-
1
-
-
84940502214
-
Predicting effective microRNA target sites in mammalian mRNAs
-
Agarwal, V., Bell, G.W., Nam, J.W., Bartel, D.P., Predicting effective microRNA target sites in mammalian mRNAs. eLife, 4, 2015, 10.7554/eLife.05005.
-
(2015)
eLife
, vol.4
-
-
Agarwal, V.1
Bell, G.W.2
Nam, J.W.3
Bartel, D.P.4
-
2
-
-
84975246805
-
Functional characterization of somatic mutations in cancer using network-based inference of protein activity
-
Alvarez, M.J., Shen, Y., Giorgi, F.M., Lachmann, A., Ding, B.B., Ye, B.H., Califano, A., Functional characterization of somatic mutations in cancer using network-based inference of protein activity. Nat. Genet. 48 (2016), 838–847.
-
(2016)
Nat. Genet.
, vol.48
, pp. 838-847
-
-
Alvarez, M.J.1
Shen, Y.2
Giorgi, F.M.3
Lachmann, A.4
Ding, B.B.5
Ye, B.H.6
Califano, A.7
-
3
-
-
85019852504
-
Mutant IDH1 regulates the tumor-associated immune system in gliomas
-
Amankulor, N.M., Kim, Y., Arora, S., Kargl, J., Szulzewsky, F., Hanke, M., Margineantu, D.H., Rao, A., Bolouri, H., Delrow, J., et al. Mutant IDH1 regulates the tumor-associated immune system in gliomas. Genes Dev. 31 (2017), 774–786.
-
(2017)
Genes Dev.
, vol.31
, pp. 774-786
-
-
Amankulor, N.M.1
Kim, Y.2
Arora, S.3
Kargl, J.4
Szulzewsky, F.5
Hanke, M.6
Margineantu, D.H.7
Rao, A.8
Bolouri, H.9
Delrow, J.10
-
4
-
-
44149084690
-
Using genetic markers to orient the edges in quantitative trait networks: the NEO software
-
Aten, J.E., Fuller, T.F., Lusis, A.J., Horvath, S., Using genetic markers to orient the edges in quantitative trait networks: the NEO software. BMC Syst. Biol., 2, 2008, 34.
-
(2008)
BMC Syst. Biol.
, vol.2
, pp. 34
-
-
Aten, J.E.1
Fuller, T.F.2
Lusis, A.J.3
Horvath, S.4
-
5
-
-
67849122320
-
MEME SUITE: tools for motif discovery and searching
-
W202-208
-
Bailey, T.L., Boden, M., Buske, F.A., Frith, M., Grant, C.E., Clementi, L., Ren, J., Li, W.W., Noble, W.S., MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res., 37, 2009 W202-208.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Bailey, T.L.1
Boden, M.2
Buske, F.A.3
Frith, M.4
Grant, C.E.5
Clementi, L.6
Ren, J.7
Li, W.W.8
Noble, W.S.9
-
6
-
-
84960194345
-
Genomic analyses identify molecular subtypes of pancreatic cancer
-
Bailey, P., Chang, D.K., Nones, K., Johns, A.L., Patch, A.M., Gingras, M.C., Miller, D.K., Christ, A.N., Bruxner, T.J., Quinn, M.C., et al. Genomic analyses identify molecular subtypes of pancreatic cancer. Nature 531 (2016), 47–52.
-
(2016)
Nature
, vol.531
, pp. 47-52
-
-
Bailey, P.1
Chang, D.K.2
Nones, K.3
Johns, A.L.4
Patch, A.M.5
Gingras, M.C.6
Miller, D.K.7
Christ, A.N.8
Bruxner, T.J.9
Quinn, M.C.10
-
7
-
-
70449091786
-
Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1
-
Barbie, D.A., Tamayo, P., Boehm, J.S., Kim, S.Y., Moody, S.E., Dunn, I.F., Schinzel, A.C., Sandy, P., Meylan, E., Scholl, C., et al. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature 462 (2009), 108–112.
-
(2009)
Nature
, vol.462
, pp. 108-112
-
-
Barbie, D.A.1
Tamayo, P.2
Boehm, J.S.3
Kim, S.Y.4
Moody, S.E.5
Dunn, I.F.6
Schinzel, A.C.7
Sandy, P.8
Meylan, E.9
Scholl, C.10
-
8
-
-
61349148145
-
The macrophage colony-stimulating factor 1 response signature in breast carcinoma
-
Beck, A.H., Espinosa, I., Edris, B., Li, R., Montgomery, K., Zhu, S., Varma, S., Marinelli, R.J., van de Rijn, M., West, R.B., The macrophage colony-stimulating factor 1 response signature in breast carcinoma. Clin. Cancer Res. 15 (2009), 778–787.
-
(2009)
Clin. Cancer Res.
, vol.15
, pp. 778-787
-
-
Beck, A.H.1
Espinosa, I.2
Edris, B.3
Li, R.4
Montgomery, K.5
Zhu, S.6
Varma, S.7
Marinelli, R.J.8
van de Rijn, M.9
West, R.B.10
-
9
-
-
84960093795
-
Disentangling the relationship between tumor genetic programs and immune responsiveness
-
Bedognetti, D., Hendrickx, W., Ceccarelli, M., Miller, L.D., Seliger, B., Disentangling the relationship between tumor genetic programs and immune responsiveness. Curr. Opin. Immunol. 39 (2016), 150–158.
-
(2016)
Curr. Opin. Immunol.
, vol.39
, pp. 150-158
-
-
Bedognetti, D.1
Hendrickx, W.2
Ceccarelli, M.3
Miller, L.D.4
Seliger, B.5
-
10
-
-
84991030621
-
BTN3A molecules considerably improve Vgamma9Vdelta2T cells-based immunotherapy in acute myeloid leukemia
-
Benyamine, A., Le Roy, A., Mamessier, E., Gertner-Dardenne, J., Castanier, C., Orlanducci, F., Pouyet, L., Goubard, A., Collette, Y., Vey, N., et al. BTN3A molecules considerably improve Vgamma9Vdelta2T cells-based immunotherapy in acute myeloid leukemia. OncoImmunology, 5, 2016, e1146843.
-
(2016)
OncoImmunology
, vol.5
, pp. e1146843
-
-
Benyamine, A.1
Le Roy, A.2
Mamessier, E.3
Gertner-Dardenne, J.4
Castanier, C.5
Orlanducci, F.6
Pouyet, L.7
Goubard, A.8
Collette, Y.9
Vey, N.10
-
11
-
-
77549083441
-
Transforming growth factor beta (TGF-beta) and inflammation in cancer
-
Bierie, B., Moses, H.L., Transforming growth factor beta (TGF-beta) and inflammation in cancer. Cytokine Growth Factor Rev. 21 (2010), 49–59.
-
(2010)
Cytokine Growth Factor Rev.
, vol.21
, pp. 49-59
-
-
Bierie, B.1
Moses, H.L.2
-
12
-
-
84885724091
-
Spatiotemporal dynamics of intratumoral immune cells reveal the immune landscape in human cancer
-
Bindea, G., Mlecnik, B., Tosolini, M., Kirilovsky, A., Waldner, M., Obenauf, A.C., Angell, H., Fredriksen, T., Lafontaine, L., Berger, A., et al. Spatiotemporal dynamics of intratumoral immune cells reveal the immune landscape in human cancer. Immunity 39 (2013), 782–795.
-
(2013)
Immunity
, vol.39
, pp. 782-795
-
-
Bindea, G.1
Mlecnik, B.2
Tosolini, M.3
Kirilovsky, A.4
Waldner, M.5
Obenauf, A.C.6
Angell, H.7
Fredriksen, T.8
Lafontaine, L.9
Berger, A.10
-
13
-
-
84883462993
-
MiTCR: software for T-cell receptor sequencing data analysis
-
Bolotin, D.A., Shugay, M., Mamedov, I.Z., Putintseva, E.V., Turchaninova, M.A., Zvyagin, I.V., Britanova, O.V., Chudakov, D.M., MiTCR: software for T-cell receptor sequencing data analysis. Nat. Methods 10 (2013), 813–814.
-
(2013)
Nat. Methods
, vol.10
, pp. 813-814
-
-
Bolotin, D.A.1
Shugay, M.2
Mamedov, I.Z.3
Putintseva, E.V.4
Turchaninova, M.A.5
Zvyagin, I.V.6
Britanova, O.V.7
Chudakov, D.M.8
-
14
-
-
84966283954
-
Near-optimal probabilistic RNA-seq quantification
-
Bray, N.L., Pimentel, H., Melsted, P., Pachter, L., Near-optimal probabilistic RNA-seq quantification. Nat. Biotechnol. 34 (2016), 525–527.
-
(2016)
Nat. Biotechnol.
, vol.34
, pp. 525-527
-
-
Bray, N.L.1
Pimentel, H.2
Melsted, P.3
Pachter, L.4
-
15
-
-
84899836282
-
Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival
-
Brown, S.D., Warren, R.L., Gibb, E.A., Martin, S.D., Spinelli, J.J., Nelson, B.H., Holt, R.A., Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival. Genome Res. 24 (2014), 743–750.
-
(2014)
Genome Res.
, vol.24
, pp. 743-750
-
-
Brown, S.D.1
Warren, R.L.2
Gibb, E.A.3
Martin, S.D.4
Spinelli, J.J.5
Nelson, B.H.6
Holt, R.A.7
-
16
-
-
84948737706
-
Profiling tissue-resident T cell repertoires by RNA sequencing
-
Brown, S.D., Raeburn, L.A., Holt, R.A., Profiling tissue-resident T cell repertoires by RNA sequencing. Genome Med., 7, 2015, 125.
-
(2015)
Genome Med.
, vol.7
, pp. 125
-
-
Brown, S.D.1
Raeburn, L.A.2
Holt, R.A.3
-
17
-
-
67649421579
-
Effects of infiltrating lymphocytes and estrogen receptor on gene expression and prognosis in breast cancer
-
Calabro, A., Beissbarth, T., Kuner, R., Stojanov, M., Benner, A., Asslaber, M., Ploner, F., Zatloukal, K., Samonigg, H., Poustka, A., et al. Effects of infiltrating lymphocytes and estrogen receptor on gene expression and prognosis in breast cancer. Breast Cancer Res. Treat. 116 (2009), 69–77.
-
(2009)
Breast Cancer Res. Treat.
, vol.116
, pp. 69-77
-
-
Calabro, A.1
Beissbarth, T.2
Kuner, R.3
Stojanov, M.4
Benner, A.5
Asslaber, M.6
Ploner, F.7
Zatloukal, K.8
Samonigg, H.9
Poustka, A.10
-
18
-
-
84860782006
-
Absolute quantification of somatic DNA alterations in human cancer
-
Carter, S.L., Cibulskis, K., Helman, E., McKenna, A., Shen, H., Zack, T., Laird, P.W., Onofrio, R.C., Winckler, W., Weir, B.A., et al. Absolute quantification of somatic DNA alterations in human cancer. Nat. Biotechnol. 30 (2012), 413–421.
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 413-421
-
-
Carter, S.L.1
Cibulskis, K.2
Helman, E.3
McKenna, A.4
Shen, H.5
Zack, T.6
Laird, P.W.7
Onofrio, R.C.8
Winckler, W.9
Weir, B.A.10
-
19
-
-
84955561447
-
Molecular profiling reveals biologically discrete subsets and pathways of progression in diffuse glioma
-
Ceccarelli, M., Barthel, F.P., Malta, T.M., Sabedot, T.S., Salama, S.R., Murray, B.A., Morozova, O., Newton, Y., Radenbaugh, A., Pagnotta, S.M., et al. Molecular profiling reveals biologically discrete subsets and pathways of progression in diffuse glioma. Cell 164 (2016), 550–563.
-
(2016)
Cell
, vol.164
, pp. 550-563
-
-
Ceccarelli, M.1
Barthel, F.P.2
Malta, T.M.3
Sabedot, T.S.4
Salama, S.R.5
Murray, B.A.6
Morozova, O.7
Newton, Y.8
Radenbaugh, A.9
Pagnotta, S.M.10
-
20
-
-
19344363035
-
Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds
-
Chang, H.Y., Sneddon, J.B., Alizadeh, A.A., Sood, R., West, R.B., Montgomery, K., Chi, J.T., van de Rijn, M., Botstein, D., Brown, P.O., Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. PLoS Biol., 2, 2004, E7.
-
(2004)
PLoS Biol.
, vol.2
, pp. E7
-
-
Chang, H.Y.1
Sneddon, J.B.2
Alizadeh, A.A.3
Sood, R.4
West, R.B.5
Montgomery, K.6
Chi, J.T.7
van de Rijn, M.8
Botstein, D.9
Brown, P.O.10
-
21
-
-
85009106590
-
Pan-cancer immunogenomic analyses reveal genotype-immunophenotype pelationships and predictors of response to checkpoint blockade
-
Charoentong, P., Finotello, F., Angelova, M., Mayer, C., Efremova, M., Rieder, D., Hackl, H., Trajanoski, Z., Pan-cancer immunogenomic analyses reveal genotype-immunophenotype pelationships and predictors of response to checkpoint blockade. Cell Rep. 18 (2017), 248–262.
-
(2017)
Cell Rep.
, vol.18
, pp. 248-262
-
-
Charoentong, P.1
Finotello, F.2
Angelova, M.3
Mayer, C.4
Efremova, M.5
Rieder, D.6
Hackl, H.7
Trajanoski, Z.8
-
22
-
-
84915815121
-
Identification of causal genetic drivers of human disease through systems-level analysis of regulatory networks
-
Chen, J.C., Alvarez, M.J., Talos, F., Dhruv, H., Rieckhof, G.E., Iyer, A., Diefes, K.L., Aldape, K., Berens, M., Shen, M.M., et al. Identification of causal genetic drivers of human disease through systems-level analysis of regulatory networks. Cell 159 (2014), 402–414.
-
(2014)
Cell
, vol.159
, pp. 402-414
-
-
Chen, J.C.1
Alvarez, M.J.2
Talos, F.3
Dhruv, H.4
Rieckhof, G.E.5
Iyer, A.6
Diefes, K.L.7
Aldape, K.8
Berens, M.9
Shen, M.M.10
-
23
-
-
84874763866
-
Biomolecular events in cancer revealed by attractor metagenes
-
Cheng, W.Y., Ou Yang, T.H., Anastassiou, D., Biomolecular events in cancer revealed by attractor metagenes. PLoS Comput. Biol., 9, 2013, e1002920.
-
(2013)
PLoS Comput. Biol.
, vol.9
, pp. e1002920
-
-
Cheng, W.Y.1
Ou Yang, T.H.2
Anastassiou, D.3
-
24
-
-
84877737214
-
Development of a prognostic model for breast cancer survival in an open challenge environment
-
Cheng, W.Y., Ou Yang, T.H., Anastassiou, D., Development of a prognostic model for breast cancer survival in an open challenge environment. Sci. Transl. Med., 5, 2013, 181ra150.
-
(2013)
Sci. Transl. Med.
, vol.5
, pp. 181ra150
-
-
Cheng, W.Y.1
Ou Yang, T.H.2
Anastassiou, D.3
-
25
-
-
84925552713
-
BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters
-
Chu, J., Sadeghi, S., Raymond, A., Jackman, S.D., Nip, K.M., Mar, R., Mohamadi, H., Butterfield, Y.S., Robertson, A.G., Birol, I., BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters. Bioinformatics 30 (2014), 3402–3404.
-
(2014)
Bioinformatics
, vol.30
, pp. 3402-3404
-
-
Chu, J.1
Sadeghi, S.2
Raymond, A.3
Jackman, S.D.4
Nip, K.M.5
Mar, R.6
Mohamadi, H.7
Butterfield, Y.S.8
Robertson, A.G.9
Birol, I.10
-
26
-
-
84966269471
-
TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data
-
Colaprico, A., Silva, T.C., Olsen, C., Garofano, L., Cava, C., Garolini, D., Sabedot, T.S., Malta, T.M., Pagnotta, S.M., Castiglioni, I., et al. TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data. Nucleic Acids Res., 44, 2016, e71.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. e71
-
-
Colaprico, A.1
Silva, T.C.2
Olsen, C.3
Garofano, L.4
Cava, C.5
Garolini, D.6
Sabedot, T.S.7
Malta, T.M.8
Pagnotta, S.M.9
Castiglioni, I.10
-
27
-
-
79851504402
-
CD277 is a negative co-stimulatory molecule universally expressed by ovarian cancer microenvironmental cells
-
Cubillos-Ruiz, J.R., Martinez, D., Scarlett, U.K., Rutkowski, M.R., Nesbeth, Y.C., Camposeco-Jacobs, A.L., Conejo-Garcia, J.R., CD277 is a negative co-stimulatory molecule universally expressed by ovarian cancer microenvironmental cells. Oncotarget 1 (2010), 329–338.
-
(2010)
Oncotarget
, vol.1
, pp. 329-338
-
-
Cubillos-Ruiz, J.R.1
Martinez, D.2
Scarlett, U.K.3
Rutkowski, M.R.4
Nesbeth, Y.C.5
Camposeco-Jacobs, A.L.6
Conejo-Garcia, J.R.7
-
28
-
-
84871809302
-
STAR: ultrafast universal RNA-seq aligner
-
Dobin, A., Davis, C.A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., Gingeras, T.R., STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29 (2013), 15–21.
-
(2013)
Bioinformatics
, vol.29
, pp. 15-21
-
-
Dobin, A.1
Davis, C.A.2
Schlesinger, F.3
Drenkow, J.4
Zaleski, C.5
Jha, S.6
Batut, P.7
Chaisson, M.8
Gingeras, T.R.9
-
29
-
-
84981318520
-
Phosphoproteome integration reveals patient-specific networks in prostate cancer
-
Drake, J.M., Paull, E.O., Graham, N.A., Lee, J.K., Smith, B.A., Titz, B., Stoyanova, T., Faltermeier, C.M., Uzunangelov, V., Carlin, D.E., et al. Phosphoproteome integration reveals patient-specific networks in prostate cancer. Cell 166 (2016), 1041–1054.
-
(2016)
Cell
, vol.166
, pp. 1041-1054
-
-
Drake, J.M.1
Paull, E.O.2
Graham, N.A.3
Lee, J.K.4
Smith, B.A.5
Titz, B.6
Stoyanova, T.7
Faltermeier, C.M.8
Uzunangelov, V.9
Carlin, D.E.10
-
30
-
-
85044569292
-
Scalable open science approach for mutation calling of tumor exomes using multiple genomic pipelines
-
Ellrott, K., Bailey, M.H., Saksena, G., Covington, K.R., Kandoth, C., Stewart, C., Hess, J., Ma, S., McLellan, M., Sofia, H.J., et al. Scalable open science approach for mutation calling of tumor exomes using multiple genomic pipelines. Cell Syst., 6, 2018, 10.1016/j.cels.2018.03.002.
-
(2018)
Cell Syst.
, vol.6
-
-
Ellrott, K.1
Bailey, M.H.2
Saksena, G.3
Covington, K.R.4
Kandoth, C.5
Stewart, C.6
Hess, J.7
Ma, S.8
McLellan, M.9
Sofia, H.J.10
-
31
-
-
77950537175
-
Regularization paths for generalized linear models via coordinate descent
-
Friedman, J., Hastie, T., Tibshirani, R., Regularization paths for generalized linear models via coordinate descent. J. Stat. Softw. 33 (2010), 1–22.
-
(2010)
J. Stat. Softw.
, vol.33
, pp. 1-22
-
-
Friedman, J.1
Hastie, T.2
Tibshirani, R.3
-
32
-
-
84880704621
-
The continuum of cancer immunosurveillance: prognostic, predictive, and mechanistic signatures
-
Galon, J., Angell, H.K., Bedognetti, D., Marincola, F.M., The continuum of cancer immunosurveillance: prognostic, predictive, and mechanistic signatures. Immunity 39 (2013), 11–26.
-
(2013)
Immunity
, vol.39
, pp. 11-26
-
-
Galon, J.1
Angell, H.K.2
Bedognetti, D.3
Marincola, F.M.4
-
33
-
-
84938984463
-
The prognostic landscape of genes and infiltrating immune cells across human cancers
-
Gentles, A.J., Newman, A.M., Liu, C.L., Bratman, S.V., Feng, W., Kim, D., Nair, V.S., Xu, Y., Khuong, A., Hoang, C.D., et al. The prognostic landscape of genes and infiltrating immune cells across human cancers. Nat. Med. 21 (2015), 938–945.
-
(2015)
Nat. Med.
, vol.21
, pp. 938-945
-
-
Gentles, A.J.1
Newman, A.M.2
Liu, C.L.3
Bratman, S.V.4
Feng, W.5
Kim, D.6
Nair, V.S.7
Xu, Y.8
Khuong, A.9
Hoang, C.D.10
-
34
-
-
84958925144
-
Compendium of immune signatures identifies conserved and species-specific biology in response to inflammation
-
Godec, J., Tan, Y., Liberzon, A., Tamayo, P., Bhattacharya, S., Butte, A.J., Mesirov, J.P., Haining, W.N., Compendium of immune signatures identifies conserved and species-specific biology in response to inflammation. Immunity 44 (2016), 194–206.
-
(2016)
Immunity
, vol.44
, pp. 194-206
-
-
Godec, J.1
Tan, Y.2
Liberzon, A.3
Tamayo, P.4
Bhattacharya, S.5
Butte, A.J.6
Mesirov, J.P.7
Haining, W.N.8
-
35
-
-
84867307317
-
iBBiG: iterative binary bi-clustering of gene sets
-
Gusenleitner, D., Howe, E.A., Bentink, S., Quackenbush, J., Culhane, A.C., iBBiG: iterative binary bi-clustering of gene sets. Bioinformatics 28 (2012), 2484–2492.
-
(2012)
Bioinformatics
, vol.28
, pp. 2484-2492
-
-
Gusenleitner, D.1
Howe, E.A.2
Bentink, S.3
Quackenbush, J.4
Culhane, A.C.5
-
36
-
-
79952284127
-
Hallmarks of cancer: the next generation
-
Hanahan, D., Weinberg, R.A., Hallmarks of cancer: the next generation. Cell 144 (2011), 646–674.
-
(2011)
Cell
, vol.144
, pp. 646-674
-
-
Hanahan, D.1
Weinberg, R.A.2
-
37
-
-
84872202078
-
GSVA: gene set variation analysis for microarray and RNA-seq data
-
Hänzelmann, S., Castelo, R., Guinney, J., GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics, 14, 2013, 7.
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 7
-
-
Hänzelmann, S.1
Castelo, R.2
Guinney, J.3
-
38
-
-
84865760395
-
GENCODE: the reference human genome annotation for The ENCODE Project
-
Harrow, J., Frankish, A., Gonzalez, J.M., Tapanari, E., Diekhans, M., Kokocinski, F., Aken, B.L., Barrell, D., Zadissa, A., Searle, S., et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 22 (2012), 1760–1774.
-
(2012)
Genome Res.
, vol.22
, pp. 1760-1774
-
-
Harrow, J.1
Frankish, A.2
Gonzalez, J.M.3
Tapanari, E.4
Diekhans, M.5
Kokocinski, F.6
Aken, B.L.7
Barrell, D.8
Zadissa, A.9
Searle, S.10
-
39
-
-
85011817556
-
Identification of genetic determinants of breast cancer immune phenotypes by integrative genome-scale analysis
-
Hendrickx, W., Simeone, I., Anjum, S., Mokrab, Y., Bertucci, F., Finetti, P., Curigliano, G., Seliger, B., Cerulo, L., Tomei, S., et al. Identification of genetic determinants of breast cancer immune phenotypes by integrative genome-scale analysis. OncoImmunology, 6, 2017, e1253654.
-
(2017)
OncoImmunology
, vol.6
, pp. e1253654
-
-
Hendrickx, W.1
Simeone, I.2
Anjum, S.3
Mokrab, Y.4
Bertucci, F.5
Finetti, P.6
Curigliano, G.7
Seliger, B.8
Cerulo, L.9
Tomei, S.10
-
40
-
-
27544491443
-
A CLUE for CLUster ensembles
-
Hornik, K., A CLUE for CLUster ensembles. J. Stat. Softw. 14 (2005), 1–25.
-
(2005)
J. Stat. Softw.
, vol.14
, pp. 1-25
-
-
Hornik, K.1
-
41
-
-
84961221351
-
Genomic and transcriptomic features of response to anti-PD-1 therapy in metastatic melanoma
-
Hugo, W., Zaretsky, J.M., Sun, L., Song, C., Moreno, B.H., Hu-Lieskovan, S., Berent-Maoz, B., Pang, J., Chmielowski, B., Cherry, G., et al. Genomic and transcriptomic features of response to anti-PD-1 therapy in metastatic melanoma. Cell 165 (2016), 35–44.
-
(2016)
Cell
, vol.165
, pp. 35-44
-
-
Hugo, W.1
Zaretsky, J.M.2
Sun, L.3
Song, C.4
Moreno, B.H.5
Hu-Lieskovan, S.6
Berent-Maoz, B.7
Pang, J.8
Chmielowski, B.9
Cherry, G.10
-
42
-
-
84957108846
-
pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens
-
Hundal, J., Carreno, B.M., Petti, A.A., Linette, G.P., Griffith, O.L., Mardis, E.R., Griffith, M., pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens. Genome Med., 8, 2016, 11.
-
(2016)
Genome Med.
, vol.8
, pp. 11
-
-
Hundal, J.1
Carreno, B.M.2
Petti, A.A.3
Linette, G.P.4
Griffith, O.L.5
Mardis, E.R.6
Griffith, M.7
-
43
-
-
85014834973
-
Genomic analysis of immune cell infiltrates across 11 tumor types
-
Iglesia, M.D., Parker, J.S., Hoadley, K.A., Serody, J.S., Perou, C.M., Vincent, B.G., Genomic analysis of immune cell infiltrates across 11 tumor types. J. Natl. Cancer Inst., 108, 2016, 10.1093/jnci/djw144.
-
(2016)
J. Natl. Cancer Inst.
, vol.108
-
-
Iglesia, M.D.1
Parker, J.S.2
Hoadley, K.A.3
Serody, J.S.4
Perou, C.M.5
Vincent, B.G.6
-
44
-
-
84917673811
-
Effects of BRAF mutations and BRAF inhibition on immune responses to melanoma
-
Ilieva, K.M., Correa, I., Josephs, D.H., Karagiannis, P., Egbuniwe, I.U., Cafferkey, M.J., Spicer, J.F., Harries, M., Nestle, F.O., Lacy, K.E., et al. Effects of BRAF mutations and BRAF inhibition on immune responses to melanoma. Mol. Cancer Ther. 13 (2014), 2769–2783.
-
(2014)
Mol. Cancer Ther.
, vol.13
, pp. 2769-2783
-
-
Ilieva, K.M.1
Correa, I.2
Josephs, D.H.3
Karagiannis, P.4
Egbuniwe, I.U.5
Cafferkey, M.J.6
Spicer, J.F.7
Harries, M.8
Nestle, F.O.9
Lacy, K.E.10
-
45
-
-
34748821761
-
The role of site accessibility in microRNA target recognition
-
Kertesz, M., Iovino, N., Unnerstall, U., Gaul, U., Segal, E., The role of site accessibility in microRNA target recognition. Nat. Genet. 39 (2007), 1278–1284.
-
(2007)
Nat. Genet.
, vol.39
, pp. 1278-1284
-
-
Kertesz, M.1
Iovino, N.2
Unnerstall, U.3
Gaul, U.4
Segal, E.5
-
46
-
-
84876009220
-
Interpretation of genomic variants using a unified biological network approach
-
Khurana, E., Fu, Y., Chen, J., Gerstein, M., Interpretation of genomic variants using a unified biological network approach. PLoS Comput. Biol., 9, 2013, e1002886.
-
(2013)
PLoS Comput. Biol.
, vol.9
, pp. e1002886
-
-
Khurana, E.1
Fu, Y.2
Chen, J.3
Gerstein, M.4
-
47
-
-
85044676615
-
Genomic and molecular landscape of DNA damage repair deficiency across The Cancer Genome Atlas
-
Knijnenburg, T., Wang, L., Zimmermann, M., Chambwe, N., Gao, G., Cherniack, A., Fan, H., Shen, H., Way, G., Greene, C., et al. Genomic and molecular landscape of DNA damage repair deficiency across The Cancer Genome Atlas. Cell Rep., 23, 2018, 10.1016/j.celrep.2018.03.076.
-
(2018)
Cell Rep.
, vol.23
-
-
Knijnenburg, T.1
Wang, L.2
Zimmermann, M.3
Chambwe, N.4
Gao, G.5
Cherniack, A.6
Fan, H.7
Shen, H.8
Way, G.9
Greene, C.10
-
48
-
-
41449085571
-
Eigengene networks for studying the relationships between co-expression modules
-
Langfelder, P., Horvath, S., Eigengene networks for studying the relationships between co-expression modules. BMC Syst. Biol., 1, 2007, 54.
-
(2007)
BMC Syst. Biol.
, vol.1
, pp. 54
-
-
Langfelder, P.1
Horvath, S.2
-
49
-
-
60549111634
-
WGCNA: an R package for weighted correlation network analysis
-
Langfelder, P., Horvath, S., WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics, 9, 2008, 559.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 559
-
-
Langfelder, P.1
Horvath, S.2
-
50
-
-
58149316094
-
IMGT, the international ImMunoGeneTics information system
-
Lefranc, M.P., Giudicelli, V., Ginestoux, C., Jabado-Michaloud, J., Folch, G., Bellahcene, F., Wu, Y., Gemrot, E., Brochet, X., Lane, J., et al. IMGT, the international ImMunoGeneTics information system. Nucleic Acids Res. 37 (2009), D1006–D1012.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. D1006-D1012
-
-
Lefranc, M.P.1
Giudicelli, V.2
Ginestoux, C.3
Jabado-Michaloud, J.4
Folch, G.5
Bellahcene, F.6
Wu, Y.7
Gemrot, E.8
Brochet, X.9
Lane, J.10
-
51
-
-
84946057476
-
The promise of gammadelta T cells and the gammadelta T cell receptor for cancer immunotherapy
-
Legut, M., Cole, D.K., Sewell, A.K., The promise of gammadelta T cells and the gammadelta T cell receptor for cancer immunotherapy. Cell. Mol. Immunol. 12 (2015), 656–668.
-
(2015)
Cell. Mol. Immunol.
, vol.12
, pp. 656-668
-
-
Legut, M.1
Cole, D.K.2
Sewell, A.K.3
-
52
-
-
79961123152
-
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
-
Li, B., Dewey, C.N., RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics, 12, 2011, 323.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 323
-
-
Li, B.1
Dewey, C.N.2
-
53
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li, H., Durbin, R., Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25 (2009), 1754–1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
54
-
-
84862260334
-
Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets
-
Li, M.X., Yeung, J.M., Cherny, S.S., Sham, P.C., Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets. Hum. Genet. 131 (2012), 747–756.
-
(2012)
Hum. Genet.
, vol.131
, pp. 747-756
-
-
Li, M.X.1
Yeung, J.M.2
Cherny, S.S.3
Sham, P.C.4
-
55
-
-
84983347823
-
Comprehensive analyses of tumor immunity: implications for cancer immunotherapy
-
Li, B., Severson, E., Pignon, J.C., Zhao, H., Li, T., Novak, J., Jiang, P., Shen, H., Aster, J.C., Rodig, S., et al. Comprehensive analyses of tumor immunity: implications for cancer immunotherapy. Genome Biol., 17, 2016, 174.
-
(2016)
Genome Biol.
, vol.17
, pp. 174
-
-
Li, B.1
Severson, E.2
Pignon, J.C.3
Zhao, H.4
Li, T.5
Novak, J.6
Jiang, P.7
Shen, H.8
Aster, J.C.9
Rodig, S.10
-
56
-
-
84928774817
-
microRNAs function in CD8+T cell biology
-
Liang, Y., Pan, H.F., Ye, D.Q., microRNAs function in CD8+T cell biology. J. Leukoc. Biol. 97 (2015), 487–497.
-
(2015)
J. Leukoc. Biol.
, vol.97
, pp. 487-497
-
-
Liang, Y.1
Pan, H.F.2
Ye, D.Q.3
-
57
-
-
85044905247
-
An Integrated TCGA Pan-Cancer Clinical Data Resource to drive high quality survival outcome analytics
-
Liu, J., Lichtenberg, T., Hoadley, K.A., Poisson, L.M., Lazar, A.J., Cherniack, A.D., Kovatich, A.J., Benz, C.C., Levine, D.A., Lee, A.V., et al. An Integrated TCGA Pan-Cancer Clinical Data Resource to drive high quality survival outcome analytics. Cell, 173, 2018, 10.1016/j.cell.2018.02.052.
-
(2018)
Cell
, vol.173
-
-
Liu, J.1
Lichtenberg, T.2
Hoadley, K.A.3
Poisson, L.M.4
Lazar, A.J.5
Cherniack, A.D.6
Kovatich, A.J.7
Benz, C.C.8
Levine, D.A.9
Lee, A.V.10
-
58
-
-
26644452073
-
Macrophage polarization comes of age
-
Mantovani, A., Sica, A., Locati, M., Macrophage polarization comes of age. Immunity 23 (2005), 344–346.
-
(2005)
Immunity
, vol.23
, pp. 344-346
-
-
Mantovani, A.1
Sica, A.2
Locati, M.3
-
59
-
-
33947305781
-
ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
-
Margolin, A.A., Nemenman, I., Basso, K., Wiggins, C., Stolovitzky, G., Dalla Favera, R., Califano, A., ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics, 7(Suppl 1), 2006, S7.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. S7
-
-
Margolin, A.A.1
Nemenman, I.2
Basso, K.3
Wiggins, C.4
Stolovitzky, G.5
Dalla Favera, R.6
Califano, A.7
-
60
-
-
84983479616
-
A reference panel of 64,976 haplotypes for genotype imputation
-
McCarthy, S., Das, S., Kretzschmar, W., Delaneau, O., Wood, A.R., Teumer, A., Kang, H.M., Fuchsberger, C., Danecek, P., Sharp, K., et al. A reference panel of 64,976 haplotypes for genotype imputation. Nat. Genet. 48 (2016), 1279–1283.
-
(2016)
Nat. Genet.
, vol.48
, pp. 1279-1283
-
-
McCarthy, S.1
Das, S.2
Kretzschmar, W.3
Delaneau, O.4
Wood, A.R.5
Teumer, A.6
Kang, H.M.7
Fuchsberger, C.8
Danecek, P.9
Sharp, K.10
-
61
-
-
50849087987
-
Mastermind-like transcriptional co-activators: emerging roles in regulating cross talk among multiple signaling pathways
-
McElhinny, A.S., Li, J.L., Wu, L., Mastermind-like transcriptional co-activators: emerging roles in regulating cross talk among multiple signaling pathways. Oncogene 27 (2008), 5138–5147.
-
(2008)
Oncogene
, vol.27
, pp. 5138-5147
-
-
McElhinny, A.S.1
Li, J.L.2
Wu, L.3
-
62
-
-
84962301577
-
Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade
-
McGranahan, N., Furness, A.J., Rosenthal, R., Ramskov, S., Lyngaa, R., Saini, S.K., Jamal-Hanjani, M., Wilson, G.A., Birkbak, N.J., Hiley, C.T., et al. Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade. Science 351 (2016), 1463–1469.
-
(2016)
Science
, vol.351
, pp. 1463-1469
-
-
McGranahan, N.1
Furness, A.J.2
Rosenthal, R.3
Ramskov, S.4
Lyngaa, R.5
Saini, S.K.6
Jamal-Hanjani, M.7
Wilson, G.A.8
Birkbak, N.J.9
Hiley, C.T.10
-
63
-
-
84973338712
-
The Ensembl Variant Effect Predictor
-
McLaren, W., Gil, L., Hunt, S.E., Riat, H.S., Ritchie, G.R., Thormann, A., Flicek, P., Cunningham, F., The Ensembl Variant Effect Predictor. Genome Biol., 17, 2016, 122.
-
(2016)
Genome Biol.
, vol.17
, pp. 122
-
-
McLaren, W.1
Gil, L.2
Hunt, S.E.3
Riat, H.S.4
Ritchie, G.R.5
Thormann, A.6
Flicek, P.7
Cunningham, F.8
-
64
-
-
79955166265
-
GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers
-
Mermel, C.H., Schumacher, S.E., Hill, B., Meyerson, M.L., Beroukhim, R., Getz, G., GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol., 12, 2011, R41.
-
(2011)
Genome Biol.
, vol.12
, pp. R41
-
-
Mermel, C.H.1
Schumacher, S.E.2
Hill, B.3
Meyerson, M.L.4
Beroukhim, R.5
Getz, G.6
-
65
-
-
85040072272
-
Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma
-
Miao, D., Margolis, C.A., Gao, W., Voss, M.H., Li, W., Martini, D.J., Norton, C., Bosse, D., Wankowicz, S.M., Cullen, D., et al. Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma. Science 359 (2018), 801–806.
-
(2018)
Science
, vol.359
, pp. 801-806
-
-
Miao, D.1
Margolis, C.A.2
Gao, W.3
Voss, M.H.4
Li, W.5
Martini, D.J.6
Norton, C.7
Bosse, D.8
Wankowicz, S.M.9
Cullen, D.10
-
66
-
-
84961572813
-
Pan-cancer analysis of intratumor heterogeneity as a prognostic determinant of survival
-
Morris, L.G., Riaz, N., Desrichard, A., Senbabaoglu, Y., Hakimi, A.A., Makarov, V., Reis-Filho, J.S., Chan, T.A., Pan-cancer analysis of intratumor heterogeneity as a prognostic determinant of survival. Oncotarget 7 (2016), 10051–10063.
-
(2016)
Oncotarget
, vol.7
, pp. 10051-10063
-
-
Morris, L.G.1
Riaz, N.2
Desrichard, A.3
Senbabaoglu, Y.4
Hakimi, A.A.5
Makarov, V.6
Reis-Filho, J.S.7
Chan, T.A.8
-
67
-
-
85012208605
-
Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V'DJer
-
Mose, L.E., Selitsky, S.R., Bixby, L.M., Marron, D.L., Iglesia, M.D., Serody, J.S., Perou, C.M., Vincent, B.G., Parker, J.S., Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V'DJer. Bioinformatics 32 (2016), 3729–3734.
-
(2016)
Bioinformatics
, vol.32
, pp. 3729-3734
-
-
Mose, L.E.1
Selitsky, S.R.2
Bixby, L.M.3
Marron, D.L.4
Iglesia, M.D.5
Serody, J.S.6
Perou, C.M.7
Vincent, B.G.8
Parker, J.S.9
-
68
-
-
84928927858
-
Robust enumeration of cell subsets from tissue expression profiles
-
Newman, A.M., Liu, C.L., Green, M.R., Gentles, A.J., Feng, W., Xu, Y., Hoang, C.D., Diehn, M., Alizadeh, A.A., Robust enumeration of cell subsets from tissue expression profiles. Nat. Methods 12 (2015), 453–457.
-
(2015)
Nat. Methods
, vol.12
, pp. 453-457
-
-
Newman, A.M.1
Liu, C.L.2
Green, M.R.3
Gentles, A.J.4
Feng, W.5
Xu, Y.6
Hoang, C.D.7
Diehn, M.8
Alizadeh, A.A.9
-
69
-
-
84962905590
-
NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets
-
Nielsen, M., Andreatta, M., NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets. Genome Med., 8, 2016, 33.
-
(2016)
Genome Med.
, vol.8
, pp. 33
-
-
Nielsen, M.1
Andreatta, M.2
-
70
-
-
84884403849
-
Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE)
-
Paull, E.O., Carlin, D.E., Niepel, M., Sorger, P.K., Haussler, D., Stuart, J.M., Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE). Bioinformatics 29 (2013), 2757–2764.
-
(2013)
Bioinformatics
, vol.29
, pp. 2757-2764
-
-
Paull, E.O.1
Carlin, D.E.2
Niepel, M.3
Sorger, P.K.4
Haussler, D.5
Stuart, J.M.6
-
71
-
-
43749099620
-
Using Weeder for the discovery of conserved transcription factor binding sites
-
Unit 2 11
-
Pavesi, G., Pesole, G., Using Weeder for the discovery of conserved transcription factor binding sites. Curr Protoc Bioinformatics, Chapter 2, 2006 Unit 2 11.
-
(2006)
Curr Protoc Bioinformatics
, vol.Chapter 2
-
-
Pavesi, G.1
Pesole, G.2
-
72
-
-
3242770671
-
Overall C as a measure of discrimination in survival analysis: model specific population value and confidence interval estimation
-
Pencina, M.J., D'Agostino, R.B., Overall C as a measure of discrimination in survival analysis: model specific population value and confidence interval estimation. Stat. Med. 23 (2004), 2109–2123.
-
(2004)
Stat. Med.
, vol.23
, pp. 2109-2123
-
-
Pencina, M.J.1
D'Agostino, R.B.2
-
73
-
-
70349656509
-
A systems genetics approach implicates USF1, FADS3, and other causal candidate genes for familial combined hyperlipidemia
-
Plaisier, C.L., Horvath, S., Huertas-Vazquez, A., Cruz-Bautista, I., Herrera, M.F., Tusie-Luna, T., Aguilar-Salinas, C., Pajukanta, P., A systems genetics approach implicates USF1, FADS3, and other causal candidate genes for familial combined hyperlipidemia. PLoS Genet., 5, 2009, e1000642.
-
(2009)
PLoS Genet.
, vol.5
, pp. e1000642
-
-
Plaisier, C.L.1
Horvath, S.2
Huertas-Vazquez, A.3
Cruz-Bautista, I.4
Herrera, M.F.5
Tusie-Luna, T.6
Aguilar-Salinas, C.7
Pajukanta, P.8
-
74
-
-
84868326494
-
A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers
-
Plaisier, C.L., Pan, M., Baliga, N.S., A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers. Genome Res. 22 (2012), 2302–2314.
-
(2012)
Genome Res.
, vol.22
, pp. 2302-2314
-
-
Plaisier, C.L.1
Pan, M.2
Baliga, N.S.3
-
75
-
-
84978811202
-
Causal mechanistic regulatory network for glioblastoma deciphered using systems genetics network analysis
-
Plaisier, C.L., O'Brien, S., Bernard, B., Reynolds, S., Simon, Z., Toledo, C.M., Ding, Y., Reiss, D.J., Paddison, P.J., Baliga, N.S., Causal mechanistic regulatory network for glioblastoma deciphered using systems genetics network analysis. Cell Syst. 3 (2016), 172–186.
-
(2016)
Cell Syst.
, vol.3
, pp. 172-186
-
-
Plaisier, C.L.1
O'Brien, S.2
Bernard, B.3
Reynolds, S.4
Simon, Z.5
Toledo, C.M.6
Ding, Y.7
Reiss, D.J.8
Paddison, P.J.9
Baliga, N.S.10
-
76
-
-
85016134484
-
Mutation drivers of immunological responses to cancer
-
Porta-Pardo, E., Godzik, A., Mutation drivers of immunological responses to cancer. Cancer Immunol. Res. 4 (2016), 789–798.
-
(2016)
Cancer Immunol. Res.
, vol.4
, pp. 789-798
-
-
Porta-Pardo, E.1
Godzik, A.2
-
77
-
-
33746512512
-
Principal components analysis corrects for stratification in genome-wide association studies
-
Price, A.L., Patterson, N.J., Plenge, R.M., Weinblatt, M.E., Shadick, N.A., Reich, D., Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38 (2006), 904–909.
-
(2006)
Nat. Genet.
, vol.38
, pp. 904-909
-
-
Price, A.L.1
Patterson, N.J.2
Plenge, R.M.3
Weinblatt, M.E.4
Shadick, N.A.5
Reich, D.6
-
78
-
-
84954566376
-
The correlations between IL-17 vs. Th17 cells and cancer patient survival: a systematic review
-
Punt, S., Langenhoff, J.M., Putter, H., Fleuren, G.J., Gorter, A., Jordanova, E.S., The correlations between IL-17 vs. Th17 cells and cancer patient survival: a systematic review. OncoImmunology, 4, 2015, e984547.
-
(2015)
OncoImmunology
, vol.4
, pp. e984547
-
-
Punt, S.1
Langenhoff, J.M.2
Putter, H.3
Fleuren, G.J.4
Gorter, A.5
Jordanova, E.S.6
-
79
-
-
84937934040
-
A draft network of ligand-receptor-mediated multicellular signalling in human
-
Ramilowski, J.A., Goldberg, T., Harshbarger, J., Kloppmann, E., Lizio, M., Satagopam, V.P., Itoh, M., Kawaji, H., Carninci, P., Rost, B., et al. A draft network of ligand-receptor-mediated multicellular signalling in human. Nat. Commun., 6, 2015, 7866.
-
(2015)
Nat. Commun.
, vol.6
, pp. 7866
-
-
Ramilowski, J.A.1
Goldberg, T.2
Harshbarger, J.3
Kloppmann, E.4
Lizio, M.5
Satagopam, V.P.6
Itoh, M.7
Kawaji, H.8
Carninci, P.9
Rost, B.10
-
80
-
-
84939604164
-
cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism
-
Reiss, D.J., Plaisier, C.L., Wu, W.J., Baliga, N.S., cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism. Nucleic Acids Res., 43, 2015, e87.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. e87
-
-
Reiss, D.J.1
Plaisier, C.L.2
Wu, W.J.3
Baliga, N.S.4
-
81
-
-
84920962202
-
Molecular and genetic properties of tumors associated with local immune cytolytic activity
-
Rooney, M.S., Shukla, S.A., Wu, C.J., Getz, G., Hacohen, N., Molecular and genetic properties of tumors associated with local immune cytolytic activity. Cell 160 (2015), 48–61.
-
(2015)
Cell
, vol.160
, pp. 48-61
-
-
Rooney, M.S.1
Shukla, S.A.2
Wu, C.J.3
Getz, G.4
Hacohen, N.5
-
82
-
-
85044586207
-
Spatial organization and molecular correlation of tumor infiltrating lymphocytes using deep learning on pathology images
-
Saltz, J.H., Gupta, R., Hou, L., Kurc, T., Singh, P., Nguyen, V., Samaras, D., Shroyer, K.R., Zhao, T., Batiste, R., et al. Spatial organization and molecular correlation of tumor infiltrating lymphocytes using deep learning on pathology images. Cell Rep., 23, 2018, 10.1016/j.celrep.2018.03.086.
-
(2018)
Cell Rep.
, vol.23
-
-
Saltz, J.H.1
Gupta, R.2
Hou, L.3
Kurc, T.4
Singh, P.5
Nguyen, V.6
Samaras, D.7
Shroyer, K.R.8
Zhao, T.9
Batiste, R.10
-
83
-
-
85044966521
-
Oncogenic signaling pathways in The Cancer Genome Atlas
-
Sanchez-Vega, F., Mina, M., Armenia, J., Chatila, W.K., Luna, A., La, K., Dimitriadoy, S., Liu, D.L., Kantheti, H.S., Saghafinia, S., et al. Oncogenic signaling pathways in The Cancer Genome Atlas. Cell, 173, 2018.
-
(2018)
Cell
, vol.173
-
-
Sanchez-Vega, F.1
Mina, M.2
Armenia, J.3
Chatila, W.K.4
Luna, A.5
La, K.6
Dimitriadoy, S.7
Liu, D.L.8
Kantheti, H.S.9
Saghafinia, S.10
-
84
-
-
85010390664
-
mclust 5: clustering, classification and density estimation using Gaussian finite mixture models
-
Scrucca, L., Fop, M., Murphy, T.B., Raftery, A.E., mclust 5: clustering, classification and density estimation using Gaussian finite mixture models. R J. 8 (2016), 289–317.
-
(2016)
R J.
, vol.8
, pp. 289-317
-
-
Scrucca, L.1
Fop, M.2
Murphy, T.B.3
Raftery, A.E.4
-
85
-
-
85002930854
-
Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures
-
Senbabaoglu, Y., Gejman, R.S., Winer, A.G., Liu, M., Van Allen, E.M., de Velasco, G., Miao, D., Ostrovnaya, I., Drill, E., Luna, A., et al. Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures. Genome Biol., 17, 2016, 231.
-
(2016)
Genome Biol.
, vol.17
, pp. 231
-
-
Senbabaoglu, Y.1
Gejman, R.S.2
Winer, A.G.3
Liu, M.4
Van Allen, E.M.5
de Velasco, G.6
Miao, D.7
Ostrovnaya, I.8
Drill, E.9
Luna, A.10
-
86
-
-
84946565788
-
Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes
-
Shukla, S.A., Rooney, M.S., Rajasagi, M., Tiao, G., Dixon, P.M., Lawrence, M.S., Stevens, J., Lane, W.J., Dellagatta, J.L., Steelman, S., et al. Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes. Nat. Biotechnol. 33 (2015), 1152–1158.
-
(2015)
Nat. Biotechnol.
, vol.33
, pp. 1152-1158
-
-
Shukla, S.A.1
Rooney, M.S.2
Rajasagi, M.3
Tiao, G.4
Dixon, P.M.5
Lawrence, M.S.6
Stevens, J.7
Lane, W.J.8
Dellagatta, J.L.9
Steelman, S.10
-
87
-
-
85013753091
-
TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages
-
Silva, T.C., Colaprico, A., Olsen, C., D'Angelo, F., Bontempi, G., Ceccarelli, M., Noushmehr, H., TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages. F1000Res., 5, 2016, 1542.
-
(2016)
F1000Res.
, vol.5
, pp. 1542
-
-
Silva, T.C.1
Colaprico, A.2
Olsen, C.3
D'Angelo, F.4
Bontempi, G.5
Ceccarelli, M.6
Noushmehr, H.7
-
88
-
-
84876548372
-
Fast and accurate read mapping with approximate seeds and multiple backtracking
-
Siragusa, E., Weese, D., Reinert, K., Fast and accurate read mapping with approximate seeds and multiple backtracking. Nucleic Acids Res., 41, 2013, e78.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. e78
-
-
Siragusa, E.1
Weese, D.2
Reinert, K.3
-
89
-
-
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., Paulovich, A., Pomeroy, S.L., Golub, T.R., Lander, E.S., Mesirov, J.P., Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102 (2005), 15545–15550.
-
(2005)
Proc. Natl. Acad. Sci. USA
, 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
-
90
-
-
84925550130
-
OptiType: precision HLA typing from next-generation sequencing data
-
Szolek, A., Schubert, B., Mohr, C., Sturm, M., Feldhahn, M., Kohlbacher, O., OptiType: precision HLA typing from next-generation sequencing data. Bioinformatics 30 (2014), 3310–3316.
-
(2014)
Bioinformatics
, vol.30
, pp. 3310-3316
-
-
Szolek, A.1
Schubert, B.2
Mohr, C.3
Sturm, M.4
Feldhahn, M.5
Kohlbacher, O.6
-
91
-
-
85039543315
-
Comprehensive analysis of the clinical immuno-oncology landscape
-
Tang, J., Shalabi, A., Hubbard-Lucey, V.M., Comprehensive analysis of the clinical immuno-oncology landscape. Ann. Oncol. 29 (2018), 84–91.
-
(2018)
Ann. Oncol.
, vol.29
, pp. 84-91
-
-
Tang, J.1
Shalabi, A.2
Hubbard-Lucey, V.M.3
-
92
-
-
85017402367
-
A cloud-based workflow to quantify transcript-expression levels in public cancer compendia
-
Tatlow, P.J., Piccolo, S.R., A cloud-based workflow to quantify transcript-expression levels in public cancer compendia. Sci. Rep., 6, 2016, 39259.
-
(2016)
Sci. Rep.
, vol.6
, pp. 39259
-
-
Tatlow, P.J.1
Piccolo, S.R.2
-
93
-
-
85044906084
-
Genomic and functional approaches to understanding cancer aneuploidy
-
Taylor, A.M., Shih, J., Ha, G., Gao, G.F., Zhang, X., Berger, A.C., Schumacher, S.E., Wang, C., Hu, H., Liu, J., et al. Genomic and functional approaches to understanding cancer aneuploidy. Cancer Cell, 33, 2018, 10.1016/j.ccell.2018.03.007.
-
(2018)
Cancer Cell
, vol.33
-
-
Taylor, A.M.1
Shih, J.2
Ha, G.3
Gao, G.F.4
Zhang, X.5
Berger, A.C.6
Schumacher, S.E.7
Wang, C.8
Hu, H.9
Liu, J.10
-
94
-
-
78049396399
-
Improved prognostic classification of breast cancer defined by antagonistic activation patterns of immune response pathway modules
-
Teschendorff, A.E., Gomez, S., Arenas, A., El-Ashry, D., Schmidt, M., Gehrmann, M., Caldas, C., Improved prognostic classification of breast cancer defined by antagonistic activation patterns of immune response pathway modules. BMC Cancer, 10, 2010, 604.
-
(2010)
BMC Cancer
, vol.10
, pp. 604
-
-
Teschendorff, A.E.1
Gomez, S.2
Arenas, A.3
El-Ashry, D.4
Schmidt, M.5
Gehrmann, M.6
Caldas, C.7
-
95
-
-
84935009372
-
Genomic classification of cutaneous melanoma
-
The Cancer Genome Atlas Network. Genomic classification of cutaneous melanoma. Cell 161 (2015), 1681–1696.
-
(2015)
Cell
, vol.161
, pp. 1681-1696
-
-
-
96
-
-
79959838081
-
Integrated genomic analyses of ovarian carcinoma
-
The Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 474 (2011), 609–615.
-
(2011)
Nature
, vol.474
, pp. 609-615
-
-
-
97
-
-
26644472430
-
Cluster validation by prediction strength
-
Tibshirani, R., Walther, G., Cluster validation by prediction strength. J. Comput. Graph. Stat. 14 (2005), 511–528.
-
(2005)
J. Comput. Graph. Stat.
, vol.14
, pp. 511-528
-
-
Tibshirani, R.1
Walther, G.2
-
98
-
-
85016574289
-
Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq
-
Venteicher, A.S., Tirosh, I., Hebert, C., Yizhak, K., Neftel, C., Filbin, M.G., Hovestadt, V., Escalante, L.E., Shaw, M.L., Rodman, C., et al. Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq. Science, 355, 2017, 10.1126/science.aai8478.
-
(2017)
Science
, vol.355
-
-
Venteicher, A.S.1
Tirosh, I.2
Hebert, C.3
Yizhak, K.4
Neftel, C.5
Filbin, M.G.6
Hovestadt, V.7
Escalante, L.E.8
Shaw, M.L.9
Rodman, C.10
-
99
-
-
84876529769
-
TFClass: an expandable hierarchical classification of human transcription factors
-
Wingender, E., Schoeps, T., Donitz, J., TFClass: an expandable hierarchical classification of human transcription factors. Nucleic Acids Res. 41 (2013), D165–D170.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D165-D170
-
-
Wingender, E.1
Schoeps, T.2
Donitz, J.3
-
100
-
-
84895739525
-
Gene co-expression modules as clinically relevant hallmarks of breast cancer diversity
-
Wolf, D.M., Lenburg, M.E., Yau, C., Boudreau, A., van ’t Veer, L.J., Gene co-expression modules as clinically relevant hallmarks of breast cancer diversity. PLoS ONE, 9, 2014, e88309.
-
(2014)
PLoS ONE
, vol.9
, pp. e88309
-
-
Wolf, D.M.1
Lenburg, M.E.2
Yau, C.3
Boudreau, A.4
van ’t Veer, L.J.5
-
101
-
-
84885008220
-
Pan-cancer patterns of somatic copy number alteration
-
Zack, T.I., Schumacher, S.E., Carter, S.L., Cherniack, A.D., Saksena, G., Tabak, B., Lawrence, M.S., Zhsng, C.Z., Wala, J., Mermel, C.H., et al. Pan-cancer patterns of somatic copy number alteration. Nat. Genet. 45 (2013), 1134–1140.
-
(2013)
Nat. Genet.
, vol.45
, pp. 1134-1140
-
-
Zack, T.I.1
Schumacher, S.E.2
Carter, S.L.3
Cherniack, A.D.4
Saksena, G.5
Tabak, B.6
Lawrence, M.S.7
Zhsng, C.Z.8
Wala, J.9
Mermel, C.H.10
-
102
-
-
84867881743
-
Structure-based prediction of protein-protein interactions on a genome-wide scale
-
Zhang, Q.C., Petrey, D., Deng, L., Qiang, L., Shi, Y., Thu, C.A., Bisikirska, B., Lefebvre, C., Accili, D., Hunter, T., et al. Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature 490 (2012), 556–560.
-
(2012)
Nature
, vol.490
, pp. 556-560
-
-
Zhang, Q.C.1
Petrey, D.2
Deng, L.3
Qiang, L.4
Shi, Y.5
Thu, C.A.6
Bisikirska, B.7
Lefebvre, C.8
Accili, D.9
Hunter, T.10
|