-
1
-
-
70449369491
-
Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information
-
Acencio ML, Lemke N. Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information. BMC Bioinforma 2009, 10:290-307.
-
(2009)
BMC Bioinforma
, vol.10
, pp. 290-307
-
-
Acencio, M.L.1
Lemke, N.2
-
2
-
-
33747019241
-
Differences in the evolutionary history of disease genes affected by dominant or recessive mutations
-
10.1186/1471-2164-7-165, 1534034, 16817963
-
Furney SJ, Albà M, Lóez-Bigas N. Differences in the evolutionary history of disease genes affected by dominant or recessive mutations. BMC Genomics 2006, 7:165. 10.1186/1471-2164-7-165, 1534034, 16817963.
-
(2006)
BMC Genomics
, vol.7
, pp. 165
-
-
Furney, S.J.1
Albà, M.2
Lóez-Bigas, N.3
-
3
-
-
2442691018
-
Bioinformatical assay of human gene morbidity
-
10.1093/nar/gkh330, 390328, 15020709
-
Kondrashov FA, Ogurtsov AY, Kondrashov AS. Bioinformatical assay of human gene morbidity. Nucl Acids Res 2004, 32(5):1731-1737. 10.1093/nar/gkh330, 390328, 15020709.
-
(2004)
Nucl Acids Res
, vol.32
, Issue.5
, pp. 1731-1737
-
-
Kondrashov, F.A.1
Ogurtsov, A.Y.2
Kondrashov, A.S.3
-
4
-
-
0036699060
-
Systematic screen for human disease genes in yeast
-
Steinmetz LM, Scharfe C, Deutschbauer AM, Mokranjac D, Herman ZS, et al. Systematic screen for human disease genes in yeast. Nature Gene 2002, 31:400-404.
-
(2002)
Nature Gene
, vol.31
, pp. 400-404
-
-
Steinmetz, L.M.1
Scharfe, C.2
Deutschbauer, A.M.3
Mokranjac, D.4
Herman, Z.S.5
-
5
-
-
0038472048
-
A postgenomic method for predicting essential genes at subsaturation levels of mutagenesis: application to Mycobacterium tuberculosis
-
10.1073/pnas.1231432100, 165855, 12775759
-
Lamichhane G, Zignol M, Blades NJ, Geiman DE, Dougherty A, Grosset J, Broman KW, Bishai WR. A postgenomic method for predicting essential genes at subsaturation levels of mutagenesis: application to Mycobacterium tuberculosis. PNAS 2003, 100(12):7213-7218. 10.1073/pnas.1231432100, 165855, 12775759.
-
(2003)
PNAS
, vol.100
, Issue.12
, pp. 7213-7218
-
-
Lamichhane, G.1
Zignol, M.2
Blades, N.J.3
Geiman, D.E.4
Dougherty, A.5
Grosset, J.6
Broman, K.W.7
Bishai, W.R.8
-
6
-
-
17844405878
-
Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation
-
10.1186/1471-2180-5-8, 1079855, 15752426
-
Becker SA, Palsson BO. Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation. BMC Microbiol 2005, 5:8. 10.1186/1471-2180-5-8, 1079855, 15752426.
-
(2005)
BMC Microbiol
, vol.5
, pp. 8
-
-
Becker, S.A.1
Palsson, B.O.2
-
7
-
-
0033529707
-
Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis
-
10.1126/science.285.5429.901, 10436161
-
Winzeler FA, Shoemaker DD, Astromoff A, Liang H, Anderson K, et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 1999, 285:901-906. 10.1126/science.285.5429.901, 10436161.
-
(1999)
Science
, vol.285
, pp. 901-906
-
-
Winzeler, F.A.1
Shoemaker, D.D.2
Astromoff, A.3
Liang, H.4
Anderson, K.5
-
8
-
-
0037448540
-
Systematic functional analysis of the Caenorhabditis elegans genome using RNAi
-
10.1038/nature01278, 12529635
-
Kamath RS, Fraser AG, Dong Y, Poulin G, Durbin R, et al. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 2003, 421:231-237. 10.1038/nature01278, 12529635.
-
(2003)
Nature
, vol.421
, pp. 231-237
-
-
Kamath, R.S.1
Fraser, A.G.2
Dong, Y.3
Poulin, G.4
Durbin, R.5
-
9
-
-
0037173615
-
Functional profiling of the Saccharomyces cerevisiae genome
-
10.1038/nature00935, 12140549
-
Giaever G, Chu AM, Ni L, et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature 2002, 418(6896):387-391. 10.1038/nature00935, 12140549.
-
(2002)
Nature
, vol.418
, Issue.6896
, pp. 387-391
-
-
Giaever, G.1
Chu, A.M.2
Ni, L.3
-
10
-
-
20444424942
-
Genome-wide screening for gene function using RNAi in mammalian cells
-
10.1111/j.1440-1711.2005.01332.x, 15877598
-
Cullen LM, Arndt GM. Genome-wide screening for gene function using RNAi in mammalian cells. Immunol Cell Biol 2005, 83(3):217-223. 10.1111/j.1440-1711.2005.01332.x, 15877598.
-
(2005)
Immunol Cell Biol
, vol.83
, Issue.3
, pp. 217-223
-
-
Cullen, L.M.1
Arndt, G.M.2
-
11
-
-
0141818929
-
Large-scale essential gene identification in Candida albicans and applications to antifungal drug discovery
-
10.1046/j.1365-2958.2003.03697.x, 14507372
-
Roemer T, Jiang B, Davison J, et al. Large-scale essential gene identification in Candida albicans and applications to antifungal drug discovery. Mol Microbiol 2003, 50:167-181. 10.1046/j.1365-2958.2003.03697.x, 14507372.
-
(2003)
Mol Microbiol
, vol.50
, pp. 167-181
-
-
Roemer, T.1
Jiang, B.2
Davison, J.3
-
12
-
-
2442477788
-
Genomic analysis of essentiality within protein networks
-
10.1016/j.tig.2004.04.008, 15145574
-
Yu H, Greenbaum D, Lu HX, Zhu X, Gerstein M. Genomic analysis of essentiality within protein networks. Trends Genet 2004, 20(6):227-231. 10.1016/j.tig.2004.04.008, 15145574.
-
(2004)
Trends Genet
, vol.20
, Issue.6
, pp. 227-231
-
-
Yu, H.1
Greenbaum, D.2
Lu, H.X.3
Zhu, X.4
Gerstein, M.5
-
13
-
-
16344381521
-
Comparative Genomics of Centrality and Essentiality in Three Eukaryotic Protein Interaction Networks
-
Hahn MW, Kern AD. Comparative Genomics of Centrality and Essentiality in Three Eukaryotic Protein Interaction Networks. Mol Biol Evol 2004, 22(4):803-806.
-
(2004)
Mol Biol Evol
, vol.22
, Issue.4
, pp. 803-806
-
-
Hahn, M.W.1
Kern, A.D.2
-
14
-
-
0035799707
-
Lethality and centrality in protein networks
-
10.1038/35075138, 11333967
-
Jeong H, Mason SP, et al. Lethality and centrality in protein networks. Nature 2001, 411(6833):41-42. 10.1038/35075138, 11333967.
-
(2001)
Nature
, vol.411
, Issue.6833
, pp. 41-42
-
-
Jeong, H.1
Mason, S.P.2
-
15
-
-
53349117774
-
High-Quality Binary Protein Interaction Map of the Yeast Interactome Network
-
10.1126/science.1158684, 2746753, 18719252
-
Yu H, Braun P, Yildirim MA, et al. High-Quality Binary Protein Interaction Map of the Yeast Interactome Network. Science 2008, 322(5898):104-110. 10.1126/science.1158684, 2746753, 18719252.
-
(2008)
Science
, vol.322
, Issue.5898
, pp. 104-110
-
-
Yu, H.1
Braun, P.2
Yildirim, M.A.3
-
16
-
-
33745712594
-
Why Do Hubs Tend to Be Essential in Protein Networks?
-
He X, Zhang J. Why Do Hubs Tend to Be Essential in Protein Networks?. PLoS Genet 2006, 2(6):0826-0834.
-
(2006)
PLoS Genet
, vol.2
, Issue.6
, pp. 826-834
-
-
He, X.1
Zhang, J.2
-
17
-
-
50949092459
-
Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality
-
Zotenko E, Mestre J, O'Leary DP, Przytycka TM. Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality. PLoS Comput Biol 2008, 4(8):1-16.
-
(2008)
PLoS Comput Biol
, vol.4
, Issue.8
, pp. 1-16
-
-
Zotenko, E.1
Mestre, J.2
O'Leary, D.P.3
Przytycka, T.M.4
-
18
-
-
77957726465
-
Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology
-
Ning K, Ng HK, Srihari S, et al. Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology. BMC Bioinforma 2010, 11:505.
-
(2010)
BMC Bioinforma
, vol.11
, pp. 505
-
-
Ning, K.1
Ng, H.K.2
Srihari, S.3
-
19
-
-
33746631391
-
Evolutionary and physiological importance of hub proteins
-
10.1371/journal.pcbi.0020088, 1500817, 16839197
-
Batada NN, Hurst LD, Tyers M. Evolutionary and physiological importance of hub proteins. PLoS Comput Biol 2006, 2(7):e88. 10.1371/journal.pcbi.0020088, 1500817, 16839197.
-
(2006)
PLoS Comput Biol
, vol.2
, Issue.7
-
-
Batada, N.N.1
Hurst, L.D.2
Tyers, M.3
-
20
-
-
65449152586
-
Identifying Hubs in Protein Interaction Networks
-
Vallabhajosyula R, Chakravarti D, Lutfeali S, Ray A, Raval A. Identifying Hubs in Protein Interaction Networks. PLoS One 2009, 4(4):1-10.
-
(2009)
PLoS One
, vol.4
, Issue.4
, pp. 1-10
-
-
Vallabhajosyula, R.1
Chakravarti, D.2
Lutfeali, S.3
Ray, A.4
Raval, A.5
-
21
-
-
31344478575
-
Virtual identification of essential proteins within the protein interaction network of yeast
-
10.1002/pmic.200500209, 16281187
-
Estrada E. Virtual identification of essential proteins within the protein interaction network of yeast. Proteomics 2006, 6(1):35-40. 10.1002/pmic.200500209, 16281187.
-
(2006)
Proteomics
, vol.6
, Issue.1
, pp. 35-40
-
-
Estrada, E.1
-
22
-
-
27744469130
-
High-betweenness proteins in the yeast protein interaction network
-
Joy M, et al. High-betweenness proteins in the yeast protein interaction network. J Biomed Biotechnol 2005, 2:96-103.
-
(2005)
J Biomed Biotechnol
, vol.2
, pp. 96-103
-
-
Joy, M.1
-
23
-
-
0038700482
-
Centers of complex networks
-
10.1016/S0022-5193(03)00071-7, 12782116
-
Wuchty S, Stadler PF. Centers of complex networks. J Theor Biol 2003, 223:45-53. 10.1016/S0022-5193(03)00071-7, 12782116.
-
(2003)
J Theor Biol
, vol.223
, pp. 45-53
-
-
Wuchty, S.1
Stadler, P.F.2
-
24
-
-
48449102450
-
Hubba: hub objects analyzer-a framework of interactome hubs identification for network biology
-
Lin CY, Chin CH, Wu HH, Chen SH, Ho CW, Ko MT. Hubba: hub objects analyzer-a framework of interactome hubs identification for network biology. Nucleic Acids Res 2008, 36:438-443.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 438-443
-
-
Lin, C.Y.1
Chin, C.H.2
Wu, H.H.3
Chen, S.H.4
Ho, C.W.5
Ko, M.T.6
-
25
-
-
79959695371
-
A local average connectivity-based method for identifying essential proteins from the network level
-
10.1016/j.compbiolchem.2011.04.002, 21704260
-
Li M, Wang J, Chen X, Wang H, Pan Y. A local average connectivity-based method for identifying essential proteins from the network level. Comput Biol Chem 2011, 35:143-150. 10.1016/j.compbiolchem.2011.04.002, 21704260.
-
(2011)
Comput Biol Chem
, vol.35
, pp. 143-150
-
-
Li, M.1
Wang, J.2
Chen, X.3
Wang, H.4
Pan, Y.5
-
27
-
-
79955839284
-
A New Method for Identifying Essential Proteins Based on Edge Clustering Coefficient
-
Wang H, Li M, Wang J, Pan Y. A New Method for Identifying Essential Proteins Based on Edge Clustering Coefficient. ISBRA 2011, LNBI 2010, 6674:87-98.
-
(2010)
ISBRA 2011, LNBI
, vol.6674
, pp. 87-98
-
-
Wang, H.1
Li, M.2
Wang, J.3
Pan, Y.4
-
28
-
-
77953785685
-
Essential Proteins Discovery from Weighted Protein Interaction Networks
-
Li M, Wang J, Wang H, Pan Y. Essential Proteins Discovery from Weighted Protein Interaction Networks. ISBRA2010, LNBI 2010, 6053:89-100.
-
(2010)
ISBRA2010, LNBI
, vol.6053
, pp. 89-100
-
-
Li, M.1
Wang, J.2
Wang, H.3
Pan, Y.4
-
31
-
-
79959575935
-
Leaders in Social Networks, the Delicious Case
-
10.1371/journal.pone.0021202, 3124485, 21738620
-
Lu L, Zhang YC, Yeung CH, Zhou T. Leaders in Social Networks, the Delicious Case. PLoS One 2011, 6:e21202. 10.1371/journal.pone.0021202, 3124485, 21738620.
-
(2011)
PLoS One
, vol.6
-
-
Lu, L.1
Zhang, Y.C.2
Yeung, C.H.3
Zhou, T.4
-
32
-
-
79961076379
-
A Parameterized Centrality Metrics for Network Analysis
-
Gosh R, Lerman K. A Parameterized Centrality Metrics for Network Analysis. Phys Rev 2011, E 83:066118.
-
(2011)
Phys Rev
, vol.E 83
, pp. 066118
-
-
Gosh, R.1
Lerman, K.2
-
33
-
-
77958564958
-
Community landscapes: an integrative approach to determine overlapping network module hierarchy, identify key nodes and predict network dynamics
-
10.1371/journal.pone.0012528, 2932713, 20824084
-
Kovács IA, Palotai R, Szalay MS, Csermely P. Community landscapes: an integrative approach to determine overlapping network module hierarchy, identify key nodes and predict network dynamics. PLoS One 2010, 5:e12528. 10.1371/journal.pone.0012528, 2932713, 20824084.
-
(2010)
PLoS One
, vol.5
-
-
Kovács, I.A.1
Palotai, R.2
Szalay, M.S.3
Csermely, P.4
-
34
-
-
79955847235
-
Prediction of essential proteins by integration of PPI network topology andprotein complexes information
-
Ren J, Wang J, Li L, Wang H, Liu B. Prediction of essential proteins by integration of PPI network topology andprotein complexes information. ISBRA 2011, LNBI 2010, 6674:12-24.
-
(2010)
ISBRA 2011, LNBI
, vol.6674
, pp. 12-24
-
-
Ren, J.1
Wang, J.2
Li, L.3
Wang, H.4
Liu, B.5
-
36
-
-
84936824655
-
Power and centrality: A family of measures
-
Bonacich P. Power and centrality: A family of measures. Am J Sociol 1987, 92(5):1170-1182.
-
(1987)
Am J Sociol
, vol.92
, Issue.5
, pp. 1170-1182
-
-
Bonacich, P.1
-
37
-
-
45249126392
-
Rethinking centrality: Methods and examples
-
Stephenson K, Zelen M. Rethinking centrality: Methods and examples. Social Networks 1989, 11:1-37.
-
(1989)
Social Networks
, vol.11
, pp. 1-37
-
-
Stephenson, K.1
Zelen, M.2
-
38
-
-
1342330546
-
Functional topology in a network of protein interactions
-
10.1093/bioinformatics/btg415, 14960460
-
Pržulj N, Wigle DA, Jurisica I. Functional topology in a network of protein interactions. Bioinformatics 2004, 20(3):340-348. 10.1093/bioinformatics/btg415, 14960460.
-
(2004)
Bioinformatics
, vol.20
, Issue.3
, pp. 340-348
-
-
Pržulj, N.1
Wigle, D.A.2
Jurisica, I.3
-
39
-
-
34247622363
-
The importance of bottlenecks in protein networks: Correlation with gene essentiality and expression dynamics
-
10.1371/journal.pcbi.0030059, 1853125, 17447836
-
Yu H, Kim PM, Sprecher E, Trifonov V, Gerstein M. The importance of bottlenecks in protein networks: Correlation with gene essentiality and expression dynamics. PLoS Comput Biol 2007, 3(4):e59. 10.1371/journal.pcbi.0030059, 1853125, 17447836.
-
(2007)
PLoS Comput Biol
, vol.3
, Issue.4
-
-
Yu, H.1
Kim, P.M.2
Sprecher, E.3
Trifonov, V.4
Gerstein, M.5
-
40
-
-
33845955474
-
Inferring topology from clustering coefficients in protein-protein interaction networks
-
Friedel C, Zimmer R. Inferring topology from clustering coefficients in protein-protein interaction networks. BMC Bioinforma 2006, 7:519.
-
(2006)
BMC Bioinforma
, vol.7
, pp. 519
-
-
Friedel, C.1
Zimmer, R.2
-
41
-
-
1542357701
-
Defining and identifying communities in networks
-
10.1073/pnas.0400054101, 365677, 14981240
-
Radicchi F, Castellano C, Cecconi F, Loreto V, Parisi D. Defining and identifying communities in networks. PNAS 2004, 101:2658-2663. 10.1073/pnas.0400054101, 365677, 14981240.
-
(2004)
PNAS
, vol.101
, pp. 2658-2663
-
-
Radicchi, F.1
Castellano, C.2
Cecconi, F.3
Loreto, V.4
Parisi, D.5
-
42
-
-
51549100406
-
A Fast Agglomerate Algorithm for Mining Functional Modules in Protein Interaction Networks
-
IEEE press
-
Li M, Wang J, Chen J. A Fast Agglomerate Algorithm for Mining Functional Modules in Protein Interaction Networks. BMEI 2008 2008, 1:3-7. IEEE press.
-
(2008)
BMEI 2008
, vol.1
, pp. 3-7
-
-
Li, M.1
Wang, J.2
Chen, J.3
-
43
-
-
84862790604
-
-
http://en.wikipedia.org/wiki/Pearson%27s_correlation_coefficient
-
-
-
-
44
-
-
0037050026
-
Functional organization of the yeast proteome by systematic analysis of protein complexes
-
10.1038/415123a, 11805813
-
Gavin AC, et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002, 415(6868):123-124. 10.1038/415123a, 11805813.
-
(2002)
Nature
, vol.415
, Issue.6868
, pp. 123-124
-
-
Gavin, A.C.1
-
45
-
-
34547787599
-
A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality
-
Hart GT, Lee I, Marcotte EM. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. BMC Bioinforma 2007, 8:236.
-
(2007)
BMC Bioinforma
, vol.8
, pp. 236
-
-
Hart, G.T.1
Lee, I.2
Marcotte, E.M.3
-
46
-
-
0033971642
-
DIP: the database of interacting proteins
-
10.1093/nar/28.1.289, 102387, 10592249
-
Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D. DIP: the database of interacting proteins. Nucleic Acids Res 2000, 28(1):289-291. 10.1093/nar/28.1.289, 102387, 10592249.
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.1
, pp. 289-291
-
-
Xenarios, I.1
Rice, D.W.2
Salwinski, L.3
Baron, M.K.4
Marcotte, E.M.5
Eisenberg, D.6
-
47
-
-
33644875537
-
MIPS: analysis and annotation of proteins from whole genomes in 2005
-
10.1093/nar/gkj148, 1347510, 16381839
-
Mewes HW, et al. MIPS: analysis and annotation of proteins from whole genomes in 2005. Nucleic Acids Res 2006, 34:D169-D172. 10.1093/nar/gkj148, 1347510, 16381839.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Mewes, H.W.1
-
48
-
-
0031858914
-
SGD: Saccharomyces Genome Database
-
Cherry JM, et al. SGD: Saccharomyces Genome Database. Nucleic Acids Res 1988, 26(1):73-79.
-
(1988)
Nucleic Acids Res
, vol.26
, Issue.1
, pp. 73-79
-
-
Cherry, J.M.1
-
49
-
-
58149197597
-
DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes
-
2686491, 18974178
-
Zhang R, Lin Y. DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. Nucleic Acids Res 2009, 37(1):D455-D458. 2686491, 18974178.
-
(2009)
Nucleic Acids Res
, vol.37
, Issue.1
-
-
Zhang, R.1
Lin, Y.2
-
50
-
-
84879688507
-
Saccharomyces Genome Deletion Project
-
Saccharomyces Genome Deletion Project. , http://www-sequence.stanford.edu/group/
-
-
-
-
51
-
-
27944487902
-
Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes
-
10.1126/science.1120499, 16254148
-
Tu BP, Kudlicki A, Rowicka M, McKnight SL. Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science 2005, 310:1152-1158. 10.1126/science.1120499, 16254148.
-
(2005)
Science
, vol.310
, pp. 1152-1158
-
-
Tu, B.P.1
Kudlicki, A.2
Rowicka, M.3
McKnight, S.L.4
|