.3
Lee, L.4
Nolan, G.P.5
-
25
-
-
18344396568
-
Minimum information about a microarray experiment (MIAME)-toward standards for microarray data
-
Brazma A., Hingamp P., Quackenbush J., Sherlock G., Spellman P., Stoeckert C., et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nature Genetics 2001, 29:365-372.
-
(2001)
Nature Genetics
, vol.29
, pp. 365-372
-
-
Brazma, A.1
Hingamp, P.2
Quackenbush, J.3
Sherlock, G.4
Spellman, P.5
Stoeckert, C.6
-
26
-
-
53049110682
-
MIFlowCyt: the minimum information about a Flow Cytometry Experiment
-
Lee J.A., Spidlen J., Boyce K., Cai J., Crosbie N., Dalphin M., et al. MIFlowCyt: the minimum information about a Flow Cytometry Experiment. Cytometry Part A 2008, 73:926-930.
-
(2008)
Cytometry Part A
, vol.73
, pp. 926-930
-
-
Lee, J.A.1
Spidlen, J.2
Boyce, K.3
Cai, J.4
Crosbie, N.5
Dalphin, M.6
-
27
-
-
79952325548
-
Flow cytometry data standards
-
Spidlen J., Shooshtari P., Kollmann T.R., Brinkman R.R. Flow cytometry data standards. BMC Research Notes 2011, 4:50.
-
(2011)
BMC Research Notes
, vol.4
, pp. 50
-
-
Spidlen, J.1
Shooshtari, P.2
Kollmann, T.R.3
Brinkman, R.R.4
-
28
-
-
70349833381
-
MIATA-Minimal Information about T Cell Assays
-
Janetzki S., Britten C.M., Kalos M., Levitsky H.I., Maecker H.T., Melief C.J., et al. MIATA-Minimal Information about T Cell Assays. Immunity 2009, 31:527-528.
-
(2009)
Immunity
, vol.31
, pp. 527-528
-
-
Janetzki, S.1
Britten, C.M.2
Kalos, M.3
Levitsky, H.I.4
Maecker, H.T.5
Melief, C.J.6
-
30
-
-
60749090295
-
Gene-set analysis and reduction
-
Dinu I., Potter J.D., Mueller T., Liu Q., Adewale A.J., Jhangri G.S., et al. Gene-set analysis and reduction. Briefings in Bioinformatics 2009, 10:24-34.
-
(2009)
Briefings in Bioinformatics
, vol.10
, pp. 24-34
-
-
Dinu, I.1
Potter, J.D.2
Mueller, T.3
Liu, Q.4
Adewale, A.J.5
Jhangri, G.S.6
-
31
-
-
84861123691
-
Ten years of pathway analysis: current approaches and outstanding challenges
-
Khatri P., Sirota M., Butte A.J. Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Computational Biology 2012, 8:e1002375.
-
(2012)
PLoS Computational Biology
, vol.8
-
-
Khatri, P.1
Sirota, M.2
Butte, A.J.3
-
32
-
-
33644874819
-
From genomics to chemical genomics: new developments in KEGG
-
D354-D7
-
Kanehisa M., Goto S., Hattori M., Aoki-Kinoshita K.F., Itoh M., Kawashima S., et al. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Research 2006, 34. D354-D7.
-
(2006)
Nucleic Acids Research
, vol.34
-
-
Kanehisa, M.1
Goto, S.2
Hattori, M.3
Aoki-Kinoshita, K.F.4
Itoh, M.5
Kawashima, S.6
-
33
-
-
58149186477
-
PID: the pathway interaction database
-
D674-D9
-
Schaefer C.F., Anthony K., Krupa S., Buchoff J., Day M., Hannay T., et al. PID: the pathway interaction database. Nucleic Acids Research 2009, 37. D674-D9.
-
(2009)
Nucleic Acids Research
, vol.37
-
-
Schaefer, C.F.1
Anthony, K.2
Krupa, S.3
Buchoff, J.4
Day, M.5
Hannay, T.6
-
34
-
-
27344435774
-
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian A., Tamayo P., Mootha V.K., Mukherjee S., Ebert B.L., Gillette M.A., et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America 2005, 102:15545-15550.
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
Mukherjee, S.4
Ebert, B.L.5
Gillette, M.A.6
-
35
-
-
34250191844
-
Reactome: a knowledge base of biologic pathways and processes
-
Vastrik I., D'Eustachio P., Schmidt E., Joshi-Tope G., Gopinath G., Croft D., et al. Reactome: a knowledge base of biologic pathways and processes. Genome Biology 2007, 8:R39.
-
(2007)
Genome Biology
, vol.8
-
-
Vastrik, I.1
D'Eustachio, P.2
Schmidt, E.3
Joshi-Tope, G.4
Gopinath, G.5
Croft, D.6
-
36
-
-
51049113607
-
InnateDB: facilitating systems-level analyses of the mammalian innate immune response
-
Lynn D.J., Winsor G.L., Chan C., Richard N., Laird M.R., Barsky A., et al. InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Molecular Systems Biology 2008, 2008.
-
(2008)
Molecular Systems Biology
, pp. 2008
-
-
Lynn, D.J.1
Winsor, G.L.2
Chan, C.3
Richard, N.4
Laird, M.R.5
Barsky, A.6
-
37
-
-
46749152178
-
A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus
-
Chaussabel D., Quinn C., Shen J., Patel P., Glaser C., Baldwin N., et al. A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus. Immunity 2008, 29:150-164.
-
(2008)
Immunity
, vol.29
, pp. 150-164
-
-
Chaussabel, D.1
Quinn, C.2
Shen, J.3
Patel, P.4
Glaser, C.5
Baldwin, N.6
-
38
-
-
77955894773
-
An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis
-
Berry M.P., Graham C.M., McNab F.W., Xu Z., Bloch S.A., Oni T., et al. An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis. Nature 2010, 466:973-977.
-
(2010)
Nature
, vol.466
, pp. 973-977
-
-
Berry, M.P.1
Graham, C.M.2
McNab, F.W.3
Xu, Z.4
Bloch, S.A.5
Oni, T.6
-
39
-
-
77954384233
-
Assessing the human immune system through blood transcriptomics
-
Chaussabel D., Pascual V., Banchereau J. Assessing the human immune system through blood transcriptomics. BMC Biology 2010, 8:84.
-
(2010)
BMC Biology
, vol.8
, pp. 84
-
-
Chaussabel, D.1
Pascual, V.2
Banchereau, J.3
-
40
-
-
79953323633
-
A multicentre, randomised, double-blind, placebo-controlled trial with the interleukin-1 receptor antagonist anakinra in patients with systemic-onset juvenile idiopathic arthritis (ANAJIS trial)
-
Quartier P., Allantaz F., Cimaz R., Pillet P., Messiaen C., Bardin C., et al. A multicentre, randomised, double-blind, placebo-controlled trial with the interleukin-1 receptor antagonist anakinra in patients with systemic-onset juvenile idiopathic arthritis (ANAJIS trial). Annals of the Rheumatic Diseases 2011, 70:747-754.
-
(2011)
Annals of the Rheumatic Diseases
, vol.70
, pp. 747-754
-
-
Quartier, P.1
Allantaz, F.2
Cimaz, R.3
Pillet, P.4
Messiaen, C.5
Bardin, C.6
-
41
-
-
84857497003
-
Systems biology approaches reveal a specific interferon-inducible signature in HTLV-1 associated myelopathy
-
Tattermusch S., Skinner J.A., Chaussabel D., Banchereau J., Berry M.P., McNab F.W., et al. Systems biology approaches reveal a specific interferon-inducible signature in HTLV-1 associated myelopathy. PLoS Pathogens 2012, 8:e1002480.
-
(2012)
PLoS Pathogens
, vol.8
-
-
Tattermusch, S.1
Skinner, J.A.2
Chaussabel, D.3
Banchereau, J.4
Berry, M.P.5
McNab, F.W.6
-
43
-
-
33748351161
-
Computational expression deconvolution in a complex mammalian organ
-
Wang M., Master S.R., Chodosh L.A. Computational expression deconvolution in a complex mammalian organ. BMC Bioinformatics 2006, 7:328.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 328
-
-
Wang, M.1
Master, S.R.2
Chodosh, L.A.3
-
44
-
-
67749112023
-
Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus
-
Abbas A.R., Wolslegel K., Seshasayee D., Modrusan Z., Clark H.F. Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus. PloS One 2009, 4:e6098.
-
(2009)
PloS One
, vol.4
-
-
Abbas, A.R.1
Wolslegel, K.2
Seshasayee, D.3
Modrusan, Z.4
Clark, H.F.5
-
45
-
-
77951634577
-
Cell type-specific gene expression differences in complex tissues
-
Shen-Orr S.S., Tibshirani R., Khatri P., Bodian D.L., Staedtler F., Perry N.M., et al. Cell type-specific gene expression differences in complex tissues. Nature Methods 2010, 7:287-289.
-
(2010)
Nature Methods
, vol.7
, pp. 287-289
-
-
Shen-Orr, S.S.1
Tibshirani, R.2
Khatri, P.3
Bodian, D.L.4
Staedtler, F.5
Perry, N.M.6
-
47
-
-
67650895858
-
Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans
-
Chikina M.D., Huttenhower C., Murphy C.T., Troyanskaya O.G. Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans. PLoS Computational Biology 2009, 5:e1000417.
-
(2009)
PLoS Computational Biology
, vol.5
-
-
Chikina, M.D.1
Huttenhower, C.2
Murphy, C.T.3
Troyanskaya, O.G.4
-
48
-
-
21344446363
-
Immune response in silico (IRIS): immune-specific genes identified from a compendium of microarray expression data
-
Abbas A., Baldwin D., Ma Y., Ouyang W., Gurney A., Martin F., et al. Immune response in silico (IRIS): immune-specific genes identified from a compendium of microarray expression data. Genes and Immunity 2005, 6:319-331.
-
(2005)
Genes and Immunity
, vol.6
, pp. 319-331
-
-
Abbas, A.1
Baldwin, D.2
Ma, Y.3
Ouyang, W.4
Gurney, A.5
Martin, F.6
-
49
-
-
33745259517
-
Cell-type specific gene expression profiles of leukocytes in human peripheral blood
-
Palmer C., Diehn M., Alizadeh A.A., Brown P.O. Cell-type specific gene expression profiles of leukocytes in human peripheral blood. BMC Genomics 2006, 7:115.
-
(2006)
BMC Genomics
, vol.7
, pp. 115
-
-
Palmer, C.1
Diehn, M.2
Alizadeh, A.A.3
Brown, P.O.4
-
50
-
-
52649097448
-
The Immunological Genome Project: networks of gene expression in immune cells
-
Heng T.S., Painter M.W., Elpek K., Lukacs-Kornek V., Mauermann N., Turley S.J., et al. The Immunological Genome Project: networks of gene expression in immune cells. Nature Immunology 2008, 9:1091-1094.
-
(2008)
Nature Immunology
, vol.9
, pp. 1091-1094
-
-
Heng, T.S.1
Painter, M.W.2
Elpek, K.3
Lukacs-Kornek, V.4
Mauermann, N.5
Turley, S.J.6
-
51
-
-
78651486442
-
Densely interconnected transcriptional circuits control cell states in human hematopoiesis
-
Novershtern N., Subramanian A., Lawton L.N., Mak R.H., Haining W.N., McConkey M.E., et al. Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell 2011, 144:296-309.
-
(2011)
Cell
, vol.144
, pp. 296-309
-
-
Novershtern, N.1
Subramanian, A.2
Lawton, L.N.3
Mak, R.H.4
Haining, W.N.5
McConkey, M.E.6
-
52
-
-
79955750055
-
Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum
-
Bendall S.C., Simonds E.F., Qiu P., Amir E-aD, Krutzik P.O., Finck R., et al. Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science Signalling 2011, 332:687.
-
(2011)
Science Signalling
, vol.332
, pp. 687
-
-
Bendall, S.C.1
Simonds, E.F.2
Qiu, P.3
Amir, E.-A.D.4
Krutzik, P.O.5
Finck, R.6
-
53
-
-
84856278095
-
Cytometry by time-of-flight shows combinatorial cytokine expression and virus-specific cell niches within a continuum of CD8+ T cell phenotypes
-
Newell E.W., Sigal N., Bendall S.C., Nolan G.P., Davis M.M. Cytometry by time-of-flight shows combinatorial cytokine expression and virus-specific cell niches within a continuum of CD8+ T cell phenotypes. Immunity 2012, 36:142-152.
-
(2012)
Immunity
, vol.36
, pp. 142-152
-
-
Newell, E.W.1
Sigal, N.2
Bendall, S.C.3
Nolan, G.P.4
Davis, M.M.5
-
54
-
-
69849105361
-
Machine learning framework for classification in medicine and biology
-
Lee E. Machine learning framework for classification in medicine and biology. Lecture Notes in Computer Science 2009, 5547:1-7.
-
(2009)
Lecture Notes in Computer Science
, vol.5547
, pp. 1-7
-
-
Lee, E.1
-
55
-
-
1542473171
-
Application of independent component analysis to microarrays
-
Lee S-I., Batzoglou S. Application of independent component analysis to microarrays. Genome Biology 2003, 4:76.
-
(2003)
Genome Biology
, vol.4
, pp. 76
-
-
Lee, S.-I.1
Batzoglou, S.2
-
56
-
-
77955160229
-
K-Nearest neighbor models for microarray gene expression analysis and clinical outcome prediction
-
Parry R., Jones W., Stokes T., Phan J., Moffitt R., Fang H., et al. k-Nearest neighbor models for microarray gene expression analysis and clinical outcome prediction. The Pharmacogenomics Journal 2010, 10:292-309.
-
(2010)
The Pharmacogenomics Journal
, vol.10
, pp. 292-309
-
-
Parry, R.1
Jones, W.2
Stokes, T.3
Phan, J.4
Moffitt, R.5
Fang, H.6
-
57
-
-
0037076272
-
Diagnosis of multiple cancer types by shrunken centroids of gene expression
-
Tibshirani R., Hastie T., Narasimhan B., Chu G. Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proceedings of the National Academy of Sciences of the United States of America 2002, 99:6567-6572.
-
(2002)
Proceedings of the National Academy of Sciences of the United States of America
, vol.99
, pp. 6567-6572
-
-
Tibshirani, R.1
Hastie, T.2
Narasimhan, B.3
Chu, G.4
-
58
-
-
33845703344
-
What is a support vector machine
-
Noble W.S. What is a support vector machine. Nature Biotechnology 2006, 24:1565-1567.
-
(2006)
Nature Biotechnology
, vol.24
, pp. 1565-1567
-
-
Noble, W.S.1
-
59
-
-
30644464444
-
Gene selection and classification of microarray data using random forest
-
Díaz-Uriarte R., De Andres S.A. Gene selection and classification of microarray data using random forest. BMC Bioinformatics 2006, 7:3.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 3
-
-
Díaz-Uriarte, R.1
De Andres, S.A.2
-
60
-
-
33846978784
-
Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting
-
Dupuy A., Simon R.M. Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting. Journal of the National Cancer Institute 2007, 99:147-157.
-
(2007)
Journal of the National Cancer Institute
, vol.99
, pp. 147-157
-
-
Dupuy, A.1
Simon, R.M.2
-
61
-
-
78650735473
-
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models
-
Shi L., Campbell G., Jones W.D., Campagne F., Wen Z., Walker S.J., et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nature Biotechnology 2010, 28:827.
-
(2010)
Nature Biotechnology
, vol.28
, pp. 827
-
-
Shi, L.1
Campbell, G.2
Jones, W.D.3
Campagne, F.4
Wen, Z.5
Walker, S.J.6
-
62
-
-
57149092133
-
Inferring pathway activity toward precise disease classification
-
Lee E., Chuang H-Y., Kim J-W., Ideker T., Lee D. Inferring pathway activity toward precise disease classification. PLoS Computational Biology 2008, 4:e1000217.
-
(2008)
PLoS Computational Biology
, vol.4
-
-
Lee, E.1
Chuang, H.-Y.2
Kim, J.-W.3
Ideker, T.4
Lee, D.5
-
63
-
-
35348891430
-
Network-based classification of breast cancer metastasis
-
Chuang H-Y., Lee E., Liu Y-T., Lee D., Ideker T. Network-based classification of breast cancer metastasis. Molecular Systems Biology 2007, 2007.
-
(2007)
Molecular Systems Biology
, pp. 2007
-
-
Chuang, H.-Y.1
Lee, E.2
Liu, Y.-T.3
Lee, D.4
Ideker, T.5
-
64
-
-
84862683516
-
Identifying gnostic predictors of the vaccine response
-
Haining W.N., Pulendran B. Identifying gnostic predictors of the vaccine response. Current Opinion in Immunology 2012, 24:332-336.
-
(2012)
Current Opinion in Immunology
, vol.24
, pp. 332-336
-
-
Haining, W.N.1
Pulendran, B.2
-
65
-
-
78049415626
-
An integrative multi-network and multi-classifier approach to predict genetic interactions
-
Pandey G., Zhang B., Chang A.N., Myers C.L., Zhu J., Kumar V., et al. An integrative multi-network and multi-classifier approach to predict genetic interactions. PLoS Computational Biology 2010, 6:e1000928.
-
(2010)
PLoS Computational Biology
, vol.6
-
-
Pandey, G.1
Zhang, B.2
Chang, A.N.3
Myers, C.L.4
Zhu, J.5
Kumar, V.6
-
66
-
-
82255175259
-
Strategies to discover regulatory circuits of the mammalian immune system
-
Amit I., Regev A., Hacohen N. Strategies to discover regulatory circuits of the mammalian immune system. Nature Reviews Immunology 2011, 11:873-880.
-
(2011)
Nature Reviews Immunology
, vol.11
, pp. 873-880
-
-
Amit, I.1
Regev, A.2
Hacohen, N.3
-
68
-
-
84858414020
-
Cellular metabolism and disease: what do metabolic outliers teach us
-
DeBerardinis R.J., Thompson C.B. Cellular metabolism and disease: what do metabolic outliers teach us. Cell 2012, 148:1132-1144.
-
(2012)
Cell
, vol.148
, pp. 1132-1144
-
-
DeBerardinis, R.J.1
Thompson, C.B.2
-
69
-
-
84860451927
-
Metabolomics: the final frontier?
-
Veenstra T.D. Metabolomics: the final frontier?. Genome Medicine 2012, 4:40.
-
(2012)
Genome Medicine
, vol.4
, pp. 40
-
-
Veenstra, T.D.1
-
70
-
-
53649110425
-
Systems-level metabolic flux profiling identifies fatty acid synthesis as a target for antiviral therapy
-
Munger J., Bennett B.D., Parikh A., Feng X-J., McArdle J., Rabitz H.A., et al. Systems-level metabolic flux profiling identifies fatty acid synthesis as a target for antiviral therapy. Nature Biotechnology 2008, 26:1179-1186.
-
(2008)
Nature Biotechnology
, vol.26
, pp. 1179-1186
-
-
Munger, J.1
Bennett, B.D.2
Parikh, A.3
Feng, X.-J.4
McArdle, J.5
Rabitz, H.A.6
-
71
-
-
79955660777
-
Branched tricarboxylic acid metabolism in Plasmodium falciparum
-
Olszewski K.L., Mather M.W., Morrisey J.M., Garcia B.A., Vaidya A.B., Rabinowitz J.D., et al. Branched tricarboxylic acid metabolism in Plasmodium falciparum. Nature 2010, 466:774-778.
-
(2010)
Nature
, vol.466
, pp. 774-778
-
-
Olszewski, K.L.1
Mather, M.W.2
Morrisey, J.M.3
Garcia, B.A.4
Vaidya, A.B.5
Rabinowitz, J.D.6
-
72
-
-
72049125350
-
Cancer-associated IDH1 mutations produce 2-hydroxyglutarate
-
Dang L., White D.W., Gross S., Bennett B.D., Bittinger M.A., Driggers E.M., et al. Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature 2009, 462:739-744.
-
(2009)
Nature
, vol.462
, pp. 739-744
-
-
Dang, L.1
White, D.W.2
Gross, S.3
Bennett, B.D.4
Bittinger, M.A.5
Driggers, E.M.6
-
73
-
-
60149091657
-
Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression
-
Sreekumar A., Poisson L.M., Rajendiran T.M., Khan A.P., Cao Q., Yu J., et al. Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature 2009, 457:910-914.
-
(2009)
Nature
, vol.457
, pp. 910-914
-
-
Sreekumar, A.1
Poisson, L.M.2
Rajendiran, T.M.3
Khan, A.P.4
Cao, Q.5
Yu, J.6
-
74
-
-
62649151803
-
Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites
-
Wikoff W.R., Anfora A.T., Liu J., Schultz P.G., Lesley S.A., Peters E.C., et al. Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proceedings of the National Academy of Sciences of the United States of America 2009, 106:3698-3703.
-
(2009)
Proceedings of the National Academy of Sciences of the United States of America
, vol.106
, pp. 3698-3703
-
-
Wikoff, W.R.1
Anfora, A.T.2
Liu, J.3
Schultz, P.G.4
Lesley, S.A.5
Peters, E.C.6
-
75
-
-
77952545479
-
Metabolic oxidation regulates embryonic stem cell differentiation
-
Yanes O., Clark J., Wong D.M., Patti G.J., Sánchez-Ruiz A., Benton H.P., et al. Metabolic oxidation regulates embryonic stem cell differentiation. Nature Chemical Biology 2010, 6:411-417.
-
(2010)
Nature Chemical Biology
, vol.6
, pp. 411-417
-
-
Yanes, O.1
Clark, J.2
Wong, D.M.3
Patti, G.J.4
Sánchez-Ruiz, A.5
Benton, H.P.6
-
76
-
-
80053456051
-
Serum metabolomics reveals higher levels of polyunsaturated Fatty acids in lepromatous leprosy: potential markers for susceptibility and pathogenesis
-
Al-Mubarak R., Vander Heiden J., Broeckling C.D., Balagon M., Brennan P.J., Vissa V.D. Serum metabolomics reveals higher levels of polyunsaturated Fatty acids in lepromatous leprosy: potential markers for susceptibility and pathogenesis. PLoS Neglected Tropical Diseases 2011, 5:e1303.
-
(2011)
PLoS Neglected Tropical Diseases
, vol.5
-
-
Al-Mubarak, R.1
Vander Heiden, J.2
Broeckling, C.D.3
Balagon, M.4
Brennan, P.J.5
Vissa, V.D.6
-
77
-
-
84858433310
-
Personal omics profiling reveals dynamic molecular and medical phenotypes
-
Chen R., Mias G.I., Li-Pook-Than J., Jiang L., Lam H.Y., Chen R., et al. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell 2012, 148:1293-1307.
-
(2012)
Cell
, vol.148
, pp. 1293-1307
-
-
Chen, R.1
Mias, G.I.2
Li-Pook-Than, J.3
Jiang, L.4
Lam, H.Y.5
Chen, R.6
-
78
-
-
79953307254
-
Impact of Salmonella infection on host hormone metabolism revealed by metabolomics
-
Antunes L.C.M., Arena E.T., Menendez A., Han J., Ferreira R.B., Buckner M.M., et al. Impact of Salmonella infection on host hormone metabolism revealed by metabolomics. Infection and Immunity 2011, 79:1759-1769.
-
(2011)
Infection and Immunity
, vol.79
, pp. 1759-1769
-
-
Antunes, L.C.M.1
Arena, E.T.2
Menendez, A.3
Han, J.4
Ferreira, R.B.5
Buckner, M.M.6
-
79
-
-
67650400646
-
Response and recovery in the plasma metabolome tracks the acute LCMV-induced immune response
-
Wikoff W.R., Kalisak E., Trauger S., Manchester M., Siuzdak G. Response and recovery in the plasma metabolome tracks the acute LCMV-induced immune response. Journal of Proteome Research 2009, 8:3578-3587.
-
(2009)
Journal of Proteome Research
, vol.8
, pp. 3578-3587
-
-
Wikoff, W.R.1
Kalisak, E.2
Trauger, S.3
Manchester, M.4
Siuzdak, G.5
-
80
-
-
60649112444
-
Host-parasite interactions revealed by Plasmodium falciparum metabolomics
-
Olszewski K.L., Morrisey J.M., Wilinski D., Burns J.M., Vaidya A.B., Rabinowitz J.D., et al. Host-parasite interactions revealed by Plasmodium falciparum metabolomics. Cell Host & Microbe 2009, 5:191-199.
-
(2009)
Cell Host & Microbe
, vol.5
, pp. 191-199
-
-
Olszewski, K.L.1
Morrisey, J.M.2
Wilinski, D.3
Burns, J.M.4
Vaidya, A.B.5
Rabinowitz, J.D.6
-
81
-
-
77956419824
-
Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network
-
Plata G., Hsiao T-L., Olszewski K.L., Llinás M., Vitkup D. Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network. Molecular Systems Biology 2010, 2010.
-
(2010)
Molecular Systems Biology
, pp. 2010
-
-
Plata, G.1
Hsiao, T.-L.2
Olszewski, K.L.3
Llinás, M.4
Vitkup, D.5
-
82
-
-
33750827770
-
Glutamate released by dendritic cells as a novel modulator of T cell activation
-
Pacheco R., Oliva H., Martinez-Navío J.M., Climent N., Ciruela F., Gatell J.M., et al. Glutamate released by dendritic cells as a novel modulator of T cell activation. The Journal of Immunology 2006, 177:6695-6704.
-
(2006)
The Journal of Immunology
, vol.177
, pp. 6695-6704
-
-
Pacheco, R.1
Oliva, H.2
Martinez-Navío, J.M.3
Climent, N.4
Ciruela, F.5
Gatell, J.M.6
-
83
-
-
77955360587
-
Glutamate joins the ranks of immunomodulators
-
Hansen A.M., Caspi R.R. Glutamate joins the ranks of immunomodulators. Nature Medicine 2010, 16:856-858.
-
(2010)
Nature Medicine
, vol.16
, pp. 856-858
-
-
Hansen, A.M.1
Caspi, R.R.2
-
86
-
-
34250351459
-
Adenosine generation catalyzed by CD39 and CD73 expressed on regulatory T cells mediates immune suppression
-
Deaglio S., Dwyer K.M., Gao W., Friedman D., Usheva A., Erat A., et al. Adenosine generation catalyzed by CD39 and CD73 expressed on regulatory T cells mediates immune suppression. The Journal of Experimental Medicine 2007, 204:1257-1265.
-
(2007)
The Journal of Experimental Medicine
, vol.204
, pp. 1257-1265
-
-
Deaglio, S.1
Dwyer, K.M.2
Gao, W.3
Friedman, D.4
Usheva, A.5
Erat, A.6
-
87
-
-
51049101334
-
Adenosine receptors: therapeutic aspects for inflammatory and immune diseases
-
Haskó G., Linden J., Cronstein B., Pacher P. Adenosine receptors: therapeutic aspects for inflammatory and immune diseases. Nature Reviews Drug Discovery 2008, 7:759-770.
-
(2008)
Nature Reviews Drug Discovery
, vol.7
, pp. 759-770
-
-
Haskó, G.1
Linden, J.2
Cronstein, B.3
Pacher, P.4
-
88
-
-
23444456772
-
Regulation of immune responses by l-arginine metabolism
-
Bronte V., Zanovello P. Regulation of immune responses by l-arginine metabolism. Nature Reviews Immunology 2005, 5:641-654.
-
(2005)
Nature Reviews Immunology
, vol.5
, pp. 641-654
-
-
Bronte, V.1
Zanovello, P.2
-
89
-
-
33750110432
-
Fatty acids as modulators of the immune response
-
Fritsche K. Fatty acids as modulators of the immune response. Annual Review of Nutrition 2006, 26:45-73.
-
(2006)
Annual Review of Nutrition
, vol.26
, pp. 45-73
-
-
Fritsche, K.1
-
90
-
-
84866254082
-
New families of bioactive oxidized phospholipids generated by immune cells: identification and signaling actions
-
O'Donnell V.B., Murphy R.C. New families of bioactive oxidized phospholipids generated by immune cells: identification and signaling actions. Blood 2012, 120:1985-1992.
-
(2012)
Blood
, vol.120
, pp. 1985-1992
-
-
O'Donnell, V.B.1
Murphy, R.C.2
-
92
-
-
79957742886
-
Thyroxine is a potential endogenous antagonist of macrophage migration inhibitory factor (MIF) activity
-
Al-Abed Y., Metz C.N., Cheng K.F., Aljabari B., VanPatten S., Blau S., et al. Thyroxine is a potential endogenous antagonist of macrophage migration inhibitory factor (MIF) activity. Proceedings of the National Academy of Sciences of the United States of America 2011, 108:8224-8227.
-
(2011)
Proceedings of the National Academy of Sciences of the United States of America
, vol.108
, pp. 8224-8227
-
-
Al-Abed, Y.1
Metz, C.N.2
Cheng, K.F.3
Aljabari, B.4
VanPatten, S.5
Blau, S.6
-
93
-
-
67650096912
-
Enhancing CD8 T-cell memory by modulating fatty acid metabolism
-
Pearce E.L., Walsh M.C., Cejas P.J., Harms G.M., Shen H., Wang L-S., et al. Enhancing CD8 T-cell memory by modulating fatty acid metabolism. Nature 2009, 460:103-107.
-
(2009)
Nature
, vol.460
, pp. 103-107
-
-
Pearce, E.L.1
Walsh, M.C.2
Cejas, P.J.3
Harms, G.M.4
Shen, H.5
Wang, L.-S.6
-
94
-
-
84880851838
-
Predicting network activity from high throughput metabolomics
-
in press
-
Li S., Park Y., Duraisingham S., Strobel F.H., Khan N., Soltow Q.A., et al. Predicting network activity from high throughput metabolomics. PLoS Computational Biology 2013, in press. 10.1371/journal.pcbi.1003123.
-
(2013)
PLoS Computational Biology
-
-
Li, S.1
Park, Y.2
Duraisingham, S.3
Strobel, F.H.4
Khan, N.5
Soltow, Q.A.6
-
95
-
-
0021940473
-
Genetic regulation of immunoglobulin and specific antibody levels in twins reared apart
-
Kohler P.F., Rivera V.J., Eckert E., Bouchard T.J., Heston L.L. Genetic regulation of immunoglobulin and specific antibody levels in twins reared apart. Journal of Clinical Investigation 1985, 75:883.
-
(1985)
Journal of Clinical Investigation
, vol.75
, pp. 883
-
-
Kohler, P.F.1
Rivera, V.J.2
Eckert, E.3
Bouchard, T.J.4
Heston, L.L.5
-
96
-
-
0035925676
-
Twin studies of immunogenicity-determining the genetic contribution to vaccine failure
-
Tan P-L., Jacobson R.M., Poland G.A., Jacobsen S.J., Pankratz V.S. Twin studies of immunogenicity-determining the genetic contribution to vaccine failure. Vaccine 2001, 19:2434-2439.
-
(2001)
Vaccine
, vol.19
, pp. 2434-2439
-
-
Tan, P.-L.1
Jacobson, R.M.2
Poland, G.A.3
Jacobsen, S.J.4
Pankratz, V.S.5
-
97
-
-
33744517008
-
Influence of genetic and environmental factors on the immunogenicity of Hib vaccine in Gambian twins
-
Lee Y., Newport M., Goetghebuer T., Siegrist C., Weiss H., Pollard A., et al. Influence of genetic and environmental factors on the immunogenicity of Hib vaccine in Gambian twins. Vaccine 2006, 24:5335-5340.
-
(2006)
Vaccine
, vol.24
, pp. 5335-5340
-
-
Lee, Y.1
Newport, M.2
Goetghebuer, T.3
Siegrist, C.4
Weiss, H.5
Pollard, A.6
-
99
-
-
77956643281
-
Infectious diseases not immune to genome-wide association
-
de Bakker P.I., Telenti A. Infectious diseases not immune to genome-wide association. Nature Genetics 2010, 42:731.
-
(2010)
Nature Genetics
, vol.42
, pp. 731
-
-
de Bakker, P.I.1
Telenti, A.2
-
100
-
-
74249086566
-
Common genetic variation and the control of HIV-1 in humans
-
Fellay J., Ge D., Shianna K.V., Colombo S., Ledergerber B., Cirulli E.T., et al. Common genetic variation and the control of HIV-1 in humans. PLoS Genetics 2009, 5:e1000791.
-
(2009)
PLoS Genetics
, vol.5
-
-
Fellay, J.1
Ge, D.2
Shianna, K.V.3
Colombo, S.4
Ledergerber, B.5
Cirulli, E.T.6
-
101
-
-
67349160018
-
A genome-wide association study identifies variants in the HLA-DP locus associated with chronic hepatitis B in Asians
-
Kamatani Y., Wattanapokayakit S., Ochi H., Kawaguchi T., Takahashi A., Hosono N., et al. A genome-wide association study identifies variants in the HLA-DP locus associated with chronic hepatitis B in Asians. Nature Genetics 2009, 41:591-595.
-
(2009)
Nature Genetics
, vol.41
, pp. 591-595
-
-
Kamatani, Y.1
Wattanapokayakit, S.2
Ochi, H.3
Kawaguchi, T.4
Takahashi, A.5
Hosono, N.6
-
102
-
-
74049127960
-
Genomewide association study of leprosy
-
Zhang F-R., Huang W., Chen S-M., Sun L-D., Liu H., Li Y., et al. Genomewide association study of leprosy. New England Journal of Medicine 2009, 361:2609-2618.
-
(2009)
New England Journal of Medicine
, vol.361
, pp. 2609-2618
-
-
Zhang, F.-R.1
Huang, W.2
Chen, S.-M.3
Sun, L.-D.4
Liu, H.5
Li, Y.6
-
103
-
-
78650084232
-
The major genetic determinants of HIV-1 control affect HLA class I peptide presentation
-
Pereyra F., Jia X., McLaren P.J., Telenti A., de Bakker P.I., Walker B.D., et al. The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science 2010, 330:1551.
-
(2010)
Science
, vol.330
, pp. 1551
-
-
Pereyra, F.1
Jia, X.2
McLaren, P.J.3
Telenti, A.4
de Bakker, P.I.5
Walker, B.D.6
-
104
-
-
84861715100
-
Genome-wide association study of antibody response to smallpox vaccine
-
Ovsyannikova I.G., Kennedy R.B., O'Byrne M., Jacobson R.M., Pankratz V.S., Poland G.A. Genome-wide association study of antibody response to smallpox vaccine. Vaccine 2012, 30:4182-4189.
-
(2012)
Vaccine
, vol.30
, pp. 4182-4189
-
-
Ovsyannikova, I.G.1
Kennedy, R.B.2
O'Byrne, M.3
Jacobson, R.M.4
Pankratz, V.S.5
Poland, G.A.6
-
105
-
-
84866739066
-
Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients
-
Kennedy R.B., Ovsyannikova I.G., Shane Pankratz V., Haralambieva I.H., Vierkant R.A., Poland G.A. Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients. Human Genetics 2012, 1-19.
-
(2012)
Human Genetics
, pp. 1-19
-
-
Kennedy, R.B.1
Ovsyannikova, I.G.2
Shane Pankratz, V.3
Haralambieva, I.H.4
Vierkant, R.A.5
Poland, G.A.6
-
106
-
-
78649701338
-
Surfing a genetic association interaction network to identify modulators of antibody response to smallpox vaccine
-
Davis N., Crowe J., Pajewski N., McKinney B. Surfing a genetic association interaction network to identify modulators of antibody response to smallpox vaccine. Genes and Immunity 2010, 11:630-636.
-
(2010)
Genes and Immunity
, vol.11
, pp. 630-636
-
-
Davis, N.1
Crowe, J.2
Pajewski, N.3
McKinney, B.4
-
107
-
-
79960800986
-
Targeting TLRs expands the antibody repertoire in response to a malaria vaccine
-
93ra69
-
Wiley S.R., Raman V.S., Desbien A., Bailor H.R., Bhardwaj R., Shakri A.R., et al. Targeting TLRs expands the antibody repertoire in response to a malaria vaccine. Science Translational Medicine 2011, 3. 93ra69.
-
(2011)
Science Translational Medicine
, vol.3
-
-
Wiley, S.R.1
Raman, V.S.2
Desbien, A.3
Bailor, H.R.4
Bhardwaj, R.5
Shakri, A.R.6
-
108
-
-
85027927719
-
Enterotypes of the human gut microbiome
-
Arumugam M., Raes J., Pelletier E., Le Paslier D., Yamada T., Mende D.R., et al. Enterotypes of the human gut microbiome. Nature 2011, 473:174-180.
-
(2011)
Nature
, vol.473
, pp. 174-180
-
-
Arumugam, M.1
Raes, J.2
Pelletier, E.3
Le Paslier, D.4
Yamada, T.5
Mende, D.R.6
-
109
-
-
84862276328
-
Structure, function and diversity of the healthy human microbiome
-
Huttenhower C., Gevers D., Knight R., Abubucker S., Badger J.H., Chinwalla A.T., et al. Structure, function and diversity of the healthy human microbiome. Nature 2012, 486:207-214.
-
(2012)
Nature
, vol.486
, pp. 207-214
-
-
Huttenhower, C.1
Gevers, D.2
Knight, R.3
Abubucker, S.4
Badger, J.H.5
Chinwalla, A.T.6
-
110
-
-
75249107844
-
PyNAST: a flexible tool for aligning sequences to a template alignment
-
Caporaso J.G., Bittinger K., Bushman F.D., DeSantis T.Z., Andersen G.L., Knight R. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 2010, 26:266-267.
-
(2010)
Bioinformatics
, vol.26
, pp. 266-267
-
-
Caporaso, J.G.1
Bittinger, K.2
Bushman, F.D.3
DeSantis, T.Z.4
Andersen, G.L.5
Knight, R.6
-
111
-
-
40149103278
-
Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex
-
Hamady M., Walker J.J., Harris J.K., Gold N.J., Knight R. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nature Methods 2008, 5:235-237.
-
(2008)
Nature Methods
, vol.5
, pp. 235-237
-
-
Hamady, M.1
Walker, J.J.2
Harris, J.K.3
Gold, N.J.4
Knight, R.5
-
112
-
-
84857049212
-
Interleukin-1β (IL-1β) promotes susceptibility of Toll-like receptor 5 (TLR5) deficient mice to colitis
-
Carvalho F.A., Nalbantoglu I., Ortega-Fernandez S., Aitken J.D., Su Y., Koren O., et al. Interleukin-1β (IL-1β) promotes susceptibility of Toll-like receptor 5 (TLR5) deficient mice to colitis. Gut 2012, 61:373-384.
-
(2012)
Gut
, vol.61
, pp. 373-384
-
-
Carvalho, F.A.1
Nalbantoglu, I.2
Ortega-Fernandez, S.3
Aitken, J.D.4
Su, Y.5
Koren, O.6
-
113
-
-
53649100675
-
ATP drives lamina propria TH17 cell differentiation
-
Atarashi K., Nishimura J., Shima T., Umesaki Y., Yamamoto M., Onoue M., et al. ATP drives lamina propria TH17 cell differentiation. Nature 2008, 455:808-812.
-
(2008)
Nature
, vol.455
, pp. 808-812
-
-
Atarashi, K.1
Nishimura, J.2
Shima, T.3
Umesaki, Y.4
Yamamoto, M.5
Onoue, M.6
-
114
-
-
0032935617
-
Influences of microbiota on intestinal immune system development
-
Cebra J.J. Influences of microbiota on intestinal immune system development. The American Journal of Clinical Nutrition 1999, 69:1046-1051.
-
(1999)
The American Journal of Clinical Nutrition
, vol.69
, pp. 1046-1051
-
-
Cebra, J.J.1
-
115
-
-
53349164200
-
Commensal DNA limits regulatory T cell conversion and is a natural adjuvant of intestinal immune responses
-
Hall J.A., Bouladoux N., Sun C.M., Wohlfert E.A., Blank R.B., Zhu Q., et al. Commensal DNA limits regulatory T cell conversion and is a natural adjuvant of intestinal immune responses. Immunity 2008, 29:637-649.
-
(2008)
Immunity
, vol.29
, pp. 637-649
-
-
Hall, J.A.1
Bouladoux, N.2
Sun, C.M.3
Wohlfert, E.A.4
Blank, R.B.5
Zhu, Q.6
-
116
-
-
53349173070
-
Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine
-
Ivanov I.I., Frutos RdL.Manel N., Yoshinaga K., Rifkin D.B., Sartor R.B., et al. Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine. Cell Host & Microbe 2008, 4:337-349.
-
(2008)
Cell Host & Microbe
, vol.4
, pp. 337-349
-
-
Ivanov, I.I.1
Frutos Rde Manel, N.2
Yoshinaga, K.3
Rifkin, D.B.4
Sartor, R.B.5
-
117
-
-
67349250428
-
The gut microbiota shapes intestinal immune responses during health and disease
-
Round J.L., Mazmanian S.K. The gut microbiota shapes intestinal immune responses during health and disease. Nature Reviews Immunology 2009, 9:313-323.
-
(2009)
Nature Reviews Immunology
, vol.9
, pp. 313-323
-
-
Round, J.L.1
Mazmanian, S.K.2
-
119
-
-
70350343544
-
Induction of intestinal Th17 cells by segmented filamentous bacteria
-
Ivanov I.I., Atarashi K., Manel N., Brodie E.L., Shima T., Karaoz U., et al. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 2009, 139:485-498.
-
(2009)
Cell
, vol.139
, pp. 485-498
-
-
Ivanov, I.I.1
Atarashi, K.2
Manel, N.3
Brodie, E.L.4
Shima, T.5
Karaoz, U.6
-
120
-
-
22144490199
-
An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system
-
Mazmanian S.K., Liu C.H., Tzianabos A.O., Kasper D.L. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 2005, 122:107-118.
-
(2005)
Cell
, vol.122
, pp. 107-118
-
-
Mazmanian, S.K.1
Liu, C.H.2
Tzianabos, A.O.3
Kasper, D.L.4
-
121
-
-
44449106055
-
A microbial symbiosis factor prevents intestinal inflammatory disease
-
Mazmanian S.K., Round J.L., Kasper D.L. A microbial symbiosis factor prevents intestinal inflammatory disease. Nature 2008, 453:620-625.
-
(2008)
Nature
, vol.453
, pp. 620-625
-
-
Mazmanian, S.K.1
Round, J.L.2
Kasper, D.L.3
-
122
-
-
85027947787
-
Induction of colonic regulatory T cells by indigenous Clostridium species
-
Atarashi K., Tanoue T., Shima T., Imaoka A., Kuwahara T., Momose Y., et al. Induction of colonic regulatory T cells by indigenous Clostridium species. Science Signalling 2011, 331:337.
-
(2011)
Science Signalling
, vol.331
, pp. 337
-
-
Atarashi, K.1
Tanoue, T.2
Shima, T.3
Imaoka, A.4
Kuwahara, T.5
Momose, Y.6
-
123
-
-
77957075815
-
Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa
-
De Filippo C., Cavalieri D., Di Paola M., Ramazzotti M., Poullet J.B., Massart S., et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proceedings of the National Academy of Sciences of the United States of America 2010, 107:14691-14696.
-
(2010)
Proceedings of the National Academy of Sciences of the United States of America
, vol.107
, pp. 14691-14696
-
-
De Filippo, C.1
Cavalieri, D.2
Di Paola, M.3
Ramazzotti, M.4
Poullet, J.B.5
Massart, S.6
-
124
-
-
3242664636
-
Recognition of commensal microflora by Toll-like receptors is required for intestinal homeostasis
-
Rakoff-Nahoum S., Paglino J., Eslami-Varzaneh F., Edberg S., Medzhitov R. Recognition of commensal microflora by Toll-like receptors is required for intestinal homeostasis. Cell 2004, 118:229-241.
-
(2004)
Cell
, vol.118
, pp. 229-241
-
-
Rakoff-Nahoum, S.1
Paglino, J.2
Eslami-Varzaneh, F.3
Edberg, S.4
Medzhitov, R.5
-
125
-
-
77249163771
-
Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis
-
Hill D.A., Hoffmann C., Abt M.C., Du Y., Kobuley D., Kirn T.J., et al. Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis. Mucosal Immunology 2009, 3:148-158.
-
(2009)
Mucosal Immunology
, vol.3
, pp. 148-158
-
-
Hill, D.A.1
Hoffmann, C.2
Abt, M.C.3
Du, Y.4
Kobuley, D.5
Kirn, T.J.6
-
126
-
-
84864311450
-
Commensal bacteria calibrate the activation threshold of innate antiviral immunity
-
Abt M.C., Osborne L.C., Monticelli L.A., Doering T.A., Alenghat T., Sonnenberg G.F., et al. Commensal bacteria calibrate the activation threshold of innate antiviral immunity. Immunity 2012, 37:158-170.
-
(2012)
Immunity
, vol.37
, pp. 158-170
-
-
Abt, M.C.1
Osborne, L.C.2
Monticelli, L.A.3
Doering, T.A.4
Alenghat, T.5
Sonnenberg, G.F.6
-
127
-
-
84862777474
-
Commensal bacteria-derived signals regulate basophil hematopoiesis and allergic inflammation
-
Hill D.A., Siracusa M.C., Abt M.C., Kim B.S., Kobuley D., Kubo M., et al. Commensal bacteria-derived signals regulate basophil hematopoiesis and allergic inflammation. Nature Medicine 2012, 18:538-546.
-
(2012)
Nature Medicine
, vol.18
, pp. 538-546
-
-
Hill, D.A.1
Siracusa, M.C.2
Abt, M.C.3
Kim, B.S.4
Kobuley, D.5
Kubo, M.6
-
128
-
-
79955121049
-
Microbiota regulates immune defense against respiratory tract influenza A virus infection
-
Ichinohe T., Pang I.K., Kumamoto Y., Peaper D.R., Ho J.H., Murray T.S., et al. Microbiota regulates immune defense against respiratory tract influenza A virus infection. Science Signalling 2011, 108:5354.
-
(2011)
Science Signalling
, vol.108
, pp. 5354
-
-
Ichinohe, T.1
Pang, I.K.2
Kumamoto, Y.3
Peaper, D.R.4
Ho, J.H.5
Murray, T.S.6
-
129
-
-
84860317030
-
Genetics of gene expression in primary immune cells identifies cell type-specific master regulators and roles of HLA alleles
-
Fairfax B.P., Makino S., Radhakrishnan J., Plant K., Leslie S., Dilthey A., et al. Genetics of gene expression in primary immune cells identifies cell type-specific master regulators and roles of HLA alleles. Nature Genetics 2012, 44:502-510.
-
(2012)
Nature Genetics
, vol.44
, pp. 502-510
-
-
Fairfax, B.P.1
Makino, S.2
Radhakrishnan, J.3
Plant, K.4
Leslie, S.5
Dilthey, A.6
-
130
-
-
61349114190
-
Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity
-
Yeger-Lotem E., Riva L., Su L.J., Gitler A.D., Cashikar A.G., King O.D., et al. Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity. Nature Genetics 2009, 41:316-323.
-
(2009)
Nature Genetics
, vol.41
, pp. 316-323
-
-
Yeger-Lotem, E.1
Riva, L.2
Su, L.J.3
Gitler, A.D.4
Cashikar, A.G.5
King, O.D.6
-
131
-
-
40749105508
-
Variations in DNA elucidate molecular networks that cause disease
-
Chen Y., Zhu J., Lum P.Y., Yang X., Pinto S., MacNeil D.J., et al. Variations in DNA elucidate molecular networks that cause disease. Nature 2008, 452:429-435.
-
(2008)
Nature
, vol.452
, pp. 429-435
-
-
Chen, Y.1
Zhu, J.2
Lum, P.Y.3
Yang, X.4
Pinto, S.5
MacNeil, D.J.6
-
132
-
-
70249134919
-
Molecular networks as sensors and drivers of common human diseases
-
Schadt E.E. Molecular networks as sensors and drivers of common human diseases. Nature 2009, 461:218-223.
-
(2009)
Nature
, vol.461
, pp. 218-223
-
-
Schadt, E.E.1
-
133
-
-
33646841491
-
Elucidating the murine brain transcriptional network in a segregating mouse population to identify core functional modules for obesity and diabetes
-
Lum P.Y., Chen Y., Zhu J., Lamb J., Melmed S., Wang S., et al. Elucidating the murine brain transcriptional network in a segregating mouse population to identify core functional modules for obesity and diabetes. Journal of Neurochemistry 2006, 97:50-62.
-
(2006)
Journal of Neurochemistry
, vol.97
, pp. 50-62
-
-
Lum, P.Y.1
Chen, Y.2
Zhu, J.3
Lamb, J.4
Melmed, S.5
Wang, S.6
-
134
-
-
63449132586
-
Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks
-
Yang X., Deignan J.L., Qi H., Zhu J., Qian S., Zhong J., et al. Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks. Nature Genetics 2009, 41:415-423.
-
(2009)
Nature Genetics
, vol.41
, pp. 415-423
-
-
Yang, X.1
Deignan, J.L.2
Qi, H.3
Zhu, J.4
Qian, S.5
Zhong, J.6
-
135
-
-
41349095280
-
Genetics of gene expression and its effect on disease
-
Emilsson V., Thorleifsson G., Zhang B., Leonardson A.S., Zink F., Zhu J., et al. Genetics of gene expression and its effect on disease. Nature 2008, 452:423-428.
-
(2008)
Nature
, vol.452
, pp. 423-428
-
-
Emilsson, V.1
Thorleifsson, G.2
Zhang, B.3
Leonardson, A.S.4
Zink, F.5
Zhu, J.6
-
136
-
-
0033707946
-
Using Bayesian networks to analyze expression data
-
Friedman N., Linial M., Nachman I., Pe'er D. Using Bayesian networks to analyze expression data. Journal of Computational Biology 2000, 7:601-620.
-
(2000)
Journal of Computational Biology
, vol.7
, pp. 601-620
-
-
Friedman, N.1
Linial, M.2
Nachman, I.3
Pe'er, D.4
-
137
-
-
17644427718
-
Causal protein-signaling networks derived from multiparameter single-cell data
-
Sachs K., Perez O., Pe'er D., Lauffenburger D.A., Nolan G.P. Causal protein-signaling networks derived from multiparameter single-cell data. Science Signalling 2005, 308:523.
-
(2005)
Science Signalling
, vol.308
, pp. 523
-
-
Sachs, K.1
Perez, O.2
Pe'er, D.3
Lauffenburger, D.A.4
Nolan, G.P.5
-
138
-
-
19544362938
-
Bayesian model averaging: development of an improved multi-class, gene selection and classification tool for microarray data
-
Yeung K.Y., Bumgarner R.E., Raftery A.E. Bayesian model averaging: development of an improved multi-class, gene selection and classification tool for microarray data. Bioinformatics 2005, 21:2394-2402.
-
(2005)
Bioinformatics
, vol.21
, pp. 2394-2402
-
-
Yeung, K.Y.1
Bumgarner, R.E.2
Raftery, A.E.3
-
139
-
-
79953670434
-
Causal modeling using network ensemble simulations of genetic and gene expression data predicts genes involved in rheumatoid arthritis
-
Xing H., McDonagh P.D., Bienkowska J., Cashorali T., Runge K., Miller R.E., et al. Causal modeling using network ensemble simulations of genetic and gene expression data predicts genes involved in rheumatoid arthritis. PLoS Computational Biology 2011, 7:e1001105.
-
(2011)
PLoS Computational Biology
, vol.7
-
-
Xing, H.1
McDonagh, P.D.2
Bienkowska, J.3
Cashorali, T.4
Runge, K.5
Miller, R.E.6
-
141
-
-
78649346852
-
Constructing a fish metabolic network model
-
Li S., Pozhitkov A., Ryan R.A., Manning C.S., Brown-Peterson N., Brouwer M. Constructing a fish metabolic network model. Genome Biology 2010, 11:R115.
-
(2010)
Genome Biology
, vol.11
-
-
Li, S.1
Pozhitkov, A.2
Ryan, R.A.3
Manning, C.S.4
Brown-Peterson, N.5
Brouwer, M.6
-
143
-
-
0036371443
-
Modelling viral and immune system dynamics
-
Perelson A.S. Modelling viral and immune system dynamics. Nature Reviews Immunology 2002, 2:28-36.
-
(2002)
Nature Reviews Immunology
, vol.2
, pp. 28-36
-
-
Perelson, A.S.1
-
144
-
-
67650441757
-
Simulation and prediction of the adaptive immune response to influenza A virus infection
-
Lee H.Y., Topham D.J., Park S.Y., Hollenbaugh J., Treanor J., Mosmann T.R., et al. Simulation and prediction of the adaptive immune response to influenza A virus infection. Journal of Virology 2009, 83:7151-7165.
-
(2009)
Journal of Virology
, vol.83
, pp. 7151-7165
-
-
Lee, H.Y.1
Topham, D.J.2
Park, S.Y.3
Hollenbaugh, J.4
Treanor, J.5
Mosmann, T.R.6
-
146
-
-
27844541328
-
Modeling T cell antigen discrimination based on feedback control of digital ERK responses
-
Altan-Bonnet G., Germain R.N. Modeling T cell antigen discrimination based on feedback control of digital ERK responses. PLoS Biology 2005, 3:e356.
-
(2005)
PLoS Biology
, vol.3
-
-
Altan-Bonnet, G.1
Germain, R.N.2
-
147
-
-
79957566441
-
An incoherent regulatory network architecture that orchestrates B cell diversification in response to antigen signaling
-
Sciammas R., Li Y., Warmflash A., Song Y., Dinner A.R., Singh H. An incoherent regulatory network architecture that orchestrates B cell diversification in response to antigen signaling. Molecular Systems Biology 2011, 2011.
-
(2011)
Molecular Systems Biology
, pp. 2011
-
-
Sciammas, R.1
Li, Y.2
Warmflash, A.3
Song, Y.4
Dinner, A.R.5
Singh, H.6
-
148
-
-
62849092708
-
Function of C/EBPδ in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals
-
Litvak V., Ramsey S.A., Rust A.G., Zak D.E., Kennedy K.A., Lampano A.E., et al. Function of C/EBPδ in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals. Nature Immunology 2009, 10:437-443.
-
(2009)
Nature Immunology
, vol.10
, pp. 437-443
-
-
Litvak, V.1
Ramsey, S.A.2
Rust, A.G.3
Zak, D.E.4
Kennedy, K.A.5
Lampano, A.E.6
-
149
-
-
33947236071
-
Toward a multiscale model of antigen presentation in immunity
-
Kirschner D.E., Chang S.T., Riggs T.W., Perry N., Linderman J.J. Toward a multiscale model of antigen presentation in immunity. Immunological Reviews 2007, 216:93-118.
-
(2007)
Immunological Reviews
, vol.216
, pp. 93-118
-
-
Kirschner, D.E.1
Chang, S.T.2
Riggs, T.W.3
Perry, N.4
Linderman, J.J.5
-
150
-
-
45449110225
-
Systems biology of persistent infection: tuberculosis as a case study
-
Young D., Stark J., Kirschner D. Systems biology of persistent infection: tuberculosis as a case study. Nature Reviews Microbiology 2008, 6:520-528.
-
(2008)
Nature Reviews Microbiology
, vol.6
, pp. 520-528
-
-
Young, D.1
Stark, J.2
Kirschner, D.3
-
151
-
-
77953397764
-
Systems medicine: the future of medical genomics and healthcare
-
Auffray C., Chen Z., Hood L. Systems medicine: the future of medical genomics and healthcare. Genome Medicine 2009, 1:2.
-
(2009)
Genome Medicine
, vol.1
, pp. 2
-
-
Auffray, C.1
Chen, Z.2
Hood, L.3
-
153
-
-
80052942203
-
Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing
-
Wu X., Zhou T., Zhu J., Zhang B., Georgiev I., Wang C., et al. Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing. Science 2011, 333:1593-1602.
-
(2011)
Science
, vol.333
, pp. 1593-1602
-
-
Wu, X.1
Zhou, T.2
Zhu, J.3
Zhang, B.4
Georgiev, I.5
Wang, C.6
-
154
-
-
34247388467
-
Harnessing bioinformatics to discover new vaccines
-
Davies M.N., Flower D.R. Harnessing bioinformatics to discover new vaccines. Drug Discovery Today 2007, 12:389-395.
-
(2007)
Drug Discovery Today
, vol.12
, pp. 389-395
-
-
Davies, M.N.1
Flower, D.R.2
-
155
-
-
58049203835
-
Systems biology of innate immunity
-
Zak D.E., Aderem A. Systems biology of innate immunity. Immunological Reviews 2008, 227:264-282.
-
(2008)
Immunological Reviews
, vol.227
, pp. 264-282
-
-
Zak, D.E.1
Aderem, A.2
-
157
-
-
69949148793
-
Gene expression signatures diagnose influenza and other symptomatic respiratory viral infections in humans
-
Zaas A.K., Chen M., Varkey J., Veldman T., Hero A.O., Lucas J., et al. Gene expression signatures diagnose influenza and other symptomatic respiratory viral infections in humans. Cell Host & Microbe 2009, 6:207-217.
-
(2009)
Cell Host & Microbe
, vol.6
, pp. 207-217
-
-
Zaas, A.K.1
Chen, M.2
Varkey, J.3
Veldman, T.4
Hero, A.O.5
Lucas, J.6
-
158
-
-
80052320333
-
Temporal dynamics of host molecular responses differentiate symptomatic and asymptomatic influenza a infection
-
Huang Y., Zaas A.K., Rao A., Dobigeon N., Woolf P.J., Veldman T., et al. Temporal dynamics of host molecular responses differentiate symptomatic and asymptomatic influenza a infection. PLoS Genetics 2011, 7:e1002234.
-
(2011)
PLoS Genetics
, vol.7
-
-
Huang, Y.1
Zaas, A.K.2
Rao, A.3
Dobigeon, N.4
Woolf, P.J.5
Veldman, T.6
-
159
-
-
36849029833
-
Systems biology and the host response to viral infection
-
Tan S-L., Ganji G., Paeper B., Proll S., Katze M.G. Systems biology and the host response to viral infection. Nature Biotechnology 2007, 25:1383-1389.
-
(2007)
Nature Biotechnology
, vol.25
, pp. 1383-1389
-
-
Tan, S.-L.1
Ganji, G.2
Paeper, B.3
Proll, S.4
Katze, M.G.5
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