-
1
-
-
0141593601
-
Conserved pathways within bacteria and yeast as revealed by global protein network alignment
-
Kelley BP, et al. (2003) Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc Natl Acad Sci USA 100(20):11394-11399.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, Issue.20
, pp. 11394-11399
-
-
Kelley, B.P.1
-
2
-
-
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(6):1974-1979.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, Issue.6
, pp. 1974-1979
-
-
Sharan, R.1
-
3
-
-
33645985807
-
Pairwise alignment of protein interaction networks
-
Koyutürk M, et al. (2006) Pairwise alignment of protein interaction networks. J Comput Biol 13(2):182-199.
-
(2006)
J Comput Biol
, vol.13
, Issue.2
, pp. 182-199
-
-
Koyutürk, M.1
-
4
-
-
34548755675
-
Comparing protein interaction networks via a graph match-and-split algorithm
-
Narayanan M, Karp RM (2007) Comparing protein interaction networks via a graph match-and-split algorithm. J Comput Biol 14(7):892-907.
-
(2007)
J Comput Biol
, vol.14
, Issue.7
, pp. 892-907
-
-
Narayanan, M.1
Karp, R.M.2
-
5
-
-
84861515900
-
Algorithms to detect multiprotein modularity conserved during evolution
-
Hodgkinson L, Karp RM (2012) Algorithms to detect multiprotein modularity conserved during evolution. IEEE/ACM Trans Comput Biol Bioinform 9(4):1046-1058.
-
(2012)
IEEE/ACM Trans Comput Biol Bioinform
, vol.9
, Issue.4
, pp. 1046-1058
-
-
Hodgkinson, L.1
Karp, R.M.2
-
6
-
-
84859699831
-
The gene ontology: Enhancements for 2011
-
Gene Ontology Consortium
-
Gene Ontology Consortium (2012) The Gene Ontology: Enhancements for 2011. Nucleic Acids Res 40(Database issue):D559-D564.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.DATABASE ISSUE
-
-
-
7
-
-
12344269924
-
GO:TermFinder - Open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
-
Boyle EI, et al. (2004) GO:TermFinder - Open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 20(18):3710-3715.
-
(2004)
Bioinformatics
, vol.20
, Issue.18
, pp. 3710-3715
-
-
Boyle, E.I.1
-
8
-
-
36448946146
-
Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis
-
Grossmann S, Bauer S, Robinson PN, Vingron M (2007) Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis. Bioinformatics 23(22):3024-3031.
-
(2007)
Bioinformatics
, vol.23
, Issue.22
, pp. 3024-3031
-
-
Grossmann, S.1
Bauer, S.2
Robinson, P.N.3
Vingron, M.4
-
9
-
-
47049099111
-
Ontologizer 2.0 - A multifunctional tool for GOtermenrichment analysis and data exploration
-
Bauer S, Grossmann S, Vingron M, Robinson PN (2008) Ontologizer 2.0 - A multifunctional tool for GOtermenrichment analysis and data exploration. Bioinformatics 24(14):1650-1651.
-
(2008)
Bioinformatics
, vol.24
, Issue.14
, pp. 1650-1651
-
-
Bauer, S.1
Grossmann, S.2
Vingron, M.3
Robinson, P.N.4
-
10
-
-
84859609641
-
Analyzing proteinprotein interaction networks
-
Koh GCKW, Porras P, Aranda B, Hermjakob H, Orchard SE (2012) Analyzing proteinprotein interaction networks. J Proteome Res 11(4):2014-2031.
-
(2012)
J Proteome Res
, vol.11
, Issue.4
, pp. 2014-2031
-
-
Koh, G.C.K.W.1
Porras, P.2
Aranda, B.3
Hermjakob, H.4
Orchard, S.E.5
-
11
-
-
84898957407
-
Conductance and the rapid mixing property for Markov chains: The approximation of permanent resolved
-
(ACM, New York)
-
Jerrum M, Sinclair A (1988) Conductance and the rapid mixing property for Markov chains: The approximation of permanent resolved. Proceedings of the twentieth annual ACM symposium on Theory of computing (ACM, New York), pp 235-244.
-
(1988)
Proceedings of the Twentieth Annual ACM Symposium on Theory of Computing
, pp. 235-244
-
-
Jerrum, M.1
Sinclair, A.2
-
13
-
-
37649028224
-
Finding and evaluating community structure in networks
-
Newman ME, Girvan M (2004) Finding and evaluating community structure in networks. Phys Rev E Stat Nonlin Soft Matter Phys 69(2 Pt 2):026113.
-
(2004)
Phys Rev e Stat Nonlin Soft Matter Phys
, vol.69
, Issue.2 PART 2
, pp. 026113
-
-
Newman, M.E.1
Girvan, M.2
-
14
-
-
40449109730
-
Consistent dissection of the protein interaction network by combining global and local metrics
-
Wang C, Ding C, Yang Q, Holbrook SR (2007) Consistent dissection of the protein interaction network by combining global and local metrics. Genome Biol 8(12):R271.
-
(2007)
Genome Biol
, vol.8
, Issue.12
-
-
Wang, C.1
Ding, C.2
Yang, Q.3
Holbrook, S.R.4
-
15
-
-
84856944883
-
An iterative network partition algorithm for accurate identification of dense network modules
-
Sun S, Dong X, Fu Y, Tian W (2012) An iterative network partition algorithm for accurate identification of dense network modules. Nucleic Acids Res 40(3):e18.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.3
-
-
Sun, S.1
Dong, X.2
Fu, Y.3
Tian, W.4
-
17
-
-
80052036327
-
Biological interaction networks are conserved at the module level
-
Zinman GE, Zhong S, Bar-Joseph Z (2011) Biological interaction networks are conserved at the module level. BMC Syst Biol 5:134.
-
(2011)
BMC Syst Biol
, vol.5
, pp. 134
-
-
Zinman, G.E.1
Zhong, S.2
Bar-Joseph, Z.3
-
18
-
-
33847249901
-
Specificity and evolvability in eukaryotic protein interaction networks
-
Beltrao P, Serrano L (2007) Specificity and evolvability in eukaryotic protein interaction networks. PLOS Comput Biol 3(2):e25.
-
(2007)
PLOS Comput Biol
, vol.3
, Issue.2
-
-
Beltrao, P.1
Serrano, L.2
-
19
-
-
33644617753
-
Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets
-
Gandhi TKB, et al. (2006) Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet 38(3):285-293.
-
(2006)
Nat Genet
, vol.38
, Issue.3
, pp. 285-293
-
-
Gandhi, T.K.B.1
-
20
-
-
0035211290
-
Identification of potential interaction networks using sequence- based searches for conserved protein-protein interactions or "interologs"
-
Matthews LR, et al. (2001) Identification of potential interaction networks using sequence- based searches for conserved protein-protein interactions or "interologs" Genome Res 11(12):2120-2126.
-
(2001)
Genome Res
, vol.11
, Issue.12
, pp. 2120-2126
-
-
Matthews, L.R.1
-
21
-
-
75949120438
-
How and when should interactome-derived clusters be used to predict functional modules and protein function?
-
Song J, Singh M (2009) How and when should interactome-derived clusters be used to predict functional modules and protein function? Bioinformatics 25(23):3143-3150.
-
(2009)
Bioinformatics
, vol.25
, Issue.23
, pp. 3143-3150
-
-
Song, J.1
Singh, M.2
-
23
-
-
54949127160
-
IRefIndex: A consolidated protein interaction database with provenance
-
Razick S, Magklaras G, Donaldson IM (2008) iRefIndex: A consolidated protein interaction database with provenance. BMC Bioinformatics 9:405.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 405
-
-
Razick, S.1
Magklaras, G.2
Donaldson, I.M.3
-
24
-
-
79959846617
-
PSICQUIC and PSISCORE: Accessing and scoring molecular interactions
-
Aranda B, et al. (2011) PSICQUIC and PSISCORE: Accessing and scoring molecular interactions. Nat Methods 8(7):528-529.
-
(2011)
Nat Methods
, vol.8
, Issue.7
, pp. 528-529
-
-
Aranda, B.1
-
25
-
-
84859204939
-
The IntAct molecular interaction database in 2012
-
Kerrien S, et al. (2012) The IntAct molecular interaction database in 2012. Nucleic Acids Res 40(Database issue):D841-D846.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.DATABASE ISSUE
-
-
Kerrien, S.1
-
26
-
-
78651328883
-
The BioGRID interaction database: 2011 update
-
Stark C, et al. (2011) The BioGRID interaction database: 2011 update. Nucleic Acids Res 39(Database issue):D698-D704.
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.DATABASE ISSUE
-
-
Stark, C.1
-
27
-
-
0347755535
-
The database of interacting proteins: 2004 update
-
Salwinski L, et al. (2004) The database of interacting proteins: 2004 update. Nucleic Acids Res 32(Database issue):D449-D451.
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.DATABASE ISSUE
-
-
Salwinski, L.1
-
28
-
-
58149193222
-
Human Protein Reference Database - 2009 update
-
Keshava Prasad TS, et al. (2009) Human Protein Reference Database - 2009 update. Nucleic Acids Res 37(Database issue):D767-D772.
-
(2009)
Nucleic Acids Res
, vol.37
, Issue.DATABASE ISSUE
-
-
Keshava Prasad, T.S.1
-
30
-
-
84860918589
-
MINT, the molecular interaction database: 2012 update
-
Licata L, et al. (2012) MINT, the molecular interaction database: 2012 update. Nucleic Acids Res 40(Database issue):D857-D861.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.DATABASE ISSUE
-
-
Licata, L.1
-
31
-
-
78651331299
-
MIPS: Curated databases and comprehensive secondary data resources in 2010
-
Mewes HW, et al. (2011) MIPS: Curated databases and comprehensive secondary data resources in 2010. Nucleic Acids Res 39(Database issue):D220-D224.
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.DATABASE ISSUE
-
-
Mewes, H.W.1
-
32
-
-
51049113607
-
InnateDB: Facilitating systems-level analyses of the mammalian innate immune response
-
Lynn DJ, et al. (2008) InnateDB: Facilitating systems-level analyses of the mammalian innate immune response. Mol Syst Biol 4:218.
-
(2008)
Mol Syst Biol
, vol.4
, pp. 218
-
-
Lynn, D.J.1
-
33
-
-
78651301312
-
MatrixDB, the extracellular matrix interaction database
-
Chautard E, Fatoux-Ardore M, Ballut L, Thierry-Mieg N, Ricard-Blum S (2011) MatrixDB, the extracellular matrix interaction database. Nucleic Acids Res 39(Database issue):D235-D240.
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.DATABASE ISSUE
-
-
Chautard, E.1
Fatoux-Ardore, M.2
Ballut, L.3
Thierry-Mieg, N.4
Ricard-Blum, S.5
-
34
-
-
84860833500
-
Reorganizing the protein space at the Universal Protein Resource (UniProt)
-
UniProt Consortium
-
UniProt Consortium (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 40(Database issue):D71-D75.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.DATABASE ISSUE
-
-
-
35
-
-
84857745267
-
Detabase resources of the National Center for Biotechnology Information
-
Sayers EW, et al. (2012) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 40(Database issue):D13-D25.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.DATABASE ISSUE
-
-
Sayers, E.W.1
-
36
-
-
35448974490
-
Fossils and phylogenies: Integrating multiple lines of evidence to investigate the origin of early major metazoan lineages
-
Cartwright P, Collins A (2007) Fossils and phylogenies: Integrating multiple lines of evidence to investigate the origin of early major metazoan lineages. Integr Comp Biol 47(5): 744-751.
-
(2007)
Integr Comp Biol
, vol.47
, Issue.5
, pp. 744-751
-
-
Cartwright, P.1
Collins, A.2
-
37
-
-
80053278126
-
Eukaryotic genome complexity
-
Pray LA (2008) Eukaryotic genome complexity. Nature Education. Available online at http://www.nature.com/scitable/topicpage/eukaryotic-genome-complexity- 437.
-
(2008)
Nature Education
-
-
Pray, L.A.1
-
38
-
-
84865247976
-
Parallel software architecture for experimental workflows in computational biology on clouds
-
eds Wyrzykowski R, Dongarra J, Karczewski K, Wa-sniewski J, Part II Springer, Berlin)
-
Hodgkinson L, Rosa J, Brewer EA (2012) Parallel software architecture for experimental workflows in computational biology on clouds. Proceedings of the 9th international conference on Parallel Processing and Applied Mathematics - Volume Part II, eds Wyrzykowski R, Dongarra J, Karczewski K, Wa-sniewski J, Part II (Springer, Berlin), pp 281-291.
-
(2012)
Proceedings of the 9th International Conference on Parallel Processing and Applied Mathematics - Volume Part I.I.
, pp. 281-291
-
-
Hodgkinson, L.1
Rosa, J.2
Brewer, E.A.3
-
39
-
-
84863304598
-
-
R Development Core Team (R Foundation for Statistical Computing, Vienna)
-
R Development Core Team (2012) R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, Vienna).
-
(2012)
R: A Language and Environment for Statistical Computing
-
-
-
40
-
-
0003802343
-
-
Chapman & Hall/CRC, Boca Raton, FL)
-
Breiman L, Friedman JH, Olshen RA, Stone CJ (1984) Classification and Regression Trees (Chapman & Hall/CRC, Boca Raton, FL).
-
(1984)
Classification and Regression Trees
-
-
Breiman, L.1
Friedman, J.H.2
Olshen, R.A.3
Stone, C.J.4
-
41
-
-
33750228994
-
Relative importance for linear regression in R: The package relaimpo
-
Groemping U (2006) Relative importance for linear regression in R: The package relaimpo. J Stat Softw 17(1):17.
-
(2006)
J Stat Softw
, vol.17
, Issue.1
, pp. 17
-
-
Groemping, U.1
-
42
-
-
34248397223
-
Estimators of relative importance in linear regression based on variance decomposition
-
Groemping U (2007) Estimators of relative importance in linear regression based on variance decomposition. Am Stat 61(2):139-147.
-
(2007)
Am Stat
, vol.61
, Issue.2
, pp. 139-147
-
-
Groemping, U.1
-
43
-
-
0032439915
-
On variable importance in linear regression
-
Thomas DR, Hughes E, Zumbo BD (1998) On variable importance in linear regression. Soc Indic Res 45(1-3):253-275.
-
(1998)
Soc Indic Res
, vol.45
, Issue.1-3
, pp. 253-275
-
-
Thomas, D.R.1
Hughes, E.2
Zumbo, B.D.3
|