-
1
-
-
0029279295
-
Travel and the emergence of infectious diseases
-
Wilson ME. Travel and the emergence of infectious diseases. Emerg Infect Dis 1995, 1(2):39-46.
-
(1995)
Emerg Infect Dis
, vol.1
, Issue.2
, pp. 39-46
-
-
Wilson, M.E.1
-
2
-
-
0000842940
-
What is a pathogen?
-
ASM News
-
Falkow S. What is a pathogen? ASM News 1997, 63(7):359-365.
-
(1997)
, vol.63
, Issue.7
, pp. 359-365
-
-
Falkow, S.1
-
3
-
-
0034444550
-
Host-pathogen interactions: basic concepts of microbial commensalism, colonization, infection, and disease
-
Casadevall A, Pirofski LA. Host-pathogen interactions: basic concepts of microbial commensalism, colonization, infection, and disease. Infect Immun 2000, 68(12):6511-6518.
-
(2000)
Infect Immun
, vol.68
, Issue.12
, pp. 6511-6518
-
-
Casadevall, A.1
Pirofski, L.A.2
-
4
-
-
73349098458
-
Antigenic diversity, transmission mechanisms, and the evolution of pathogens
-
Lange A, Ferguson NM. Antigenic diversity, transmission mechanisms, and the evolution of pathogens. PLoS Comput Biol 2009, 5(10):e1000536.
-
(2009)
PLoS Comput Biol
, vol.5
, Issue.10
-
-
Lange, A.1
Ferguson, N.M.2
-
5
-
-
0028361849
-
Evolution of antigen drift/switching: continuously evading pathogens
-
Sasaki A. Evolution of antigen drift/switching: continuously evading pathogens. J Theor Biol 1994, 168(3):291-308.
-
(1994)
J Theor Biol
, vol.168
, Issue.3
, pp. 291-308
-
-
Sasaki, A.1
-
6
-
-
0031589843
-
Evolutionary pattern of intra-host-pathogen antigenic drift: effect of cross-reactivity in immune response
-
Haraguchi Y, Sasaki A. Evolutionary pattern of intra-host-pathogen antigenic drift: effect of cross-reactivity in immune response. Philos Trans R Soc Lond B Biol Sci 1997, 352(1349):11-20.
-
(1997)
Philos Trans R Soc Lond B Biol Sci
, vol.352
, Issue.1349
, pp. 11-20
-
-
Haraguchi, Y.1
Sasaki, A.2
-
7
-
-
0031916242
-
Rates of spontaneous mutation
-
Drake JW, Charlesworth B, Charlesworth D, Crow JF. Rates of spontaneous mutation. Genetics 1998, 148(4):1667-1686.
-
(1998)
Genetics
, vol.148
, Issue.4
, pp. 1667-1686
-
-
Drake, J.W.1
Charlesworth, B.2
Charlesworth, D.3
Crow, J.F.4
-
8
-
-
0036234053
-
What is a pathogen
-
Ann Med
-
Casadevall A, Pirofski LA. What is a pathogen? Ann Med 2002, 34(1):2-4.
-
(2002)
, vol.34
, Issue.1
, pp. 2-4
-
-
Casadevall, A.1
Pirofski, L.A.2
-
9
-
-
33645343816
-
Host-pathogen systems biology
-
Forst CV. Host-pathogen systems biology. Drug Discov Today 2006, 11(5-6):220-227.
-
(2006)
Drug Discov Today
, vol.11
, Issue.5-6
, pp. 220-227
-
-
Forst, C.V.1
-
10
-
-
77951111554
-
Integration of 'omics' data: does it lead to new insights into host-microbe interactions
-
Kint G, Fierro C, Marchal K, Vanderleyden J, De Keersmaecker SCJ. Integration of 'omics' data: does it lead to new insights into host-microbe interactions? Future Microbiol 2010, 5(2):313-328.
-
(2010)
Future Microbiol
, vol.5
, Issue.2
, pp. 313-328
-
-
Kint, G.1
Fierro, C.2
Marchal, K.3
Vanderleyden, J.4
De Keersmaecker, S.C.J.5
-
11
-
-
0035166979
-
The comprehensive microbial resource
-
Peterson JD, Umayam LA, Dickinson T, Hickey EK, White O. The comprehensive microbial resource. Nucleic Acids Res 2001, 29(1):123-125.
-
(2001)
Nucleic Acids Res
, vol.29
, Issue.1
, pp. 123-125
-
-
Peterson, J.D.1
Umayam, L.A.2
Dickinson, T.3
Hickey, E.K.4
White, O.5
-
12
-
-
35148882499
-
Transcript profiling in host-pathogen interactions
-
Wise RP, Moscou MJ, Bogdanove AJ, Whitham SA. Transcript profiling in host-pathogen interactions. Annu Rev Phytopathol 2007, 45(1):329-369.
-
(2007)
Annu Rev Phytopathol
, vol.45
, Issue.1
, pp. 329-369
-
-
Wise, R.P.1
Moscou, M.J.2
Bogdanove, A.J.3
Whitham, S.A.4
-
13
-
-
23844442475
-
Genome-wide RNAi screen for host factors required for intracellular bacterial infection
-
Agaisse H, Burrack LS, Philips JA, Rubin EJ, Perrimon N, Higgins DE. Genome-wide RNAi screen for host factors required for intracellular bacterial infection. Science 2005, 309(5738):1248-1251.
-
(2005)
Science
, vol.309
, Issue.5738
, pp. 1248-1251
-
-
Agaisse, H.1
Burrack, L.S.2
Philips, J.A.3
Rubin, E.J.4
Perrimon, N.5
Higgins, D.E.6
-
14
-
-
77951620158
-
Dynamic imaging of host-pathogen interactions in vivo
-
Coombes JL, Robey EA. Dynamic imaging of host-pathogen interactions in vivo. Nat Rev Immunol 2010, 10(5):353-364.
-
(2010)
Nat Rev Immunol
, vol.10
, Issue.5
, pp. 353-364
-
-
Coombes, J.L.1
Robey, E.A.2
-
15
-
-
77954407941
-
Phenomics: expanding the role of clinical evaluation in genomic studies
-
Lanktree MB, Hassell RG, Lahiry P, Hegele RA. Phenomics: expanding the role of clinical evaluation in genomic studies. J Investig Med 2010, 58(5):700-706.
-
(2010)
J Investig Med
, vol.58
, Issue.5
, pp. 700-706
-
-
Lanktree, M.B.1
Hassell, R.G.2
Lahiry, P.3
Hegele, R.A.4
-
16
-
-
34248674621
-
Serial analysis of gene expression
-
Hu M, Polyak K. Serial analysis of gene expression. Nat Protoc 2006, 1(4):1743-1760.
-
(2006)
Nat Protoc
, vol.1
, Issue.4
, pp. 1743-1760
-
-
Hu, M.1
Polyak, K.2
-
17
-
-
0042972838
-
A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: support vector machine classification of peptide MS/MS spectra and SEQUEST scores
-
Anderson DC, Li W, Payan DG, Noble WS. A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: support vector machine classification of peptide MS/MS spectra and SEQUEST scores. J Proteome Res 2003, 2(2):137-146.
-
(2003)
J Proteome Res
, vol.2
, Issue.2
, pp. 137-146
-
-
Anderson, D.C.1
Li, W.2
Payan, D.G.3
Noble, W.S.4
-
18
-
-
67650527108
-
Comparison of feature selection and classification for MALDI-MS data
-
Liu Q, Sung AH, Qiao M, Chen Z, Yang JY, Yang MQ, Huang X, Deng Y. Comparison of feature selection and classification for MALDI-MS data. BMC Genomics 2009, 10(Suppl 1):S3.
-
(2009)
BMC Genomics
, vol.10
, Issue.SUPPL. 1
-
-
Liu, Q.1
Sung, A.H.2
Qiao, M.3
Chen, Z.4
Yang, J.Y.5
Yang, M.Q.6
Huang, X.7
Deng, Y.8
-
19
-
-
80855134793
-
PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species
-
Gillespie JJ, Wattam AR, Cammer SA, Gabbard JL, Shukla MP, Dalay O, Driscoll T, Hix D, Mane SP, Mao C, et al. PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species. Infect Immun 2011, 79(11):4286-4298.
-
(2011)
Infect Immun
, vol.79
, Issue.11
, pp. 4286-4298
-
-
Gillespie, J.J.1
Wattam, A.R.2
Cammer, S.A.3
Gabbard, J.L.4
Shukla, M.P.5
Dalay, O.6
Driscoll, T.7
Hix, D.8
Mane, S.P.9
Mao, C.10
-
20
-
-
84862167820
-
ViPR: an open bioinformatics database and analysis resource for virology research
-
Pickett BE, Sadat EL, Zhang Y, Noronha JM, Squires RB, Hunt V, Liu M, Kumar S, Zaremba S, Gu Z, et al. ViPR: an open bioinformatics database and analysis resource for virology research. Nucleic Acids Res 2012, 40(D1):D593-D598.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.D1
-
-
Pickett, B.E.1
Sadat, E.L.2
Zhang, Y.3
Noronha, J.M.4
Squires, R.B.5
Hunt, V.6
Liu, M.7
Kumar, S.8
Zaremba, S.9
Gu, Z.10
-
21
-
-
84867723807
-
Influenza research database: an integrated bioinformatics resource for influenza research and surveillance
-
Squires RB, Noronha J, Hunt V, García-Sastre A, Macken C, Baumgarth N, Suarez D, Pickett BE, Zhang Y, Larsen CN, et al. Influenza research database: an integrated bioinformatics resource for influenza research and surveillance. Influenza Other Respir Viruses 2012, 6(6):404-416.
-
(2012)
Influenza Other Respir Viruses
, vol.6
, Issue.6
, pp. 404-416
-
-
Squires, R.B.1
Noronha, J.2
Hunt, V.3
García-Sastre, A.4
Macken, C.5
Baumgarth, N.6
Suarez, D.7
Pickett, B.E.8
Zhang, Y.9
Larsen, C.N.10
-
22
-
-
75549083482
-
EuPathDB: a portal to eukaryotic pathogen databases
-
Aurrecoechea C, Brestelli J, Brunk BP, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, et al. EuPathDB: a portal to eukaryotic pathogen databases. Nucleic Acids Res 2010, 38(Suppl 1):D415-D419.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.SUPPL. 1
-
-
Aurrecoechea, C.1
Brestelli, J.2
Brunk, B.P.3
Fischer, S.4
Gajria, B.5
Gao, X.6
Gingle, A.7
Grant, G.8
Harb, O.S.9
Heiges, M.10
-
23
-
-
33846119130
-
The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation
-
Database issue
-
McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes S, Hwang K, Kubal M, et al. The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic Acids Res 2007, 35(Database issue):D347-D353.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
McNeil, L.K.1
Reich, C.2
Aziz, R.K.3
Bartels, D.4
Cohoon, M.5
Disz, T.6
Edwards, R.A.7
Gerdes, S.8
Hwang, K.9
Kubal, M.10
-
24
-
-
51049113607
-
InnateDB: facilitating systems-level analyses of the mammalian innate immune response
-
Lynn DJ, Winsor GL, Chan C, Richard N, Laird MR, Barsky A, Gardy JL, Roche FM, Chan THW, Shah N, et al. InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Mol Syst Biol 2008, 4:218.
-
(2008)
Mol Syst Biol
, vol.4
, pp. 218
-
-
Lynn, D.J.1
Winsor, G.L.2
Chan, C.3
Richard, N.4
Laird, M.R.5
Barsky, A.6
Gardy, J.L.7
Roche, F.M.8
Chan, T.H.W.9
Shah, N.10
-
25
-
-
41149084666
-
The Innate Immune Database (IIDB)
-
Korb M, Rust A, Thorsson V, Battail C, Li B, Hwang D, Kennedy K, Roach J, Rosenberger C, Gilchrist M, et al. The Innate Immune Database (IIDB). BMC Immunol 2008, 9(1):7.
-
(2008)
BMC Immunol
, vol.9
, Issue.1
, pp. 7
-
-
Korb, M.1
Rust, A.2
Thorsson, V.3
Battail, C.4
Li, B.5
Hwang, D.6
Kennedy, K.7
Roach, J.8
Rosenberger, C.9
Gilchrist, M.10
-
26
-
-
29244485462
-
GPX-Macrophage Expression Atlas: a database for expression profiles of macrophages challenged with a variety of pro-inflammatory, anti-inflammatory, benign and pathogen insults
-
Grimes GR, Moodie S, Beattie JS, Craigon M, Dickinson P, Forster T, Livingston AD, Mewissen M, Robertson KA, Ross AJ, et al. GPX-Macrophage Expression Atlas: a database for expression profiles of macrophages challenged with a variety of pro-inflammatory, anti-inflammatory, benign and pathogen insults. BMC Genomics 2005, 6:178.
-
(2005)
BMC Genomics
, vol.6
, pp. 178
-
-
Grimes, G.R.1
Moodie, S.2
Beattie, J.S.3
Craigon, M.4
Dickinson, P.5
Forster, T.6
Livingston, A.D.7
Mewissen, M.8
Robertson, K.A.9
Ross, A.J.10
-
27
-
-
52649097448
-
The Immunological Genome Project: networks of gene expression in immune cells
-
Heng TS, Painter MW. The Immunological Genome Project: networks of gene expression in immune cells. Nat Immunol 2008, 9(10):1091-1094.
-
(2008)
Nat Immunol
, vol.9
, Issue.10
, pp. 1091-1094
-
-
Heng, T.S.1
Painter, M.W.2
-
28
-
-
33644873422
-
PHI-base: a new database for pathogen host interactions
-
Database issue
-
Winnenburg R, Baldwin TK, Urban M, Rawlings C, Köhler J, Hammond-Kosack KE. PHI-base: a new database for pathogen host interactions. Nucleic Acids Res 2006, 34(Database issue):D459-D464.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Winnenburg, R.1
Baldwin, T.K.2
Urban, M.3
Rawlings, C.4
Köhler, J.5
Hammond-Kosack, K.E.6
-
29
-
-
38549139547
-
PHIDIAS: a pathogen-host interaction data integration and analysis system
-
Xiang Z, Tian Y, He Y. PHIDIAS: a pathogen-host interaction data integration and analysis system. Genome Biol 2007, 8(7):R150.
-
(2007)
Genome Biol
, vol.8
, Issue.7
-
-
Xiang, Z.1
Tian, Y.2
He, Y.3
-
30
-
-
77957719439
-
HPIDB-a unified resource for host-pathogen interactions
-
Kumar R, Nanduri B. HPIDB-a unified resource for host-pathogen interactions. BMC Bioinformatics 2010, 11(Suppl 6):S16.
-
(2010)
BMC Bioinformatics
, vol.11
, Issue.SUPPL. 6
-
-
Kumar, R.1
Nanduri, B.2
-
31
-
-
33747884345
-
Gene expression omnibus: microarray data storage, submission, retrieval, and analysis
-
Barrett T, Edgar R. Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. Methods Enzymol 2006, 411:352-369.
-
(2006)
Methods Enzymol
, vol.411
, pp. 352-369
-
-
Barrett, T.1
Edgar, R.2
-
32
-
-
13444249955
-
ArrayExpress-a public repository for microarray gene expression data at the EBI
-
Database issue
-
Parkinson H, Sarkans U, Shojatalab M, Abeygunawardena N, Contrino S, Coulson R, Farne A, Lara GG, Holloway E, Kapushesky M, et al. ArrayExpress-a public repository for microarray gene expression data at the EBI. Nucleic Acids Res 2005, 33(Database issue):D553-D555.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Parkinson, H.1
Sarkans, U.2
Shojatalab, M.3
Abeygunawardena, N.4
Contrino, S.5
Coulson, R.6
Farne, A.7
Lara, G.G.8
Holloway, E.9
Kapushesky, M.10
-
33
-
-
76649122816
-
Expander: from expression microarrays to networks and functions
-
Ulitsky I, Maron-Katz A, Shavit S, Sagir D, Linhart C, Elkon R, Tanay A, Sharan R, Shiloh Y, Shamir R. Expander: from expression microarrays to networks and functions. Nat Protoc 2010, 5(2):303-322.
-
(2010)
Nat Protoc
, vol.5
, Issue.2
, pp. 303-322
-
-
Ulitsky, I.1
Maron-Katz, A.2
Shavit, S.3
Sagir, D.4
Linhart, C.5
Elkon, R.6
Tanay, A.7
Sharan, R.8
Shiloh, Y.9
Shamir, R.10
-
34
-
-
18744403988
-
MAGIC Tool: integrated microarray data analysis
-
Heyer LJ, Moskowitz DZ, Abele JA, Karnik P, Choi D, Campbell AM, Oldham EE, Akin BK. MAGIC Tool: integrated microarray data analysis. Bioinformatics 2005, 21(9):2114-2115.
-
(2005)
Bioinformatics
, vol.21
, Issue.9
, pp. 2114-2115
-
-
Heyer, L.J.1
Moskowitz, D.Z.2
Abele, J.A.3
Karnik, P.4
Choi, D.5
Campbell, A.M.6
Oldham, E.E.7
Akin, B.K.8
-
35
-
-
33747885673
-
Bioconductor: an open source framework for bioinformatics and computational biology
-
Reimers M, Carey VJ. Bioconductor: an open source framework for bioinformatics and computational biology. Methods Enzymol 2006, 411:119-134.
-
(2006)
Methods Enzymol
, vol.411
, pp. 119-134
-
-
Reimers, M.1
Carey, V.J.2
-
36
-
-
78651324347
-
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
-
Database issue
-
Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, et al. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 2011, 39(Database issue):D561-D568.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Szklarczyk, D.1
Franceschini, A.2
Kuhn, M.3
Simonovic, M.4
Roth, A.5
Minguez, P.6
Doerks, T.7
Stark, M.8
Muller, J.9
Bork, P.10
-
37
-
-
84859204939
-
The IntAct molecular interaction database in 2012
-
Database issue
-
Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, Chen C, Duesbury M, Dumousseau M, Feuermann M, Hinz U, et al. The IntAct molecular interaction database in 2012. Nucleic Acids Res 2012, 40(Database issue):D841-D846.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Kerrien, S.1
Aranda, B.2
Breuza, L.3
Bridge, A.4
Broackes-Carter, F.5
Chen, C.6
Duesbury, M.7
Dumousseau, M.8
Feuermann, M.9
Hinz, U.10
-
38
-
-
0036088133
-
DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions
-
Xenarios I, Salwinski L, Duan XJ, Higney P, Kim SM, Eisenberg D. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res 2002, 30(1):303-305.
-
(2002)
Nucleic Acids Res
, vol.30
, Issue.1
, pp. 303-305
-
-
Xenarios, I.1
Salwinski, L.2
Duan, X.J.3
Higney, P.4
Kim, S.M.5
Eisenberg, D.6
-
39
-
-
0037245913
-
BIND: the Biomolecular Interaction Network Database
-
Bader GD, Betel D, Hogue CW. BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res 2003, 31(1):248-250.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.1
, pp. 248-250
-
-
Bader, G.D.1
Betel, D.2
Hogue, C.W.3
-
40
-
-
33846073818
-
MINT: the Molecular INTeraction database
-
Database issue
-
Chatr-aryamontri A, Ceol A, Palazzi LM, Nardelli G, Schneider MV, Castagnoli L, Cesareni G. MINT: the Molecular INTeraction database. Nucleic Acids Res 2007, 35(Database issue):D572-D574.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Chatr-aryamontri, A.1
Ceol, A.2
Palazzi, L.M.3
Nardelli, G.4
Schneider, M.V.5
Castagnoli, L.6
Cesareni, G.7
-
41
-
-
78651328883
-
The BioGRID Interaction Database: 2011 update
-
Database issue
-
Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, Livstone MS, Nixon J, Van Auken K, Wang X, Shi X, et al. The BioGRID Interaction Database: 2011 update. Nucleic Acids Res 2011, 39(Database issue):D698-D704.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Stark, C.1
Breitkreutz, B.J.2
Chatr-Aryamontri, A.3
Boucher, L.4
Oughtred, R.5
Livstone, M.S.6
Nixon, J.7
Van Auken, K.8
Wang, X.9
Shi, X.10
-
42
-
-
58149193222
-
Human Protein Reference Database-2009 update
-
Database issue
-
Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, et al. Human Protein Reference Database-2009 update. Nucleic Acids Res 2009, 37(Database issue):D767-D772.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Keshava Prasad, T.S.1
Goel, R.2
Kandasamy, K.3
Keerthikumar, S.4
Kumar, S.5
Mathivanan, S.6
Telikicherla, D.7
Raju, R.8
Shafreen, B.9
Venugopal, A.10
-
43
-
-
0033982936
-
KEGG: kyoto encyclopedia of genes and genomes
-
Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28(1):27-30.
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.1
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
44
-
-
78651275182
-
Reactome: a database of reactions, pathways and biological processes
-
Database issue
-
Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, Matthews L, Caudy M, Garapati P, Gopinath G, Jassal B, et al. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 2011, 39(Database issue):D691-D697.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Croft, D.1
O'Kelly, G.2
Wu, G.3
Haw, R.4
Gillespie, M.5
Matthews, L.6
Caudy, M.7
Garapati, P.8
Gopinath, G.9
Jassal, B.10
-
45
-
-
78651332286
-
Pathway Commons, a web resource for biological pathway data
-
Database issue
-
Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, Schultz N, Bader GD, Sander C. Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res 2011, 39(Database issue):D685-D690.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Cerami, E.G.1
Gross, B.E.2
Demir, E.3
Rodchenkov, I.4
Babur, O.5
Anwar, N.6
Schultz, N.7
Bader, G.D.8
Sander, C.9
-
46
-
-
13444312083
-
The PANTHER database of protein families, subfamilies, functions and pathways
-
Database issue
-
Mi H, Lazareva-Ulitsky B, Loo R, Kejariwal A, Vandergriff J, Rabkin S, Guo N, Muruganujan A, Doremieux O, Campbell MJ, et al. The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Res 2005, 33(Database issue):D284-D288.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Mi, H.1
Lazareva-Ulitsky, B.2
Loo, R.3
Kejariwal, A.4
Vandergriff, J.5
Rabkin, S.6
Guo, N.7
Muruganujan, A.8
Doremieux, O.9
Campbell, M.J.10
-
47
-
-
0036165418
-
BRENDA: a resource for enzyme data and metabolic information
-
Schomburg I, Chang A, Hofmann O, Ebeling C, Ehrentreich F, Schomburg D. BRENDA: a resource for enzyme data and metabolic information. Trends Biochem Sci 2002, 27(1):54-56.
-
(2002)
Trends Biochem Sci
, vol.27
, Issue.1
, pp. 54-56
-
-
Schomburg, I.1
Chang, A.2
Hofmann, O.3
Ebeling, C.4
Ehrentreich, F.5
Schomburg, D.6
-
48
-
-
27244436714
-
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes
-
Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky L, Kaipa P, Ahren D, Tsoka S, Darzentas N, Kunin V, Lopez-Bigas N. Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res 2005, 33(19):6083-6089.
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.19
, pp. 6083-6089
-
-
Karp, P.D.1
Ouzounis, C.A.2
Moore-Kochlacs, C.3
Goldovsky, L.4
Kaipa, P.5
Ahren, D.6
Tsoka, S.7
Darzentas, N.8
Kunin, V.9
Lopez-Bigas, N.10
-
49
-
-
77953934646
-
BioModels Database: an enhanced, curated and annotated resource for published quantitative kinetic models
-
Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, et al. BioModels Database: an enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol 2010, 4:92.
-
(2010)
BMC Syst Biol
, vol.4
, pp. 92
-
-
Li, C.1
Donizelli, M.2
Rodriguez, N.3
Dharuri, H.4
Endler, L.5
Chelliah, V.6
Li, L.7
He, E.8
Henry, A.9
Stefan, M.I.10
-
50
-
-
0037433037
-
The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks
-
Sivakumaran S, Hariharaputran S, Mishra J, Bhalla US. The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks. Bioinformatics 2003, 19(3):408-415.
-
(2003)
Bioinformatics
, vol.19
, Issue.3
, pp. 408-415
-
-
Sivakumaran, S.1
Hariharaputran, S.2
Mishra, J.3
Bhalla, U.S.4
-
51
-
-
51749096446
-
The CellML Model Repository
-
Lloyd CM, Lawson JR, Hunter PJ, Nielsen PF. The CellML Model Repository. Bioinformatics 2008, 24(18):2122-2123.
-
(2008)
Bioinformatics
, vol.24
, Issue.18
, pp. 2122-2123
-
-
Lloyd, C.M.1
Lawson, J.R.2
Hunter, P.J.3
Nielsen, P.F.4
-
53
-
-
0242490780
-
Cytoscape: a software environment for integrated models of biomolecular interaction networks
-
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13(11):2498-2504.
-
(2003)
Genome Res
, vol.13
, Issue.11
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
-
54
-
-
33645830948
-
CFinder: locating cliques and overlapping modules in biological networks
-
Adamcsek B, Palla G, Farkas IJ, Derenyi I, Vicsek T. CFinder: locating cliques and overlapping modules in biological networks. Bioinformatics 2006, 22(8):1021-1023.
-
(2006)
Bioinformatics
, vol.22
, Issue.8
, pp. 1021-1023
-
-
Adamcsek, B.1
Palla, G.2
Farkas, I.J.3
Derenyi, I.4
Vicsek, T.5
-
55
-
-
75249086155
-
NAViGaTOR. Network Analysis, Visualization and Graphing Toronto
-
Brown KR, Otasek D, Ali M, McGuffin MJ, Xie W, Devani B, Toch IL, Jurisica I. NAViGaTOR. Network Analysis, Visualization and Graphing Toronto. Bioinformatics 2009, 25(24):3327-3329.
-
(2009)
Bioinformatics
, vol.25
, Issue.24
, pp. 3327-3329
-
-
Brown, K.R.1
Otasek, D.2
Ali, M.3
McGuffin, M.J.4
Xie, W.5
Devani, B.6
Toch, I.L.7
Jurisica, I.8
-
57
-
-
0035455635
-
Distributing MCell simulations on the Grid
-
3
-
Casanova H, Bartol T, Stiles J, Berman F. Distributing MCell simulations on the Grid. Int J High Perform Comput Appl 2001, 14(3):243-257.
-
(2001)
Int J High Perform Comput Appl
, vol.14
, pp. 243-257
-
-
Casanova, H.1
Bartol, T.2
Stiles, J.3
Berman, F.4
-
58
-
-
0033031386
-
E-CELL: software environment for whole-cell simulation
-
Tomita M, Hashimoto K, Takahashi K, Shimizu TS, Matsuzaki Y, Miyoshi F, Saito K, Tanida S, Yugi K, Venter JC, et al. E-CELL: software environment for whole-cell simulation. Bioinformatics 1999, 15(1):72-84.
-
(1999)
Bioinformatics
, vol.15
, Issue.1
, pp. 72-84
-
-
Tomita, M.1
Hashimoto, K.2
Takahashi, K.3
Shimizu, T.S.4
Matsuzaki, Y.5
Miyoshi, F.6
Saito, K.7
Tanida, S.8
Yugi, K.9
Venter, J.C.10
-
59
-
-
65649138437
-
Computational modeling of biochemical networks using COPASI
-
Mendes P, Hoops S, Sahle S, Gauges R, Dada J, Kummer U. Computational modeling of biochemical networks using COPASI. Methods Mol Biol 2009, 500:17-59.
-
(2009)
Methods Mol Biol
, vol.500
, pp. 17-59
-
-
Mendes, P.1
Hoops, S.2
Sahle, S.3
Gauges, R.4
Dada, J.5
Kummer, U.6
-
60
-
-
3042595010
-
Cellware-a multi-algorithmic software for computational systems biology
-
Dhar P, Meng TC, Somani S, Ye L, Sairam A, Chitre M, Hao Z, Sakharkar K. Cellware-a multi-algorithmic software for computational systems biology. Bioinformatics 2004, 20(8):1319-1321.
-
(2004)
Bioinformatics
, vol.20
, Issue.8
, pp. 1319-1321
-
-
Dhar, P.1
Meng, T.C.2
Somani, S.3
Ye, L.4
Sairam, A.5
Chitre, M.6
Hao, Z.7
Sakharkar, K.8
-
62
-
-
33746595848
-
Key role of local regulation in chemosensing revealed by a new molecular interaction-based modeling method
-
Meier-Schellersheim M, Xu X, Angermann B, Kunkel EJ, Jin T, Germain RN. Key role of local regulation in chemosensing revealed by a new molecular interaction-based modeling method. PloS Comput Biol 2006, 2(7):e82.
-
(2006)
PloS Comput Biol
, vol.2
, Issue.7
-
-
Meier-Schellersheim, M.1
Xu, X.2
Angermann, B.3
Kunkel, E.J.4
Jin, T.5
Germain, R.N.6
-
63
-
-
58049164511
-
Boolean network simulations for life scientists
-
Albert I, Thakar J, Li S, Zhang R, Albert R. Boolean network simulations for life scientists. Source Code Biol Med 2008, 3:16.
-
(2008)
Source Code Biol Med
, vol.3
, pp. 16
-
-
Albert, I.1
Thakar, J.2
Li, S.3
Zhang, R.4
Albert, R.5
-
64
-
-
34447551397
-
Structural and functional analysis of cellular networks with CellNetAnalyzer
-
Klamt S, Saez-Rodriguez J, Gilles ED. Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst Biol 2007, 1:2.
-
(2007)
BMC Syst Biol
, vol.1
, pp. 2
-
-
Klamt, S.1
Saez-Rodriguez, J.2
Gilles, E.D.3
-
65
-
-
77952851181
-
BoolNet-an R package for generation, reconstruction and analysis of Boolean networks
-
Mussel C, Hopfensitz M, Kestler HA. BoolNet-an R package for generation, reconstruction and analysis of Boolean networks. Bioinformatics 2010, 26(10):1378-1380.
-
(2010)
Bioinformatics
, vol.26
, Issue.10
, pp. 1378-1380
-
-
Mussel, C.1
Hopfensitz, M.2
Kestler, H.A.3
-
66
-
-
75249087912
-
SimBoolNet-a Cytoscape plugin for dynamic simulation of signaling networks
-
Zheng J, Zhang D, Przytycki PF, Zielinski R, Capala J, Przytycka TM. SimBoolNet-a Cytoscape plugin for dynamic simulation of signaling networks. Bioinformatics 2010, 26(1):141-142.
-
(2010)
Bioinformatics
, vol.26
, Issue.1
, pp. 141-142
-
-
Zheng, J.1
Zhang, D.2
Przytycki, P.F.3
Zielinski, R.4
Capala, J.5
Przytycka, T.M.6
-
67
-
-
67650351960
-
ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists
-
Helikar T, Rogers JA. ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists. BMC Syst Biol 2009, 3:58.
-
(2009)
BMC Syst Biol
, vol.3
, pp. 58
-
-
Helikar, T.1
Rogers, J.A.2
-
68
-
-
65649154507
-
Rule-based modeling of biochemical systems with BioNetGen
-
Maly IV, Faeder J, Blinov M, Hlavacek W. Rule-based modeling of biochemical systems with BioNetGen. Methods Mol Biol 2009, 500: 113-167.
-
(2009)
Methods Mol Biol
, vol.500
, pp. 113-167
-
-
Maly, I.V.1
Faeder, J.2
Blinov, M.3
Hlavacek, W.4
-
69
-
-
34347258175
-
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox
-
Becker SA, Feist AM, Mo ML, Hannum G, Palsson BO, Herrgard MJ. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc 2007, 2(3):727-738.
-
(2007)
Nat Protoc
, vol.2
, Issue.3
, pp. 727-738
-
-
Becker, S.A.1
Feist, A.M.2
Mo, M.L.3
Hannum, G.4
Palsson, B.O.5
Herrgard, M.J.6
-
70
-
-
78651553577
-
FASIMU: flexible software for flux-balance computation series in large metabolic networks
-
Hoppe A, Hoffmann S, Gerasch A, Gille C, Holzhutter HG. FASIMU: flexible software for flux-balance computation series in large metabolic networks. BMC Bioinformatics 2011, 12:28.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 28
-
-
Hoppe, A.1
Hoffmann, S.2
Gerasch, A.3
Gille, C.4
Holzhutter, H.G.5
-
71
-
-
84983163202
-
MetNetMaker: a free and open-source tool for the creation of novel metabolic networks in SBML format
-
Forth T, McConkey GA, Westhead DR. MetNetMaker: a free and open-source tool for the creation of novel metabolic networks in SBML format. Bioinformatics 2012, 26(18):2352-2353.
-
(2012)
Bioinformatics
, vol.26
, Issue.18
, pp. 2352-2353
-
-
Forth, T.1
McConkey, G.A.2
Westhead, D.R.3
-
72
-
-
79955979079
-
Structurally robust biological networks
-
Blanchini F, Franco E. Structurally robust biological networks. BMC Syst Biol 2011, 5:74.
-
(2011)
BMC Syst Biol
, vol.5
, pp. 74
-
-
Blanchini, F.1
Franco, E.2
-
73
-
-
7644238181
-
Biological robustness
-
Kitano H. Biological robustness. Nat Rev Genet 2004, 5(11):826-837.
-
(2004)
Nat Rev Genet
, vol.5
, Issue.11
, pp. 826-837
-
-
Kitano, H.1
-
74
-
-
34548825690
-
Towards a theory of biological robustness
-
Kitano H. Towards a theory of biological robustness. Mol Syst Biol 2007, 3:137.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 137
-
-
Kitano, H.1
-
75
-
-
33846903329
-
Biological robustness in complex host-pathogen systems
-
Kitano H. Biological robustness in complex host-pathogen systems. Prog Drug Res 2007, 64(239):241-263.
-
(2007)
Prog Drug Res
, vol.64
, Issue.239
, pp. 241-263
-
-
Kitano, H.1
-
76
-
-
84867635448
-
Biological robustness: paradigms, mechanisms, and systems principles
-
Whitacre JM. Biological robustness: paradigms, mechanisms, and systems principles. Front Genet 2012, 3:67.
-
(2012)
Front Genet
, vol.3
, pp. 67
-
-
Whitacre, J.M.1
-
77
-
-
45449094504
-
A methodology for performing global uncertainty and sensitivity analysis in systems biology
-
Marino S, Hogue IB, Ray CJ, Kirschner DE. A methodology for performing global uncertainty and sensitivity analysis in systems biology. J Theor Biol 2008, 254(1):178-196.
-
(2008)
J Theor Biol
, vol.254
, Issue.1
, pp. 178-196
-
-
Marino, S.1
Hogue, I.B.2
Ray, C.J.3
Kirschner, D.E.4
-
79
-
-
58049164600
-
Dynamics of a delay differential equation model of hepatitis B virus infection
-
Gourley SA, Kuang Y, Nagy JD. Dynamics of a delay differential equation model of hepatitis B virus infection. J Biol Dyn 2008, 2(2):140-153.
-
(2008)
J Biol Dyn
, vol.2
, Issue.2
, pp. 140-153
-
-
Gourley, S.A.1
Kuang, Y.2
Nagy, J.D.3
-
80
-
-
0036297271
-
Mathematical analysis of delay differential equation models of HIV-1 infection
-
Nelson PW, Perelson AS. Mathematical analysis of delay differential equation models of HIV-1 infection. Math Biosci 2002, 179(1):73-94.
-
(2002)
Math Biosci
, vol.179
, Issue.1
, pp. 73-94
-
-
Nelson, P.W.1
Perelson, A.S.2
-
81
-
-
79960556453
-
Mathematical models of malaria-a review
-
Mandal S, Sarkar RR, Sinha S. Mathematical models of malaria-a review. Malar J 2011, 10:202.
-
(2011)
Malar J
, vol.10
, pp. 202
-
-
Mandal, S.1
Sarkar, R.R.2
Sinha, S.3
-
82
-
-
34249736324
-
Biological impacts and context of network theory
-
Almaas E. Biological impacts and context of network theory. J Exp Biol 2007, 210(9):1548-1558.
-
(2007)
J Exp Biol
, vol.210
, Issue.9
, pp. 1548-1558
-
-
Almaas, E.1
-
83
-
-
79959834606
-
Integrative analysis of many weighted co-expression networks using tensor computation
-
Li W, Liu C-C, Zhang T, Li H, Waterman MS, Zhou XJ. Integrative analysis of many weighted co-expression networks using tensor computation. PLoS Comput Biol 2011, 7(6):e1001106.
-
(2011)
PLoS Comput Biol
, vol.7
, Issue.6
-
-
Li, W.1
Liu, C.-C.2
Zhang, T.3
Li, H.4
Waterman, M.S.5
Zhou, X.J.6
-
84
-
-
37849020261
-
Network inference, analysis, and modeling in systems biology
-
Albert R. Network inference, analysis, and modeling in systems biology. Plant Cell 2007, 19(11):3327-3338.
-
(2007)
Plant Cell
, vol.19
, Issue.11
, pp. 3327-3338
-
-
Albert, R.1
-
85
-
-
0034564487
-
Analysis of gene expression data with pathway scores
-
Zien A, Küffner R, Zimmer R, Lengauer T. Analysis of gene expression data with pathway scores. Proc Int Conf Intell Syst Mol Biol 2000, 8:407-417.
-
(2000)
Proc Int Conf Intell Syst Mol Biol
, vol.8
, pp. 407-417
-
-
Zien, A.1
Küffner, R.2
Zimmer, R.3
Lengauer, T.4
-
86
-
-
84859748911
-
Causal reasoning on biological networks: interpreting transcriptional changes
-
Chindelevitch L, Ziemek D, Enayetallah A, Randhawa R, Sidders B, Brockel C, Huang ES. Causal reasoning on biological networks: interpreting transcriptional changes. Bioinformatics 2012, 28(8):1114-1121.
-
(2012)
Bioinformatics
, vol.28
, Issue.8
, pp. 1114-1121
-
-
Chindelevitch, L.1
Ziemek, D.2
Enayetallah, A.3
Randhawa, R.4
Sidders, B.5
Brockel, C.6
Huang, E.S.7
-
87
-
-
78049316294
-
Pairwise network mechanisms in the host signaling response to coxsackievirus B3 infection
-
Garmaroudi FS, Marchant D, Si X, Khalili A, Bashashati A, Wong BW, Tabet A, Ng RT, Murphy K, Luo H, et al. Pairwise network mechanisms in the host signaling response to coxsackievirus B3 infection. Proc Natl Acad Sci USA 2010, 107(39):17053-17058.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, Issue.39
, pp. 17053-17058
-
-
Garmaroudi, F.S.1
Marchant, D.2
Si, X.3
Khalili, A.4
Bashashati, A.5
Wong, B.W.6
Tabet, A.7
Ng, R.T.8
Murphy, K.9
Luo, H.10
-
88
-
-
77955707911
-
Dynamic models of immune responses: what is the ideal level of detail
-
Theor Biol Med Model
-
Thakar J, Poss M, Albert R, Long GH, Zhang R. Dynamic models of immune responses: what is the ideal level of detail? Theor Biol Med Model 2010, 7:35.
-
(2010)
, vol.7
, pp. 35
-
-
Thakar, J.1
Poss, M.2
Albert, R.3
Long, G.H.4
Zhang, R.5
-
89
-
-
77951962279
-
Odefy-from discrete to continuous models
-
Krumsiek J, Polsterl S, Wittmann DM, Theis FJ. Odefy-from discrete to continuous models. BMC Bioinformatics 2010, 11:233.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 233
-
-
Krumsiek, J.1
Polsterl, S.2
Wittmann, D.M.3
Theis, F.J.4
-
90
-
-
34547825448
-
Simulation study in Probabilistic Boolean Network models for genetic regulatory networks
-
Zhang SQ, Ching WK, Ng MK, Akutsu T. Simulation study in Probabilistic Boolean Network models for genetic regulatory networks. Int J Data Min Bioinform 2007, 1(3):217-240.
-
(2007)
Int J Data Min Bioinform
, vol.1
, Issue.3
, pp. 217-240
-
-
Zhang, S.Q.1
Ching, W.K.2
Ng, M.K.3
Akutsu, T.4
-
91
-
-
84867272347
-
Boolean modeling in systems biology: an overview of methodology and applications
-
Wang RS, Saadatpour A, Albert R. Boolean modeling in systems biology: an overview of methodology and applications. Phys Biol 2012, 9:055001.
-
(2012)
Phys Biol
, vol.9
, pp. 055001
-
-
Wang, R.S.1
Saadatpour, A.2
Albert, R.3
-
92
-
-
80054062207
-
Rule-based multi-level modeling of cell biological systems
-
Maus C, Rybacki S, Uhrmacher A. Rule-based multi-level modeling of cell biological systems. BMC Syst Biol 2011, 5(1):166.
-
(2011)
BMC Syst Biol
, vol.5
, Issue.1
, pp. 166
-
-
Maus, C.1
Rybacki, S.2
Uhrmacher, A.3
-
93
-
-
38149083357
-
-
In Caires L, Vasconcelos VT, eds. . Proceedings of the Eighteenth International Conference on Concurrency Theory, CONCUR'07. Lecture Notes in Computer Science 4703, Berlin, Germany: Springer
-
Danos V, Feret J, Fontana W, Harmer R, Krivine J. In Caires L, Vasconcelos VT, eds. Rule-based modelling of cellular signalling, invited paper. Proceedings of the Eighteenth International Conference on Concurrency Theory, CONCUR'07. Lecture Notes in Computer Science 4703, Berlin, Germany: Springer, 2007, 17-41.
-
(2007)
Rule-based modelling of cellular signalling, invited paper
, pp. 17-41
-
-
Danos, V.1
Feret, J.2
Fontana, W.3
Harmer, R.4
Krivine, J.5
-
94
-
-
0027415226
-
Cellular automata approaches to biological modelling
-
Ermentrout GB, Edelstein-Keshet L. Cellular automata approaches to biological modelling. J Theor Biol 1993, 160(1):97-133.
-
(1993)
J Theor Biol
, vol.160
, Issue.1
, pp. 97-133
-
-
Ermentrout, G.B.1
Edelstein-Keshet, L.2
-
95
-
-
0036025778
-
From factors to actors: computational sociology and agent-based modeling
-
Macy MW, Willer R. From factors to actors: computational sociology and agent-based modeling. Annu Rev Sociol 2002, 28:143-166.
-
(2002)
Annu Rev Sociol
, vol.28
, pp. 143-166
-
-
Macy, M.W.1
Willer, R.2
-
98
-
-
0026556477
-
A computer model of cellular interactions in the immune system
-
Celada F, Seiden PE. A computer model of cellular interactions in the immune system. Immunol Today 1992, 13(2):56-62.
-
(1992)
Immunol Today
, vol.13
, Issue.2
, pp. 56-62
-
-
Celada, F.1
Seiden, P.E.2
-
99
-
-
61449214048
-
Agent-based modeling of host-pathogen systems: the successes and challenges
-
Bauer AL, Beauchemin CA, Perelson AS. Agent-based modeling of host-pathogen systems: the successes and challenges. Inf Sci (NY) 2009, 179(10):1379-1389.
-
(2009)
Inf Sci (NY)
, vol.179
, Issue.10
, pp. 1379-1389
-
-
Bauer, A.L.1
Beauchemin, C.A.2
Perelson, A.S.3
-
101
-
-
28444483647
-
A multiscale model for avascular tumor growth
-
Jiang Y, Pjesivac-Grbovic J, Cantrell C, Freyer JP. A multiscale model for avascular tumor growth. Biophys J 2005, 89(6):3884-3894.
-
(2005)
Biophys J
, vol.89
, Issue.6
, pp. 3884-3894
-
-
Jiang, Y.1
Pjesivac-Grbovic, J.2
Cantrell, C.3
Freyer, J.P.4
-
102
-
-
0035491584
-
Agent-based computer simulation and sirs: building a bridge between basic science and clinical trials
-
An G. Agent-based computer simulation and sirs: building a bridge between basic science and clinical trials. Shock 2001, 16(4):266-273.
-
(2001)
Shock
, vol.16
, Issue.4
, pp. 266-273
-
-
An, G.1
-
103
-
-
0036389411
-
Exploring the formation of Alzheimer's disease senile plaques in silico
-
Edelstein-keshet L, Spiros A. Exploring the formation of Alzheimer's disease senile plaques in silico. J Theor Biol 2002, 216(3):301-326.
-
(2002)
J Theor Biol
, vol.216
, Issue.3
, pp. 301-326
-
-
Edelstein-keshet, L.1
Spiros, A.2
-
104
-
-
0142124428
-
The impact of "search precision" in an agent-based tumor model
-
Mansury Y, Deisboeck TS. The impact of "search precision" in an agent-based tumor model. J Theor Biol 2003, 224(3):325-337.
-
(2003)
J Theor Biol
, vol.224
, Issue.3
, pp. 325-337
-
-
Mansury, Y.1
Deisboeck, T.S.2
-
105
-
-
70450278800
-
Hybrid cellular automaton modeling of nutrient modulated cell growth in tissue engineering constructs
-
Chung CA, Lin TH, Chen SD, Huang HI. Hybrid cellular automaton modeling of nutrient modulated cell growth in tissue engineering constructs. J Theor Biol 2009, 262(2):267-278.
-
(2009)
J Theor Biol
, vol.262
, Issue.2
, pp. 267-278
-
-
Chung, C.A.1
Lin, T.H.2
Chen, S.D.3
Huang, H.I.4
-
106
-
-
33644890522
-
A cellular automata model of tumor-immune system interactions
-
Mallet DG, De Pillis LG. A cellular automata model of tumor-immune system interactions. J Theor Biol 2006, 239(3):334-350.
-
(2006)
J Theor Biol
, vol.239
, Issue.3
, pp. 334-350
-
-
Mallet, D.G.1
De Pillis, L.G.2
-
107
-
-
34548302044
-
Petri net modelling of biological networks
-
Chaouiya C. Petri net modelling of biological networks. Brief Bioinform 2007, 8(4):210-219.
-
(2007)
Brief Bioinform
, vol.8
, Issue.4
, pp. 210-219
-
-
Chaouiya, C.1
-
108
-
-
10944244598
-
Modeling and simulation of molecular biology systems using Petri nets: modeling goals of various approaches
-
Hardy S, Robillard PN. Modeling and simulation of molecular biology systems using Petri nets: modeling goals of various approaches. J Bioinform Comput Biol 2004, 2(04):619-637.
-
(2004)
J Bioinform Comput Biol
, vol.2
, Issue.4
, pp. 619-637
-
-
Hardy, S.1
Robillard, P.N.2
-
109
-
-
84855891503
-
Petri nets in snoopy: a unifying framework for the graphical display, computational modelling, and simulation of bacterial regulatory networks
-
In van Helden J, Toussaint A, Thieffry D, eds. . New York: Springer;
-
Helden J, Toussaint A, Thieffry D, Marwan W, Rohr C, Heiner M. Petri nets in snoopy: a unifying framework for the graphical display, computational modelling, and simulation of bacterial regulatory networks. In van Helden J, Toussaint A, Thieffry D, eds. Bacterial Molecular Networks. New York: Springer; 2012, 409-437.
-
(2012)
Bacterial Molecular Networks
, pp. 409-437
-
-
Helden, J.1
Toussaint, A.2
Thieffry, D.3
Marwan, W.4
Rohr, C.5
Heiner, M.6
-
111
-
-
84859339035
-
Spatial modeling of cell signaling networks
-
Cowan AE, Moraru I, Schaff JC, Slepchenko BM, Loew LM. Spatial modeling of cell signaling networks. Methods Cell Biol 2012, 110:195-221.
-
(2012)
Methods Cell Biol
, vol.110
, pp. 195-221
-
-
Cowan, A.E.1
Moraru, I.2
Schaff, J.C.3
Slepchenko, B.M.4
Loew, L.M.5
-
112
-
-
33644552113
-
Use of constraint-based modeling for the prediction and validation of antimicrobial targets
-
Trawick JD, Schilling CH. Use of constraint-based modeling for the prediction and validation of antimicrobial targets. Biochem Pharmacol 2006, 71(7):1026-1035.
-
(2006)
Biochem Pharmacol
, vol.71
, Issue.7
, pp. 1026-1035
-
-
Trawick, J.D.1
Schilling, C.H.2
-
113
-
-
9544253891
-
Genome-scale models of microbial cells: evaluating the consequences of constraints
-
Price ND, Reed JL, Palsson BO. Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Micro 2004, 2(11):886-897.
-
(2004)
Nat Rev Micro
, vol.2
, Issue.11
, pp. 886-897
-
-
Price, N.D.1
Reed, J.L.2
Palsson, B.O.3
-
115
-
-
0002021736
-
Equilibrium points in n-person games
-
Nash JF. Equilibrium points in n-person games. Proc Natl Acad Sci USA 1950, 36(1):48-49.
-
(1950)
Proc Natl Acad Sci USA
, vol.36
, Issue.1
, pp. 48-49
-
-
Nash, J.F.1
-
117
-
-
67649973270
-
On validation and invalidation of biological models
-
Anderson J, Papachristodoulou A. On validation and invalidation of biological models. BMC Bioinformatics 2009, 10(1):132.
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.1
, pp. 132
-
-
Anderson, J.1
Papachristodoulou, A.2
-
118
-
-
0029967721
-
HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time
-
Perelson AS, Neumann AU, Markowitz M, Leonard JM, Ho DD. HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time. Science 1996, 271(5255):1582-1586.
-
(1996)
Science
, vol.271
, Issue.5255
, pp. 1582-1586
-
-
Perelson, A.S.1
Neumann, A.U.2
Markowitz, M.3
Leonard, J.M.4
Ho, D.D.5
-
119
-
-
40349106161
-
The landscape of human proteins interacting with viruses and other pathogens
-
Dyer MD, Murali TM, Sobral BW. The landscape of human proteins interacting with viruses and other pathogens. PloS Pathog 2008, 4(2):e32.
-
(2008)
PloS Pathog
, vol.4
, Issue.2
-
-
Dyer, M.D.1
Murali, T.M.2
Sobral, B.W.3
-
120
-
-
78651526843
-
When the human viral infectome and diseasome networks collide: towards a systems biology platform for the aetiology of human diseases
-
Navratil V, de Chassey B, Combe C, Lotteau V. When the human viral infectome and diseasome networks collide: towards a systems biology platform for the aetiology of human diseases. BMC Syst Biol 2011, 5(1):13.
-
(2011)
BMC Syst Biol
, vol.5
, Issue.1
, pp. 13
-
-
Navratil, V.1
de Chassey, B.2
Combe, C.3
Lotteau, V.4
-
121
-
-
77954367520
-
System-level comparison of protein-protein interactions between viruses and the human type I interferon system network
-
Navratil V, de Chassey B, Meyniel L, Pradezynski F, AndreÌ P, Rabourdin-Combe C, Lotteau V. System-level comparison of protein-protein interactions between viruses and the human type I interferon system network. J Proteome Res 2010, 9(7):3527-3536.
-
(2010)
J Proteome Res
, vol.9
, Issue.7
, pp. 3527-3536
-
-
Navratil, V.1
de Chassey, B.2
Meyniel, L.3
Pradezynski, F.4
Andreì, P.5
Rabourdin-Combe, C.6
Lotteau, V.7
-
122
-
-
78049296111
-
Patterns of HIV-1 protein interaction identify perturbed host-cellular subsystems
-
MacPherson JI, Dickerson JE, Pinney JW, Robertson DL. Patterns of HIV-1 protein interaction identify perturbed host-cellular subsystems. PloS Comput Biol 2010, 6(7):e1000863.
-
(2010)
PloS Comput Biol
, vol.6
, Issue.7
-
-
MacPherson, J.I.1
Dickerson, J.E.2
Pinney, J.W.3
Robertson, D.L.4
-
123
-
-
79960617916
-
Structural principles within the human-virus protein-protein interaction network
-
Franzosa EA, Xia Y. Structural principles within the human-virus protein-protein interaction network. Proc Natl Acad Sci USA 2011, 108(26):10538-10543.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, Issue.26
, pp. 10538-10543
-
-
Franzosa, E.A.1
Xia, Y.2
-
124
-
-
79960040671
-
Domain-domain interactions underlying herpesvirus-human protein-protein interaction networks
-
Itzhaki Z. Domain-domain interactions underlying herpesvirus-human protein-protein interaction networks. PLoS One 2011, 6(7):e21724.
-
(2011)
PLoS One
, vol.6
, Issue.7
-
-
Itzhaki, Z.1
-
125
-
-
44749087331
-
A viral load-based cellular automata approach to modeling HIV dynamics and drug treatment
-
Shi V, Tridane A, Kuang Y. A viral load-based cellular automata approach to modeling HIV dynamics and drug treatment. J Theor Biol 2008, 253(1):24-35.
-
(2008)
J Theor Biol
, vol.253
, Issue.1
, pp. 24-35
-
-
Shi, V.1
Tridane, A.2
Kuang, Y.3
-
126
-
-
79955412523
-
Scoring protein relationships in functional interaction networks predicted from sequence data
-
Mazandu GK, Mulder NJ. Scoring protein relationships in functional interaction networks predicted from sequence data. PLoS One 2011, 6(4):e18607.
-
(2011)
PLoS One
, vol.6
, Issue.4
-
-
Mazandu, G.K.1
Mulder, N.J.2
-
127
-
-
80052768783
-
Rule-based modelling of iron homeostasis in tuberculosis
-
Ghosh S, Prasad KVS, Vishveshwara S, Chandra N. Rule-based modelling of iron homeostasis in tuberculosis. Mol Biosyst 2011, 7(10):2750-2768.
-
(2011)
Mol Biosyst
, vol.7
, Issue.10
, pp. 2750-2768
-
-
Ghosh, S.1
Prasad, K.V.S.2
Vishveshwara, S.3
Chandra, N.4
-
128
-
-
70450282392
-
Identification and functional characterization of the iron-dependent regulator (IdeR) of Mycobacterium avium subsp. paratuberculosis
-
Janagama HK, Senthilkumar TMA, Bannantine JP, Rodriguez GM, Smith I, Paustian ML, McGarvey JA, Sreevatsan S. Identification and functional characterization of the iron-dependent regulator (IdeR) of Mycobacterium avium subsp. paratuberculosis. Microbiology 2009, 155(Pt 11):3683-3690.
-
(2009)
Microbiology
, vol.155
, Issue.PART 11
, pp. 3683-3690
-
-
Janagama, H.K.1
Senthilkumar, T.M.A.2
Bannantine, J.P.3
Rodriguez, G.M.4
Smith, I.5
Paustian, M.L.6
McGarvey, J.A.7
Sreevatsan, S.8
-
129
-
-
33847654799
-
Flux balance analysis of mycolic acid pathway: targets for anti-tubercular drugs
-
Raman K, Rajagopalan P, Chandra N. Flux balance analysis of mycolic acid pathway: targets for anti-tubercular drugs. PloS Comput Biol 2005, 1(5):e46.
-
(2005)
PloS Comput Biol
, vol.1
, Issue.5
-
-
Raman, K.1
Rajagopalan, P.2
Chandra, N.3
-
130
-
-
77249117661
-
A systems perspective of host-pathogen interactions: predicting disease outcome in tuberculosis
-
Raman K, Bhat AG, Chandra N. A systems perspective of host-pathogen interactions: predicting disease outcome in tuberculosis. Mol Biosyst 2010, 6(3):516-530.
-
(2010)
Mol Biosyst
, vol.6
, Issue.3
, pp. 516-530
-
-
Raman, K.1
Bhat, A.G.2
Chandra, N.3
-
131
-
-
84879529605
-
-
Global tuberculosis control. WHO Report .
-
Global tuberculosis control. WHO Report 2011.
-
(2011)
-
-
-
132
-
-
58149083837
-
The role of the granuloma in expansion and dissemination of early tuberculous infection
-
Davis JM, Ramakrishnan L. The role of the granuloma in expansion and dissemination of early tuberculous infection. Cell 2009, 136(1):37-49.
-
(2009)
Cell
, vol.136
, Issue.1
, pp. 37-49
-
-
Davis, J.M.1
Ramakrishnan, L.2
-
133
-
-
6344281115
-
Identifying control mechanisms of granuloma formation during M. tuberculosis infection using an agent-based model
-
Segovia-Juarez JL, Ganguli S, Kirschner D. Identifying control mechanisms of granuloma formation during M. tuberculosis infection using an agent-based model. J Theor Biol 2004, 231(3):357-376.
-
(2004)
J Theor Biol
, vol.231
, Issue.3
, pp. 357-376
-
-
Segovia-Juarez, J.L.1
Ganguli, S.2
Kirschner, D.3
-
134
-
-
79954611569
-
A hybrid multi-compartment model of granuloma formation and T cell priming in tuberculosis
-
Marino S, El-Kebir M, Kirschner D. A hybrid multi-compartment model of granuloma formation and T cell priming in tuberculosis. J Theor Biol 2011, 280(1):50-62.
-
(2011)
J Theor Biol
, vol.280
, Issue.1
, pp. 50-62
-
-
Marino, S.1
El-Kebir, M.2
Kirschner, D.3
-
135
-
-
35349001069
-
The equilibria that allow bacterial persistence in human hosts
-
Blaser MJ, Kirschner D. The equilibria that allow bacterial persistence in human hosts. Nature 2007, 449(7164):843-849.
-
(2007)
Nature
, vol.449
, Issue.7164
, pp. 843-849
-
-
Blaser, M.J.1
Kirschner, D.2
-
136
-
-
65549115896
-
Location of pathogenic bacteria during persistent infections: insights from an analysis using game theory
-
Eswarappa SM. Location of pathogenic bacteria during persistent infections: insights from an analysis using game theory. PLoS One 2009, 4(4):e5383.
-
(2009)
PLoS One
, vol.4
, Issue.4
-
-
Eswarappa, S.M.1
-
137
-
-
34347333614
-
Modeling systems-level regulation of host immune responses
-
Thakar J, Pilione M, Kirimanjeswara G, Harvill ET, Albert R. Modeling systems-level regulation of host immune responses. PloS Comput Biol 2007, 3(6):e109.
-
(2007)
PloS Comput Biol
, vol.3
, Issue.6
-
-
Thakar, J.1
Pilione, M.2
Kirimanjeswara, G.3
Harvill, E.T.4
Albert, R.5
-
138
-
-
77956416193
-
Systems approach to investigating host-pathogen interactions in infections with the biothreat agent Francisella. Constraints-based model of Francisella tularensis
-
Raghunathan A, Shin S, Daefler S. Systems approach to investigating host-pathogen interactions in infections with the biothreat agent Francisella. Constraints-based model of Francisella tularensis. BMC Syst Biol 2010, 4(1):118.
-
(2010)
BMC Syst Biol
, vol.4
, Issue.1
, pp. 118
-
-
Raghunathan, A.1
Shin, S.2
Daefler, S.3
-
139
-
-
34347332311
-
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
-
Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 2007, 3:121.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 121
-
-
Feist, A.M.1
Henry, C.S.2
Reed, J.L.3
Krummenacker, M.4
Joyce, A.R.5
Karp, P.D.6
Broadbelt, L.J.7
Hatzimanikatis, V.8
Palsson, B.O.9
-
140
-
-
65649105134
-
Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction
-
Raghunathan A, Reed J, Shin S, Palsson B, Daefler S. Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction. BMC Syst Biol 2009, 3(1):38.
-
(2009)
BMC Syst Biol
, vol.3
, Issue.1
, pp. 38
-
-
Raghunathan, A.1
Reed, J.2
Shin, S.3
Palsson, B.4
Daefler, S.5
-
141
-
-
70449449392
-
Genome scale reconstruction of a Salmonella metabolic model: comparison of similarity and differences with a commensal Escherichia coli strain
-
AbuOun M, Suthers PF, Jones GI, Carter BR, Saunders MP, Maranas CD, Woodward MJ, Anjum MF. Genome scale reconstruction of a Salmonella metabolic model: comparison of similarity and differences with a commensal Escherichia coli strain. J Biol Chem 2009, 284(43):29480-29488.
-
(2009)
J Biol Chem
, vol.284
, Issue.43
, pp. 29480-29488
-
-
Abuoun, M.1
Suthers, P.F.2
Jones, G.I.3
Carter, B.R.4
Saunders, M.P.5
Maranas, C.D.6
Woodward, M.J.7
Anjum, M.F.8
-
142
-
-
0033580813
-
Systems properties of the Haemophilus influenzae Rd metabolic genotype
-
Edwards JS, Palsson BO. Systems properties of the Haemophilus influenzae Rd metabolic genotype. J Biol Chem 1999, 274(25):17410-17416.
-
(1999)
J Biol Chem
, vol.274
, Issue.25
, pp. 17410-17416
-
-
Edwards, J.S.1
Palsson, B.O.2
-
143
-
-
0037313750
-
Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network
-
Forster J, Famili I, Fu P, Palsson BO, Nielsen J. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 2003, 13(2):244-253.
-
(2003)
Genome Res
, vol.13
, Issue.2
, pp. 244-253
-
-
Forster, J.1
Famili, I.2
Fu, P.3
Palsson, B.O.4
Nielsen, J.5
-
144
-
-
34447317247
-
Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets
-
Jamshidi N, Palsson B. Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets. BMC Syst Biol 2007, 1(1):26.
-
(2007)
BMC Syst Biol
, vol.1
, Issue.1
, pp. 26
-
-
Jamshidi, N.1
Palsson, B.2
-
145
-
-
23644452487
-
Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants
-
Thiele I, Vo TD, Price ND, Palsson BÃ. Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants. J Bacteriol 2005, 187(16):5818-5830.
-
(2005)
J Bacteriol
, vol.187
, Issue.16
, pp. 5818-5830
-
-
Thiele, I.1
Vo, T.D.2
Price, N.D.3
Palsson, BA.4
-
146
-
-
77956419824
-
Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network
-
Plata G, Hsiao T-L, Olszewski KL, Llinas Manuel, Vitkup D. Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network. Mol Syst Biol 2010, 6:408.
-
(2010)
Mol Syst Biol
, vol.6
, pp. 408
-
-
Plata, G.1
Hsiao, T.-L.2
Olszewski, K.L.3
Llinas, M.4
Vitkup, D.5
-
147
-
-
41149169317
-
Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major
-
Chavali AK, Whittemore JD, Eddy JA, Williams KT, Papin JA. Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major. Mol Syst Biol 2008, 4:177.
-
(2008)
Mol Syst Biol
, vol.4
, pp. 177
-
-
Chavali, A.K.1
Whittemore, J.D.2
Eddy, J.A.3
Williams, K.T.4
Papin, J.A.5
-
148
-
-
73849090293
-
Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology
-
Milne CB, Kim PJ, Eddy JA, Price ND. Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology. Biotechnol J 2009, 4(12):1653-1670.
-
(2009)
Biotechnol J
, vol.4
, Issue.12
, pp. 1653-1670
-
-
Milne, C.B.1
Kim, P.J.2
Eddy, J.A.3
Price, N.D.4
-
149
-
-
33846910173
-
Global reconstruction of the human metabolic network based on genomic and bibliomic data
-
Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, Srivas R, Palsson BÃ. Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci USA 2007, 104(6):1777-1782.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, Issue.6
, pp. 1777-1782
-
-
Duarte, N.C.1
Becker, S.A.2
Jamshidi, N.3
Thiele, I.4
Mo, M.L.5
Vo, T.D.6
Srivas, R.7
Palsson, BA.8
-
150
-
-
84855929956
-
Using the reconstructed genome-scale human metabolic network to study physiology and pathology
-
Bordbar APB. Using the reconstructed genome-scale human metabolic network to study physiology and pathology. J Inter Med 2012, 271(2):131-141.
-
(2012)
J Inter Med
, vol.271
, Issue.2
, pp. 131-141
-
-
Bordbar, A.P.B.1
-
151
-
-
0036709912
-
Network genomics-a novel approach for the analysis of biological systems in the post-genomic era
-
Forst CV. Network genomics-a novel approach for the analysis of biological systems in the post-genomic era. Mol Biol Rep 2002, 29: 265-280.
-
(2002)
Mol Biol Rep
, vol.29
, pp. 265-280
-
-
Forst, C.V.1
|