-
1
-
-
84903754137
-
Targeted immune interventions for type 1 diabetes: Not as easy as it looks!
-
M. R. Rigby, M. R. Ehlers, Targeted immune interventions for type 1 diabetes: Not as easy as it looks! Curr. Opin. Endocrinol. Diabetes Obes. 21, 271–278 (2014).
-
(2014)
Curr. Opin. Endocrinol. Diabetes Obes.
, vol.21
, pp. 271-278
-
-
Rigby, M.R.1
Ehlers, M.R.2
-
2
-
-
84861868291
-
Through the fog: Recent clinical trials to preserve b-cell function in type 1 diabetes
-
C. J. Greenbaum, D. A. Schatz, M. J. Haller, S. Sanda, Through the fog: Recent clinical trials to preserve b-cell function in type 1 diabetes. Diabetes 61, 1323–1330 (2012).
-
(2012)
Diabetes
, vol.61
, pp. 1323-1330
-
-
Greenbaum, C.J.1
Schatz, D.A.2
Haller, M.J.3
Sanda, S.4
-
3
-
-
84888439466
-
Immune mechanisms in type 1 diabetes
-
M. Wållberg, A. Cooke, Immune mechanisms in type 1 diabetes. Trends Immunol. 34, 583–591 (2013).
-
(2013)
Trends Immunol
, vol.34
, pp. 583-591
-
-
Wållberg, M.1
Cooke, A.2
-
4
-
-
84877059916
-
T cell anergy, exhaustion, senescence, and stemness in the tumor microenvironment
-
J. Crespo, H. Sun, T. H. Welling, Z. Tian, W. Zou, T cell anergy, exhaustion, senescence, and stemness in the tumor microenvironment. Curr. Opin. Immunol. 25, 214–221 (2013).
-
(2013)
Curr. Opin. Immunol.
, vol.25
, pp. 214-221
-
-
Crespo, J.1
Sun, H.2
Welling, T.H.3
Tian, Z.4
Zou, W.5
-
5
-
-
84893711428
-
Tolerance and exhaustion: Defining mechanisms of T cell dysfunction
-
A. Schietinger, P. D. Greenberg, Tolerance and exhaustion: Defining mechanisms of T cell dysfunction. Trends Immunol. 35, 51–60 (2014).
-
(2014)
Trends Immunol
, vol.35
, pp. 51-60
-
-
Schietinger, A.1
Greenberg, P.D.2
-
7
-
-
84877028141
-
Comprehensive molecular portraits of human breast tumours
-
Cancer Genome Atlas Network
-
Cancer Genome Atlas Network, Comprehensive molecular portraits of human breast tumours. Nature 490, 61–70 (2012).
-
(2012)
Nature
, vol.490
, pp. 61-70
-
-
-
8
-
-
84926507971
-
Limma powers differential expression analyses for RNA-sequencing and microarray studies
-
M. E. Ritchie, B. Phipson, D. Wu, Y. Hu, C. W. Law, W. Shi, G. K. Smyth, limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47 (2015).
-
(2015)
Nucleic Acids Res
, vol.43
, pp. e47
-
-
Ritchie, M.E.1
Phipson, B.2
Wu, D.3
Hu, Y.4
Law, C.W.5
Shi, W.6
Smyth, G.K.7
-
9
-
-
84937837169
-
Molecular and cellular insights into T cell exhaustion
-
E. J. Wherry, M. Kurachi, Molecular and cellular insights into T cell exhaustion. Nat. Rev. Immunol. 15, 486–499 (2015).
-
(2015)
Nat. Rev. Immunol.
, vol.15
, pp. 486-499
-
-
Wherry, E.J.1
Kurachi, M.2
-
10
-
-
84894258518
-
+ T cell dysfunction during chronic infection
-
+ T cell dysfunction during chronic infection. Immunity 40, 289–302 (2014).
-
(2014)
Immunity
, vol.40
, pp. 289-302
-
-
Crawford, A.1
Angelosanto, J.M.2
Kao, C.3
Doering, T.A.4
Odorizzi, P.M.5
Barnett, B.E.6
Wherry, E.J.7
-
11
-
-
79956077563
-
T cell exhaustion
-
E. J. Wherry, T cell exhaustion. Nat. Immunol. 12, 492–499 (2011).
-
(2011)
Nat. Immunol.
, vol.12
, pp. 492-499
-
-
Wherry, E.J.1
-
12
-
-
84938397867
-
T-cell exhaustion, costimulation and clinical outcome in autoimmunity and infection
-
E. F. McKinney, J. C. Lee, D. R. W. Jayne, P. A. Lyons, K. G. C. Smith, T-cell exhaustion, costimulation and clinical outcome in autoimmunity and infection. Nature 523, 612–616 (2015).
-
(2015)
Nature
, vol.523
, pp. 612-616
-
-
McKinney, E.F.1
Lee, J.C.2
Jayne, D.R.W.3
Lyons, P.A.4
Smith, K.G.C.5
-
13
-
-
77951499602
-
Specific gene expression signature associated with development of autoimmune type-I diabetes using whole-blood microarray analysis
-
F. Reynier, A. Pachot, M. Paye, Q. Xu, F. Turrel-Davin, F. Petit, A. Hot, C. Auffray, N. Bendelac, M. Nicolino, B. Mougin, C. Thivolet, Specific gene expression signature associated with development of autoimmune type-I diabetes using whole-blood microarray analysis. Genes Immun. 11, 269–278 (2010).
-
(2010)
Genes Immun
, vol.11
, pp. 269-278
-
-
Reynier, F.1
Pachot, A.2
Paye, M.3
Xu, Q.4
Turrel-Davin, F.5
Petit, F.6
Hot, A.7
Auffray, C.8
Bendelac, N.9
Nicolino, M.10
Mougin, B.11
Thivolet, C.12
-
14
-
-
84887052291
-
Teplizumab (anti-CD3 mAb) treatment preserves C-peptide responses in patients with new-onset type 1 diabetes in a randomized controlled trial: Metabolic and immunologic features at baseline identify a subgroup of responders
-
K. C. Herold, S. E. Gitelman, M. R. Ehlers, P. A. Gottlieb, C. J. Greenbaum, W. Hagopian, K. D. Boyle, L. Keyes-Elstein, S. Aggarwal, D. Phippard, P. H. Sayre, J. McNamara, J. A. Bluestone; AbATE Study Team, Teplizumab (anti-CD3 mAb) treatment preserves C-peptide responses in patients with new-onset type 1 diabetes in a randomized controlled trial: Metabolic and immunologic features at baseline identify a subgroup of responders. Diabetes 62, 3766–3774 (2013).
-
(2013)
Diabetes
, vol.62
, pp. 3766-3774
-
-
Herold, K.C.1
Gitelman, S.E.2
Ehlers, M.R.3
Gottlieb, P.A.4
Greenbaum, C.J.5
Hagopian, W.6
Boyle, K.D.7
Keyes-Elstein, L.8
Aggarwal, S.9
Phippard, D.10
Sayre, P.H.11
McNamara, J.12
Bluestone, J.A.13
-
15
-
-
84907994039
-
Copy number loss of the interferon gene cluster in melanomas is linked to reduced T cell infiltrate and poor patient prognosis
-
P. S. Linsley, C. Speake, E. Whalen, D. Chaussabel, Copy number loss of the interferon gene cluster in melanomas is linked to reduced T cell infiltrate and poor patient prognosis. PLOS ONE 9, e109760 (2014).
-
(2014)
PLOS ONE
, vol.9
-
-
Linsley, P.S.1
Speake, C.2
Whalen, E.3
Chaussabel, D.4
-
16
-
-
78651486442
-
Densely interconnected transcriptional circuits control cell states in human hematopoiesis
-
N. Novershtern, A. Subramanian, L. N. Lawton, R. H. Mak, W. N. Haining, M. E. McConkey, N. Habib, N. Yosef, C. Y. Chang, T. Shay, G. M. Frampton, A. C. B. Drake, I. Leskov, B. Nilsson, F. Preffer, D. Dombkowski, J. W. Evans, T. Liefeld, J. S. Smutko, J. Chen, N. Friedman, R. A. Young, T. R. Golub, A. Regev, B. L. Ebert, Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell 144, 296–309 (2011).
-
(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
Habib, N.7
Yosef, N.8
Chang, C.Y.9
Shay, T.10
Frampton, G.M.11
Drake, A.C.B.12
Leskov, I.13
Nilsson, B.14
Preffer, F.15
Dombkowski, D.16
Evans, J.W.17
Liefeld, T.18
Smutko, J.S.19
Chen, J.20
Friedman, N.21
Young, R.A.22
Golub, T.R.23
Regev, A.24
Ebert, B.L.25
more..
-
17
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
A. Subramanian, P. Tamayo, V. K. Mootha, S. Mukherjee, B. L. Ebert, M. A. Gillette, A. Paulovich, S. L. Pomeroy, T. R. Golub, E. S. Lander, J. P. Mesirov, Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. U.S.A. 102, 15545–15550 (2005).
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, 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
Paulovich, A.7
Pomeroy, S.L.8
Golub, T.R.9
Lander, E.S.10
Mesirov, J.P.11
-
18
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
A. Mortazavi, B. A. Williams, K. McCue, L. Schaeffer, B. Wold, Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621–628 (2008).
-
(2008)
Nat. Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
19
-
-
84876515907
-
String v9.1: Protein-protein interaction networks, with increased coverage and integration
-
A. Franceschini, D. Szklarczyk, S. Frankild, M. Kuhn, M. Simonovic, A. Roth, J. Lin, P. Minguez, P. Bork, C. von Mering, L. J. Jensen, STRING v9.1: Protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 41, D808–D815 (2013).
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D808-D815
-
-
Franceschini, A.1
Szklarczyk, D.2
Frankild, S.3
Kuhn, M.4
Simonovic, M.5
Roth, A.6
Lin, J.7
Minguez, P.8
Bork, P.9
Von Mering, C.10
Jensen, L.J.11
-
20
-
-
84953839594
-
Changes in T-cell subsets identify responders to FcR-nonbinding anti-CD3 mAb (teplizumab) in patients with type 1 diabetes
-
J. E. Tooley, N. Vudattu, J. Choi, C. Cotsapas, L. Devine, K. Raddassi, M. R. Ehlers, J. G. McNamara, K. M. Harris, S. Kanaparthi, D. Phippard, K. C. Herold, Changes in T-cell subsets identify responders to FcR-nonbinding anti-CD3 mAb (teplizumab) in patients with type 1 diabetes. Eur. J. Immunol. 46, 230–241 (2016).
-
(2016)
Eur. J. Immunol.
, vol.46
, pp. 230-241
-
-
Tooley, J.E.1
Vudattu, N.2
Choi, J.3
Cotsapas, C.4
Devine, L.5
Raddassi, K.6
Ehlers, M.R.7
McNamara, J.G.8
Harris, K.M.9
Kanaparthi, S.10
Phippard, D.11
Herold, K.C.12
-
21
-
-
33845190339
-
Structural determinants of T-cell receptor bias in immunity
-
S. J. Turner, P. C. Doherty, J. McCluskey, J. Rossjohn, Structural determinants of T-cell receptor bias in immunity. Nat. Rev. Immunol. 6, 883–894 (2006).
-
(2006)
Nat. Rev. Immunol.
, vol.6
, pp. 883-894
-
-
Turner, S.J.1
Doherty, P.C.2
McCluskey, J.3
Rossjohn, J.4
-
22
-
-
84874424688
-
Structural features underlying T-cell receptor sensitivity to concealed MHC class I micropolymorphisms
-
G. B. Stewart-Jones, P. Simpson, P. A. van der Merwe, P. Easterbrook, A. J. McMichael, S. L. Rowland-Jones, E. Y. Jones, G. M. Gillespie, Structural features underlying T-cell receptor sensitivity to concealed MHC class I micropolymorphisms. Proc. Natl. Acad. Sci. U.S.A. 109, E3483–E3492 (2012).
-
(2012)
Proc. Natl. Acad. Sci. U.S.A.
, vol.109
, pp. E3483-E3492
-
-
Stewart-Jones, G.B.1
Simpson, P.2
Van Der Merwe, P.A.3
Easterbrook, P.4
McMichael, A.J.5
Rowland-Jones, S.L.6
Jones, E.Y.7
Gillespie, G.M.8
-
23
-
-
84962748059
-
+ T-cell pathogenicity in Rasmussen encephalitis elucidated by large-scale T-cell receptor sequencing
-
+ T-cell pathogenicity in Rasmussen encephalitis elucidated by large-scale T-cell receptor sequencing. Nat. Commun. 7, 11153 (2016).
-
(2016)
Nat. Commun.
, vol.7
, pp. 11153
-
-
Schneider-Hohendorf, T.1
Mohan, H.2
Bien, C.G.3
Breuer, J.4
Becker, A.5
Görlich, D.6
Kuhlmann, T.7
Widman, G.8
Herich, S.9
Elpers, C.10
Melzer, N.11
Dornmair, K.12
Kurlemann, G.13
Wiendl, H.14
Schwab, N.15
-
24
-
-
84905122431
-
A molecular basis underpinning the T cell receptor heterogeneity of mucosal-associated invariant T cells
-
S. B. G. Eckle, R. W. Birkinshaw, L. Kostenko, A. J. Corbett, H. E. G. McWilliam, R. Reantragoon, Z. Chen, N. A. Gherardin, T. Beddoe, L. Liu, O. Patel, B. Meehan, D. P. Fairlie, J. A. Villadangos, D. I. Godfrey, L. Kjer-Nielsen, J. McCluskey, J. Rossjohn, A molecular basis underpinning the T cell receptor heterogeneity of mucosal-associated invariant T cells. J. Exp. Med. 211, 1585–1600 (2014).
-
(2014)
J. Exp. Med.
, vol.211
, pp. 1585-1600
-
-
Eckle, S.B.G.1
Birkinshaw, R.W.2
Kostenko, L.3
Corbett, A.J.4
McWilliam, H.E.G.5
Reantragoon, R.6
Chen, Z.7
Gherardin, N.A.8
Beddoe, T.9
Liu, L.10
Patel, O.11
Meehan, B.12
Fairlie, D.P.13
Villadangos, J.A.14
Godfrey, D.I.15
Kjer-Nielsen, L.16
McCluskey, J.17
Rossjohn, J.18
-
25
-
-
0027178514
-
Analysis of T cell antigen receptor (TCR) expression by human peripheral blood CD4-8- A/b T cells demonstrates preferential use of several Vb genes and an invariant TCR a chain
-
S. Porcelli, C. E. Yockey, M. B. Brenner, S. P. Balk, Analysis of T cell antigen receptor (TCR) expression by human peripheral blood CD4-8- a/b T cells demonstrates preferential use of several Vb genes and an invariant TCR a chain. J. Exp. Med. 178, 1–16 (1993).
-
(1993)
J. Exp. Med.
, vol.178
, pp. 1-16
-
-
Porcelli, S.1
Yockey, C.E.2
Brenner, M.B.3
Balk, S.P.4
-
26
-
-
84958878687
-
Diversity of T cells restricted by the MHC class I-related molecule MR1 facilitates differential antigen recognition
-
N. A. Gherardin, A. N. Keller, R. E. Woolley, J. Le Nours, D. S. Ritchie, P. J. Neeson, R. W. Birkinshaw, S. B. G. Eckle, J. N. Waddington, L. Liu, D. P. Fairlie, A. P. Uldrich, D. G. Pellicci, J. McCluskey, D. I. Godfrey, J. Rossjohn, Diversity of T cells restricted by the MHC class I-related molecule MR1 facilitates differential antigen recognition. Immunity 44, 32–45 (2016).
-
(2016)
Immunity
, vol.44
, pp. 32-45
-
-
Gherardin, N.A.1
Keller, A.N.2
Woolley, R.E.3
Le Nours, J.4
Ritchie, D.S.5
Neeson, P.J.6
Birkinshaw, R.W.7
Eckle, S.B.G.8
Waddington, J.N.9
Liu, L.10
Fairlie, D.P.11
Uldrich, A.P.12
Pellicci, D.G.13
McCluskey, J.14
Godfrey, D.I.15
Rossjohn, J.16
-
27
-
-
85030484213
-
Single-cell analysis of glandular T cell receptors in Sjögren’s syndrome
-
M. L. Joachims, K. M. Leehan, C. Lawrence, R. C. Pelikan, J. S. Moore, Z. Pan, A. Rasmussen, L. Radfar, D. M. Lewis, K. M. Grundahl, J. A. Kelly, G. B. Wiley, M. Shugay, D. M. Chudakov, C. J. Lessard, D. U. Stone, R. H. Scofield, C. G. Montgomery, K. L. Sivils, L. F. Thompson, A. D. Farris, Single-cell analysis of glandular T cell receptors in Sjögren’s syndrome. JCI Insight 1, e85609 (2016).
-
(2016)
JCI Insight
, vol.1
, pp. e85609
-
-
Joachims, M.L.1
Leehan, K.M.2
Lawrence, C.3
Pelikan, R.C.4
Moore, J.S.5
Pan, Z.6
Rasmussen, A.7
Radfar, L.8
Lewis, D.M.9
Grundahl, K.M.10
Kelly, J.A.11
Wiley, G.B.12
Shugay, M.13
Chudakov, D.M.14
Lessard, C.J.15
Stone, D.U.16
Scofield, R.H.17
Montgomery, C.G.18
Sivils, K.L.19
Thompson, L.F.20
Farris, A.D.21
more..
-
28
-
-
34547976869
-
TCR spectratyping revealed T lymphocytes associated with graft-versus-host disease after allogeneic hematopoietic stem cell transplantation
-
J.-W. Du, J.-Y. Gu, J. Liu, X.-N. Cen, Y. Zhang, Y. Ou, B. Chu, P. Zhu, TCR spectratyping revealed T lymphocytes associated with graft-versus-host disease after allogeneic hematopoietic stem cell transplantation. Leuk. Lymphoma 48, 1618–1627 (2007).
-
(2007)
Leuk. Lymphoma
, vol.48
, pp. 1618-1627
-
-
Du, J.-W.1
Gu, J.-Y.2
Liu, J.3
Cen, X.-N.4
Zhang, Y.5
Ou, Y.6
Chu, B.7
Zhu, P.8
-
29
-
-
84945157647
-
+ T cell expansion in acute EBV infection
-
+ T cell expansion in acute EBV infection. J. Immunol. 195, 4185–4197 (2015).
-
(2015)
J. Immunol.
, vol.195
, pp. 4185-4197
-
-
Greenough, T.C.1
Straubhaar, J.R.2
Kamga, L.3
Weiss, E.R.4
Brody, R.M.5
McManus, M.M.6
Lambrecht, L.K.7
Somasundaran, M.8
Luzuriaga, K.F.9
-
30
-
-
84935121294
-
Inhibitory receptors beyond T cell exhaustion
-
S. A. Fuertes Marraco, N. J. Neubert, G. Verdeil, D. E. Speiser, Inhibitory receptors beyond T cell exhaustion. Front. Immunol. 6, 310 (2015).
-
(2015)
Front. Immunol.
, vol.6
, pp. 310
-
-
Marraco, S.A.F.1
Neubert, N.J.2
Verdeil, G.3
Speiser, D.E.4
-
31
-
-
57649095902
-
Generation and function of human regulatory CD8+ T cells induced by a humanized OKT3 monoclonal antibody hOKT3g1 (Ala-Ala)
-
V. Ablamunits, K. C. Herold, Generation and function of human regulatory CD8+ T cells induced by a humanized OKT3 monoclonal antibody hOKT3g1 (Ala-Ala). Hum. Immunol. 69, 732–736 (2008).
-
(2008)
Hum. Immunol.
, vol.69
, pp. 732-736
-
-
Ablamunits, V.1
Herold, K.C.2
-
33
-
-
77957855176
-
+ T cells are involved in development and control of human autoimmune type 1 diabetes
-
+ T cells are involved in development and control of human autoimmune type 1 diabetes. J. Clin. Invest. 120, 3641–3650 (2010).
-
(2010)
J. Clin. Invest.
, vol.120
, pp. 3641-3650
-
-
Jiang, H.1
Canfield, S.M.2
Gallagher, M.P.3
Jiang, H.H.4
Jiang, Y.5
Zheng, Z.6
Chess, L.7
-
34
-
-
34250722076
-
+ T cells enter reactive lymph nodes and kill dendritic cells
-
+ T cells enter reactive lymph nodes and kill dendritic cells. Nat. Immunol. 8, 743–752 (2007).
-
(2007)
Nat. Immunol.
, vol.8
, pp. 743-752
-
-
Guarda, G.1
Hons, M.2
Soriano, S.F.3
Huang, A.Y.4
Polley, R.5
Martín-Fontecha, A.6
Stein, J.V.7
Germain, R.N.8
Lanzavecchia, A.9
Sallusto, F.10
-
35
-
-
33749315579
-
+ T-cell–mediated killing of donor dendritic cells prevents alloreactive T helper type-2 responses in vivo
-
+ T-cell–mediated killing of donor dendritic cells prevents alloreactive T helper type-2 responses in vivo. Blood 108, 2257–2264 (2006).
-
(2006)
Blood
, vol.108
, pp. 2257-2264
-
-
Laffont, S.1
Coudert, J.D.2
Garidou, L.3
Delpy, L.4
Wiedemann, A.5
Demur, C.6
Coureau, C.7
Guéry, J.-C.8
-
37
-
-
84858619527
-
+ NKT cell development
-
+ NKT cell development. PLOS Pathog. 6, e1000915 (2010).
-
(2010)
PLOS Pathog
, vol.6
-
-
Yuling, H.1
Ruijing, X.2
Xiang, J.3
Li, L.4
Lang, C.5
Jie, X.6
Wei, X.7
Yujuan, W.8
Lijun, Z.9
Rui, Z.10
Xinti, T.11
Yongyi, B.12
Yan-Ping, J.13
Youxin, J.14
Jinquan, T.15
-
38
-
-
32544459770
-
Restoring function in exhausted CD8 T cells during chronic viral infection
-
D. L. Barber, E. J. Wherry, D. Masopust, B. Zhu, J. P. Allison, A. H. Sharpe, G. J. Freeman, R. Ahmed, Restoring function in exhausted CD8 T cells during chronic viral infection. Nature 439, 682–687 (2006).
-
(2006)
Nature
, vol.439
, pp. 682-687
-
-
Barber, D.L.1
Wherry, E.J.2
Masopust, D.3
Zhu, B.4
Allison, J.P.5
Sharpe, A.H.6
Freeman, G.J.7
Ahmed, R.8
-
39
-
-
35349014587
-
+ T cell exhaustion during chronic viral infection
-
+ T cell exhaustion during chronic viral infection. Immunity 27, 670–684 (2007).
-
(2007)
Immunity
, vol.27
, pp. 670-684
-
-
Wherry, E.J.1
Ha, S.-J.2
Kaech, S.M.3
Haining, W.N.4
Sarkar, S.5
Kalia, V.6
Subramaniam, S.7
Blattman, J.N.8
Barber, D.L.9
Ahmed, R.10
-
40
-
-
84880706152
-
Oncology meets immunology: The cancer-immunity cycle
-
D. S. Chen, I. Mellman, Oncology meets immunology: The cancer-immunity cycle. Immunity 39, 1–10 (2013).
-
(2013)
Immunity
, vol.39
, pp. 1-10
-
-
Chen, D.S.1
Mellman, I.2
-
41
-
-
84962198249
-
Precipitation of autoimmune diabetes with anti-PD-1 immunotherapy
-
J. Hughes, N. Vudattu, M. Sznol, S. Gettinger, H. Kluger, B. Lupsa, K. C. Herold, Precipitation of autoimmune diabetes with anti-PD-1 immunotherapy. Diabetes Care 38, e55–e57 (2015).
-
(2015)
Diabetes Care
, vol.38
, pp. e55-e57
-
-
Hughes, J.1
Vudattu, N.2
Sznol, M.3
Gettinger, S.4
Kluger, H.5
Lupsa, B.6
Herold, K.C.7
-
42
-
-
46249088370
-
LUMI: A pipeline for processing Illumina microarray
-
P. Du, W. A. Kibbe, S. M. Lin, lumi: A pipeline for processing Illumina microarray. Bioinformatics 24, 1547–1548 (2008).
-
(2008)
Bioinformatics
, vol.24
, pp. 1547-1548
-
-
Du, P.1
Kibbe, W.A.2
Lin, S.M.3
-
43
-
-
34250705360
-
NuID: A universal naming scheme of oligonucleotides for illumina, Affymetrix, and other microarrays
-
P. Du, W. A. Kibbe, S. M. Lin, nuID: A universal naming scheme of oligonucleotides for illumina, Affymetrix, and other microarrays. Biol. Direct 2, 16 (2007).
-
(2007)
Biol. Direct
, vol.2
, pp. 16
-
-
Du, P.1
Kibbe, W.A.2
Lin, S.M.3
-
44
-
-
60549111634
-
WGCNA: An R package for weighted correlation network analysis
-
P. Langfelder, S. Horvath, WGCNA: An R package for weighted correlation network analysis. BMC Bioinf. 9, 559 (2008).
-
(2008)
BMC Bioinf
, vol.9
, pp. 559
-
-
Langfelder, P.1
Horvath, S.2
-
45
-
-
84893910301
-
Quantitative assessment of single-cell RNA-sequencing methods
-
A. R. Wu, N. F. Neff, T. Kalisky, P. Dalerba, B. Treutlein, M. E. Rothenberg, F. M. Mburu, G. L. Mantalas, S. Sim, M. F. Clarke, S. R. Quake, Quantitative assessment of single-cell RNA-sequencing methods. Nat. Methods 11, 41–46 (2014).
-
(2014)
Nat. Methods
, vol.11
, pp. 41-46
-
-
Wu, A.R.1
Neff, N.F.2
Kalisky, T.3
Dalerba, P.4
Treutlein, B.5
Rothenberg, M.E.6
Mburu, F.M.7
Mantalas, G.L.8
Sim, S.9
Clarke, M.F.10
Quake, S.R.11
-
46
-
-
25844449770
-
Galaxy: A platform for interactive large-scale genome analysis
-
B. Giardine, C. Riemer, R. C. Hardison, R. Burhans, L. Elnitski, P. Shah, Y. Zhang, D. Blankenberg, I. Albert, J. Taylor, W. Miller, W. J. Kent, A. Nekrutenko, Galaxy: A platform for interactive large-scale genome analysis. Genome Res. 15, 1451–1455 (2005).
-
(2005)
Genome Res
, vol.15
, pp. 1451-1455
-
-
Giardine, B.1
Riemer, C.2
Hardison, R.C.3
Burhans, R.4
Elnitski, L.5
Shah, P.6
Zhang, Y.7
Blankenberg, D.8
Albert, I.9
Taylor, J.10
Miller, W.11
Kent, W.J.12
Nekrutenko, A.13
-
47
-
-
84973094812
-
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update
-
E. Afgan, D. Baker, M. van den Beek, D. Blankenberg, D. Bouvier, M. Čech, J. Chilton, D. Clements, N. Coraor, C. Eberhard, B. Grüning, A. Guerler, J. Hillman-Jackson, G. Von Kuster, E. Rasche, N. Soranzo, N. Turaga, J. Taylor, A. Nekrutenko, J. Goecks, The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 44, W3–W10 (2016).
-
(2016)
Nucleic Acids Res
, vol.44
, pp. W3-W10
-
-
Afgan, E.1
Baker, D.2
Van Den Beek, M.3
Blankenberg, D.4
Bouvier, D.5
Čech, M.6
Chilton, J.7
Clements, D.8
Coraor, N.9
Eberhard, C.10
Grüning, B.11
Guerler, A.12
Hillman-Jackson, J.13
Von Kuster, G.14
Rasche, E.15
Soranzo, N.16
Turaga, N.17
Taylor, J.18
Nekrutenko, A.19
Goecks, J.20
more..
-
48
-
-
65449136284
-
Tophat: Discovering splice junctions with RNA-Seq
-
C. Trapnell, L. Pachter, S. L. Salzberg, 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
-
49
-
-
84928987900
-
HTSeq—A Python framework to work with high-throughput sequencing data
-
S. Anders, P. T. Pyl, W. Huber, 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
-
50
-
-
77953176036
-
A scaling normalization method for differential expression analysis of RNA-seq data
-
M. D. Robinson, A. Oshlack, A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 11, R25 (2010).
-
(2010)
Genome Biol
, vol.11
, pp. R25
-
-
Robinson, M.D.1
Oshlack, A.2
-
51
-
-
75249087100
-
Edger: A Bioconductor package for differential expression analysis of digital gene expression data
-
M. D. Robinson, D. J. McCarthy, G. K. Smyth, edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
52
-
-
84896735766
-
VooM: Precision weights unlock linear model analysis tools for RNA-seq read counts
-
C. W. Law, Y. Chen, W. Shi, G. K. Smyth, voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 15, R29 (2014).
-
(2014)
Genome Biol
, vol.15
, pp. R29
-
-
Law, C.W.1
Chen, Y.2
Shi, W.3
Smyth, G.K.4
-
53
-
-
79960264362
-
Full-length transcriptome assembly from RNA-Seq data without a reference genome
-
M. G. Grabherr, B. J. Haas, M. Yassour, J. Z. Levin, D. A. Thompson, I. Amit, X. Adiconis, L. Fan, R. Raychowdhury, Q. Zeng, Z. Chen, E. Mauceli, N. Hacohen, A. Gnirke, N. Rhind, F. di Palma, B. W. Birren, C. Nusbaum, K. Lindblad-Toh, N. Friedman, A. Regev, Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644–652 (2011).
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 644-652
-
-
Grabherr, M.G.1
Haas, B.J.2
Yassour, M.3
Levin, J.Z.4
Thompson, D.A.5
Amit, I.6
Adiconis, X.7
Fan, L.8
Raychowdhury, R.9
Zeng, Q.10
Chen, Z.11
Mauceli, E.12
Hacohen, N.13
Gnirke, A.14
Rhind, N.15
Di Palma, F.16
Birren, B.W.17
Nusbaum, C.18
Lindblad-Toh, K.19
Friedman, N.20
Regev, A.21
more..
-
54
-
-
48449094247
-
IMGT/V-QUEST: The highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis
-
X. Brochet, M.-P. Lefranc, V. Giudicelli, IMGT/V-QUEST: The highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis. Nucleic Acids Res. 36, W503–W508 (2008).
-
(2008)
Nucleic Acids Res
, vol.36
, pp. W503-W508
-
-
Brochet, X.1
Lefranc, M.-P.2
Giudicelli, V.3
-
55
-
-
0242490780
-
Cytoscape: A software environment for integrated models of biomolecular interaction networks
-
P. Shannon, A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang, D. Ramage, N. Amin, B. Schwikowski, T. Ideker, Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003).
-
(2003)
Genome Res
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
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