-
1
-
-
33748257786
-
Græmlin: General and robust alignment of multiple large interaction networks
-
J. Flannick, A. Novak, B. S. Srinivasan, H. H. McAdams, and S. Batzoglou, "Græmlin: General and robust alignment of multiple large interaction networks," Genome Res., vol. 16, no. 9, pp. 1169-1181, 2006.
-
(2006)
Genome Res.
, vol.16
, Issue.9
, pp. 1169-1181
-
-
Flannick, J.1
Novak, A.2
Srinivasan, B.S.3
McAdams, H.H.4
Batzoglou, S.5
-
2
-
-
47249149365
-
Automatic parameter learning for multiple network alignment
-
Proceedings of the 12th annual international conference on Research in computational molecular biology, ser. Springer- Verlag
-
J. Flannick, A. Novak, C. B. Do, B. S. Srinivasan, and S. Batzoglou, "Automatic parameter learning for multiple network alignment," in Proceedings of the 12th annual international conference on Research in computational molecular biology, ser. RECOMB'08. Springer-Verlag, 2008, pp. 214-231.
-
(2008)
RECOMB'08
, pp. 214-231
-
-
Flannick, J.1
Novak, A.2
Do, C.B.3
Srinivasan, B.S.4
Batzoglou, S.5
-
3
-
-
77956576710
-
Topological network alignment uncovers biological function and phylogeny
-
O. Kuchaiev, T. Milenkovik, V. Memisevic, W. Hayes, and N. Przulj, "Topological network alignment uncovers biological function and phylogeny," Journal of The Royal Society Interface, vol. 7, no. 50, pp. 1341-1354, 2010.
-
(2010)
Journal of the Royal Society Interface
, vol.7
, Issue.50
, pp. 1341-1354
-
-
Kuchaiev, O.1
Milenkovik, T.2
Memisevic, V.3
Hayes, W.4
Przulj, N.5
-
4
-
-
77955499935
-
Optimal network alignment with graphlet degree vectors
-
[Online]. Available
-
T. Milenković, W. L. L. Ng, W. Hayes, and N. Przulj, "Optimal network alignment with graphlet degree vectors." Cancer informatics, vol. 9, pp. 121-137, 2010. [Online]. Available: http://www.ncbi.nlm.nih.gov/pmc/ articles/PMC2901631/
-
(2010)
Cancer Informatics
, vol.9
, pp. 121-137
-
-
Milenković, T.1
Ng, W.L.L.2
Hayes, W.3
Przulj, N.4
-
5
-
-
79955751671
-
Integrative network alignment reveals large regions of global network similarity in yeast and human
-
May
-
O. Kuchaiev and N. Pržulj, "Integrative network alignment reveals large regions of global network similarity in yeast and human," Bioinformatics, vol. 27, no. 10, pp. 1390-1396, May 2011.
-
(2011)
Bioinformatics
, vol.27
, Issue.10
, pp. 1390-1396
-
-
Kuchaiev, O.1
Pržulj, N.2
-
6
-
-
51349087811
-
Global alignment of multiple protein interaction networks with application to functional orthology detection
-
R. Singh, J. Xu, and B. Berger, "Global alignment of multiple protein interaction networks with application to functional orthology detection," PNAS, vol. 105, no. 35, pp. 12 763-12 768, 2008.
-
(2008)
PNAS
, vol.105
, Issue.35
, pp. 12763-12768
-
-
Singh, R.1
Xu, J.2
Berger, B.3
-
7
-
-
66349108229
-
Isorankn: Spectral methods for global alignment of multiple protein networks
-
C.-S. Liao, K. Lu, M. Baym, R. Singh, and B. Berger, "Isorankn: spectral methods for global alignment of multiple protein networks," Bioinformatics, vol. 25, no. 12, pp. i253-i258, 2009.
-
(2009)
Bioinformatics
, vol.25
, Issue.12
-
-
Liao, C.-S.1
Lu, K.2
Baym, M.3
Singh, R.4
Berger, B.5
-
8
-
-
66349124837
-
Domain-oriented edge-based alignment of protein interaction networks
-
X. Guo and A. J. Hartemink, "Domain-oriented edge-based alignment of protein interaction networks," Bioinformatics, vol. 25, no. 12, pp. i240-1246, 2009.
-
(2009)
Bioinformatics
, vol.25
, Issue.12
-
-
Guo, X.1
Hartemink, A.J.2
-
9
-
-
34547840254
-
Identification of functional modules from conserved ancestral protein protein interactions
-
J. Dutkowski and J. Tiuryn, "Identification of functional modules from conserved ancestral protein protein interactions," Bioinformatics, vol. 23, no. 13, pp. i149-158, 2007.
-
(2007)
Bioinformatics
, vol.23
, Issue.13
-
-
Dutkowski, J.1
Tiuryn, J.2
-
10
-
-
84860471091
-
PINALOG: A novel approach to align protein interaction networksimplications for complex detection and function prediction
-
May
-
H. T. T. Phan and M. J. E. Sternberg, "PINALOG: a novel approach to align protein interaction networksimplications for complex detection and function prediction," Bioinformatics, vol. 28, no. 9, pp. 1239-1245, May 2012.
-
(2012)
Bioinformatics
, vol.28
, Issue.9
, pp. 1239-1245
-
-
Phan, H.T.T.1
Sternberg, M.J.E.2
-
11
-
-
0001373628
-
Random neural networks with positive and negative signals and product form solution
-
E. Gelenbe, "Random neural networks with positive and negative signals and product form solution," Neural Computation, vol. 1, no. 4, pp. 502-510, 1989.
-
(1989)
Neural Computation
, vol.1
, Issue.4
, pp. 502-510
-
-
Gelenbe, E.1
-
12
-
-
0001366019
-
Parallel algorithm for colour texture generation using the random neural network model
-
V. Atalay and E. Gelenbe, "Parallel algorithm for colour texture generation using the random neural network model," International Journal of Pattern Recognition and Artificial Intelligence, vol. 6, no. 2&3, pp. 437-466, 1992.
-
(1992)
International Journal of Pattern Recognition and Artificial Intelligence
, vol.6
, Issue.2-3
, pp. 437-466
-
-
Atalay, V.1
Gelenbe, E.2
-
13
-
-
0033871374
-
Video quality and traffic qos in learning-based subsampled and receiver-interpolated video sequences
-
C. Cramer and E. Gelenbe, "Video quality and traffic qos in learning-based subsampled and receiver-interpolated video sequences," IEEE Journal on Selected Areas in Communications, vol. 18, no. 2, pp. 150-167, 2000.
-
(2000)
IEEE Journal on Selected Areas in Communications
, vol.18
, Issue.2
, pp. 150-167
-
-
Cramer, C.1
Gelenbe, E.2
-
14
-
-
0031999425
-
Learning neural networks for detection and classification of synchronous recurrent transient signals
-
E. Gelenbe, K. Harmanci, and J. Krolik, "Learning neural networks for detection and classification of synchronous recurrent transient signals," Signal processing, vol. 64, no. 3, pp. 233-247, 1998.
-
(1998)
Signal Processing
, vol.64
, Issue.3
, pp. 233-247
-
-
Gelenbe, E.1
Harmanci, K.2
Krolik, J.3
-
15
-
-
0030270952
-
Neural network methods for volumnetric magnetic resonance imaging of the human brain
-
E. Gelenbe, T. Feng, and K. Krishnan, "Neural network methods for volumnetric magnetic resonance imaging of the human brain," Proceedings of the IEEE, vol. 84, no. 10, pp. 1488-1496, 1996.
-
(1996)
Proceedings of the IEEE
, vol.84
, Issue.10
, pp. 1488-1496
-
-
Gelenbe, E.1
Feng, T.2
Krishnan, K.3
-
16
-
-
55449106994
-
Synchronized interactions in spiked neuronal networks
-
E. Gelenbe and S. Timotheou, "Synchronized interactions in spiked neuronal networks," The Computer Journal, vol. 51, no. 6, pp. 723-730, 2008.
-
(2008)
The Computer Journal
, vol.51
, Issue.6
, pp. 723-730
-
-
Gelenbe, E.1
Timotheou, S.2
-
17
-
-
67650079730
-
Steps toward self-aware networks
-
E. Gelenbe, "Steps toward self-aware networks," Communications ACM, vol. 52, no. 7, pp. 66-75, 2009.
-
(2009)
Communications ACM
, vol.52
, Issue.7
, pp. 66-75
-
-
Gelenbe, E.1
-
18
-
-
0026243013
-
Global behavior of homogeneous random neural systems
-
E. Gelenbe and A. Stafylopatis, "Global behavior of homogeneous random neural systems," Applied Mathematical Modelling, vol. 15, no. 10, pp. 534-541, 1991.
-
(1991)
Applied Mathematical Modelling
, vol.15
, Issue.10
, pp. 534-541
-
-
Gelenbe, E.1
Stafylopatis, A.2
-
19
-
-
34548854836
-
Steady-state solution of probabilistic gene regulatory networks
-
E. Gelenbe, "Steady-state solution of probabilistic gene regulatory networks," Physical Review E, vol. 76, no. 3, pp. 031 903+, 2007.
-
(2007)
Physical Review E
, vol.76
, Issue.3
, pp. 031903
-
-
Gelenbe, E.1
-
20
-
-
71549166029
-
Anomaly detection in gene expression via stochastic models of gene regulatory networks
-
H. Kim and E. Gelenbe, "Anomaly detection in gene expression via stochastic models of gene regulatory networks," BMC Genomics, vol. 10, no. Suppl 3, p. S26, 2009.
-
(2009)
BMC Genomics
, vol.10
, Issue.SUPPL. 3
-
-
Kim, H.1
Gelenbe, E.2
-
21
-
-
0033369033
-
Exploiting the past and the future in protein secondary structure prediction
-
Nov.
-
P. Baldi, S. Brunak, P. Frasconi, G. Soda, and G. Pollastri, "Exploiting the past and the future in protein secondary structure prediction," Bioinformatics, vol. 15, no. 11, pp. 937-946, Nov. 1999.
-
(1999)
Bioinformatics
, vol.15
, Issue.11
, pp. 937-946
-
-
Baldi, P.1
Brunak, S.2
Frasconi, P.3
Soda, G.4
Pollastri, G.5
-
22
-
-
0036568279
-
Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles
-
G. Pollastri, D. Przybylski, B. Rost, and P. Baldi, "Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles," Proteins, vol. 47, no. 2, pp. 228-235, 2002.
-
(2002)
Proteins
, vol.47
, Issue.2
, pp. 228-235
-
-
Pollastri, G.1
Przybylski, D.2
Rost, B.3
Baldi, P.4
-
23
-
-
17844392864
-
Combining prediction of secondary structure and solvent accessibility in proteins
-
May
-
R. Adamczak, A. Porollo, and J. Meller, "Combining prediction of secondary structure and solvent accessibility in proteins," Proteins: Structure, Function, and Bioinformatics, vol. 59, no. 3, pp. 467-475, May 2005.
-
(2005)
Proteins: Structure, Function, and Bioinformatics
, vol.59
, Issue.3
, pp. 467-475
-
-
Adamczak, R.1
Porollo, A.2
Meller, J.3
-
24
-
-
33745610096
-
A two-stage approach for improved prediction of residue contact maps
-
Mar.
-
A. Vullo, I. Walsh, and G. Pollastri, "A two-stage approach for improved prediction of residue contact maps." BMC Bioinformatics, vol. 7, no. 1, Mar. 2006.
-
(2006)
BMC Bioinformatics
, vol.7
, Issue.1
-
-
Vullo, A.1
Walsh, I.2
Pollastri, G.3
-
25
-
-
0010357963
-
Dynamical random neural approach to the traveling salesman problem
-
E. Gelenbe, V. Koubi, and F. Pekegrin, "Dynamical random neural approach to the traveling salesman problem," ELEKTRIK, vol. 2, no. 2, pp. 1-10, 1994.
-
(1994)
ELEKTRIK
, vol.2
, Issue.2
, pp. 1-10
-
-
Gelenbe, E.1
Koubi, V.2
Pekegrin, F.3
-
26
-
-
0031076521
-
Improved neural heuristics for multicast routing
-
E. Gelenbe, A. Ghanwani, and V. Srivivasan, "Improved neural heuristics for multicast routing," IEEE Journal of Selected Areas of Communications, vol. 15, no. 2, pp. 147-155, 1997.
-
(1997)
IEEE Journal of Selected Areas of Communications
, vol.15
, Issue.2
, pp. 147-155
-
-
Gelenbe, E.1
Ghanwani, A.2
Srivivasan, V.3
-
27
-
-
0343266993
-
Une généralisation probabiliste du problème sat
-
E. Gelenbe, "Une généralisation probabiliste du problème sat," Comptes-Rendus Acad. Sci., vol. 313, no. II, pp. 339- 342, 1992.
-
(1992)
Comptes-Rendus Acad. Sci.
, vol.313
, Issue.2
, pp. 339-342
-
-
Gelenbe, E.1
-
28
-
-
0000428263
-
Learning in the recurrent random network
-
E. Gelenbe, "Learning in the recurrent random network," Neural Computation, no. 4, pp. 154-164, 1993.
-
(1993)
Neural Computation
, Issue.4
, pp. 154-164
-
-
Gelenbe, E.1
-
29
-
-
21344486418
-
G-networks: A unifying model for neural and queueing networks
-
E. Gelenbe, "G-networks: A unifying model for neural and queueing networks," Annals of Operations Research, vol. 48, no. 5, pp. 433-461, 1994.
-
(1994)
Annals of Operations Research
, vol.48
, Issue.5
, pp. 433-461
-
-
Gelenbe, E.1
-
31
-
-
0033561945
-
Random neural networks with multiple classes of signals
-
E. Gelenbe and J. Fourneau, "Random neural networks with multiple classes of signals," Neural Computation, vol. 11, no. 4, pp. 953-963, 1999.
-
(1999)
Neural Computation
, vol.11
, Issue.4
, pp. 953-963
-
-
Gelenbe, E.1
Fourneau, J.2
-
32
-
-
0000428263
-
Learning in the Recurrent Random Neural Network
-
Jan.
-
E. Gelenbe, "Learning in the Recurrent Random Neural Network," Neural Computation, vol. 5, no. 1, pp. 154-164, Jan. 1993.
-
(1993)
Neural Computation
, vol.5
, Issue.1
, pp. 154-164
-
-
Gelenbe, E.1
-
33
-
-
77955495879
-
Local optimization for global alignment of protein interaction networks
-
L. Chindelevitch, C. Liao, and B. Berger, "Local optimization for global alignment of protein interaction networks," in Pacific Symposium on Biocomputing, 2010, pp. 123-132.
-
Pacific Symposium on Biocomputing, 2010
, pp. 123-132
-
-
Chindelevitch, L.1
Liao, C.2
Berger, B.3
-
34
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
-
May
-
M. Ashburner, C. A. Ball, J. A. Blake, D. Botstein, H. Butler, J. M. Cherry, A. P. Davis, K. Dolinski, S. S. Dwight, J. T. Eppig, M. A. Harris, D. P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J. C. Matese, J. E. Richardson, M. Ringwald, G. M. Rubin, and G. Sherlock, "Gene ontology: tool for the unification of biology. The Gene Ontology Consortium." Nature Genetics, vol. 25, no. 1, pp. 25-29, May 2000.
-
(2000)
Nature Genetics
, vol.25
, Issue.1
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
35
-
-
33645821454
-
Assessing semantic similarity measures for the characterization of human regulatory pathways
-
X. Guo, R. Liu, C. D. Shriver, H. Hu, and M. N. Liebman, "Assessing semantic similarity measures for the characterization of human regulatory pathways," Bioinformatics, vol. 22, no. 8, pp. 967-973, 2006.
-
(2006)
Bioinformatics
, vol.22
, Issue.8
, pp. 967-973
-
-
Guo, X.1
Liu, R.2
Shriver, C.D.3
Hu, H.4
Liebman, M.N.5
-
36
-
-
33748335463
-
A new measure for functional similarity of gene products based on gene ontology
-
A. Schlicker, F. Domingues, J. Rahnenfuhrer, and T. Lengauer, "A new measure for functional similarity of gene products based on gene ontology," BMC Bioinformatics, vol. 7, no. 1, p. 302, 2006.
-
(2006)
BMC Bioinformatics
, vol.7
, Issue.1
, pp. 302
-
-
Schlicker, A.1
Domingues, F.2
Rahnenfuhrer, J.3
Lengauer, T.4
-
37
-
-
58149312546
-
Evaluation of go-based functional similarity measures using s. cerevisiae protein interaction and expression profile data
-
T. Xu, L. Du, and Y. Zhou, "Evaluation of go-based functional similarity measures using s. cerevisiae protein interaction and expression profile data," BMC Bioinformatics, vol. 9, no. 1, p. 472, 2008.
-
(2008)
BMC Bioinformatics
, vol.9
, Issue.1
, pp. 472
-
-
Xu, T.1
Du, L.2
Zhou, Y.3
-
39
-
-
75549087047
-
The IntAct molecular interaction database in 2010
-
Oct.
-
B. Aranda, P. Achuthan, Y. Alam-Faruque, I. Armean, A. Bridge, C. Derow, M. Feuermann, A. T. Ghanbarian, S. Kerrien, J. Khadake, J. Kerssemakers, C. Leroy, M. Menden, M. Michaut, L. Montecchi-Palazzi, S. N. Neuhauser, S. Orchard, V. Perreau, B. Roechert, K. van Eijk, and H. Hermjakob, "The IntAct molecular interaction database in 2010," Nucleic Acids Research, vol. 38, no. Database issue, pp. D525-D531, Oct. 2009.
-
(2009)
Nucleic Acids Research
, vol.38
, Issue.DATABASE ISSUE
-
-
Aranda, B.1
Achuthan, P.2
Alam-Faruque, Y.3
Armean, I.4
Bridge, A.5
Derow, C.6
Feuermann, M.7
Ghanbarian, A.T.8
Kerrien, S.9
Khadake, J.10
Kerssemakers, J.11
Leroy, C.12
Menden, M.13
Michaut, M.14
Montecchi-Palazzi, L.15
Neuhauser, S.N.16
Orchard, S.17
Perreau, V.18
Roechert, B.19
Van Eijk, K.20
Hermjakob, H.21
more..
-
40
-
-
13444293344
-
Database resources of the National Center for Biotechnology Information
-
D. L. Wheeler, T. Barrett, D. A. Benson, S. H. Bryant, K. Canese, V. Chetvernin, D. M. Church, M. DiCuccio, R. Edgar, S. Federhen, L. Y. Geer, W. Helmberg, Y. Kapustin, D. L. Kenton, O. Khovayko, D. J. Lipman, T. L. Madden, D. R. Maglott, J. Ostell, K. D. Pruitt, G. D. Schuler, L. M. Schriml, E. Sequeira, S. T. Sherry, K. Sirotkin, A. Souvorov, G. Starchenko, T. O. Suzek, R. Tatusov, T. A. Tatusova, L. Wagner, and E. Yaschenko, "Database resources of the National Center for Biotechnology Information." Nucleic Acids Research, vol. 33, no. suppl 1, pp. D39-D45, 2006.
-
(2006)
Nucleic Acids Research
, vol.33
, Issue.SUPPL. 1
-
-
Wheeler, D.L.1
Barrett, T.2
Benson, D.A.3
Bryant, S.H.4
Canese, K.5
Chetvernin, V.6
Church, D.M.7
DiCuccio, M.8
Edgar, R.9
Federhen, S.10
Geer, L.Y.11
Helmberg, W.12
Kapustin, Y.13
Kenton, D.L.14
Khovayko, O.15
Lipman, D.J.16
Madden, T.L.17
Maglott, D.R.18
Ostell, J.19
Pruitt, K.D.20
Schuler, G.D.21
Schriml, L.M.22
Sequeira, E.23
Sherry, S.T.24
Sirotkin, K.25
Souvorov, A.26
Starchenko, G.27
Suzek, T.O.28
Tatusov, R.29
Tatusova, T.A.30
Wagner, L.31
Yaschenko, E.32
more..
-
41
-
-
3042569597
-
Annotation transfer between genomes: Protein-protein interologs and protein-DNA regulogs
-
H. Yu, N. M. Luscombe, H. X. X. Lu, X. Zhu, Y. Xia, J.-D. D. Han, N. Bertin, S. Chung, M. Vidal, and M. Gerstein, "Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs." Genome Research, vol. 14, no. 6, pp. 1107-1118, 2004.
-
(2004)
Genome Research
, vol.14
, Issue.6
, pp. 1107-1118
-
-
Yu, H.1
Luscombe, N.M.2
Lu, H.X.X.3
Zhu, X.4
Xia, Y.5
Han, J.-D.D.6
Bertin, N.7
Chung, S.8
Vidal, M.9
Gerstein, M.10
-
42
-
-
38549159946
-
FunSimMat: A comprehensive functional similarity database
-
A. Schlicker and M. Albrecht, "FunSimMat: a comprehensive functional similarity database," Nucleic Acids Research, vol. 36, no. suppl 1, pp. D434-439, 2008.
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.SUPPL. 1
-
-
Schlicker, A.1
Albrecht, M.2
-
43
-
-
38349164409
-
Computing topological parameters of biological networks
-
Jan.
-
Y. Assenov, F. Ramirez, S.-E. Schelhorn, T. Lengauer, and M. Albrecht, "Computing topological parameters of biological networks," Bioinformatics, vol. 24, no. 2, pp. 282-284, Jan. 2008.
-
(2008)
Bioinformatics
, vol.24
, Issue.2
, pp. 282-284
-
-
Assenov, Y.1
Ramirez, F.2
Schelhorn, S.-E.3
Lengauer, T.4
Albrecht, M.5
-
44
-
-
79551587720
-
Cytoscape 2.8: New features for data integration and network visualization
-
Feb.
-
M. E. Smoot, K. Ono, J. Ruscheinski, P.-L. L. Wang, and T. Ideker, "Cytoscape 2.8: new features for data integration and network visualization." Bioinformatics, vol. 27, no. 3, pp. 431-432, Feb. 2011.
-
(2011)
Bioinformatics
, vol.27
, Issue.3
, pp. 431-432
-
-
Smoot, M.E.1
Ono, K.2
Ruscheinski, J.3
Wang, P.-L.L.4
Ideker, T.5
-
45
-
-
84941871856
-
The Kolmogorov-Smirnov test for goodness of fit
-
F. J. Massey, "The Kolmogorov-Smirnov test for goodness of fit," Journal of the American Statistical Association, vol. 46, no. 253, pp. 68-78, 1951.
-
(1951)
Journal of the American Statistical Association
, vol.46
, Issue.253
, pp. 68-78
-
-
Massey, F.J.1
-
46
-
-
70349193233
-
Fast and Accurate Alignment of Multiple Protein Networks
-
M. Kalaev, V. Bafna, and R. Sharan, " Fast and Accurate Alignment of Multiple Protein Networks," Journal of Computational Biology, vol. 16, pp. 989-999, 2009.
-
(2009)
Journal of Computational Biology
, vol.16
, pp. 989-999
-
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Kalaev, M.1
Bafna, V.2
Sharan, R.3
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