-
1
-
-
77649248957
-
Compound classification using image-based cellular phenotypes
-
Adams CL, Kutsyy V, Coleman DA, Cong G, Crompton AM, Elias KA, Oestreicher DR, Trautman JK, Vaisberg E. 2006. Compound classification using image-based cellular phenotypes. Methods Enzymol 2006: 414440-414468.
-
(2006)
Methods Enzymol
, vol.2006
, pp. 414440-414468
-
-
Adams, C.L.1
Kutsyy, V.2
Coleman, D.A.3
Cong, G.4
Crompton, A.M.5
Elias, K.A.6
Oestreicher, D.R.7
Trautman, J.K.8
Vaisberg, E.9
-
2
-
-
27944493925
-
Scale-free networks in cell biology
-
Albert R. 2005. Scale-free networks in cell biology. J Cell Sci 118: 4947-4957.
-
(2005)
J Cell Sci
, vol.118
, pp. 4947-4957
-
-
Albert, R.1
-
3
-
-
34250882643
-
Quantitative morphological signatures define local signaling networks regulating cell morphology
-
Bakal C, Aach J, Church G, Perrimon N. 2007. Quantitative morphological signatures define local signaling networks regulating cell morphology. Science 316: 1753-1756.
-
(2007)
Science
, vol.316
, pp. 1753-1756
-
-
Bakal, C.1
Aach, J.2
Church, G.3
Perrimon, N.4
-
4
-
-
54249117296
-
Phosphorylation networks regulating JNK activity in diverse genetic backgrounds
-
Bakal C, Linding R, Llense F, Heffern E, Martin-Blanco E, Pawson T, Perrimon N. 2008. Phosphorylation networks regulating JNK activity in diverse genetic backgrounds. Science 322: 453-456.
-
(2008)
Science
, vol.322
, pp. 453-456
-
-
Bakal, C.1
Linding, R.2
Llense, F.3
Heffern, E.4
Martin-Blanco, E.5
Pawson, T.6
Perrimon, N.7
-
6
-
-
0035913909
-
Regulating axon branch stability: The role of p190 RhoGAP in repressing a retraction signaling pathway
-
Billuart P, Winter CG, Maresh A, Zhao X, Luo L. 2001. Regulating axon branch stability: The role of p190 RhoGAP in repressing a retraction signaling pathway. Cell 107: 195-207.
-
(2001)
Cell
, vol.107
, pp. 195-207
-
-
Billuart, P.1
Winter, C.G.2
Maresh, A.3
Zhao, X.4
Luo, L.5
-
7
-
-
0036139314
-
A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cells
-
Boland MV, Murphy RF. 2001. A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cells. Bioinformatics 17: 1213-1223.
-
(2001)
Bioinformatics
, vol.17
, pp. 1213-1223
-
-
Boland, M.V.1
Murphy, R.F.2
-
8
-
-
0032212323
-
Automated recognition of patterns characteristic of subcellular structures in fluorescence microscopy images
-
Boland MV, Markey MK, Murphy RF. 1998. Automated recognition of patterns characteristic of subcellular structures in fluorescence microscopy images. Cytometry 33: 366-375.
-
(1998)
Cytometry
, vol.33
, pp. 366-375
-
-
Boland, M.V.1
Markey, M.K.2
Murphy, R.F.3
-
9
-
-
33845792555
-
CellProfiler: Image analysis software for identifying and quantifying cell phenotypes
-
doi: 10.1186/1471-2105-9-482
-
Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, Guertin DA, Chang JH, Lindquist RA, Moffat J, et al. 2006. CellProfiler: Image analysis software for identifying and quantifying cell phenotypes. Genome Biol 7: R100. doi: 10.1186/1471-2105-9-482.
-
(2006)
Genome Biol
, vol.7
-
-
Carpenter, A.E.1
Jones, T.R.2
Lamprecht, M.R.3
Clarke, C.4
Kang, I.H.5
Friman, O.6
Guertin, D.A.7
Chang, J.H.8
Lindquist, R.A.9
Moffat, J.10
-
10
-
-
77649245492
-
Automated interpretation of protein subcellular location patterns
-
Chen X, Murphy RF. 2006. Automated interpretation of protein subcellular location patterns. Int Rev Cytol 2006: 249193-249227.
-
(2006)
Int Rev Cytol
, vol.2006
, pp. 249193-249227
-
-
Chen, X.1
Murphy, R.F.2
-
11
-
-
34147217542
-
Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map
-
Collins SR, Miller KM, Maas NL, Roguev A, Fillingham J, Chu CS, Schuldiner M, Gebbia M, Recht J, Shales M, et al. 2007. Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature 446: 806-810.
-
(2007)
Nature
, vol.446
, pp. 806-810
-
-
Collins, S.R.1
Miller, K.M.2
Maas, N.L.3
Roguev, A.4
Fillingham, J.5
Chu, C.S.6
Schuldiner, M.7
Gebbia, M.8
Recht, J.9
Shales, M.10
-
12
-
-
4344670936
-
Bow ties, metabolism and disease
-
Csete M, Doyle J. 2004. Bow ties, metabolism and disease. Trends Biotechnol 22: 446-450.
-
(2004)
Trends Biotechnol
, vol.22
, pp. 446-450
-
-
Csete, M.1
Doyle, J.2
-
13
-
-
61349119934
-
Functional organization of the S. cerevisiae phosphorylation network
-
Fiedler D, Braberg H, Mehta M, Chechik G, Cagney G, Mukherjee P, Silva AC, Shales M, Collins SR, van Wageningen S, et al. 2009. Functional organization of the S. cerevisiae phosphorylation network. Cell 136: 952-963.
-
(2009)
Cell
, vol.136
, pp. 952-963
-
-
Fiedler, D.1
Braberg, H.2
Mehta, M.3
Chechik, G.4
Cagney, G.5
Mukherjee, P.6
Silva, A.C.7
Shales, M.8
Collins, S.R.9
van Wageningen, S.10
-
14
-
-
0842288337
-
Inferring cellular networks using probabilistic graphical models
-
Friedman N. 2004. Inferring cellular networks using probabilistic graphical models. Science 303: 799-805.
-
(2004)
Science
, vol.303
, pp. 799-805
-
-
Friedman, N.1
-
15
-
-
33846326304
-
Genetic screening for signal transduction in the era of network biology
-
Friedman A, Perrimon N. 2007. Genetic screening for signal transduction in the era of network biology. Cell 128: 225-231.
-
(2007)
Cell
, vol.128
, pp. 225-231
-
-
Friedman, A.1
Perrimon, N.2
-
17
-
-
0037108618
-
Image analysis and morphometry in the diagnosis of breast cancer
-
Gil J, Wu H, Wang BY. 2002. Image analysis and morphometry in the diagnosis of breast cancer. Microsc Res Tech 59: 109-118.
-
(2002)
Microsc Res Tech
, vol.59
, pp. 109-118
-
-
Gil, J.1
Wu, H.2
Wang, B.Y.3
-
18
-
-
33845760114
-
Automated subcellular location determination and high-throughput microscopy
-
Glory E, Murphy RF. 2007. Automated subcellular location determination and high-throughput microscopy. Dev Cell 12: 7-16.
-
(2007)
Dev Cell
, vol.12
, pp. 7-16
-
-
Glory, E.1
Murphy, R.F.2
-
19
-
-
33644873681
-
FlyBase: Anatomical data, images and queries
-
The FlyBase Consortium
-
Grumbling G, Strelets V, The FlyBase Consortium. 2006. FlyBase: Anatomical data, images and queries. Nucleic Acids Res 34: D484-D488.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Grumbling, G.1
Strelets, V.2
-
20
-
-
3042848952
-
Evidence for dynamically organized modularity in the yeast protein-protein interaction network
-
Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF, Zhang LV, Dupuy D, Walhout AJM, CusickME, Roth FP, et al. 2004. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430: 88-93.
-
(2004)
Nature
, vol.430
, pp. 88-93
-
-
Han, J.D.1
Bertin, N.2
Hao, T.3
Goldberg, D.S.4
Berriz, G.F.5
Zhang, L.V.6
Dupuy, D.7
Walhout, A.J.M.8
Cusick, M.E.9
Roth, F.P.10
-
21
-
-
29244431643
-
Genetics in the age of systems biology
-
Hiesinger PR, Hassan BA. 2005. Genetics in the age of systems biology. Cell 123: 1173-1174.
-
(2005)
Cell
, vol.123
, pp. 1173-1174
-
-
Hiesinger, P.R.1
Hassan, B.A.2
-
22
-
-
0015529008
-
Mapping of behaviour in Drosophila mosaics
-
Hotta Y, Benzer S. 1972.Mapping of behaviour in Drosophila mosaics. Nature 240: 527-535.
-
(1972)
Nature
, vol.240
, pp. 527-535
-
-
Hotta, Y.1
Benzer, S.2
-
23
-
-
60549104030
-
Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning
-
Jones TR, Carpenter AE, Lamprecht MR, Moffat J, Silver SJ, Grenier JK, Castoreno AB, Eggert US, Root DE, Golland P, et al. 2009. Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning. Proc Natl Acad Sci 106: 1826-1831.
-
(2009)
Proc Natl Acad Sci
, vol.106
, pp. 1826-1831
-
-
Jones, T.R.1
Carpenter, A.E.2
Lamprecht, M.R.3
Moffat, J.4
Silver, S.J.5
Grenier, J.K.6
Castoreno, A.B.7
Eggert, U.S.8
Root, D.E.9
Golland, P.10
-
24
-
-
22844450110
-
Systematic interpretation of genetic interactions using protein networks
-
Kelley R, Ideker T. 2005. Systematic interpretation of genetic interactions using protein networks. Nat Biotechnol 23: 561-566.
-
(2005)
Nat Biotechnol
, vol.23
, pp. 561-566
-
-
Kelley, R.1
Ideker, T.2
-
25
-
-
0242361514
-
A functional genomic analysis of cell morphology using RNA interference
-
doi: 10.1186/1475-4924-2-27
-
Kiger A, Baum B, Jones S, Jones M, Coulson A, Echeverri C, Perrimon N. 2003. A functional genomic analysis of cell morphology using RNA interference. J Biol 2: 27. doi: 10.1186/1475-4924-2-27.
-
(2003)
J Biol
, vol.2
, pp. 27
-
-
Kiger, A.1
Baum, B.2
Jones, S.3
Jones, M.4
Coulson, A.5
Echeverri, C.6
Perrimon, N.7
-
26
-
-
56849091295
-
Network hubs buffer environmental variation in Saccharomyces cerevisiae
-
doi: 10.1371/journal.pbio.0060264
-
Levy SF, Siegal ML. 2008. Network hubs buffer environmental variation in Saccharomyces cerevisiae. PLoS Biol 6: e264. doi: 10.1371/journal.pbio.0060264.
-
(2008)
PLoS Biol
, vol.6
-
-
Levy, S.F.1
Siegal, M.L.2
-
27
-
-
34250216344
-
Image-based multivariate profiling of drug responses from single cells
-
Loo L,Wu LF, Altschuler SJ. 2007. Image-based multivariate profiling of drug responses from single cells. Nat Methods 4: 445-453.
-
(2007)
Nat Methods
, vol.4
, pp. 445-453
-
-
Loo, L.1
Wu, L.F.2
Altschuler, S.J.3
-
28
-
-
4444379134
-
Vilse, a conserved Rac/Cdc42 GAP mediating Robo repulsion in tracheal cells and axons
-
LundströmA, Gallio M, Englund C, Steneberg P, Hemphälä J, AspenströmP, Keleman K, Falileeva L, Dickson BJ, Samakovlis C. 2004. Vilse, a conserved Rac/Cdc42 GAP mediating Robo repulsion in tracheal cells and axons. Genes & Dev 18: 2161-2171.
-
(2004)
Genes & Dev
, vol.18
, pp. 2161-2171
-
-
Lundström, A.1
Gallio, M.2
Englund, C.3
Steneberg, P.4
Hemphälä, J.5
Aspenström, P.6
Keleman, K.7
Falileeva, L.8
Dickson, B.J.9
Samakovlis, C.10
-
29
-
-
33646033137
-
A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen
-
Moffat J, Grueneberg DA, Yang X, Kim SY, Kloepfer AM, Hinkle G, Piqani B, Eisenhaure TM, Luo B, Grenier JK, et al. 2006. A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell 124: 1283-1298.
-
(2006)
Cell
, vol.124
, pp. 1283-1298
-
-
Moffat, J.1
Grueneberg, D.A.2
Yang, X.3
Kim, S.Y.4
Kloepfer, A.M.5
Hinkle, G.6
Piqani, B.7
Eisenhaure, T.M.8
Luo, B.9
Grenier, J.K.10
-
30
-
-
33646057010
-
High-throughput RNAi screening by time-lapse imaging of live human cells
-
Neumann B, Held M, Liebel U, Erfle H, Rogers P, Pepperkok R, Ellenberg J. 2006. High-throughput RNAi screening by time-lapse imaging of live human cells. Nat Methods 3: 385-390.
-
(2006)
Nat Methods
, vol.3
, pp. 385-390
-
-
Neumann, B.1
Held, M.2
Liebel, U.3
Erfle, H.4
Rogers, P.5
Pepperkok, R.6
Ellenberg, J.7
-
31
-
-
0019133661
-
Mutations affecting segment number and polarity in Drosophila
-
Nusslein-Volhard C, Wieschaus E. 1980. Mutations affecting segment number and polarity in Drosophila. Nature 287: 795-801.
-
(1980)
Nature
, vol.287
, pp. 795-801
-
-
Nusslein-Volhard, C.1
Wieschaus, E.2
-
32
-
-
30044445643
-
High-dimensional and large-scale phenotyping of yeast mutants
-
Ohya Y, Sese J, Yukawa M, Sano F, Nakatani Y, Saito TL, Saka A, Fukuda T, Ishihara S, Oka S, et al. 2005. High-dimensional and large-scale phenotyping of yeast mutants. Proc Natl Acad Sci 102: 19015-19020.
-
(2005)
Proc Natl Acad Sci
, vol.102
, pp. 19015-19020
-
-
Ohya, Y.1
Sese, J.2
Yukawa, M.3
Sano, F.4
Nakatani, Y.5
Saito, T.L.6
Saka, A.7
Fukuda, T.8
Ishihara, S.9
Oka, S.10
-
34
-
-
8444223104
-
Multidimensional drug profiling by automated microscopy
-
Perlman ZE, Slack MD, Feng Y, Mitchison TJ, Wu LF, Altschuler SJ. 2004. Multidimensional drug profiling by automated microscopy. Science 306: 1194-1198.
-
(2004)
Science
, vol.306
, pp. 1194-1198
-
-
Perlman, Z.E.1
Slack, M.D.2
Feng, Y.3
Mitchison, T.J.4
Wu, L.F.5
Altschuler, S.J.6
-
35
-
-
0037137443
-
Gene clustering based on RNAi phenotypes of ovary-enriched genes in C. elegans
-
Piano F, Schetter AJ, Morton DG, Gunsalus KC, Reinke V, Kim SK, Kemphues KJ. 2002. Gene clustering based on RNAi phenotypes of ovary-enriched genes in C. elegans. Curr Biol 12: 1959-1964.
-
(2002)
Curr Biol
, vol.12
, pp. 1959-1964
-
-
Piano, F.1
Schetter, A.J.2
Morton, D.G.3
Gunsalus, K.C.4
Reinke, V.5
Kim, S.K.6
Kemphues, K.J.7
-
36
-
-
0035929653
-
The Rac GTPase-activating protein RotundRacGAP interferes with Drac1 and Dcdc42 signalling in Drosophila melanogaster
-
Raymond K, Bergeret E, Dagher M, Breton R, Griffin-Shea R, Fauvarque M. 2001. The Rac GTPase-activating protein RotundRacGAP interferes with Drac1 and Dcdc42 signalling in Drosophila melanogaster. J Biol Chem 276: 35909-35916.
-
(2001)
J Biol Chem
, vol.276
, pp. 35909-35916
-
-
Raymond, K.1
Bergeret, E.2
Dagher, M.3
Breton, R.4
Griffin-Shea, R.5
Fauvarque, M.6
-
37
-
-
54249107599
-
Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast
-
Roguev A, Bandyopadhyay S, Zofall M, Zhang K, Fischer T, Collins SR, Qu H, Shales M, Park H, Hayles J, et al. 2008. Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science 322: 405-410.
-
(2008)
Science
, vol.322
, pp. 405-410
-
-
Roguev, A.1
Bandyopadhyay, S.2
Zofall, M.3
Zhang, K.4
Fischer, T.5
Collins, S.R.6
Qu, H.7
Shales, M.8
Park, H.9
Hayles, J.10
-
38
-
-
17644427718
-
Causal protein-signaling networks derived from multiparameter single-cell data
-
Sachs K, Perez O, Pe'er D, Lauffenburger DA, Nolan GP. 2005. Causal protein-signaling networks derived from multiparameter single-cell data. Science 308: 523-529.
-
(2005)
Science
, vol.308
, pp. 523-529
-
-
Sachs, K.1
Perez, O.2
Pe'er, D.3
Lauffenburger, D.A.4
Nolan, G.P.5
-
39
-
-
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. 2003. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504.
-
(2003)
Genome Res
, vol.13
, 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
-
40
-
-
62149151349
-
PDGF/VEGF signaling controls cell size in Drosophila
-
doi: 10.1186/gb-2009-10-2-r20
-
Sims D, Duchek P, Baum B. 2009. PDGF/VEGF signaling controls cell size in Drosophila. Genome Biol 10: R20. doi: 10.1186/gb-2009-10-2-r20.
-
(2009)
Genome Biol
, vol.10
-
-
Sims, D.1
Duchek, P.2
Baum, B.3
-
42
-
-
0034518590
-
DRacGAP, a novel Drosophila gene, inhibits EGFR/Ras signalling in the developing imaginal wing disc
-
Sotillos S, Campuzano S. 2000. DRacGAP, a novel Drosophila gene, inhibits EGFR/Ras signalling in the developing imaginal wing disc. Development 127: 5427-5438.
-
(2000)
Development
, vol.127
, pp. 5427-5438
-
-
Sotillos, S.1
Campuzano, S.2
-
43
-
-
33644873184
-
BioGRID: A general repository for interaction datasets
-
Stark C, Breitkreutz B, Reguly T, Boucher L, Breitkreutz A, Tyers M. 2006. BioGRID: A general repository for interaction datasets. Nucleic Acids Res 34: D535-D539.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Stark, C.1
Breitkreutz, B.2
Reguly, T.3
Boucher, L.4
Breitkreutz, A.5
Tyers, M.6
-
44
-
-
21744448078
-
An unbiased cell morphology-based screen for new, biologically active small molecules
-
doi: 10.1371/journal.pbio.0030128
-
Tanaka M, Bateman R, Rauh D, Vaisberg E, Ramachandani S, Zhang C, Hansen KC, Burlingame AL, Trautman JK, Shokat KM, et al. 2005. An unbiased cell morphology-based screen for new, biologically active small molecules. PLoS Biol 3: e128. doi: 10.1371/journal.pbio.0030128.
-
(2005)
PLoS Biol
, vol.3
-
-
Tanaka, M.1
Bateman, R.2
Rauh, D.3
Vaisberg, E.4
Ramachandani, S.5
Zhang, C.6
Hansen, K.C.7
Burlingame, A.L.8
Trautman, J.K.9
Shokat, K.M.10
-
45
-
-
33846969965
-
Current knowledge of the large RhoGAP family of proteins
-
Tcherkezian J, Lamarche-Vane N. 2007. Current knowledge of the large RhoGAP family of proteins. Biol Cell 99: 67-86.
-
(2007)
Biol Cell
, vol.99
, pp. 67-86
-
-
Tcherkezian, J.1
Lamarche-Vane, N.2
-
46
-
-
0035861532
-
systematic genetic analysis with ordered arrays of yeast deletion mutants
-
Tong AHY, Evangelista M, Parsons AB, Xu H, Bader GD, Page N, Robinson M, Raghibizadeh S, Hogue CWV, Bussey H, et al. 2001. systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294: 2364-2368.
-
(2001)
Science
, vol.294
, pp. 2364-2368
-
-
Tong, A.H.Y.1
Evangelista, M.2
Parsons, A.B.3
Xu, H.4
Bader, G.D.5
Page, N.6
Robinson, M.7
Raghibizadeh, S.8
Hogue, C.W.V.9
Bussey, H.10
-
47
-
-
37749002713
-
Cellular phenotype recognition for high-content RNA interference genomewide screening
-
Wang J, Zhou X, Bradley PL, Chang S, Perrimon N,Wong ST. 2008. Cellular phenotype recognition for high-content RNA interference genomewide screening. J Biomol Screen 13: 29-39.
-
(2008)
J Biomol Screen
, vol.13
, pp. 29-39
-
-
Wang, J.1
Zhou, X.2
Bradley, P.L.3
Chang, S.4
Perrimon, N.5
Wong, S.T.6
-
48
-
-
8144227773
-
Combining biological networks to predict genetic interactions
-
Wong SL, Zhang LV, Tong AHY, Li Z, Goldberg DS, King OD, Lesage G, Vidal M, Andrews B, Bussey H, et al. 2004. Combining biological networks to predict genetic interactions. Proc Natl Acad Sci 101: 15682-15687.
-
(2004)
Proc Natl Acad Sci
, vol.101
, pp. 15682-15687
-
-
Wong, S.L.1
Zhang, L.V.2
Tong, A.H.Y.3
Li, Z.4
Goldberg, D.S.5
King, O.D.6
Lesage, G.7
Vidal, M.8
Andrews, B.9
Bussey, H.10
-
49
-
-
37249026328
-
Integrating high-content screening and ligand-target prediction to identify mechanism of action
-
Young DW, Bender A, Hoyt J, McWhinnie E, Chirn G, Tao CY, Tallarico JA, Labow M, Jenkins JL, Mitchison TJ, et al. 2008. Integrating high-content screening and ligand-target prediction to identify mechanism of action. Nat Chem Biol 1: 59-68.
-
(2008)
Nat Chem Biol
, vol.1
, pp. 59-68
-
-
Young, D.W.1
Bender, A.2
Hoyt, J.3
McWhinnie, E.4
Chirn, G.5
Tao, C.Y.6
Tallarico, J.A.7
Labow, M.8
Jenkins, J.L.9
Mitchison, T.J.10
-
50
-
-
54949120007
-
DroID: The Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions
-
doi: 1186/1471-2164-9-461
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Yu J, Pacifico S, Liu G, Finley RL. 2008. DroID: The Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions. BMC Genomics 2008: 9461. doi: 1186/1471-2164-9-461.
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(2008)
BMC Genomics
, vol.2008
, pp. 9461
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Yu, J.1
Pacifico, S.2
Liu, G.3
Finley, R.L.4
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