-
1
-
-
84875490185
-
Cancer genome landscapes
-
Vogelstein, B. et al. Cancer genome landscapes. Science 339, 1546-1558, doi:10.1126/science.1235122 (2013).
-
(2013)
Science
, vol.339
, pp. 1546-1558
-
-
Vogelstein, B.1
-
2
-
-
84875758730
-
Lessons from the cancer genome
-
Garraway, L. A.&Lander, E. S. Lessons from the cancer genome. Cell 153, 17-37, doi:10.1016/j.cell.2013.03.002 (2013).
-
(2013)
Cell
, vol.153
, pp. 17-37
-
-
Garraway, L.A.1
Lander, E.S.2
-
3
-
-
0000801240
-
-
Ideker, T., Ozier, O., Schwikowski, B.&Siegel, A. F. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 18 Suppl 1, S233-240 (2002).
-
(2002)
Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics
, vol.18
, pp. S233-S240
-
-
Ideker, T.1
Ozier, O.2
Schwikowski, B.3
Siegel, A.F.4
-
4
-
-
80052493684
-
A network-based approach to prioritize results from genome-wide association studies
-
Akula, N. et al. A network-based approach to prioritize results from genome-wide association studies. PloS one 6, e24220, doi:10.1371/journal.pone.0024220 (2011).
-
(2011)
PloS One
, vol.6
, pp. e24220
-
-
Akula, N.1
-
5
-
-
79952389826
-
Algorithms for detecting significantly mutated pathways in cancer
-
Vandin, F., Upfal, E.&Raphael, B. J. Algorithms for detecting significantly mutated pathways in cancer. Journal of computational biology : a journal of computational molecular cell biology 18, 507-522, doi:10.1089/cmb.2010.0265 (2011).
-
(2011)
Journal of Computational Biology : A Journal of Computational Molecular Cell Biology
, vol.18
, pp. 507-522
-
-
Vandin, F.1
Upfal, E.2
Raphael, B.J.3
-
6
-
-
77949446630
-
Automated network analysis identifies core pathways in glioblastoma
-
Cerami, E., Demir, E., Schultz, N., Taylor, B. S.&Sander, C. Automated network analysis identifies core pathways in glioblastoma. PloS one 5, e8918, doi:10.1371/journal.pone.0008918 (2010).
-
(2010)
PloS One
, vol.5
, pp. e8918
-
-
Cerami, E.1
Demir, E.2
Schultz, N.3
Taylor, B.S.4
Sander, C.5
-
7
-
-
84887084951
-
Network-based stratification of tumor mutations
-
Hofree, M., Shen, J. P., Carter, H., Gross, A.&Ideker, T. Network-based stratification of tumor mutations. Nature methods 10, 1108-1115, doi:10.1038/nmeth.2651 (2013).
-
(2013)
Nature Methods
, vol.10
, pp. 1108-1115
-
-
Hofree, M.1
Shen, J.P.2
Carter, H.3
Gross, A.4
Ideker, T.5
-
8
-
-
84871967106
-
Interactome3D: Adding structural details to protein networks
-
Mosca, R., Ceol, A.&Aloy, P. Interactome3D: adding structural details to protein networks. Nature methods 10, 47-53, doi:10.1038/nmeth.2289 (2013).
-
(2013)
Nature Methods
, vol.10
, pp. 47-53
-
-
Mosca, R.1
Ceol, A.2
Aloy, P.3
-
9
-
-
84863010950
-
Three-dimensional reconstruction of protein networks provides insight into human genetic disease
-
Wang, X. et al. Three-dimensional reconstruction of protein networks provides insight into human genetic disease. Nature biotechnology 30, 159-164, doi:10.1038/nbt.2106 (2012).
-
(2012)
Nature Biotechnology
, vol.30
, pp. 159-164
-
-
Wang, X.1
-
10
-
-
84857790275
-
Protein-protein interaction sites are hot spots for disease-associated nonsynonymous SNPs
-
David, A., Razali, R., Wass, M. N.&Sternberg, M. J. Protein-protein interaction sites are hot spots for disease-associated nonsynonymous SNPs. Human mutation 33, 359-363, doi:10.1002/humu.21656 (2012).
-
(2012)
Human Mutation
, vol.33
, pp. 359-363
-
-
David, A.1
Razali, R.2
Wass, M.N.3
Sternberg, M.J.4
-
11
-
-
84894309512
-
Integrating structure to proteinprotein interaction networks that drive metastasis to brain and lung in breast cancer
-
Engin, H. B., Guney, E., Keskin, O., Oliva, B.&Gursoy, A. Integrating structure to proteinprotein interaction networks that drive metastasis to brain and lung in breast cancer. PloS one 8, e81035, doi:10.1371/journal.pone.0081035 (2013).
-
(2013)
PloS One
, vol.8
, pp. e81035
-
-
Engin, H.B.1
Guney, E.2
Keskin, O.3
Oliva, B.4
Gursoy, A.5
-
12
-
-
84907569494
-
The structural network of Interleukin-10 and its implications in inflammation and cancer
-
Acuner-Ozbabacan , S. E. et al. The structural network of Interleukin-10 and its implications in inflammation and cancer. BMC Genomics 15, S2 (2014).
-
(2014)
BMC Genomics
, vol.15
, pp. S2
-
-
Acuner-Ozbabacan, S.E.1
-
13
-
-
84895765208
-
The structural pathway of interleukin 1 (IL-1) initiated signaling reveals mechanisms of oncogenic mutations and SNPs in inflammation and cancer
-
Acuner Ozbabacan, S. E., Gursoy, A., Nussinov, R.&Keskin, O. The structural pathway of interleukin 1 (IL-1) initiated signaling reveals mechanisms of oncogenic mutations and SNPs in inflammation and cancer. PLoS computational biology 10, e1003470, doi:10.1371/journal.pcbi.1003470 (2014).
-
(2014)
PLoS Computational Biology
, vol.10
, pp. e1003470
-
-
Acuner Ozbabacan, S.E.1
Gursoy, A.2
Nussinov, R.3
Keskin, O.4
-
14
-
-
72849142731
-
Edgetic perturbation models of human inherited disorders
-
Zhong, Q. et al. Edgetic perturbation models of human inherited disorders. Molecular systems biology 5, 321, doi:10.1038/msb.2009.80 (2009).
-
(2009)
Molecular Systems Biology
, vol.5
, pp. 321
-
-
Zhong, Q.1
-
15
-
-
45949108954
-
Protein interactions in human genetic diseases
-
Schuster-Bockler, B.&Bateman, A. Protein interactions in human genetic diseases. Genome biology 9, R9, doi:10.1186/gb-2008-9-1-r9 (2008).
-
(2008)
Genome Biology
, vol.9
, pp. R9
-
-
Schuster-Bockler, B.1
Bateman, A.2
-
16
-
-
84876515907
-
STRING v9.1: Protein-protein interaction networks, with increased coverage and integration
-
Franceschini, A. et al. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic acids research 41, D808-815, doi:10.1093/nar/gks1094 (2013).
-
(2013)
Nucleic Acids Research
, vol.41
, pp. D808-D815
-
-
Franceschini, A.1
-
17
-
-
84864376672
-
HINT: High-quality protein interactomes and their applications in understanding human disease
-
Das, J.&Yu, H. HINT: High-quality protein interactomes and their applications in understanding human disease. BMC systems biology 6, 92, doi:10.1186/1752-0509-6-92 (2012).
-
(2012)
BMC Systems Biology
, vol.6
, pp. 92
-
-
Das, J.1
Yu, H.2
-
18
-
-
0017751668
-
The protein data bank. A computer-based archival file for macromolecular structures
-
Bernstein, F. C. et al. The Protein Data Bank. A computer-based archival file for macromolecular structures. European journal of biochemistry / FEBS 80, 319-324 (1977).
-
(1977)
European Journal of Biochemistry / FEBS
, vol.80
, pp. 319-324
-
-
Bernstein, F.C.1
-
19
-
-
84865760395
-
GENCODE: The reference human genome annotation for the ENCODE project
-
Harrow, J. et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome research 22, 1760-1774, doi:10.1101/gr.135350.111 (2012).
-
(2012)
Genome Research
, vol.22
, pp. 1760-1774
-
-
Harrow, J.1
-
20
-
-
0037250168
-
The UCSC genome browser database
-
Karolchik, D. et al. The UCSC Genome Browser Database. Nucleic acids research 31, 51-54 (2003).
-
(2003)
Nucleic Acids Research
, vol.31
, pp. 51-54
-
-
Karolchik, D.1
-
21
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic acids research 25, 3389-3402 (1997).
-
(1997)
Nucleic Acids Research
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
-
22
-
-
28444469788
-
Mapping PDB chains to UniProtKB entries
-
Martin, A. C. Mapping PDB chains to UniProtKB entries. Bioinformatics 21, 4297-4301, doi:10.1093/bioinformatics/bti694 (2005).
-
(2005)
Bioinformatics
, vol.21
, pp. 4297-4301
-
-
Martin, A.C.1
-
23
-
-
77954294794
-
HotPoint: Hot spot prediction server for protein interfaces
-
Tuncbag, N., Keskin, O.&Gursoy, A. HotPoint: hot spot prediction server for protein interfaces. Nucleic acids research 38, W402-406, doi:10.1093/nar/gkq323 (2010).
-
(2010)
Nucleic Acids Research
, vol.38
, pp. W402-W406
-
-
Tuncbag, N.1
Keskin, O.2
Gursoy, A.3
-
24
-
-
80051576392
-
KFC2: A knowledge-based hot spot prediction method based on interface solvation, atomic density, and plasticity features
-
Zhu, X.&Mitchell, J. C. KFC2: a knowledge-based hot spot prediction method based on interface solvation, atomic density, and plasticity features. Proteins 79, 2671-2683, doi:10.1002/prot.23094 (2011).
-
(2011)
Proteins
, vol.79
, pp. 2671-2683
-
-
Zhu, X.1
Mitchell, J.C.2
-
26
-
-
76749134818
-
Associating genes and protein complexes with disease via network propagation
-
Vanunu, O., Magger, O., Ruppin, E., Shlomi, T.&Sharan, R. Associating genes and protein complexes with disease via network propagation. PLoS computational biology 6, e1000641, doi:10.1371/journal.pcbi.1000641 (2010).
-
(2010)
PLoS Computational Biology
, vol.6
, pp. e1000641
-
-
Vanunu, O.1
Magger, O.2
Ruppin, E.3
Shlomi, T.4
Sharan, R.5
-
27
-
-
28744458859
-
Bioconductor: Open software development for computational biology and bioinformatics
-
Gentleman, R. C. et al. Bioconductor: open software development for computational biology and bioinformatics. Genome biology 5, R80, doi:10.1186/gb-2004-5-10-r80 (2004).
-
(2004)
Genome Biology
, vol.5
, pp. R80
-
-
Gentleman, R.C.1
-
29
-
-
58549112996
-
Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
-
Huang da, W., Sherman, B. T.&Lempicki, R. A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic acids research 37, 1-13, doi:10.1093/nar/gkn923 (2009).
-
(2009)
Nucleic Acids Research
, vol.37
, pp. 1-13
-
-
Da Huang, W.1
Sherman, B.T.2
Lempicki, R.A.3
-
30
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The gene ontology consortium
-
Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature genetics 25, 25-29, doi:10.1038/75556 (2000).
-
(2000)
Nature Genetics
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
-
31
-
-
79960052850
-
Ras in cancer and developmental diseases
-
Fernandez-Medarde, A.&Santos, E. Ras in cancer and developmental diseases. Genes&cancer 2, 344-358, doi:10.1177/1947601911411084 (2011).
-
(2011)
Genes&cancer
, vol.2
, pp. 344-358
-
-
Fernandez-Medarde, A.1
Santos, E.2
-
32
-
-
20044363093
-
Replacement of K-ras with H-ras supports normal embryonic development despite inducing cardiovascular pathology in adult mice
-
Potenza, N. et al. Replacement of K-Ras with H-Ras supports normal embryonic development despite inducing cardiovascular pathology in adult mice. EMBO reports 6, 432-437, doi:10.1038/sj.embor.7400397 (2005).
-
(2005)
EMBO Reports
, vol.6
, pp. 432-437
-
-
Potenza, N.1
-
33
-
-
77955277111
-
Effects of KRAS, BRAF, NRAS, and PIK3CA mutations on the efficacy of cetuximab plus chemotherapy in chemotherapy-refractory metastatic colorectal cancer: A retrospective consortium analysis
-
De Roock, W. et al. Effects of KRAS, BRAF, NRAS, and PIK3CA mutations on the efficacy of cetuximab plus chemotherapy in chemotherapy-refractory metastatic colorectal cancer: a retrospective consortium analysis. The lancet oncology 11, 753-762, doi:10.1016/S1470-2045(10)70130-3 (2010).
-
(2010)
The Lancet Oncology
, vol.11
, pp. 753-762
-
-
De Roock, W.1
-
34
-
-
0035475987
-
The role of the coagulation system in tumour angiogenesis
-
Nash, G. F., Walsh, D. C.&Kakkar, A. K. The role of the coagulation system in tumour angiogenesis. The lancet oncology 2, 608-613 (2001).
-
(2001)
The Lancet Oncology
, vol.2
, pp. 608-613
-
-
Nash, G.F.1
Walsh, D.C.2
Kakkar, A.K.3
-
35
-
-
77949697909
-
Inhibition of vasculogenesis, but not angiogenesis, prevents the recurrence of glioblastoma after irradiation in mice
-
Kioi, M. et al. Inhibition of vasculogenesis, but not angiogenesis, prevents the recurrence of glioblastoma after irradiation in mice. The Journal of clinical investigation 120, 694-705, doi:10.1172/JCI40283 (2010).
-
(2010)
The Journal of Clinical Investigation
, vol.120
, pp. 694-705
-
-
Kioi, M.1
-
36
-
-
0032512655
-
Chemokine receptors in human endothelial cells. Functional expression of CXCR4 and its transcriptional regulation by inflammatory cytokines
-
Gupta, S. K., Lysko, P. G., Pillarisetti, K., Ohlstein, E.&Stadel, J. M. Chemokine receptors in human endothelial cells. Functional expression of CXCR4 and its transcriptional regulation by inflammatory cytokines. The Journal of biological chemistry 273, 4282-4287 (1998).
-
(1998)
The Journal of Biological Chemistry
, vol.273
, pp. 4282-4287
-
-
Gupta, S.K.1
Lysko, P.G.2
Pillarisetti, K.3
Ohlstein, E.4
Stadel, J.M.5
-
37
-
-
0034076189
-
Mechanisms of angiogenesis and arteriogenesis
-
Carmeliet, P. Mechanisms of angiogenesis and arteriogenesis. Nature medicine 6, 389-395, doi:10.1038/74651 (2000).
-
(2000)
Nature Medicine
, vol.6
, pp. 389-395
-
-
Carmeliet, P.1
-
38
-
-
70849134402
-
ELR+ CXC chemokines and oncogenic Rasmediated tumorigenesis
-
O'Hayer, K. M., Brady, D. C.&Counter, C. M. ELR+ CXC chemokines and oncogenic Rasmediated tumorigenesis. Carcinogenesis 30, 1841-1847, doi:10.1093/carcin/bgp198 (2009).
-
(2009)
Carcinogenesis
, vol.30
, pp. 1841-1847
-
-
O'Hayer, K.M.1
Brady, D.C.2
Counter, C.M.3
-
39
-
-
0033614962
-
Essential role for oncogenic Ras in tumour maintenance
-
Chin, L. et al. Essential role for oncogenic Ras in tumour maintenance. Nature 400, 468-472, doi:10.1038/22788 (1999).
-
(1999)
Nature
, vol.400
, pp. 468-472
-
-
Chin, L.1
-
40
-
-
80054856209
-
RAS oncogenes: Weaving a tumorigenic web
-
Pylayeva-Gupta, Y., Grabocka, E.&Bar-Sagi, D. RAS oncogenes: weaving a tumorigenic web. Nature reviews. Cancer 11, 761-774, doi:10.1038/nrc3106 (2011).
-
(2011)
Nature Reviews. Cancer
, vol.11
, pp. 761-774
-
-
Pylayeva-Gupta, Y.1
Grabocka, E.2
Bar-Sagi, D.3
-
41
-
-
0028909572
-
Ultraviolet irradiation induces acute changes in melanocytic nevi
-
Tronnier, M., Smolle, J.&Wolff, H. H. Ultraviolet irradiation induces acute changes in melanocytic nevi. The Journal of investigative dermatology 104, 475-478 (1995).
-
(1995)
The Journal of Investigative Dermatology
, vol.104
, pp. 475-478
-
-
Tronnier, M.1
Smolle, J.2
Wolff, H.H.3
-
42
-
-
79251647799
-
Interferon-gamma links ultraviolet radiation to melanomagenesis in mice
-
Zaidi, M. R. et al. Interferon-gamma links ultraviolet radiation to melanomagenesis in mice. Nature 469, 548-553, doi:10.1038/nature09666 (2011).
-
(2011)
Nature
, vol.469
, pp. 548-553
-
-
Zaidi, M.R.1
-
43
-
-
84895871023
-
Ultraviolet-radiation-induced inflammation promotes angiotropism and metastasis in melanoma
-
Bald, T. et al. Ultraviolet-radiation-induced inflammation promotes angiotropism and metastasis in melanoma. Nature 507, 109-113, doi:10.1038/nature13111 (2014).
-
(2014)
Nature
, vol.507
, pp. 109-113
-
-
Bald, T.1
-
44
-
-
34250831624
-
Loss of xeroderma pigmentosum C (Xpc) enhances melanoma photocarcinogenesis in Ink4a-arf-deficient mice
-
Yang, G., Curley, D., Bosenberg, M. W.&Tsao, H. Loss of xeroderma pigmentosum C (Xpc) enhances melanoma photocarcinogenesis in Ink4a-Arf-deficient mice. Cancer research 67, 5649-5657, doi:10.1158/0008-5472.CAN-06-3806 (2007).
-
(2007)
Cancer Research
, vol.67
, pp. 5649-5657
-
-
Yang, G.1
Curley, D.2
Bosenberg, M.W.3
Tsao, H.4
-
45
-
-
0026730948
-
Mapping of UV photoproducts within ras proto-oncogenes in UV-irradiated cells: Correlation with mutations in human skin cancer
-
Tormanen, V. T.&Pfeifer, G. P. Mapping of UV photoproducts within ras proto-oncogenes in UV-irradiated cells: correlation with mutations in human skin cancer. Oncogene 7, 1729-1736 (1992).
-
(1992)
Oncogene
, vol.7
, pp. 1729-1736
-
-
Tormanen, V.T.1
Pfeifer, G.P.2
-
46
-
-
56049114699
-
Many faces of ras activation
-
Buday, L.&Downward, J. Many faces of Ras activation. Biochimica et biophysica acta 1786, 178-187, doi:10.1016/j.bbcan.2008.05.001 (2008).
-
(2008)
Biochimica et Biophysica Acta
, vol.1786
, pp. 178-187
-
-
Buday, L.1
Downward, J.2
-
47
-
-
60749118005
-
A missense mutation in the APC tumor suppressor gene disrupts an ASF/SF2 splicing enhancer motif and causes pathogenic skipping of exon 14
-
Goncalves, V. et al. A missense mutation in the APC tumor suppressor gene disrupts an ASF/SF2 splicing enhancer motif and causes pathogenic skipping of exon 14. Mutation research 662, 33-36, doi:10.1016/j.mrfmmm.2008.12.001 (2009).
-
(2009)
Mutation Research
, vol.662
, pp. 33-36
-
-
Goncalves, V.1
-
48
-
-
0033883092
-
APC mutations in sporadic medulloblastomas
-
Huang, H. et al. APC mutations in sporadic medulloblastomas. The American journal of pathology 156, 433-437, doi:10.1016/S0002-9440(10)64747-5 (2000).
-
(2000)
The American Journal of Pathology
, vol.156
, pp. 433-437
-
-
Huang, H.1
-
49
-
-
79960063257
-
Combinatorial readout of histone H3 modifications specifies localization of ATRX to heterochromatin
-
Eustermann, S. et al. Combinatorial readout of histone H3 modifications specifies localization of ATRX to heterochromatin. Nature structural&molecular biology 18, 777-782, doi:10.1038/nsmb.2070 (2011).
-
(2011)
Nature Structural&molecular Biology
, vol.18
, pp. 777-782
-
-
Eustermann, S.1
-
50
-
-
26844541188
-
Epigenetic regulation of mammalian pericentric heterochromatin in vivo by HP1
-
Kourmouli, N., Sun, Y. M., van der Sar, S., Singh, P. B.&Brown, J. P. Epigenetic regulation of mammalian pericentric heterochromatin in vivo by HP1. Biochemical and biophysical research communications 337, 901-907, doi:10.1016/j.bbrc.2005.09.132 (2005).
-
(2005)
Biochemical and Biophysical Research Communications
, vol.337
, pp. 901-907
-
-
Kourmouli, N.1
Sun, Y.M.2
Van Der Sar, S.3
Singh, P.B.4
Brown, J.P.5
-
51
-
-
25144497571
-
The BRCA1-interacting helicase BRIP1 is deficient in fanconi anemia
-
Levran, O. et al. The BRCA1-interacting helicase BRIP1 is deficient in Fanconi anemia. Nature genetics 37, 931-933, doi:10.1038/ng1624 (2005).
-
(2005)
Nature Genetics
, vol.37
, pp. 931-933
-
-
Levran, O.1
-
52
-
-
84555196106
-
BRCA1 and BRCA2: Different roles in a common pathway of genome protection
-
Roy, R., Chun, J.&Powell, S. N. BRCA1 and BRCA2: different roles in a common pathway of genome protection. Nature reviews. Cancer 12, 68-78, doi:10.1038/nrc3181 (2012).
-
(2012)
Nature Reviews. Cancer
, vol.12
, pp. 68-78
-
-
Roy, R.1
Chun, J.2
Powell, S.N.3
-
53
-
-
33847314487
-
Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis
-
Carvalho, M. A. et al. Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis. Cancer research 67, 1494-1501, doi:10.1158/0008-5472.CAN-06-3297 (2007).
-
(2007)
Cancer Research
, vol.67
, pp. 1494-1501
-
-
Carvalho, M.A.1
-
54
-
-
84863786019
-
CBL mutation-related patterns of phosphorylation and sensitivity to tyrosine kinase inhibitors
-
Makishima, H. et al. CBL mutation-related patterns of phosphorylation and sensitivity to tyrosine kinase inhibitors. Leukemia 26, 1547-1554, doi:10.1038/leu.2012.7 (2012).
-
(2012)
Leukemia
, vol.26
, pp. 1547-1554
-
-
Makishima, H.1
-
55
-
-
0033602144
-
A direct interaction between the adaptor protein Cbl-b and the kinase zap-70 induces a positive signal in T cells
-
Zhang, Z., Elly, C., Qiu, L., Altman, A.&Liu, Y. C. A direct interaction between the adaptor protein Cbl-b and the kinase zap-70 induces a positive signal in T cells. Current biology : CB 9, 203-206 (1999).
-
(1999)
Current Biology : CB
, vol.9
, pp. 203-206
-
-
Zhang, Z.1
Elly, C.2
Qiu, L.3
Altman, A.4
Liu, Y.C.5
|