-
1
-
-
84894559216
-
Beams: Backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks
-
Alkan, F., Erten, C. (2014) Beams: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks. Bioinformatics, 30, 531-539.
-
(2014)
Bioinformatics
, vol.30
, pp. 531-539
-
-
Alkan, F.1
Erten, C.2
-
2
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
-
3
-
-
33644656793
-
Systematic identification of functional orthologs based on protein network comparison
-
Bandyopadhyay, S. et al. (2006) Systematic identification of functional orthologs based on protein network comparison. Genome Res., 16, 428-435.
-
(2006)
Genome Res.
, vol.16
, pp. 428-435
-
-
Bandyopadhyay, S.1
-
5
-
-
84874947727
-
The BioGRID interaction database: 2013 update
-
Chatr-Aryamontri, A. et al. (2013) The BioGRID interaction database: 2013 update. Nucleic Acids Res., 41, D816-D823.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D816-D823
-
-
Chatr-Aryamontri, A.1
-
6
-
-
84906243482
-
A comparison of algorithms for the pairwise alignment of biological networks
-
Clark, C., Kalita, J. (2014) A comparison of algorithms for the pairwise alignment of biological networks. Bioinformatics., 30, 2351-2359
-
(2014)
Bioinformatics
, vol.30
, pp. 2351-2359
-
-
Clark, C.1
Kalita, J.2
-
8
-
-
33749255098
-
On the equivalence of nonnegative matrix factorization and spectral clustering
-
Kargupta, H., Srivastava, J. Philadelphia, USA
-
Ding, C. et al. (2005) On the equivalence of nonnegative matrix factorization and spectral clustering. In: Kargupta, H., Srivastava, J. (eds), Proceedings of the SIAM Data Mining Conference, Philadelphia, USA, pp. 606-610.
-
(2005)
Proceedings of the SIAM Data Mining Conference
, pp. 606-610
-
-
Ding, C.1
-
9
-
-
33749575326
-
Orthogonal nonnegative matrix t-factorizations for clustering
-
Eliassi-Rad, T. (ed KDD '06, ACM, New York, NY, USA
-
Ding, C. et al. (2006) Orthogonal nonnegative matrix t-factorizations for clustering. In: Eliassi-Rad, T. (ed), Proceedings of the 12th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, KDD '06, ACM, New York, NY, USA, pp. 126-135.
-
(2006)
Proceedings of the 12th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining
, pp. 126-135
-
-
Ding, C.1
-
10
-
-
33748257786
-
Graemlin: General and robust alignment of multiple large interaction networks
-
Flannick, J. et al. (2006) Graemlin: general and robust alignment of multiple large interaction networks. Genome Res., 16, 1169-1181.
-
(2006)
Genome Res.
, vol.16
, pp. 1169-1181
-
-
Flannick, J.1
-
11
-
-
33747891871
-
Predicting the prognosis of breast cancer by integrating clinical and microarray data with Bayesian networks
-
Gevaert, O. et al. (2006) Predicting the prognosis of breast cancer by integrating clinical and microarray data with Bayesian networks. Bioinformatics, 22, e184-e190.
-
(2006)
Bioinformatics
, vol.22
, pp. e184-e190
-
-
Gevaert, O.1
-
12
-
-
84907027309
-
Integration of molecular network data reconstruct gene ontology
-
Gligorijevi-c, V. et al. (2014) Integration of molecular network data reconstruct gene ontology. Bioinformatics, 30, 1594-1600.
-
(2014)
Bioinformatics
, vol.30
, pp. 1594-1600
-
-
Gligorijevic, V.1
-
13
-
-
4043178261
-
Approximation algorithms for some graph partitioning problems
-
He, G. et al. (2000) Approximation algorithms for some graph partitioning problems. J. Graph Algorithms Appl., 4, 1-11.
-
(2000)
J. Graph Algorithms Appl.
, vol.4
, pp. 1-11
-
-
He, G.1
-
14
-
-
0037050004
-
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
-
Ho, Y. et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature, 415, 180-183.
-
(2002)
Nature
, vol.415
, pp. 180-183
-
-
Ho, Y.1
-
15
-
-
84894557914
-
NetCoffee: A fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks
-
Hu, J. et al. (2013) NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks. Bioinformatics, 30, 540-548.
-
(2013)
Bioinformatics
, vol.30
, pp. 540-548
-
-
Hu, J.1
-
16
-
-
0033974688
-
Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins
-
Ito, T. et al. (2000) Toward a protein-protein interaction map of the budding yeast: a comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins.Proc. Natl.Acad. Sci. USA, 97, 1143-1147.
-
(2000)
Proc. Natl.Acad. Sci. USA
, vol.97
, pp. 1143-1147
-
-
Ito, T.1
-
17
-
-
84928739036
-
Accurate multiple network alignment through context-sensitive random walk
-
Jeong, H., Yoon, B.J. (2015) Accurate multiple network alignment through context-sensitive random walk. BMC Syst. Biol., 9, S7.
-
(2015)
BMC Syst. Biol.
, vol.9
, pp. S7
-
-
Jeong, H.1
Yoon, B.J.2
-
19
-
-
39149087720
-
NetworkBLAST: Comparative analysis of protein networks
-
Kalaev, M. et al. (2008) NetworkBLAST: comparative analysis of protein networks. Bioinformatics, 24, 594-596.
-
(2008)
Bioinformatics
, vol.24
, pp. 594-596
-
-
Kalaev, M.1
-
20
-
-
0003037529
-
Reducibility among combinatorial problems
-
Karp, R.M. (1972) Reducibility among combinatorial problems. Complexity Comput. Comput., 6, 85-103.
-
(1972)
Complexity Comput. Comput.
, vol.6
, pp. 85-103
-
-
Karp, R.M.1
-
21
-
-
0141593601
-
Conserved pathways within bacteria and yeast as revealed by global protein network alignment
-
Kelley, B.P. et al. (2003) Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc. Natl. Acad. Sci. USA, 100, 11394-11399.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 11394-11399
-
-
Kelley, B.P.1
-
22
-
-
3442886313
-
PathBLAST: A tool for alignment of protein interaction networks
-
Kelley, B.P. et al. (2004) PathBLAST: a tool for alignment of protein interaction networks. Nucleic Acids Res., 32, W83-W88.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. W83-W88
-
-
Kelley, B.P.1
-
23
-
-
85008044987
-
Matrix factorization techniques for recommender systems
-
Koren, Y. et al. (2009) Matrix factorization techniques for recommender systems. Computer, 42, 30-37.
-
(2009)
Computer
, vol.42
, pp. 30-37
-
-
Koren, Y.1
-
24
-
-
33645985807
-
Pairwise alignment of protein interaction networks
-
Koyutü rk, M. et al. (2006) Pairwise alignment of protein interaction networks. J. Comput. Biol., 13, 182-199.
-
(2006)
J. Comput. Biol.
, vol.13
, pp. 182-199
-
-
Koyutürk, M.1
-
25
-
-
77956576710
-
Topological network alignment uncovers biological function and phylogeny
-
Kuchaiev, O. et al. (2010) Topological network alignment uncovers biological function and phylogeny. J. R. Soc. Interface, 7, 1341-1354.
-
(2010)
J. R. Soc. Interface
, vol.7
, pp. 1341-1354
-
-
Kuchaiev, O.1
-
26
-
-
8844263749
-
A statistical framework for genomic data fusion
-
Lanckriet, G.R.G. et al. (2004) A statistical framework for genomic data fusion. Bioinformatics, 20, 2626-2635.
-
(2004)
Bioinformatics
, vol.20
, pp. 2626-2635
-
-
Lanckriet, G.R.G.1
-
27
-
-
66349108229
-
IsorankN: Spectral methods for global alignment of multiple protein networks
-
Liao, C.S. et al. (2009) IsorankN: spectral methods for global alignment of multiple protein networks. Bioinformatics, 25, i253-i258.
-
(2009)
Bioinformatics
, vol.25
, pp. i253-i258
-
-
Liao, C.S.1
-
28
-
-
0038363049
-
-
North-Holland mathematics studies, North-Holland, Amsterdam, New York
-
Lovasz, L., Plummer, M. (1986) Matching theory. North-Holland mathematics studies, North-Holland, Amsterdam, New York.
-
(1986)
Matching Theory
-
-
Lovasz, L.1
Plummer, M.2
-
29
-
-
13444272087
-
Entrez gene: Gene-centered information at ncbi
-
Maglott, D. et al. (2005) Entrez gene: gene-centered information at ncbi. Nucleic Acids Res., 33, D54-D58.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. D54-D58
-
-
Maglott, D.1
-
30
-
-
84884397652
-
Integrative approaches for finding modular structure in biological networks
-
Mitra, K. et al. (2013) Integrative approaches for finding modular structure in biological networks. Nat. Rev. Genet., 14, 719-732.
-
(2013)
Nat. Rev. Genet.
, vol.14
, pp. 719-732
-
-
Mitra, K.1
-
31
-
-
0034623005
-
T-coffee: A novel method for fast and accurate multiple sequence alignment
-
Notredame, C. et al. (2000) T-coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302, 205-217.
-
(2000)
J. Mol. Biol.
, vol.302
, pp. 205-217
-
-
Notredame, C.1
-
33
-
-
78651455332
-
Protein-protein interactions: Making sense of networks via graph-theoretic modeling
-
Przulj, N. (2011) Protein-protein interactions: making sense of networks via graph-theoretic modeling. Bioessays, 33, 115-123.
-
(2011)
Bioessays
, vol.33
, pp. 115-123
-
-
Przulj, N.1
-
34
-
-
84937003898
-
Node handprinting: A scalable and accurate algorithm for aligning multiple biological networks
-
Radu, A., Charleston, M. (2015) Node handprinting: a scalable and accurate algorithm for aligning multiple biological networks. J. Comput. Biol., 22, 687-697.
-
(2015)
J. Comput. Biol.
, vol.22
, pp. 687-697
-
-
Radu, A.1
Charleston, M.2
-
35
-
-
84888001187
-
High-resolution network biology: Connecting sequence with function
-
Ryan, C.J. et al. (2013) High-resolution network biology: connecting sequence with function. Nat. Rev. Genet., 14, 865-879.
-
(2013)
Nat. Rev. Genet.
, vol.14
, pp. 865-879
-
-
Ryan, C.J.1
-
36
-
-
84880057180
-
SMETANA: Accurate and scalable algorithm for probabilistic alignment of large-scale biological networks
-
Sahraeian, S.M.E., Yoon, B.J. (2013) SMETANA: accurate and scalable algorithm for probabilistic alignment of large-scale biological networks. PLoS One, 8, e67995.
-
(2013)
PLoS One
, vol.8
, pp. e67995
-
-
Sahraeian, S.M.E.1
Yoon, B.J.2
-
37
-
-
13844314048
-
Conserved patterns of protein interaction in multiple species
-
Sharan, R. et al. (2005) Conserved patterns of protein interaction in multiple species. Proc. Natl. Acad. Sci. USA, 102, 1974-1979.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 1974-1979
-
-
Sharan, R.1
-
38
-
-
34547416529
-
Pairwise global alignment of protein interaction networks by matching neighborhood topology
-
Speed, T., Huang, H. (eds. Lecture Notes in Computer Science Springer Berlin Heidelberg, Germany
-
Singh, R. et al. (2007) Pairwise global alignment of protein interaction networks by matching neighborhood topology. In: Speed, T., Huang, H. (eds.) Research in Computational Molecular Biology, Volume 4453 of Lecture Notes in Computer Science. Springer Berlin Heidelberg, Germany, pp. 16-31.
-
(2007)
Research in Computational Molecular Biology
, vol.4453
, pp. 16-31
-
-
Singh, R.1
-
39
-
-
51349087811
-
Global alignment of multiple protein interaction networks with application to functional orthology detection
-
Singh, R. et al. (2008) Global alignment of multiple protein interaction networks with application to functional orthology detection. Proc. Natl. Acad. Sci. USA, 105, 12763-12768.
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 12763-12768
-
-
Singh, R.1
-
40
-
-
0034628508
-
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
-
Uetz, P. et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 623-627.
-
(2000)
Nature
, vol.403
, pp. 623-627
-
-
Uetz, P.1
-
41
-
-
30844443758
-
Herpesviral protein networks and their interaction with the human proteome
-
Uetz, P. et al. (2006) Herpesviral protein networks and their interaction with the human proteome. Science, 311, 239-242.
-
(2006)
Science
, vol.311
, pp. 239-242
-
-
Uetz, P.1
-
42
-
-
53849111925
-
Semi-supervised clustering via matrix factorization
-
Wang, W. (ed Philadelphia, PA, USA
-
Wang, F. et al. (2008) Semi-supervised clustering via matrix factorization. In: Wang, W. (ed), SDM, SIAM, Philadelphia, PA, USA, pp. 1-12.
-
(2008)
SDM SIAM
, pp. 1-12
-
-
Wang, F.1
-
43
-
-
83055181835
-
Simultaneous clustering of multi-type relational data via symmetric nonnegative matrix tri-factorization
-
CIKM '11. ACM, New York.
-
Wang, H. et al. (2011) Simultaneous clustering of multi-type relational data via symmetric nonnegative matrix tri-factorization. In: Proceedings of the 20th ACM International Conference on Information and Knowledge Management, CIKM '11. ACM, New York. pp. 279-284.
-
(2011)
Proceedings of the 20th ACM International Conference on Information and Knowledge Management
, pp. 279-284
-
-
Wang, H.1
-
44
-
-
84876235880
-
Predicting protein-protein interactions from multimodal biological data sources via nonnegative matrix tri-factorization
-
Wang, H. et al. (2013) Predicting protein-protein interactions from multimodal biological data sources via nonnegative matrix tri-factorization. J. Comput. Biol., 20, 344-358.
-
(2013)
J. Comput. Biol.
, vol.20
, pp. 344-358
-
-
Wang, H.1
-
45
-
-
84946046702
-
Matrix factorization-based data fusion for drug-induced liver injury prediction
-
Zitnik, M., Zupan, B. (2014a) Matrix factorization-based data fusion for drug-induced liver injury prediction. Syst. Biomed., 2, 16-22.
-
(2014)
Syst. Biomed.
, vol.2
, pp. 16-22
-
-
Zitnik, M.1
Zupan, B.2
-
46
-
-
84905884178
-
Matrix factorization-based data fusion for gene function prediction in baker's yeast and slime mold
-
Pacific Symposium on Biocomputing, Kohala Coast, Hawaii, USA World Scientific
-
Zitnik, M., Zupan, B. (2014b) Matrix factorization-based data fusion for gene function prediction in baker's yeast and slime mold. In: Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, Kohala Coast, Hawaii, USA, Vol. 19. World Scientific, pp. 400.
-
(2014)
Pacific Symposium on Biocomputing
, vol.19
, pp. 400
-
-
Zitnik, M.1
Zupan, B.2
-
47
-
-
84889679014
-
Discovering disease-disease associations by fusing systems-level molecular data
-
Zitnik, M. et al. (2013) Discovering disease-disease associations by fusing systems-level molecular data. Sci. Rep., 3, 1-9.
-
(2013)
Sci. Rep.
, vol.3
, pp. 1-9
-
-
Zitnik, M.1
|