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Volumn 2, Issue 2, 2008, Pages 58-66

Pipeline for acquisition of quantitative data on segmentation gene expression from confocal images

Author keywords

Background removal; Confocal microscopy; Gene expression; Image processing; Image segmentation; Spatial registration

Indexed keywords

ANIMAL; BIOLOGY; CONFOCAL MICROSCOPY; DROSOPHILA; GENE EXPRESSION; GENETICS; IMAGE PROCESSING; METHODOLOGY; PRENATAL DEVELOPMENT; REVIEW;

EID: 58149199098     PISSN: 19336934     EISSN: 19336942     Source Type: Journal    
DOI: 10.4161/fly.6060     Document Type: Review
Times cited : (41)

References (48)
  • 1
    • 0036277075 scopus 로고    scopus 로고
    • Functional genomics as applied to mapping transcription regulatory networks
    • Banerjee N, Zhang MQ. Functional genomics as applied to mapping transcription regulatory networks. Curr Op Microbiol 2002; 5:313-7.
    • (2002) Curr Op Microbiol , vol.5 , pp. 313-317
    • Banerjee, N.1    Zhang, M.Q.2
  • 2
    • 33745727726 scopus 로고    scopus 로고
    • The living test-tube: Imaging of real-time gene expression
    • Shav Tal Y. The living test-tube: imaging of real-time gene expression. Soft Matter 2006; 2:361-70.
    • (2006) Soft Matter , vol.2 , pp. 361-370
    • Shav, T.Y.1
  • 3
    • 0030048999 scopus 로고    scopus 로고
    • Resynthesizing evolutionary and developmental biology
    • Gilbert S, Opitz J, Raff R. Resynthesizing evolutionary and developmental biology. Developmental Biology 1996; 173:357-72.
    • (1996) Developmental Biology , vol.173 , pp. 357-372
    • Gilbert, S.1    Opitz, J.2    Raff, R.3
  • 4
    • 0001314223 scopus 로고    scopus 로고
    • Method for spatial registration of the expression patterns of Drosophila segmentation genes using wavelets
    • Kozlov K, Myasnikova E, Samsonova M, Reinitz J, Kosman D. Method for spatial registration of the expression patterns of Drosophila segmentation genes using wavelets. Computational Technologies 2000; 5:112-9.
    • (2000) Computational Technologies , vol.5 , pp. 112-119
    • Kozlov, K.1    Myasnikova, E.2    Samsonova, M.3    Reinitz, J.4    Kosman, D.5
  • 5
    • 0036014564 scopus 로고    scopus 로고
    • A method for two-dimensional registration and construction of the two-dimensional atlas of gene expression patterns in situ
    • Kozlov K, Myasnikova E, Pisarev A, Samsonova M, Reinitz J. A method for two-dimensional registration and construction of the two-dimensional atlas of gene expression patterns in situ. In Silico Biology 2002; 2:125-41.
    • (2002) In Silico Biology , vol.2 , pp. 125-141
    • Kozlov, K.1    Myasnikova, E.2    Pisarev, A.3    Samsonova, M.4    Reinitz, J.5
  • 6
    • 0035115973 scopus 로고    scopus 로고
    • Registration of the expression patterns of Drosophila segmentation genes by two independent methods
    • Myasnikova E, Samsonova A, Kozlov K, Samsonova M, Reinitz J. Registration of the expression patterns of Drosophila segmentation genes by two independent methods. Bioinformatics 2001; 17:3-12.
    • (2001) Bioinformatics , vol.17 , pp. 3-12
    • Myasnikova, E.1    Samsonova, A.2    Kozlov, K.3    Samsonova, M.4    Reinitz, J.5
  • 7
    • 4644258117 scopus 로고    scopus 로고
    • Support vector regression applied to the determination of the developmental age of a Drosophila embryo from its segmentation gene expression patterns
    • Myasnikova E, Samsonova A, Samsonova M, Reinitz J. Support vector regression applied to the determination of the developmental age of a Drosophila embryo from its segmentation gene expression patterns. Bioinformatics 2002; 18:87-95.
    • (2002) Bioinformatics , vol.18 , pp. 87-95
    • Myasnikova, E.1    Samsonova, A.2    Samsonova, M.3    Reinitz, J.4
  • 8
  • 9
    • 21344474605 scopus 로고    scopus 로고
    • Removal of background signal from in situ data on the expression of segmentation genes in Drosophila
    • Myasnikova E, Samsonova M, Kosman D, Reinitz J. Removal of background signal from in situ data on the expression of segmentation genes in Drosophila. Dev Genes Evol 2005; 215:320-6.
    • (2005) Dev Genes Evol , vol.215 , pp. 320-326
    • Myasnikova, E.1    Samsonova, M.2    Kosman, D.3    Reinitz, J.4
  • 10
    • 0031814029 scopus 로고    scopus 로고
    • Rapid preparation of a panel of polyclonal antibodies to Drosophila segmentation proteins
    • Kosman D, Small S, Reinitz J. Rapid preparation of a panel of polyclonal antibodies to Drosophila segmentation proteins. Dev Genes Evol 1998; 208:290-4.
    • (1998) Dev Genes Evol , vol.208 , pp. 290-294
    • Kosman, D.1    Small, S.2    Reinitz, J.3
  • 11
    • 0031616115 scopus 로고    scopus 로고
    • Automated assay of gene expression at cellular resolution
    • Altman R, Dunker K, Hunter L, Klein T, eds. Singapore: World Scientific Press
    • Kosman D, Reinitz J, Sharp DH. Automated assay of gene expression at cellular resolution. In: Proceedings of the 1998 Pacific Symposium on Biocomputing. Altman R, Dunker K, Hunter L, Klein T, eds. Singapore: World Scientific Press 1997; 6-17.
    • (1997) Proceedings of the 1998 Pacific Symposium On Biocomputing , pp. 6-17
    • Kosman, D.1    Reinitz, J.2    Sharp, D.H.3
  • 13
    • 0024204462 scopus 로고
    • Requirements for autosomal gene activity during precellular stages of Drosophila melanogaster
    • Merrill P, Sweeton D, Wieschaus E. Requirements for autosomal gene activity during precellular stages of Drosophila melanogaster. Development 1988; 104:495-509.
    • (1988) Development , vol.104 , pp. 495-509
    • Merrill, P.1    Sweeton, D.2    Wieschaus, E.3
  • 16
    • 84937655864 scopus 로고
    • Visual pattern recognition by moment invariants
    • Hu MK. Visual pattern recognition by moment invariants. IRE transactions of information theory 1962; 8:179-87.
    • (1962) IRE Transactions of Information Theory , vol.8 , pp. 179-187
    • Hu, M.K.1
  • 19
    • 0004094721 scopus 로고    scopus 로고
    • Learning with Kernels
    • Regularization, Optimization, and Beyond. MIT Press
    • Schölkopf B, Smola A. Learning with Kernels. In: Support Vector Machines, Regularization, Optimization, and Beyond. MIT Press 2002.
    • Support Vector Machines , pp. 2002
    • Schölkopf, B.1    Smola, A.2
  • 21
    • 0033289232 scopus 로고    scopus 로고
    • Spatiotemporal registration of the expression patterns of Drosophila segmentation genes
    • In: Lengauer T, Schneider R, Bork P, Brutlag D, Glasgow J, Mewes HW, Zimmer R, eds., Menlo Park, CA: AAAI Press
    • Myasnikova E, Kosman D, Reinitz J, Samsonova M. Spatiotemporal registration of the expression patterns of Drosophila segmentation genes. In: Lengauer T, Schneider R, Bork P, Brutlag D, Glasgow J, Mewes HW, Zimmer R, eds. Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology. Menlo Park, CA: AAAI Press 1999; 195-201.
    • (1999) Proceedings of the Seventh International Conference On Intelligent Systems For Molecular Biology , pp. 195-201
    • Myasnikova, E.1    Kosman, D.2    Reinitz, J.3    Samsonova, M.4
  • 22
    • 0344334039 scopus 로고    scopus 로고
    • Efficient cell segmentation tool for confocal microscopy tissue images and quantitative evaluation of FISH signal
    • Umesh Adiga PS, Chaudhuri BB. Efficient cell segmentation tool for confocal microscopy tissue images and quantitative evaluation of FISH signal. Microsc Res Tech 1999; 44:49-68.
    • (1999) Microsc Res Tech , vol.44 , pp. 49-68
    • Umesh, A.P.S.1    Chaudhuri, B.B.2
  • 25
  • 26
    • 0037075022 scopus 로고    scopus 로고
    • Establishment of developmental precision and proportions in the early Drosophila embryo
    • Houchmandzadeh B, Wieschaus E, Leibler S. Establishment of developmental precision and proportions in the early Drosophila embryo. Nature 2002; 415:748-9.
    • (2002) Nature , vol.415 , pp. 748-749
    • Houchmandzadeh, B.1    Wieschaus, E.2    Leibler, S.3
  • 29
    • 34447099234 scopus 로고    scopus 로고
    • Probing the Limits to Positional Information
    • Gregor T, Tank DW, Wieschaus EF, Bialek W. Probing the Limits to Positional Information. Cell 2007; 130:153-64.
    • (2007) Cell , vol.130 , pp. 153-164
    • Gregor, T.1    Tank, D.W.2    Wieschaus, E.F.3    Bialek, W.4
  • 31
    • 0041324707 scopus 로고    scopus 로고
    • Noise in the segmentation gene network of Drosophila with implications for mechanisms of body axis specification
    • In: Bezrukov SM, ed. Fuctuations and Noise in Biological, Biophysical, and Biomedical Systems
    • Holloway DM, Harrison LG, Spirov AV. Noise in the segmentation gene network of Drosophila with implications for mechanisms of body axis specification. In: Bezrukov SM, ed. Fuctuations and Noise in Biological, Biophysical, and Biomedical Systems. Proceedings of the SPIE 2003; 5110:180-91.
    • (2003) Proceedings of the SPIE , vol.5110 , pp. 180-191
    • Holloway, D.M.1    Harrison, L.G.2    Spirov, A.V.3
  • 32
    • 3142630233 scopus 로고    scopus 로고
    • Digital three-dimensional models of Drosophila development
    • Pereanu W, Hartenstein V. Digital three-dimensional models of Drosophila development. Curr Opin Genet Dev 2004; 14:382-91.
    • (2004) Curr Opin Genet Dev , vol.14 , pp. 382-391
    • Pereanu, W.1    Hartenstein, V.2
  • 35
    • 27544455325 scopus 로고    scopus 로고
    • Complex networks approach to gene expression driven phenotype imaging
    • Diambra L, Da Costa F. Complex networks approach to gene expression driven phenotype imaging. Bioinformatics 2005; 21:3846-51.
    • (2005) Bioinformatics , vol.21 , pp. 3846-3851
    • Diambra, L.1    da Costa, F.2
  • 36
    • 13844253735 scopus 로고    scopus 로고
    • Model for the robust establishment of precise proportions in the early Drosophila embryo
    • Aegerter Wilmsen T, Aegerter CM, Bisseling T. Model for the robust establishment of precise proportions in the early Drosophila embryo. J Theor Biol 2005; 234:13-9.
    • (2005) J Theor Biol , vol.234 , pp. 13-19
    • Aegerter, W.T.1    Aegerter, C.M.2    Bisseling, T.3
  • 37
    • 18144363600 scopus 로고    scopus 로고
    • Engineering gene networks to emulate Drosophila embryonic pattern formation
    • Isalan M, Lemerle C, Serrano L. Engineering gene networks to emulate Drosophila embryonic pattern formation. PLoS Biol 2005; 3:64.
    • (2005) PLoS Biol , vol.3 , pp. 64
    • Isalan, M.1    Lemerle, C.2    Serrano, L.3
  • 39
    • 33750995578 scopus 로고    scopus 로고
    • Analysis of pattern precision shows that Drosophila segmentation develops substantial independence from gradients of maternal gene products
    • Holloway DM, Harrison LG, Kosman D, Vanario-Alonso C. E, Spirov AV. Analysis of pattern precision shows that Drosophila segmentation develops substantial independence from gradients of maternal gene products. Dev Dyn 2006; 235:2949-60.
    • (2006) Dev Dyn , vol.235 , pp. 2949-2960
    • Holloway, D.M.1    Harrison, L.G.2    Kosman, D.3    Vanario-Alonso, C.E.4    Spirov, A.V.5
  • 40
    • 16344387146 scopus 로고    scopus 로고
    • Stochastic simulations of the origins and implications of long-tailed distributions in gene expression
    • Krishna S, Banerjee B, Ramakrishnan TV, Shivashankar GV. Stochastic simulations of the origins and implications of long-tailed distributions in gene expression. PNAS 2005; 102:4771-6.
    • (2005) PNAS , vol.102 , pp. 4771-4776
    • Krishna, S.1    Banerjee, B.2    Ramakrishnan, T.V.3    Shivashankar, G.V.4
  • 43
    • 30044433054 scopus 로고    scopus 로고
    • Precise outputs from a variable gradient
    • Yucel G, Small S. Morphogens: Precise outputs from a variable gradient. Curr Biol 2006; 16:29-31.
    • (2006) Curr Biol , vol.16 , pp. 29-31
    • Yucel, G.1    Morphogens, S.S.2
  • 44
    • 34249722123 scopus 로고    scopus 로고
    • Enhancer responses to similarly distributed antagonistic gradients in development
    • Zinzen R, Papatsenko D. Enhancer responses to similarly distributed antagonistic gradients in development. PLoS Computational Biology 2007; 3:84.
    • (2007) PLoS Computational Biology , vol.3 , pp. 84
    • Zinzen, R.1    Papatsenko, D.2
  • 46
    • 33749137281 scopus 로고    scopus 로고
    • Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even-skipped gene
    • Janssens H, Hou S, Jaeger J, Kim AR, Myasnikova E, Sharp D, Reinitz J. Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even-skipped gene. Nature Genetics 2006; 38:1159-65.
    • (2006) Nature Genetics , vol.38 , pp. 1159-1165
    • Janssens, H.1    Hou, S.2    Jaeger, J.3    Kim, A.R.4    Myasnikova, E.5    Sharp, D.6    Reinitz, J.7
  • 47
    • 33846359035 scopus 로고    scopus 로고
    • Known maternal gradients are not sufficient for the establishment of gap domains in Drosophila melanogaster
    • Jaeger J, Sharp D, Reinitz J. Known maternal gradients are not sufficient for the establishment of gap domains in Drosophila melanogaster. Mechanisms of Development 2007; 124:108-28.
    • (2007) Mechanisms of Development , vol.124 , pp. 108-128
    • Jaeger, J.1    Sharp, D.2    Reinitz, J.3


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