-
1
-
-
1542515338
-
A census of human cancer genes
-
Futreal PA, Coin L, Marshall M, Down T, Hubbard T, et al. (2004) A census of human cancer genes. Nat Rev Cancer 4: 177–183. 14993899
-
(2004)
Nat Rev Cancer
, vol.4
, pp. 177-183
-
-
Futreal, P.A.1
Coin, L.2
Marshall, M.3
Down, T.4
Hubbard, T.5
-
2
-
-
84866894408
-
Comprehensive genomic characterization of squamous cell lung cancers
-
Cancer Genome Atlas Research N (2012) Comprehensive genomic characterization of squamous cell lung cancers. Nature 489: 519–525. doi: 10.1038/nature11404 22960745
-
(2012)
Nature
, vol.489
, pp. 519-525
-
-
-
3
-
-
84877028141
-
Comprehensive molecular portraits of human breast tumours
-
Cancer Genome Atlas N (2012) Comprehensive molecular portraits of human breast tumours. Nature 490: 61–70. doi: 10.1038/nature11412 23000897
-
(2012)
Nature
, vol.490
, pp. 61-70
-
-
-
4
-
-
84863922124
-
Comprehensive molecular characterization of human colon and rectal cancer
-
Cancer Genome Atlas N (2012) Comprehensive molecular characterization of human colon and rectal cancer. Nature 487: 330–337. doi: 10.1038/nature11252 22810696
-
(2012)
Nature
, vol.487
, pp. 330-337
-
-
-
5
-
-
79959838081
-
Integrated genomic analyses of ovarian carcinoma
-
Cancer Genome Atlas Research N (2011) Integrated genomic analyses of ovarian carcinoma. Nature 474: 609–615. doi: 10.1038/nature10166 21720365
-
(2011)
Nature
, vol.474
, pp. 609-615
-
-
-
6
-
-
77951115122
-
International network of cancer genome projects
-
International Cancer Genome CHudson TJ, Anderson W, Artez A, Barker AD, et al. (2010) International network of cancer genome projects. Nature 464: 993–998. doi: 10.1038/nature08987 20393554
-
(2010)
Nature
, vol.464
, pp. 993-998
-
-
Hudson, T.J.1
Anderson, W.2
Artez, A.3
Barker, A.D.4
-
7
-
-
54549108740
-
Comprehensive genomic characterization defines human glioblastoma genes and core pathways
-
Cancer Genome Atlas Research N (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455: 1061–1068. doi: 10.1038/nature07385 18772890
-
(2008)
Nature
, vol.455
, pp. 1061-1068
-
-
-
8
-
-
84879890360
-
Comprehensive molecular characterization of clear cell renal cell carcinoma
-
Cancer Genome Atlas Research N (2013) Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature 499: 43–49. doi: 10.1038/nature12222 23792563
-
(2013)
Nature
, vol.499
, pp. 43-49
-
-
-
9
-
-
84878372012
-
Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia
-
Cancer Genome Atlas Research N (2013) Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med 368: 2059–2074. doi: 10.1056/NEJMoa1301689 23634996
-
(2013)
N Engl J Med
, vol.368
, pp. 2059-2074
-
-
-
10
-
-
84908695210
-
The somatic genomic landscape of chromophobe renal cell carcinoma
-
Davis CF, Ricketts CJ, Wang M, Yang L, Cherniack AD, et al. (2014) The somatic genomic landscape of chromophobe renal cell carcinoma. Cancer Cell 26: 319–330. doi: 10.1016/j.ccr.2014.07.014 25155756
-
(2014)
Cancer Cell
, vol.26
, pp. 319-330
-
-
Davis, C.F.1
Ricketts, C.J.2
Wang, M.3
Yang, L.4
Cherniack, A.D.5
-
11
-
-
84905029258
-
Comprehensive molecular profiling of lung adenocarcinoma
-
Cancer Genome Atlas Research N (2014) Comprehensive molecular profiling of lung adenocarcinoma. Nature 511: 543–550. doi: 10.1038/nature13385 25079552
-
(2014)
Nature
, vol.511
, pp. 543-550
-
-
-
12
-
-
84908335908
-
Integrated genomic characterization of papillary thyroid carcinoma
-
Cancer Genome Atlas Research N (2014) Integrated genomic characterization of papillary thyroid carcinoma. Cell 159: 676–690. doi: 10.1016/j.cell.2014.09.050 25417114
-
(2014)
Cell
, vol.159
, pp. 676-690
-
-
-
13
-
-
84907270779
-
Comprehensive molecular characterization of gastric adenocarcinoma
-
Cancer Genome Atlas Research N (2014) Comprehensive molecular characterization of gastric adenocarcinoma. Nature 513: 202–209. doi: 10.1038/nature13480 25079317
-
(2014)
Nature
, vol.513
, pp. 202-209
-
-
-
14
-
-
84897022815
-
Comprehensive molecular characterization of urothelial bladder carcinoma
-
Cancer Genome Atlas Research N (2014) Comprehensive molecular characterization of urothelial bladder carcinoma. Nature 507: 315–322. doi: 10.1038/nature12965 24476821
-
(2014)
Nature
, vol.507
, pp. 315-322
-
-
-
15
-
-
84923197605
-
Comprehensive genomic characterization of head and neck squamous cell carcinomas
-
Cancer Genome Atlas N (2015) Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature 517: 576–582. doi: 10.1038/nature14129 25631445
-
(2015)
Nature
, vol.517
, pp. 576-582
-
-
-
16
-
-
84908460595
-
Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin
-
Hoadley KA, Yau C, Wolf DM, Cherniack AD, Tamborero D, et al. (2014) Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell 158: 929–944. doi: 10.1016/j.cell.2014.06.049 25109877
-
(2014)
Cell
, vol.158
, pp. 929-944
-
-
Hoadley, K.A.1
Yau, C.2
Wolf, D.M.3
Cherniack, A.D.4
Tamborero, D.5
-
17
-
-
84885129618
-
Comprehensive identification of mutational cancer driver genes across 12 tumor types
-
Tamborero D, Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Kandoth C, et al. (2013) Comprehensive identification of mutational cancer driver genes across 12 tumor types. Sci Rep 3: 2650. doi: 10.1038/srep02650 24084849
-
(2013)
Sci Rep
, vol.3
, pp. 2650
-
-
Tamborero, D.1
Gonzalez-Perez, A.2
Perez-Llamas, C.3
Deu-Pons, J.4
Kandoth, C.5
-
18
-
-
84864598664
-
MuSiC: identifying mutational significance in cancer genomes
-
Dees ND, Zhang Q, Kandoth C, Wendl MC, Schierding W, et al. (2012) MuSiC: identifying mutational significance in cancer genomes. Genome Res 22: 1589–1598. doi: 10.1101/gr.134635.111 22759861
-
(2012)
Genome Res
, vol.22
, pp. 1589-1598
-
-
Dees, N.D.1
Zhang, Q.2
Kandoth, C.3
Wendl, M.C.4
Schierding, W.5
-
19
-
-
84892833777
-
Discovery and saturation analysis of cancer genes across 21 tumour types
-
Lawrence MS, Stojanov P, Mermel CH, Robinson JT, Garraway LA, et al. (2014) Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 505: 495–501. doi: 10.1038/nature12912 24390350
-
(2014)
Nature
, vol.505
, pp. 495-501
-
-
Lawrence, M.S.1
Stojanov, P.2
Mermel, C.H.3
Robinson, J.T.4
Garraway, L.A.5
-
20
-
-
84870599966
-
Functional impact bias reveals cancer drivers
-
Gonzalez-Perez A, Lopez-Bigas N, (2012) Functional impact bias reveals cancer drivers. Nucleic Acids Res 40: e169. doi: 10.1093/nar/gks743 22904074
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 169
-
-
Gonzalez-Perez, A.1
Lopez-Bigas, N.2
-
21
-
-
84883467378
-
OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes
-
Tamborero D, Gonzalez-Perez A, Lopez-Bigas N, (2013) OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes. Bioinformatics 29: 2238–2244. doi: 10.1093/bioinformatics/btt395 23884480
-
(2013)
Bioinformatics
, vol.29
, pp. 2238-2244
-
-
Tamborero, D.1
Gonzalez-Perez, A.2
Lopez-Bigas, N.3
-
22
-
-
84911379962
-
e-Driver: a novel method to identify protein regions driving cancer
-
Porta-Pardo E, Godzik A, (2014) e-Driver: a novel method to identify protein regions driving cancer. Bioinformatics 30: 3109–3114. doi: 10.1093/bioinformatics/btu499 25064568
-
(2014)
Bioinformatics
, vol.30
, pp. 3109-3114
-
-
Porta-Pardo, E.1
Godzik, A.2
-
23
-
-
84926157747
-
Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes
-
Leiserson MD, Vandin F, Wu HT, Dobson JR, Eldridge JV, et al. (2014) Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes. Nat Genet.
-
(2014)
Nat Genet
-
-
Leiserson, M.D.1
Vandin, F.2
Wu, H.T.3
Dobson, J.R.4
Eldridge, J.V.5
-
24
-
-
84907812291
-
The role of the interactome in the maintenance of deleterious variability in human populations
-
Garcia-Alonso L, Jimenez-Almazan J, Carbonell-Caballero J, Vela-Boza A, Santoyo-Lopez J, et al. (2014) The role of the interactome in the maintenance of deleterious variability in human populations. Mol Syst Biol 10: 752. doi: 10.15252/msb.20145222 25261458
-
(2014)
Mol Syst Biol
, vol.10
, pp. 752
-
-
Garcia-Alonso, L.1
Jimenez-Almazan, J.2
Carbonell-Caballero, J.3
Vela-Boza, A.4
Santoyo-Lopez, J.5
-
25
-
-
84873802661
-
Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers
-
Reimand J, Bader GD, (2013) Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers. Mol Syst Biol 9: 637. doi: 10.1038/msb.2012.68 23340843
-
(2013)
Mol Syst Biol
, vol.9
, pp. 637
-
-
Reimand, J.1
Bader, G.D.2
-
26
-
-
84878818533
-
Utilizing protein structure to identify non-random somatic mutations
-
Ryslik GA, Cheng Y, Cheung K-H, Modis Y, Zhao H, (2013) Utilizing protein structure to identify non-random somatic mutations. BMC Bioinformatics 14.
-
(2013)
BMC Bioinformatics
, vol.14
-
-
Ryslik, G.A.1
Cheng, Y.2
Cheung, K.-H.3
Modis, Y.4
Zhao, H.5
-
27
-
-
72849127628
-
Kinase mutations in human disease: interpreting genotype-phenotype relationships
-
Lahiry P, Torkamani A, Schork NJ, Hegele RA, (2010) Kinase mutations in human disease: interpreting genotype-phenotype relationships. Nat Rev Genet 11: 60–74. doi: 10.1038/nrg2707 20019687
-
(2010)
Nat Rev Genet
, vol.11
, pp. 60-74
-
-
Lahiry, P.1
Torkamani, A.2
Schork, N.J.3
Hegele, R.A.4
-
28
-
-
84922394461
-
Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss
-
Gross AM, Orosco RK, Shen JP, Egloff AM, Carter H, et al. (2014) Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss. Nat Genet 46: 939–943. doi: 10.1038/ng.3051 25086664
-
(2014)
Nat Genet
, vol.46
, pp. 939-943
-
-
Gross, A.M.1
Orosco, R.K.2
Shen, J.P.3
Egloff, A.M.4
Carter, H.5
-
29
-
-
33748706765
-
Global topological features of cancer proteins in the human interactome
-
Jonsson PF, Bates PA, (2006) Global topological features of cancer proteins in the human interactome. Bioinformatics 22: 2291–2297. 16844706
-
(2006)
Bioinformatics
, vol.22
, pp. 2291-2297
-
-
Jonsson, P.F.1
Bates, P.A.2
-
30
-
-
84922589272
-
A multiscale statistical mechanical framework integrates biophysical and genomic data to assemble cancer networks
-
AlQuraishi M, Koytiger G, Jenney A, MacBeath G, Sorger PK, (2014) A multiscale statistical mechanical framework integrates biophysical and genomic data to assemble cancer networks. Nat Genet 46: 1363–1371. doi: 10.1038/ng.3138 25362484
-
(2014)
Nat Genet
, vol.46
, pp. 1363-1371
-
-
AlQuraishi, M.1
Koytiger, G.2
Jenney, A.3
MacBeath, G.4
Sorger, P.K.5
-
31
-
-
84879157943
-
Cancer missense mutations alter binding properties of proteins and their interaction networks
-
Nishi H, Tyagi M, Teng S, Shoemaker BA, Hashimoto K, et al. (2013) Cancer missense mutations alter binding properties of proteins and their interaction networks. PLoS One 8: e66273. doi: 10.1371/journal.pone.0066273 23799087
-
(2013)
PLoS One
, vol.8
, pp. 66273
-
-
Nishi, H.1
Tyagi, M.2
Teng, S.3
Shoemaker, B.A.4
Hashimoto, K.5
-
32
-
-
84898646417
-
Deriving a mutation index of carcinogenicity using protein structure and protein interfaces
-
Espinosa O, Mitsopoulos K, Hakas J, Pearl F, Zvelebil M, (2014) Deriving a mutation index of carcinogenicity using protein structure and protein interfaces. PLoS One 9: e84598. doi: 10.1371/journal.pone.0084598 24454733
-
(2014)
PLoS One
, vol.9
, pp. 84598
-
-
Espinosa, O.1
Mitsopoulos, K.2
Hakas, J.3
Pearl, F.4
Zvelebil, M.5
-
34
-
-
84920962202
-
Molecular and genetic properties of tumors associated with local immune cytolytic activity
-
Rooney MS, Shukla SA, Wu CJ, Getz G, Hacohen N, (2015) Molecular and genetic properties of tumors associated with local immune cytolytic activity. Cell 160: 48–61. doi: 10.1016/j.cell.2014.12.033 25594174
-
(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
-
35
-
-
84884994218
-
The Cancer Genome Atlas Pan-Cancer analysis project
-
Cancer Genome Atlas Research NWeinstein JN, Collisson EA, Mills GB, Shaw KR, et al. (2013) The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet 45: 1113–1120. doi: 10.1038/ng.2764 24071849
-
(2013)
Nat Genet
, vol.45
, pp. 1113-1120
-
-
Weinstein, J.N.1
Collisson, E.A.2
Mills, G.B.3
Shaw, K.R.4
-
36
-
-
84880507665
-
Mutational heterogeneity in cancer and the search for new cancer-associated genes
-
Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, et al. (2013) Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499: 214–218. doi: 10.1038/nature12213 23770567
-
(2013)
Nature
, vol.499
, pp. 214-218
-
-
Lawrence, M.S.1
Stojanov, P.2
Polak, P.3
Kryukov, G.V.4
Cibulskis, K.5
-
37
-
-
84871967106
-
Interactome3D: adding structural details to protein networks
-
Mosca R, Ceol A, Aloy P, (2013) Interactome3D: adding structural details to protein networks. Nat Methods 10: 47–53. doi: 10.1038/nmeth.2289 23399932
-
(2013)
Nat Methods
, vol.10
, pp. 47-53
-
-
Mosca, R.1
Ceol, A.2
Aloy, P.3
-
38
-
-
84859415553
-
Molecular pathways: fibroblast growth factor signaling: a new therapeutic opportunity in cancer
-
Brooks AN, Kilgour E, Smith PD, (2012) Molecular pathways: fibroblast growth factor signaling: a new therapeutic opportunity in cancer. Clin Cancer Res 18: 1855–1862. doi: 10.1158/1078-0432.CCR-11-0699 22388515
-
(2012)
Clin Cancer Res
, vol.18
, pp. 1855-1862
-
-
Brooks, A.N.1
Kilgour, E.2
Smith, P.D.3
-
39
-
-
84873859431
-
ARHGAP21 protein, a new partner of alpha-tubulin involved in cell-cell adhesion formation and essential for epithelial-mesenchymal transition
-
Barcellos KS, Bigarella CL, Wagner MV, Vieira KP, Lazarini M, et al. (2013) ARHGAP21 protein, a new partner of alpha-tubulin involved in cell-cell adhesion formation and essential for epithelial-mesenchymal transition. J Biol Chem 288: 2179–2189. doi: 10.1074/jbc.M112.432716 23235160
-
(2013)
J Biol Chem
, vol.288
, pp. 2179-2189
-
-
Barcellos, K.S.1
Bigarella, C.L.2
Wagner, M.V.3
Vieira, K.P.4
Lazarini, M.5
-
40
-
-
84899836282
-
Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival
-
Brown SD, Warren RL, Gibb EA, Martin SD, Spinelli JJ, et al. (2014) Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival. Genome Res 24: 743–750. doi: 10.1101/gr.165985.113 24782321
-
(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
-
41
-
-
54549109936
-
Modulation of the antitumor immune response by complement
-
Markiewski MM, DeAngelis RA, Benencia F, Ricklin-Lichtsteiner SK, Koutoulaki A, et al. (2008) Modulation of the antitumor immune response by complement. Nat Immunol 9: 1225–1235. doi: 10.1038/ni.1655 18820683
-
(2008)
Nat Immunol
, vol.9
, pp. 1225-1235
-
-
Markiewski, M.M.1
DeAngelis, R.A.2
Benencia, F.3
Ricklin-Lichtsteiner, S.K.4
Koutoulaki, A.5
-
42
-
-
84916215272
-
Transient complement inhibition promotes a tumor-specific immune response through the implication of natural killer cells
-
Janelle V, Langlois MP, Tarrab E, Lapierre P, Poliquin L, et al. (2014) Transient complement inhibition promotes a tumor-specific immune response through the implication of natural killer cells. Cancer Immunol Res 2: 200–206. doi: 10.1158/2326-6066.CIR-13-0173 24778316
-
(2014)
Cancer Immunol Res
, vol.2
, pp. 200-206
-
-
Janelle, V.1
Langlois, M.P.2
Tarrab, E.3
Lapierre, P.4
Poliquin, L.5
-
43
-
-
84911474471
-
A proteome-scale map of the human interactome network
-
Rolland T, Tasan M, Charloteaux B, Pevzner SJ, Zhong Q, et al. (2014) A proteome-scale map of the human interactome network. Cell 159: 1212–1226. doi: 10.1016/j.cell.2014.10.050 25416956
-
(2014)
Cell
, vol.159
, pp. 1212-1226
-
-
Rolland, T.1
Tasan, M.2
Charloteaux, B.3
Pevzner, S.J.4
Zhong, Q.5
-
44
-
-
84887083535
-
TCPA: a resource for cancer functional proteomics data
-
Li J, Lu Y, Akbani R, Ju Z, Roebuck PL, et al. (2013) TCPA: a resource for cancer functional proteomics data. Nat Methods 10: 1046–1047.
-
(2013)
Nat Methods
, vol.10
, pp. 1046-1047
-
-
Li, J.1
Lu, Y.2
Akbani, R.3
Ju, Z.4
Roebuck, P.L.5
-
45
-
-
84877819562
-
Gain of interaction with IRS1 by p110alpha-helical domain mutants is crucial for their oncogenic functions
-
Hao Y, Wang C, Cao B, Hirsch BM, Song J, et al. (2013) Gain of interaction with IRS1 by p110alpha-helical domain mutants is crucial for their oncogenic functions. Cancer Cell 23: 583–593. doi: 10.1016/j.ccr.2013.03.021 23643389
-
(2013)
Cancer Cell
, vol.23
, pp. 583-593
-
-
Hao, Y.1
Wang, C.2
Cao, B.3
Hirsch, B.M.4
Song, J.5
-
46
-
-
84902009201
-
The DNA-binding domain mediates both nuclear and cytosolic functions of p53
-
Follis AV, Llambi F, Ou L, Baran K, Green DR, et al. (2014) The DNA-binding domain mediates both nuclear and cytosolic functions of p53. Nat Struct Mol Biol 21: 535–543. doi: 10.1038/nsmb.2829 24814347
-
(2014)
Nat Struct Mol Biol
, vol.21
, pp. 535-543
-
-
Follis, A.V.1
Llambi, F.2
Ou, L.3
Baran, K.4
Green, D.R.5
-
47
-
-
84868010133
-
Domain landscapes of somatic mutations in cancer
-
Nehrt NL, Peterson TA, Park D, Kann MG, (2012) Domain landscapes of somatic mutations in cancer. BMC Genomics 13 Suppl 4: S9. doi: 10.1186/1471-2164-13-S4-S9 22759657
-
(2012)
BMC Genomics
, vol.13
, pp. 9
-
-
Nehrt, N.L.1
Peterson, T.A.2
Park, D.3
Kann, M.G.4
-
48
-
-
84920956731
-
Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing
-
Yadav M, Jhunjhunwala S, Phung QT, Lupardus P, Tanguay J, et al. (2014) Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing. Nature 515: 572–576. doi: 10.1038/nature14001 25428506
-
(2014)
Nature
, vol.515
, pp. 572-576
-
-
Yadav, M.1
Jhunjhunwala, S.2
Phung, Q.T.3
Lupardus, P.4
Tanguay, J.5
-
49
-
-
84990011361
-
HLA-binding properties of tumor neoepitopes in humans
-
Fritsch EF, Rajasagi M, Ott PA, Brusic V, Hacohen N, et al. (2014) HLA-binding properties of tumor neoepitopes in humans. Cancer Immunol Res 2: 522–529. doi: 10.1158/2326-6066.CIR-13-0227 24894089
-
(2014)
Cancer Immunol Res
, vol.2
, pp. 522-529
-
-
Fritsch, E.F.1
Rajasagi, M.2
Ott, P.A.3
Brusic, V.4
Hacohen, N.5
-
50
-
-
84922262953
-
Cancer3D: understanding cancer mutations through protein structures
-
Porta-Pardo E, Hrabe T, Godzik A, (2014) Cancer3D: understanding cancer mutations through protein structures. Nucleic Acids Res.
-
(2014)
Nucleic Acids Res
-
-
Porta-Pardo, E.1
Hrabe, T.2
Godzik, A.3
-
51
-
-
84896366070
-
Synonymous mutations frequently act as driver mutations in human cancers
-
Supek F, Minana B, Valcarcel J, Gabaldon T, Lehner B, (2014) Synonymous mutations frequently act as driver mutations in human cancers. Cell 156: 1324–1335. doi: 10.1016/j.cell.2014.01.051 24630730
-
(2014)
Cell
, vol.156
, pp. 1324-1335
-
-
Supek, F.1
Minana, B.2
Valcarcel, J.3
Gabaldon, T.4
Lehner, B.5
-
52
-
-
79960001809
-
FFAS server: novel features and applications
-
Jaroszewski L, Li Z, Cai XH, Weber C, Godzik A, (2011) FFAS server: novel features and applications. Nucleic Acids Res 39: W38–44. doi: 10.1093/nar/gkr441 21715387
-
(2011)
Nucleic Acids Res
, vol.39
, pp. 38-44
-
-
Jaroszewski, L.1
Li, Z.2
Cai, X.H.3
Weber, C.4
Godzik, A.5
-
53
-
-
84904799548
-
AIDA: ab initio domain assembly server
-
Xu D, Jaroszewski L, Li Z, Godzik A, (2014) AIDA: ab initio domain assembly server. Nucleic Acids Res 42: W308–313. doi: 10.1093/nar/gku369 24831546
-
(2014)
Nucleic Acids Res
, vol.42
, pp. 308-313
-
-
Xu, D.1
Jaroszewski, L.2
Li, Z.3
Godzik, A.4
-
54
-
-
84922250630
-
Analysis of individual protein regions provides novel insights on cancer pharmacogenomics
-
Porta-Pardo E, Godzik A, (2015) Analysis of individual protein regions provides novel insights on cancer pharmacogenomics. PLoS Comput Biol 11: e1004024. doi: 10.1371/journal.pcbi.1004024 25568936
-
(2015)
PLoS Comput Biol
, vol.11
, pp. 1004024
-
-
Porta-Pardo, E.1
Godzik, A.2
-
55
-
-
72849142731
-
Edgetic perturbation models of human inherited disorders
-
Zhong Q, Simonis N, Li QR, Charloteaux B, Heuze F, et al. (2009) Edgetic perturbation models of human inherited disorders. Mol Syst Biol 5: 321. doi: 10.1038/msb.2009.80 19888216
-
(2009)
Mol Syst Biol
, vol.5
, pp. 321
-
-
Zhong, Q.1
Simonis, N.2
Li, Q.R.3
Charloteaux, B.4
Heuze, F.5
-
56
-
-
84889606541
-
Edgotype: a fundamental link between genotype and phenotype
-
Sahni N, Yi S, Zhong Q, Jailkhani N, Charloteaux B, et al. (2013) Edgotype: a fundamental link between genotype and phenotype. Curr Opin Genet Dev 23: 649–657. doi: 10.1016/j.gde.2013.11.002 24287335
-
(2013)
Curr Opin Genet Dev
, vol.23
, pp. 649-657
-
-
Sahni, N.1
Yi, S.2
Zhong, Q.3
Jailkhani, N.4
Charloteaux, B.5
-
57
-
-
84888001187
-
High-resolution network biology: connecting sequence with function
-
Ryan CJ, Cimermancic P, Szpiech ZA, Sali A, Hernandez RD, et al. (2013) High-resolution network biology: connecting sequence with function. Nat Rev Genet 14: 865–879. doi: 10.1038/nrg3574 24197012
-
(2013)
Nat Rev Genet
, vol.14
, pp. 865-879
-
-
Ryan, C.J.1
Cimermancic, P.2
Szpiech, Z.A.3
Sali, A.4
Hernandez, R.D.5
-
58
-
-
84863010950
-
Three-dimensional reconstruction of protein networks provides insight into human genetic disease
-
Wang X, Wei X, Thijssen B, Das J, Lipkin SM, et al. (2012) Three-dimensional reconstruction of protein networks provides insight into human genetic disease. Nat Biotechnol 30: 159–164. doi: 10.1038/nbt.2106 22252508
-
(2012)
Nat Biotechnol
, vol.30
, pp. 159-164
-
-
Wang, X.1
Wei, X.2
Thijssen, B.3
Das, J.4
Lipkin, S.M.5
-
59
-
-
84928389942
-
Widespread macromolecular interaction perturbations in human genetic disorders
-
Sahni N, Yi S, Taipale M, Fuxman Bass JI, Coulombe-Huntington J, et al. (2015) Widespread macromolecular interaction perturbations in human genetic disorders. Cell 161: 647–660. doi: 10.1016/j.cell.2015.04.013 25910212
-
(2015)
Cell
, vol.161
, pp. 647-660
-
-
Sahni, N.1
Yi, S.2
Taipale, M.3
Fuxman Bass, J.I.4
Coulombe-Huntington, J.5
-
60
-
-
78650372656
-
Different types of K-Ras mutations could affect drug sensitivity and tumour behaviour in non-small-cell lung cancer
-
Garassino MC, Marabese M, Rusconi P, Rulli E, Martelli O, et al. (2011) Different types of K-Ras mutations could affect drug sensitivity and tumour behaviour in non-small-cell lung cancer. Annals of Oncology 22.
-
(2011)
Annals of Oncology
, vol.22
-
-
Garassino, M.C.1
Marabese, M.2
Rusconi, P.3
Rulli, E.4
Martelli, O.5
-
61
-
-
84925970140
-
DAISY: picking synthetic lethals from cancer genomes
-
Ryan CJ, Lord CJ, Ashworth A, (2014) DAISY: picking synthetic lethals from cancer genomes. Cancer Cell 26: 306–308. doi: 10.1016/j.ccr.2014.08.008 25203319
-
(2014)
Cancer Cell
, vol.26
, pp. 306-308
-
-
Ryan, C.J.1
Lord, C.J.2
Ashworth, A.3
-
62
-
-
84874189784
-
Highly recurrent TERT promoter mutations in human melanoma
-
Huang FW, Hodis E, Xu MJ, Kryukov GV, Chin L, et al. (2013) Highly recurrent TERT promoter mutations in human melanoma. Science 339: 957–959. doi: 10.1126/science.1229259 23348506
-
(2013)
Science
, vol.339
, pp. 957-959
-
-
Huang, F.W.1
Hodis, E.2
Xu, M.J.3
Kryukov, G.V.4
Chin, L.5
-
63
-
-
84884997982
-
Emerging landscape of oncogenic signatures across human cancers
-
Ciriello G, Miller ML, Aksoy BA, Senbabaoglu Y, Schultz N, et al. (2013) Emerging landscape of oncogenic signatures across human cancers. Nat Genet 45: 1127–1133. doi: 10.1038/ng.2762 24071851
-
(2013)
Nat Genet
, vol.45
, pp. 1127-1133
-
-
Ciriello, G.1
Miller, M.L.2
Aksoy, B.A.3
Senbabaoglu, Y.4
Schultz, N.5
-
64
-
-
84928788044
-
TP53 loss creates therapeutic vulnerability in colorectal cancer
-
Liu Y, Zhang X, Han C, Wan G, Huang X, et al. (2015) TP53 loss creates therapeutic vulnerability in colorectal cancer. Nature 520: 697–701. doi: 10.1038/nature14418 25901683
-
(2015)
Nature
, vol.520
, pp. 697-701
-
-
Liu, Y.1
Zhang, X.2
Han, C.3
Wan, G.4
Huang, X.5
-
65
-
-
77955405475
-
Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor
-
McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, et al. (2010) Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26: 2069–2070. doi: 10.1093/bioinformatics/btq330 20562413
-
(2010)
Bioinformatics
, vol.26
, pp. 2069-2070
-
-
McLaren, W.1
Pritchard, B.2
Rios, D.3
Chen, Y.4
Flicek, P.5
-
66
-
-
75549083885
-
Inferred Biomolecular Interaction Server—a web server to analyze and predict protein interacting partners and binding sites
-
Shoemaker BA, Zhang D, Thangudu RR, Tyagi M, Fong JH, et al. (2010) Inferred Biomolecular Interaction Server—a web server to analyze and predict protein interacting partners and binding sites. Nucleic Acids Res 38: D518–524. doi: 10.1093/nar/gkp842 19843613
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 518-524
-
-
Shoemaker, B.A.1
Zhang, D.2
Thangudu, R.R.3
Tyagi, M.4
Fong, J.H.5
-
67
-
-
58149193222
-
Human Protein Reference Database—2009 update
-
Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, et al. (2009) Human Protein Reference Database—2009 update. Nucleic Acids Res 37: D767–772. doi: 10.1093/nar/gkn892 18988627
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 767-772
-
-
Keshava Prasad, T.S.1
Goel, R.2
Kandasamy, K.3
Keerthikumar, S.4
Kumar, S.5
-
68
-
-
84941145210
-
The BioGRID interaction database: 2015 update
-
Chatr-Aryamontri A, Breitkreutz BJ, Oughtred R, Boucher L, Heinicke S, et al. (2015) The BioGRID interaction database: 2015 update. Nucleic Acids Res 43: D470–478. doi: 10.1093/nar/gku1204 25428363
-
(2015)
Nucleic Acids Res
, vol.43
, pp. 470-478
-
-
Chatr-Aryamontri, A.1
Breitkreutz, B.J.2
Oughtred, R.3
Boucher, L.4
Heinicke, S.5
-
69
-
-
84876515907
-
STRING v9.1: protein-protein interaction networks, with increased coverage and integration
-
Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, et al. (2013) STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res 41: D808–815. doi: 10.1093/nar/gks1094 23203871
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 808-815
-
-
Franceschini, A.1
Szklarczyk, D.2
Frankild, S.3
Kuhn, M.4
Simonovic, M.5
-
70
-
-
38649138295
-
A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans
-
Lee I, Lehner B, Crombie C, Wong W, Fraser AG, et al. (2008) A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans. Nat Genet 40: 181–188. doi: 10.1038/ng.2007.70 18223650
-
(2008)
Nat Genet
, vol.40
, pp. 181-188
-
-
Lee, I.1
Lehner, B.2
Crombie, C.3
Wong, W.4
Fraser, A.G.5
-
71
-
-
79959846617
-
PSICQUIC and PSISCORE: accessing and scoring molecular interactions
-
Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, et al. (2011) PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Methods 8: 528–529. doi: 10.1038/nmeth.1637 21716279
-
(2011)
Nat Methods
, vol.8
, pp. 528-529
-
-
Aranda, B.1
Blankenburg, H.2
Kerrien, S.3
Brinkman, F.S.4
Ceol, A.5
-
72
-
-
84925028000
-
In silico prediction of physical protein interactions and characterization of interactome orphans
-
Kotlyar M, Pastrello C, Pivetta F, Lo Sardo A, Cumbaa C, et al. (2015) In silico prediction of physical protein interactions and characterization of interactome orphans. Nat Methods 12: 79–84. doi: 10.1038/nmeth.3178 25402006
-
(2015)
Nat Methods
, vol.12
, pp. 79-84
-
-
Kotlyar, M.1
Pastrello, C.2
Pivetta, F.3
Lo Sardo, A.4
Cumbaa, C.5
-
73
-
-
0036408751
-
Intrinsic Disorder in Cell-signaling and Cancer-associated Proteins
-
Iakoucheva LM, Brown CJ, Lawson JD, Obradović Z, Dunker AK, (2002) Intrinsic Disorder in Cell-signaling and Cancer-associated Proteins. Journal of Molecular Biology 323: 573–584. 12381310
-
(2002)
Journal of Molecular Biology
, vol.323
, pp. 573-584
-
-
Iakoucheva, L.M.1
Brown, C.J.2
Lawson, J.D.3
Obradović, Z.4
Dunker, A.K.5
-
74
-
-
41549139527
-
Walking the interactome for prioritization of candidate disease genes
-
Kohler S, Bauer S, Horn D, Robinson PN, (2008) Walking the interactome for prioritization of candidate disease genes. Am J Hum Genet 82: 949–958. doi: 10.1016/j.ajhg.2008.02.013 18371930
-
(2008)
Am J Hum Genet
, vol.82
, pp. 949-958
-
-
Kohler, S.1
Bauer, S.2
Horn, D.3
Robinson, P.N.4
-
75
-
-
84895774260
-
VarWalker: personalized mutation network analysis of putative cancer genes from next-generation sequencing data
-
Jia P, Zhao Z, (2014) VarWalker: personalized mutation network analysis of putative cancer genes from next-generation sequencing data. PLoS Comput Biol 10: e1003460. doi: 10.1371/journal.pcbi.1003460 24516372
-
(2014)
PLoS Comput Biol
, vol.10
, pp. 1003460
-
-
Jia, P.1
Zhao, Z.2
-
76
-
-
84907333139
-
Predicting cancer-specific vulnerability via data-driven detection of synthetic lethality
-
Jerby-Arnon L, Pfetzer N, Waldman YY, McGarry L, James D, et al. (2014) Predicting cancer-specific vulnerability via data-driven detection of synthetic lethality. Cell 158: 1199–1209. doi: 10.1016/j.cell.2014.07.027 25171417
-
(2014)
Cell
, vol.158
, pp. 1199-1209
-
-
Jerby-Arnon, L.1
Pfetzer, N.2
Waldman, Y.Y.3
McGarry, L.4
James, D.5
-
77
-
-
84887084951
-
Network-based stratification of tumor mutations
-
Hofree M, Shen JP, Carter H, Gross A, Ideker T, (2013) Network-based stratification of tumor mutations. Nat Methods 10: 1108–1115. doi: 10.1038/nmeth.2651 24037242
-
(2013)
Nat Methods
, vol.10
, pp. 1108-1115
-
-
Hofree, M.1
Shen, J.P.2
Carter, H.3
Gross, A.4
Ideker, T.5
-
78
-
-
84873292211
-
Architecture and membrane interactions of the EGF receptor
-
Arkhipov A, Shan Y, Das R, Endres NF, Eastwood MP, et al. (2013) Architecture and membrane interactions of the EGF receptor. Cell 152: 557–569. doi: 10.1016/j.cell.2012.12.030 23374350
-
(2013)
Cell
, vol.152
, pp. 557-569
-
-
Arkhipov, A.1
Shan, Y.2
Das, R.3
Endres, N.F.4
Eastwood, M.P.5
|