-
1
-
-
78650373804
-
Network medicine: A network-based approach to human disease
-
Barabási, A.-L., Gulbahce, N. & Loscalzo, J. Network medicine: A network-based approach to human disease. Nat. Rev. Genet. 12, 56-68 (2011).
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 56-68
-
-
Barabási, A.-L.1
Gulbahce, N.2
Loscalzo, J.3
-
2
-
-
0742305866
-
Network biology: Understanding the cell's functional organization
-
Barabási, A.-L. & Oltvai, Z. N. Network biology: Understanding the cell's functional organization. Nat. Rev. Genet. 5, 101-113 (2004).
-
(2004)
Nat. Rev. Genet.
, vol.5
, pp. 101-113
-
-
Barabási, A.-L.1
Oltvai, Z.N.2
-
3
-
-
0033669189
-
A network of protein-protein interactions in yeast
-
Schwikowski, B., Uetz, P. & Fields, S. A network of protein-protein interactions in yeast. Nat. Biotechnol. 18, 1257-1261 (2000).
-
(2000)
Nat. Biotechnol.
, vol.18
, pp. 1257-1261
-
-
Schwikowski, B.1
Uetz, P.2
Fields, S.3
-
4
-
-
33751255087
-
Evaluation of clustering algorithms for protein-protein interaction networks
-
Brohée, S. & van Helden, J. Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics 7, 488 (2006).
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 488
-
-
Brohée, S.1
Van Helden, J.2
-
5
-
-
75949120438
-
How and when should interactome-derived clusters be used to predict functional modules and protein function?
-
Song, J. & Singh, M. How and when should interactome-derived clusters be used to predict functional modules and protein function? Bioinformatics 25, 3143-3150 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 3143-3150
-
-
Song, J.1
Singh, M.2
-
6
-
-
33947252154
-
Network-based prediction of protein function
-
Sharan, R., Ulitsky, I. & Shamir, R. Network-based prediction of protein function. Mol. Syst. Biol. 3, 88 (2007).
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 88
-
-
Sharan, R.1
Ulitsky, I.2
Shamir, R.3
-
7
-
-
47549116997
-
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence
-
Peña-Castillo, L. et al. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol. 9 (Suppl. 1), S2 (2008).
-
(2008)
Genome Biol.
, vol.9
, pp. S2
-
-
Peña-Castillo, L.1
-
8
-
-
77951952127
-
The power of protein interaction networks for associating genes with diseases
-
Navlakha, S. & Kingsford, C. The power of protein interaction networks for associating genes with diseases. Bioinformatics 26, 1057-1063 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 1057-1063
-
-
Navlakha, S.1
Kingsford, C.2
-
9
-
-
84923306828
-
Uncovering disease-disease relationships through the incomplete interactome
-
Menche, J. et al. Uncovering disease-disease relationships through the incomplete interactome. Science 347, 1257601-1257601 (2015).
-
(2015)
Science
, vol.347
, pp. 1257601
-
-
Menche, J.1
-
10
-
-
0023179570
-
Observation of phase transitions in spreading activation networks
-
Shrager, J., Hogg, T. & Huberman, B. A. Observation of phase transitions in spreading activation networks. Science 236, 1092-1094 (1987).
-
(1987)
Science
, vol.236
, pp. 1092-1094
-
-
Shrager, J.1
Hogg, T.2
Huberman, B.A.3
-
11
-
-
39549088339
-
-
(eds Miklós, D., Sós, V. T. & Szõnyi, T.),(Janos Bolyai Mathematical Society
-
Lovász, L. in Combinatorics: Paul Erdõs is Eighty (eds Miklós, D., Sós, V. T. & Szõnyi, T.), 1-46 (Janos Bolyai Mathematical Society, 1993.
-
(1993)
Combinatorics: Paul Erdõs is Eighty
, pp. 1-46
-
-
Lovász, L.1
-
12
-
-
84966640167
-
The PageRank citation ranking: Bringing order to the web
-
Page, L., Brin, S., Motwani, R. & Winograd, T. The PageRank citation ranking: Bringing order to the web. Stanford InfoLab http://citeseer.ist.psu.edu/viewdoc/ summary?doi=10.1.1.31.1768 (1999).
-
(1999)
Stanford InfoLab
-
-
Page, L.1
Brin, S.2
Motwani, R.3
Winograd, T.4
-
13
-
-
4243148480
-
Authoritative sources in a hyperlinked environment
-
Kleinberg, J. M. Authoritative sources in a hyperlinked environment. J. of the ACM 46, 604-632 (1999).
-
(1999)
J. of the ACM
, vol.46
, pp. 604-632
-
-
Kleinberg, J.M.1
-
15
-
-
41149096059
-
Random walk with restart: Fast solutions and applications
-
Tong, H., Faloutsos, C. & Pan, J.-Y. Random walk with restart: Fast solutions and applications. Knowl. Inf. Syst. 14, 327-346 (2007).
-
(2007)
Knowl. Inf. Syst.
, vol.14
, pp. 327-346
-
-
Tong, H.1
Faloutsos, C.2
Pan, J.-Y.3
-
16
-
-
0041848443
-
Topic-sensitive pagerank: A context-sensitive ranking algorithm for web search
-
Haveliwala, T. H. Topic-sensitive pagerank: A context-sensitive ranking algorithm for web search. IEEE Trans. Knowl. Data Eng. 15, 784-796 (2003).
-
(2003)
IEEE Trans. Knowl. Data Eng.
, vol.15
, pp. 784-796
-
-
Haveliwala, T.H.1
-
21
-
-
27144509358
-
Identifying remote protein homologs by network propagation
-
Noble, W. S., Kuang, R., Leslie, C. & Weston, J. Identifying remote protein homologs by network propagation. FEBS J. 272, 5119-5128 (2005).
-
(2005)
FEBS J.
, vol.272
, pp. 5119-5128
-
-
Noble, W.S.1
Kuang, R.2
Leslie, C.3
Weston, J.4
-
22
-
-
84884397652
-
Integrative approaches for finding modular structure in biological networks
-
Mitra, K., Carvunis, A.-R., Ramesh, S. K. & Ideker, T. Integrative approaches for finding modular structure in biological networks. Nat. Rev. Genet. 14, 719-732 (2013).
-
(2013)
Nat. Rev. Genet.
, vol.14
, pp. 719-732
-
-
Mitra, K.1
Carvunis, A.-R.2
Ramesh, S.K.3
Ideker, T.4
-
23
-
-
84872037912
-
Chapter 5: Network biology approach to complex diseases
-
Cho, D.-Y., Kim, Y.-A. & Przytycka, T. M. Chapter 5: Network biology approach to complex diseases. PLoS Comput. Biol. 8, e1002820 (2012).
-
(2012)
PLoS Comput. Biol.
, vol.8
, pp. e1002820
-
-
Cho, D.-Y.1
Kim, Y.-A.2
Przytycka, T.M.3
-
24
-
-
41649119247
-
Protein networks in disease
-
Ideker, T. & Sharan, R. Protein networks in disease. Genome Res. 18, 644-652 (2008).
-
(2008)
Genome Res.
, vol.18
, pp. 644-652
-
-
Ideker, T.1
Sharan, R.2
-
25
-
-
84877580262
-
Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review
-
Csermely, P., Korcsmáros, T., Kiss, H. J. M., London, G. & Nussinov, R. Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review. Pharmacol. Ther. 138, 333-408 (2013).
-
(2013)
Pharmacol. Ther.
, vol.138
, pp. 333-408
-
-
Csermely, P.1
Korcsmáros, T.2
Kiss, H.J.M.3
London, G.4
Nussinov, R.5
-
26
-
-
33747035889
-
Predicting disease genes using protein-protein interactions
-
Oti, M., Snel, B., Huynen, M. A. & Brunner, H. G. Predicting disease genes using protein-protein interactions. J. Med. Genet. 43, 691-698 (2006).
-
(2006)
J. Med. Genet.
, vol.43
, pp. 691-698
-
-
Oti, M.1
Snel, B.2
Huynen, M.A.3
Brunner, H.G.4
-
27
-
-
33646884801
-
Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes
-
Franke, L. et al. Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. Am. J. Hum. Genet. 78, 1011-1025 (2006).
-
(2006)
Am. J. Hum. Genet.
, vol.78
, pp. 1011-1025
-
-
Franke, L.1
-
28
-
-
67749140118
-
Scale-free networks: A decade and beyond
-
Barabasi, A.-L. Scale-free networks: A decade and beyond. Science 325, 412-413 (2009).
-
(2009)
Science
, vol.325
, pp. 412-413
-
-
Barabasi, A.-L.1
-
29
-
-
84880507665
-
Mutational heterogeneity in cancer and the search for new cancer-associated genes
-
Lawrence, M. S. et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214-218 (2013).
-
(2013)
Nature
, vol.499
, pp. 214-218
-
-
Lawrence, M.S.1
-
30
-
-
84926157747
-
Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes
-
A 2D method that exploits the propagation-derived similarity matrix to infer protein modules that are associated with cancer
-
Leiserson, M. D. M. et al. Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes. Nat. Genet. 47, 106-114 (2015). A 2D method that exploits the propagation-derived similarity matrix to infer protein modules that are associated with cancer.
-
(2015)
Nat. Genet.
, vol.47
, pp. 106-114
-
-
Leiserson, M.D.M.1
-
31
-
-
84953283238
-
Network-based integration of disparate omic data to identify 'silent players' in cancer
-
Ruffalo, M., Koyutürk, M. & Sharan, R. Network-based integration of disparate omic data to identify 'silent players' in cancer. PLoS Comput. Biol. 11, e1004595 (2015).
-
(2015)
PLoS Comput. Biol.
, vol.11
, pp. e1004595
-
-
Ruffalo, M.1
Koyutürk, M.2
Sharan, R.3
-
32
-
-
84866544183
-
Systematic differences in signal emitting and receiving revealed by PageRank analysis of a human protein interactome
-
Du, D., Lee, C. F. & Li, X.-Q. Systematic differences in signal emitting and receiving revealed by PageRank analysis of a human protein interactome. PLoS ONE 7, e44872 (2012).
-
(2012)
PLoS ONE
, vol.7
, pp. e44872
-
-
Du, D.1
Lee, C.F.2
Li, X.-Q.3
-
33
-
-
80052592002
-
A directed protein interaction network for investigating intracellular signal transduction
-
Vinayagam, A. et al. A directed protein interaction network for investigating intracellular signal transduction. Sci. Signal. 4, rs8 (2011).
-
(2011)
Sci. Signal.
, vol.4
, pp. rs8
-
-
Vinayagam, A.1
-
34
-
-
84902463639
-
New directions for diffusion-based network prediction of protein function: Incorporating pathways with confidence
-
A network propagation-based approach for incorporating known biological pathways into protein function prediction
-
Cao, M. et al. New directions for diffusion-based network prediction of protein function: Incorporating pathways with confidence. Bioinformatics 30, i219-i227 (2014). A network propagation-based approach for incorporating known biological pathways into protein function prediction.
-
(2014)
Bioinformatics
, vol.30
, pp. i219-i227
-
-
Cao, M.1
-
35
-
-
2342475726
-
Protein ranking: From local to global structure in the protein similarity network
-
One of the first studies to apply the concept of network propagation to the biological domain. A propagation process over sequence similarity networks of different species is used to predict orthology
-
Weston, J., Elisseeff, A., Zhou, D., Leslie, C. S. & Noble, W. S. Protein ranking: From local to global structure in the protein similarity network. Proc. Natl Acad. Sci. USA 101, 6559-6563 (2004). One of the first studies to apply the concept of network propagation to the biological domain. A propagation process over sequence similarity networks of different species is used to predict orthology.
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 6559-6563
-
-
Weston, J.1
Elisseeff, A.2
Zhou, D.3
Leslie, C.S.4
Noble, W.S.5
-
36
-
-
27144465224
-
Motif-based protein ranking by network propagation
-
Kuang, R., Weston, J., Noble, W. S. & Leslie, C. Motif-based protein ranking by network propagation. Bioinformatics 21, 3711-3718 (2005).
-
(2005)
Bioinformatics
, vol.21
, pp. 3711-3718
-
-
Kuang, R.1
Weston, J.2
Noble, W.S.3
Leslie, C.4
-
37
-
-
49549106251
-
Improved network-based identification of protein orthologs
-
Yosef, N., Sharan, R. & Noble, W. S. Improved network-based identification of protein orthologs. Bioinformatics 24, i200-i206 (2008).
-
(2008)
Bioinformatics
, vol.24
, pp. i200-i206
-
-
Yosef, N.1
Sharan, R.2
Noble, W.S.3
-
38
-
-
51349087811
-
Global alignment of multiple protein interaction networks with application to functional orthology detection
-
Singh, R., Xu, J. & Berger, B. Global alignment of multiple protein interaction networks with application to functional orthology detection. Proc. Natl Acad. Sci. USA 105, 12763-12768 (2008).
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, pp. 12763-12768
-
-
Singh, R.1
Xu, J.2
Berger, B.3
-
39
-
-
66349108229
-
IsoRankN: Spectral methods for global alignment of multiple protein networks
-
Liao, C.-S., Lu, K., Baym, M., Singh, R. & Berger, B. IsoRankN: Spectral methods for global alignment of multiple protein networks. Bioinformatics 25, i253-i258 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. i253-i258
-
-
Liao, C.-S.1
Lu, K.2
Baym, M.3
Singh, R.4
Berger, B.5
-
40
-
-
29144442904
-
Whole-proteome prediction of protein function via graph-Theoretic analysis of interaction maps
-
Nabieva, E., Jim, K., Agarwal, A., Chazelle, B. & Singh, M. Whole-proteome prediction of protein function via graph-Theoretic analysis of interaction maps. Bioinformatics 21 (Suppl. 1), i302-i310 (2005).
-
(2005)
Bioinformatics
, vol.21
, pp. i302-i310
-
-
Nabieva, E.1
Jim, K.2
Agarwal, A.3
Chazelle, B.4
Singh, M.5
-
41
-
-
1542271409
-
Predicting protein function from protein/protein interaction data: A probabilistic approach
-
Letovsky, S. & Kasif, S. Predicting protein function from protein/protein interaction data: A probabilistic approach. Bioinformatics 19 (Suppl. 1), i197-i204 (2003).
-
(2003)
Bioinformatics
, vol.19
, pp. i197-i204
-
-
Letovsky, S.1
Kasif, S.2
-
42
-
-
0742304254
-
Prediction of protein function using protein-protein interaction data
-
Deng, M., Zhang, K., Mehta, S., Chen, T. & Sun, F. Prediction of protein function using protein-protein interaction data. J. Comput. Biol. 10, 947-960 (2003).
-
(2003)
J. Comput. Biol.
, vol.10
, pp. 947-960
-
-
Deng, M.1
Zhang, K.2
Mehta, S.3
Chen, T.4
Sun, F.5
-
43
-
-
84885655561
-
Analysis of protein-protein interaction networks using random walks
-
Can, T., Çamoglu, O. & Singh, A. K. Analysis of protein-protein interaction networks using random walks. BIOKDD '05 https://doi. org/10.1145/1134030.1134042 (2005).
-
(2005)
BIOKDD '05
-
-
Can, T.1
Çamoglu, O.2
Singh, A.K.3
-
44
-
-
73249127005
-
Spectral affinity in protein networks
-
Voevodski, K., Teng, S.-H. & Xia, Y. Spectral affinity in protein networks. BMC Syst. Biol. 3, 112 (2009).
-
(2009)
BMC Syst. Biol.
, vol.3
, pp. 112
-
-
Voevodski, K.1
Teng, S.-H.2
Xia, Y.3
-
45
-
-
42949096140
-
EQED: An efficient method for interpreting eQTL associations using protein networks
-
Suthram, S., Beyer, A., Karp, R. M., Eldar, Y. & Ideker, T. eQED: An efficient method for interpreting eQTL associations using protein networks. Mol. Syst. Biol. 4, 162 (2008).
-
(2008)
Mol. Syst. Biol.
, vol.4
, pp. 162
-
-
Suthram, S.1
Beyer, A.2
Karp, R.M.3
Eldar, Y.4
Ideker, T.5
-
46
-
-
22844450110
-
Systematic interpretation of genetic interactions using protein networks
-
Kelley, R. & Ideker, T. Systematic interpretation of genetic interactions using protein networks. Nat. Biotechnol. 23, 561-566 (2005).
-
(2005)
Nat. Biotechnol.
, vol.23
, pp. 561-566
-
-
Kelley, R.1
Ideker, T.2
-
47
-
-
57149103917
-
Finding friends and enemies in an enemies-only network: A graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions
-
Qi, Y., Suhail, Y., Lin, Y.-Y., Boeke, J. D. & Bader, J. S. Finding friends and enemies in an enemies-only network: A graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions. Genome Res. 18, 1991-2004 (2008).
-
(2008)
Genome Res.
, vol.18
, pp. 1991-2004
-
-
Qi, Y.1
Suhail, Y.2
Lin, Y.-Y.3
Boeke, J.D.4
Bader, J.S.5
-
48
-
-
84885993905
-
Going the distance for protein function prediction: A new distance metric for protein interaction networks
-
Cao, M. et al. Going the distance for protein function prediction: A new distance metric for protein interaction networks. PLoS ONE 8, e76339 (2013).
-
(2013)
PLoS ONE
, vol.8
, pp. e76339
-
-
Cao, M.1
-
49
-
-
84942636537
-
Gene function prediction from functional association networks using kernel partial least squares regression
-
Lehtinen, S., Lees, J., Bähler, J., Shawe-Taylor, J. & Orengo, C. Gene function prediction from functional association networks using kernel partial least squares regression. PLoS ONE 10, e0134668 (2015).
-
(2015)
PLoS ONE
, vol.10
, pp. e0134668
-
-
Lehtinen, S.1
Lees, J.2
Bähler, J.3
Shawe-Taylor, J.4
Orengo, C.5
-
50
-
-
47549107689
-
GeneMANIA: A real-time multiple association network integration algorithm for predicting gene function
-
Mostafavi, S., Ray, D., Warde-Farley, D., Grouios, C. & Morris, Q. GeneMANIA: A real-time multiple association network integration algorithm for predicting gene function. Genome Biol. 9 (Suppl. 1), S4 (2008).
-
(2008)
Genome Biol.
, vol.9
, pp. S4
-
-
Mostafavi, S.1
Ray, D.2
Warde-Farley, D.3
Grouios, C.4
Morris, Q.5
-
51
-
-
85026359807
-
Predicting protein functions by using unbalanced random walk algorithm on three biological networks
-
Peng, W., Li, M., Chen, L. & Wang, L. Predicting protein functions by using unbalanced random walk algorithm on three biological networks. IEEE/ACM Trans. Comput. Biol. Bioinform. 14, 360-369 (2015).
-
(2015)
IEEE/ACM Trans. Comput. Biol. Bioinform.
, vol.14
, pp. 360-369
-
-
Peng, W.1
Li, M.2
Chen, L.3
Wang, L.4
-
52
-
-
8844263749
-
A statistical framework for genomic data fusion
-
Lanckriet, G. R. G., De Bie, T., Cristianini, N., Jordan, M. I. & Noble, W. S. A statistical framework for genomic data fusion. Bioinformatics 20, 2626-2635 (2004).
-
(2004)
Bioinformatics
, vol.20
, pp. 2626-2635
-
-
Lanckriet, G.R.G.1
De Bie, T.2
Cristianini, N.3
Jordan, M.I.4
Noble, W.S.5
-
53
-
-
33645901213
-
Diffusion kernel-based logistic regression models for protein function prediction
-
Lee, H., Tu, Z., Deng, M., Sun, F. & Chen, T. Diffusion kernel-based logistic regression models for protein function prediction. OMICS 10, 40-55 (2006).
-
(2006)
OMICS
, vol.10
, pp. 40-55
-
-
Lee, H.1
Tu, Z.2
Deng, M.3
Sun, F.4
Chen, T.5
-
54
-
-
27544435126
-
Fast protein classification with multiple networks
-
Tsuda, K., Shin, H. & Schölkopf, B. Fast protein classification with multiple networks. Bioinformatics 21 (Suppl. 2), ii59-ii65 (2005).
-
(2005)
Bioinformatics
, vol.21
, pp. ii59-ii65
-
-
Tsuda, K.1
Shin, H.2
Schölkopf, B.3
-
55
-
-
19544368196
-
Learning kernels from biological networks by maximizing entropy
-
Tsuda, K. & Noble, W. S. Learning kernels from biological networks by maximizing entropy. Bioinformatics 20 (Suppl. 1), i326-i333 (2004).
-
(2004)
Bioinformatics
, vol.20
, pp. i326-i333
-
-
Tsuda, K.1
Noble, W.S.2
-
56
-
-
85006899204
-
Compact integration of multi-network topology for functional analysis of genes
-
An integrative network propagation approach for functional inference using multiple heterogeneous networks
-
Cho, H., Berger, B. & Peng, J. Compact integration of multi-network topology for functional analysis of genes. Cell Syst. 3, 540-548.e5 (2016). An integrative network propagation approach for functional inference using multiple heterogeneous networks.
-
(2016)
Cell Syst.
, vol.3
, pp. 540-548
-
-
Cho, H.1
Berger, B.2
Peng, J.3
-
57
-
-
84931061289
-
Exploiting ontology graph for predicting sparsely annotated gene function
-
Wang, S., Cho, H., Zhai, C., Berger, B. & Peng, J. Exploiting ontology graph for predicting sparsely annotated gene function. Bioinformatics 31, i357-i364 (2015).
-
(2015)
Bioinformatics
, vol.31
, pp. i357-i364
-
-
Wang, S.1
Cho, H.2
Zhai, C.3
Berger, B.4
Peng, J.5
-
58
-
-
70449359805
-
Finding local communities in protein networks
-
Voevodski, K., Teng, S.-H. & Xia, Y. Finding local communities in protein networks. BMC Bioinformatics 10, 297 (2009).
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 297
-
-
Voevodski, K.1
Teng, S.-H.2
Xia, Y.3
-
59
-
-
84923167599
-
Identification of protein complexes using weighted PageRank-nibble algorithm and core-attachment structure
-
Peng, W., Wang, J., Zhao, B. & Wang, L. Identification of protein complexes using weighted PageRank-nibble algorithm and core-attachment structure. IEEE/ACM Trans. Comput. Biol. Bioinform. 12, 179-192 (2015).
-
(2015)
IEEE/ACM Trans. Comput. Biol. Bioinform.
, vol.12
, pp. 179-192
-
-
Peng, W.1
Wang, J.2
Zhao, B.3
Wang, L.4
-
60
-
-
70349754527
-
RRW: Repeated random walks on genome-scale protein networks for local cluster discovery
-
Macropol, K., Can, T. & Singh, A. K. RRW: Repeated random walks on genome-scale protein networks for local cluster discovery. BMC Bioinformatics 10, 283 (2009).
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 283
-
-
Macropol, K.1
Can, T.2
Singh, A.K.3
-
61
-
-
27644503675
-
GeneRank: Using search engine technology for the analysis of microarray experiments
-
Morrison, J. L., Breitling, R., Higham, D. J. & Gilbert, D. R. GeneRank: Using search engine technology for the analysis of microarray experiments. BMC Bioinformatics 6, 233 (2005).
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 233
-
-
Morrison, J.L.1
Breitling, R.2
Higham, D.J.3
Gilbert, D.R.4
-
62
-
-
66249092826
-
Information flow analysis of interactome networks
-
Missiuro, P. V. et al. Information flow analysis of interactome networks. PLoS Comput. Biol. 5, e1000350 (2009).
-
(2009)
PLoS Comput. Biol.
, vol.5
, pp. e1000350
-
-
Missiuro, P.V.1
-
63
-
-
50949092459
-
Why do hubs in the yeast protein interaction network tend to be essential: Reexamining the connection between the network topology and essentiality
-
Zotenko, E., Mestre, J., O'Leary, D. P. & Przytycka, T. M. Why do hubs in the yeast protein interaction network tend to be essential: Reexamining the connection between the network topology and essentiality. PLoS Comput. Biol. 4, e1000140 (2008).
-
(2008)
PLoS Comput. Biol.
, vol.4
, pp. e1000140
-
-
Zotenko, E.1
Mestre, J.2
O'Leary, D.P.3
Przytycka, T.M.4
-
64
-
-
33747880011
-
An integrative approach for causal gene identification and gene regulatory pathway inference
-
Tu, Z., Wang, L., Arbeitman, M. N., Chen, T. & Sun, F. An integrative approach for causal gene identification and gene regulatory pathway inference. Bioinformatics 22, e489-e496 (2006).
-
(2006)
Bioinformatics
, vol.22
, pp. e489-e496
-
-
Tu, Z.1
Wang, L.2
Arbeitman, M.N.3
Chen, T.4
Sun, F.5
-
65
-
-
61349114190
-
Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity
-
Yeger-Lotem, E. et al. Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity. Nat. Genet. 41, 316-323 (2009).
-
(2009)
Nat. Genet.
, vol.41
, pp. 316-323
-
-
Yeger-Lotem, E.1
-
66
-
-
79952394490
-
An algorithmic framework for predicting side effects of drugs
-
Atias, N. & Sharan, R. An algorithmic framework for predicting side effects of drugs. J. Comput. Biol. 18, 207-218 (2011).
-
(2011)
J. Comput. Biol.
, vol.18
, pp. 207-218
-
-
Atias, N.1
Sharan, R.2
-
67
-
-
84873298120
-
A novel link prediction algorithm for reconstructing protein-protein interaction networks by topological similarity
-
Lei, C. & Ruan, J. A novel link prediction algorithm for reconstructing protein-protein interaction networks by topological similarity. Bioinformatics 29, 355-364 (2013).
-
(2013)
Bioinformatics
, vol.29
, pp. 355-364
-
-
Lei, C.1
Ruan, J.2
-
68
-
-
85028354842
-
RedNemo: Topology-based PPI network reconstruction via repeated diffusion with neighborhood modifications
-
Alkan, F. & Erten, C. RedNemo: Topology-based PPI network reconstruction via repeated diffusion with neighborhood modifications. Bioinformatics 33, 537-544 (2016).
-
(2016)
Bioinformatics
, vol.33
, pp. 537-544
-
-
Alkan, F.1
Erten, C.2
-
69
-
-
34547421112
-
Defining functional distance using manifold embeddings of gene ontology annotations
-
Lerman, G. & Shakhnovich, B. E. Defining functional distance using manifold embeddings of gene ontology annotations. Proc. Natl Acad. Sci. USA 104, 11334-11339 (2007).
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 11334-11339
-
-
Lerman, G.1
Shakhnovich, B.E.2
-
70
-
-
84871494993
-
RIDDLE: Reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network
-
Wang, P. I. et al. RIDDLE: Reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network. Genome Biol. 13, R125 (2012).
-
(2012)
Genome Biol.
, vol.13
, pp. R125
-
-
Wang, P.I.1
-
71
-
-
77952808324
-
Genome-wide inferring gene- phenotype relationship by walking on the heterogeneous network
-
Li, Y. & Patra, J. C. Genome-wide inferring gene- phenotype relationship by walking on the heterogeneous network. Bioinformatics 26, 1219-1224 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 1219-1224
-
-
Li, Y.1
Patra, J.C.2
-
72
-
-
84911363589
-
Walking the interactome for candidate prioritization in exome sequencing studies of Mendelian diseases
-
Smedley, D. et al. Walking the interactome for candidate prioritization in exome sequencing studies of Mendelian diseases. Bioinformatics 30, 3215-3222 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 3215-3222
-
-
Smedley, D.1
-
73
-
-
41549139527
-
Walking the interactome for prioritization of candidate disease genes
-
An application of network propagation to prioritize disease-causing genes
-
Köhler, S., Bauer, S., Horn, D. & Robinson, P. N. Walking the interactome for prioritization of candidate disease genes. Am. J. Hum. Genet. 82, 949-958 (2008). An application of network propagation to prioritize disease-causing genes.
-
(2008)
Am. J. Hum. Genet.
, vol.82
, pp. 949-958
-
-
Köhler, S.1
Bauer, S.2
Horn, D.3
Robinson, P.N.4
-
74
-
-
76749134818
-
Associating genes and protein complexes with disease via network propagation
-
One of the first studies to use network propagation to associate modules of multiple proteins with disease
-
Vanunu, O., Magger, O., Ruppin, E., Shlomi, T. & Sharan, R. Associating genes and protein complexes with disease via network propagation. PLoS Comput. Biol. 6, e1000641 (2010). One of the first studies to use network propagation to associate modules of multiple proteins with disease.
-
(2010)
PLoS Comput. Biol.
, vol.6
, pp. e1000641
-
-
Vanunu, O.1
Magger, O.2
Ruppin, E.3
Shlomi, T.4
Sharan, R.5
-
75
-
-
79959898376
-
Prioritizing candidate disease genes by network-based boosting of genome-wide association data
-
Lee, I., Blom, U. M., Wang, P. I., Shim, J. E. & Marcotte, E. M. Prioritizing candidate disease genes by network-based boosting of genome-wide association data. Genome Res. 21, 1109-1121 (2011).
-
(2011)
Genome Res.
, vol.21
, pp. 1109-1121
-
-
Lee, I.1
Blom, U.M.2
Wang, P.I.3
Shim, J.E.4
Marcotte, E.M.5
-
76
-
-
62849126285
-
Disease candidate gene identification and prioritization using protein interaction networks
-
Chen, J., Aronow, B. J. & Jegga, A. G. Disease candidate gene identification and prioritization using protein interaction networks. BMC Bioinformatics 10, 73 (2009).
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 73
-
-
Chen, J.1
Aronow, B.J.2
Jegga, A.G.3
-
77
-
-
39049189899
-
Mining Alzheimer disease relevant proteins from integrated protein interactome data
-
Chen, J. Y., Shen, C. & Sivachenko, A. Y. Mining Alzheimer disease relevant proteins from integrated protein interactome data. Pac. Symp. Biocomput. 2006, 367-378 (2006).
-
(2006)
Pac. Symp. Biocomput.
, vol.2006
, pp. 367-378
-
-
Chen, J.Y.1
Shen, C.2
Sivachenko, A.Y.3
-
78
-
-
77956477380
-
Candidate gene prioritization by network analysis of differential expression using machine learning approaches
-
Nitsch, D., Gonçalves, J. P., Ojeda, F., de Moor, B. & Moreau, Y. Candidate gene prioritization by network analysis of differential expression using machine learning approaches. BMC Bioinformatics 11, 460 (2010).
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 460
-
-
Nitsch, D.1
Gonçalves, J.P.2
Ojeda, F.3
De Moor, B.4
Moreau, Y.5
-
79
-
-
79953645463
-
Identifying causal genes and dysregulated pathways in complex diseases
-
Kim, Y.-A., Wuchty, S. & Przytycka, T. M. Identifying causal genes and dysregulated pathways in complex diseases. PLoS Comput. Biol. 7, e1001095 (2011).
-
(2011)
PLoS Comput. Biol.
, vol.7
, pp. e1001095
-
-
Kim, Y.-A.1
Wuchty, S.2
Przytycka, T.M.3
-
80
-
-
79959464683
-
DADA: Degree-aware algorithms for network-based disease gene prioritization
-
Erten, S., Bebek, G., Ewing, R. M. & Koyutürk, M. DADA: Degree-aware algorithms for network-based disease gene prioritization. BioData Min. 4, 19 (2011).
-
(2011)
BioData Min.
, vol.4
, pp. 19
-
-
Erten, S.1
Bebek, G.2
Ewing, R.M.3
Koyutürk, M.4
-
81
-
-
80955159942
-
Vavien: An algorithm for prioritizing candidate disease genes based on topological similarity of proteins in interaction networks
-
Erten, S., Bebek, G. & Koyutürk, M. Vavien: An algorithm for prioritizing candidate disease genes based on topological similarity of proteins in interaction networks. J. Comput. Biol. 18, 1561-1574 (2011).
-
(2011)
J. Comput. Biol.
, vol.18
, pp. 1561-1574
-
-
Erten, S.1
Bebek, G.2
Koyutürk, M.3
-
82
-
-
84877027398
-
Prediction and validation of gene-disease associations using methods inspired by social network analyses
-
Singh-Blom, U. M. et al. Prediction and validation of gene-disease associations using methods inspired by social network analyses. PLoS ONE 8, e58977 (2013).
-
(2013)
PLoS ONE
, vol.8
, pp. e58977
-
-
Singh-Blom, U.M.1
-
83
-
-
84962106951
-
Understanding genotype-phenotype effects in cancer via network approaches
-
Kim, Y.-A., Cho, D.-Y. & Przytycka, T. M. Understanding genotype-phenotype effects in cancer via network approaches. PLoS Comput. Biol. 12, e1004747 (2016).
-
(2016)
PLoS Comput. Biol.
, vol.12
, pp. e1004747
-
-
Kim, Y.-A.1
Cho, D.-Y.2
Przytycka, T.M.3
-
84
-
-
84866888440
-
Enhancing the prioritization of disease-causing genes through tissue specific protein interaction networks
-
Magger, O., Waldman, Y. Y., Ruppin, E. & Sharan, R. Enhancing the prioritization of disease-causing genes through tissue specific protein interaction networks. PLoS Comput. Biol. 8, e1002690 (2012).
-
(2012)
PLoS Comput. Biol.
, vol.8
, pp. e1002690
-
-
Magger, O.1
Waldman, Y.Y.2
Ruppin, E.3
Sharan, R.4
-
85
-
-
84976510332
-
An integer programming framework for inferring disease complexes from network data
-
Mazza, A., Klockmeier, K., Wanker, E. & Sharan, R. An integer programming framework for inferring disease complexes from network data. Bioinformatics 32, i271-i277 (2016).
-
(2016)
Bioinformatics
, vol.32
, pp. i271-i277
-
-
Mazza, A.1
Klockmeier, K.2
Wanker, E.3
Sharan, R.4
-
86
-
-
79952389826
-
Algorithms for detecting significantly mutated pathways in cancer
-
Vandin, F., Upfal, E. & Raphael, B. J. Algorithms for detecting significantly mutated pathways in cancer. J. Comput. Biol. 18, 507-522 (2011).
-
(2011)
J. Comput. Biol.
, vol.18
, pp. 507-522
-
-
Vandin, F.1
Upfal, E.2
Raphael, B.J.3
-
87
-
-
84991492394
-
Gene and network analysis of common variants reveals novel associations in multiple complex diseases
-
Nakka, P., Raphael, B. J. & Ramachandran, S. Gene and network analysis of common variants reveals novel associations in multiple complex diseases. Genetics 204, 783-798 (2016).
-
(2016)
Genetics
, vol.204
, pp. 783-798
-
-
Nakka, P.1
Raphael, B.J.2
Ramachandran, S.3
-
88
-
-
85030790909
-
Research in computational molecular biology
-
Lecture Notes in Computer Science (ed. Sharan, R.) Springer, 2014
-
Shrestha, R. et al. in Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science (ed. Sharan, R.) 293-306 (Springer, 2014).
-
(2014)
RECOMB
, pp. 293-306
-
-
Shrestha, R.1
-
89
-
-
84887084951
-
Network-based stratification of tumor mutations
-
One of the first methods to use patient-specific propagation processes to stratify patients with cancer into subtypes
-
Hofree, M., Shen, J. P., Carter, H., Gross, A. & Ideker, T. Network-based stratification of tumor mutations. Nat. Methods 10, 1108-1115 (2013). One of the first methods to use patient-specific propagation processes to stratify patients with cancer into subtypes.
-
(2013)
Nat. Methods
, vol.10
, pp. 1108-1115
-
-
Hofree, M.1
Shen, J.P.2
Carter, H.3
Gross, A.4
Ideker, T.5
-
90
-
-
84895516704
-
Similarity network fusion for aggregating data types on a genomic scale
-
Wang, B. et al. Similarity network fusion for aggregating data types on a genomic scale. Nat. Methods 11, 333-337 (2014).
-
(2014)
Nat. Methods
, vol.11
, pp. 333-337
-
-
Wang, B.1
-
91
-
-
84884403849
-
Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE)
-
An integrative method to predict cancer pathways that is based on superimposing two propagation processes that are run from nodes corresponding to mutated and differentially expressed genes
-
Paull, E. O. et al. Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE). Bioinformatics 29, 2757-2764 (2013). An integrative method to predict cancer pathways that is based on superimposing two propagation processes that are run from nodes corresponding to mutated and differentially expressed genes.
-
(2013)
Bioinformatics
, vol.29
, pp. 2757-2764
-
-
Paull, E.O.1
-
92
-
-
84981318520
-
Phosphoproteome integration reveals patient-specific networks in prostate cancer
-
Drake, J. M. et al. Phosphoproteome integration reveals patient-specific networks in prostate cancer. Cell 166, 1041-1054 (2016).
-
(2016)
Cell
, vol.166
, pp. 1041-1054
-
-
Drake, J.M.1
-
93
-
-
85012224964
-
Inference of personalized drug targets via network propagation
-
Shnaps, O., Perry, E., Silverbush, D. & Sharan, R. Inference of personalized drug targets via network propagation. Pac. Symp. Biocomput. 21, 156-167 (2016).
-
(2016)
Pac. Symp. Biocomput.
, vol.21
, pp. 156-167
-
-
Shnaps, O.1
Perry, E.2
Silverbush, D.3
Sharan, R.4
-
94
-
-
84862215494
-
Drug- target interaction prediction by random walk on the heterogeneous network
-
Chen, X., Xing, C., Ming-Xi, L. & Gui-Ying, Y. Drug- target interaction prediction by random walk on the heterogeneous network. Mol. Biosyst. 8, 1970 (2012).
-
(2012)
Mol. Biosyst.
, vol.8
, pp. 1970
-
-
Chen, X.1
Xing, C.2
Ming-Xi, L.3
Gui-Ying, Y.4
-
95
-
-
84930083700
-
Understanding multicellular function and disease with human tissue-specific networks
-
Greene, C. S. et al. Understanding multicellular function and disease with human tissue-specific networks. Nat. Genet. 47, 569-576 (2015).
-
(2015)
Nat. Genet.
, vol.47
, pp. 569-576
-
-
Greene, C.S.1
-
96
-
-
84929001104
-
Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans
-
GTEx Consortium. Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans. Science 348, 648-660 (2015).
-
(2015)
Science
, vol.348
, pp. 648-660
-
-
-
97
-
-
84899633396
-
Defining functional DNA elements in the human genome
-
Kellis, M. et al. Defining functional DNA elements in the human genome. Proc. Natl Acad. Sci. USA 111, 6131-6138 (2014).
-
(2014)
Proc. Natl Acad. Sci. USA
, vol.111
, pp. 6131-6138
-
-
Kellis, M.1
-
98
-
-
84923362619
-
Integrative analysis of 111 reference human epigenomes
-
Roadmap Epigenomics Consortium et al. Integrative analysis of 111 reference human epigenomes. Nature 518, 317-330 (2015).
-
(2015)
Nature
, vol.518
, pp. 317-330
-
-
Consortium, R.E.1
-
99
-
-
17444366585
-
Laplacians and the Cheeger inequality for directed graphs
-
Chung, F. Laplacians and the Cheeger inequality for directed graphs. Ann. Comb. 9, 1-19 (2005).
-
(2005)
Ann. Comb.
, vol.9
, pp. 1-19
-
-
Chung, F.1
-
100
-
-
84888062097
-
Clustering and community detection in directed networks: A survey
-
Malliaros, F. D. & Vazirgiannis, M. Clustering and community detection in directed networks: A survey. Phys. Rep. 533, 95-142 (2013).
-
(2013)
Phys. Rep.
, vol.533
, pp. 95-142
-
-
Malliaros, F.D.1
Vazirgiannis, M.2
-
101
-
-
84976907502
-
KEGG as a reference resource for gene and protein annotation
-
Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M. & Tanabe, M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44, D457-D462 (2016).
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D457-D462
-
-
Kanehisa, M.1
Sato, Y.2
Kawashima, M.3
Furumichi, M.4
Tanabe, M.5
-
102
-
-
84885074034
-
The somatic genomic landscape of glioblastoma
-
Brennan, C. W. et al. The somatic genomic landscape of glioblastoma. Cell 155, 462-477 (2013).
-
(2013)
Cell
, vol.155
, pp. 462-477
-
-
Brennan, C.W.1
-
103
-
-
78149262301
-
GeneMANIA Cytoscape plugin: Fast gene function predictions on the desktop
-
Montojo, J. et al. GeneMANIA Cytoscape plugin: Fast gene function predictions on the desktop. Bioinformatics 26, 2927-2928 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 2927-2928
-
-
Montojo, J.1
-
104
-
-
0242490780
-
Cytoscape: A software environment for integrated models of biomolecular interaction networks
-
Shannon, P. et al. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498-2504 (2003).
-
(2003)
Genome Res.
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
-
105
-
-
84866683906
-
Exploiting protein-protein interaction networks for genome-wide disease-gene prioritization
-
Guney, E. & Oliva, B. Exploiting protein-protein interaction networks for genome-wide disease-gene prioritization. PLoS ONE 7, e43557 (2012).
-
(2012)
PLoS ONE
, vol.7
, pp. e43557
-
-
Guney, E.1
Oliva, B.2
-
106
-
-
82255185475
-
PRINCIPLE: A tool for associating genes with diseases via network propagation
-
Gottlieb, A., Magger, O., Berman, I., Ruppin, E. & Sharan, R. PRINCIPLE: A tool for associating genes with diseases via network propagation. Bioinformatics 27, 3325-3326 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 3325-3326
-
-
Gottlieb, A.1
Magger, O.2
Berman, I.3
Ruppin, E.4
Sharan, R.5
-
107
-
-
67849130563
-
ToppGene Suite for gene list enrichment analysis and candidate gene prioritization
-
Chen, J., Bardes, E. E., Aronow, B. J. & Jegga, A. G. ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res. 37, W305-W311 (2009).
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. W305-W311
-
-
Chen, J.1
Bardes, E.E.2
Aronow, B.J.3
Jegga, A.G.4
|