메뉴 건너뛰기




Volumn 9, Issue 1, 2015, Pages

Inference of spatiotemporal effects on cellular state transitions from time-lapse microscopy

Author keywords

Cell state transition; LASSO; Single cell analysis; Spatial interaction; Time lapse microscopy

Indexed keywords

BIOLOGICAL MODEL; CELL COMMUNICATION; CELL COUNT; CELL DIFFERENTIATION; CELL FUNCTION; COMPUTER SIMULATION; MULTIVARIATE ANALYSIS; SINGLE CELL ANALYSIS; STATISTICAL MODEL; TIME LAPSE IMAGING; VALIDATION STUDY;

EID: 84959129923     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/s12918-015-0208-5     Document Type: Article
Times cited : (3)

References (52)
  • 1
    • 0004191911 scopus 로고
    • Principles of Embryology
    • New York: New York, Macmillan
    • Waddington CH. Principles of Embryology. New York: New York, Macmillan; 1956, p. 528.
    • (1956) , pp. 528
    • Waddington, C.H.1
  • 2
    • 39349096526 scopus 로고    scopus 로고
    • Hematopoiesis: an evolving paradigm for stem cell biology
    • Orkin SH, Zon LI. Hematopoiesis: an evolving paradigm for stem cell biology. Cell. 2008; 132(4):631-44.
    • (2008) Cell , vol.132 , Issue.4 , pp. 631-644
    • Orkin, S.H.1    Zon, L.I.2
  • 3
    • 84886994729 scopus 로고    scopus 로고
    • Neural stem cells: Generating and regenerating the brain
    • Gage FH, Temple S. Neural stem cells: Generating and regenerating the brain. Neuron. 2013; 80(3):588-601.
    • (2013) Neuron , vol.80 , Issue.3 , pp. 588-601
    • Gage, F.H.1    Temple, S.2
  • 4
    • 0023663888 scopus 로고
    • Expression of a single transfected cDNA converts fibroblasts to myoblasts
    • Davis RL, Weintraub H, Lassar AB. Expression of a single transfected cDNA converts fibroblasts to myoblasts. Cell. 1987; 51(6):987-1000.
    • (1987) Cell , vol.51 , Issue.6 , pp. 987-1000
    • Davis, R.L.1    Weintraub, H.2    Lassar, A.B.3
  • 5
    • 33747195353 scopus 로고    scopus 로고
    • Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors
    • Takahashi K, Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell. 2006; 126(4):663-76.
    • (2006) Cell , vol.126 , Issue.4 , pp. 663-676
    • Takahashi, K.1    Yamanaka, S.2
  • 6
    • 63049090064 scopus 로고    scopus 로고
    • A fresh look at iPS cells
    • Yamanaka S. A fresh look at iPS cells. Cell. 2009; 137(1):13-7.
    • (2009) Cell , vol.137 , Issue.1 , pp. 13-17
    • Yamanaka, S.1
  • 7
    • 84865970286 scopus 로고    scopus 로고
    • Multi-scale modeling of GMP differentiation based on single-cell genealogies
    • Marr C, Strasser M, Schwarzfischer M, Schroeder T, Theis FJ. Multi-scale modeling of GMP differentiation based on single-cell genealogies. FEBS J. 2012; 279(18):3488-500.
    • (2012) FEBS J , vol.279 , Issue.18 , pp. 3488-3500
    • Marr, C.1    Strasser, M.2    Schwarzfischer, M.3    Schroeder, T.4    Theis, F.J.5
  • 8
    • 33747410158 scopus 로고    scopus 로고
    • Optimized Neuronal Differentiation of Murine Embryonic Stem Cells: Role of Cell Density
    • Turksen K, editor.
    • Lorincz MT. Optimized Neuronal Differentiation of Murine Embryonic Stem Cells: Role of Cell Density In: Turksen K, editor. Embryonic Stem Cell Protocols. New Jersey: Humana Press: 2006. p. 55-69.
    • (2006) Embryonic Stem Cell Protocols. New Jersey: Humana Press , pp. 55-69
    • Lorincz, M.T.1
  • 9
    • 39149144034 scopus 로고    scopus 로고
    • Stem cells and niches: mechanisms that promote stem cell maintenance throughout life
    • Morrison SJ, Spradling AC. Stem cells and niches: mechanisms that promote stem cell maintenance throughout life. Cell. 2008; 132(4):598-611.
    • (2008) Cell , vol.132 , Issue.4 , pp. 598-611
    • Morrison, S.J.1    Spradling, A.C.2
  • 10
    • 84866443845 scopus 로고    scopus 로고
    • Imaging, quantification and visualization of spatio-temporal patterning in mESC colonies under different culture conditions
    • Scherf N, Herberg M, Thierbach K, Zerjatke T, Kalkan T, Humphreys P, et al.Imaging, quantification and visualization of spatio-temporal patterning in mESC colonies under different culture conditions. Bioinformatics. 2012; 28(18):556-61.
    • (2012) Bioinformatics , vol.28 , Issue.18 , pp. 556-561
    • Scherf, N.1    Herberg, M.2    Thierbach, K.3    Zerjatke, T.4    Kalkan, T.5    Humphreys, P.6
  • 11
    • 84888814610 scopus 로고    scopus 로고
    • MosaicIA: an ImageJ/Fiji plugin for spatial pattern and interaction analysis
    • Shivanandan A, Radenovic A, Sbalzarini IF. MosaicIA: an ImageJ/Fiji plugin for spatial pattern and interaction analysis. BMC Bioinformatics. 2013; 14:349.
    • (2013) BMC Bioinformatics , vol.14 , pp. 349
    • Shivanandan, A.1    Radenovic, A.2    Sbalzarini, I.F.3
  • 12
    • 43749084847 scopus 로고    scopus 로고
    • Imaging stem-cell-driven regeneration in mammals
    • Schroeder T. Imaging stem-cell-driven regeneration in mammals. Nature. 2008; 453(7193):345-51.
    • (2008) Nature , vol.453 , Issue.7193 , pp. 345-351
    • Schroeder, T.1
  • 13
    • 84907030448 scopus 로고    scopus 로고
    • Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data
    • Amat F, Lemon W, Mossing D, McDole K. Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data. Nat Methods. 2014; 11(9):951-8.
    • (2014) Nat Methods , vol.11 , Issue.9 , pp. 951-958
    • Amat, F.1    Lemon, W.2    Mossing, D.3    McDole, K.4
  • 14
    • 0037109565 scopus 로고    scopus 로고
    • Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics
    • Haseltine EL, Rawlings JB. Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics. J Chem Phys. 2002; 117(15):6959.
    • (2002) J Chem Phys , vol.117 , Issue.15 , pp. 6959
    • Haseltine, E.L.1    Rawlings, J.B.2
  • 15
    • 84949176195 scopus 로고    scopus 로고
    • Inference for Diffusion Processes: With Applications in Life Sciences
    • Berlin: Springer
    • Fuchs C. Inference for Diffusion Processes: With Applications in Life Sciences. Berlin: Springer; 2013.
    • (2013)
    • Fuchs, C.1
  • 16
    • 84884929912 scopus 로고    scopus 로고
    • An automatic method for robust and fast cell detection in bright field images from high-throughput microscopy
    • Buggenthin F, Marr C, Schwarzfischer M, Hoppe PS, Hilsenbeck O, Schroeder T, et al.An automatic method for robust and fast cell detection in bright field images from high-throughput microscopy. BMC Bioinformatics. 2013; 14(1):297.
    • (2013) BMC Bioinformatics , vol.14 , Issue.1 , pp. 297
    • Buggenthin, F.1    Marr, C.2    Schwarzfischer, M.3    Hoppe, P.S.4    Hilsenbeck, O.5    Schroeder, T.6
  • 18
  • 19
    • 60149102751 scopus 로고    scopus 로고
    • Continuous single-cell imaging of blood generation from haemogenic endothelium
    • Eilken HM, Nishikawa SI, Schroeder T. Continuous single-cell imaging of blood generation from haemogenic endothelium. Nature. 2009; 457(7231):896-900.
    • (2009) Nature , vol.457 , Issue.7231 , pp. 896-900
    • Eilken, H.M.1    Nishikawa, S.I.2    Schroeder, T.3
  • 20
    • 0030778204 scopus 로고    scopus 로고
    • Effective intercellular communication distances are determined by the relative time constants for cyto/chemokine secretion and diffusion
    • Francis K, Palsson BO. Effective intercellular communication distances are determined by the relative time constants for cyto/chemokine secretion and diffusion. Proc Natl Acad Sci U S A. 1997; 94(23):12258-62.
    • (1997) Proc Natl Acad Sci U S A , vol.94 , Issue.23 , pp. 12258-12262
    • Francis, K.1    Palsson, B.O.2
  • 22
    • 0003663926 scopus 로고
    • Generalized Linear Models
    • London: Chapman and Hall/CRC
    • McCullagh J, Nelder P. Generalized Linear Models. London: Chapman and Hall/CRC; 1989.
    • (1989)
    • McCullagh, J.1    Nelder, P.2
  • 23
    • 1642420994 scopus 로고    scopus 로고
    • A Modified Poisson Regression Approach to Prospective Studies with Binary Data
    • Zou G. A Modified Poisson Regression Approach to Prospective Studies with Binary Data. Am J Epidemiol. 2004; 159(7):702-6.
    • (2004) Am J Epidemiol , vol.159 , Issue.7 , pp. 702-706
    • Zou, G.1
  • 24
    • 85194972808 scopus 로고    scopus 로고
    • Regression shrinkage and selection via the lasso
    • Tibshirani R. Regression shrinkage and selection via the lasso. J R Stat Soc Ser B. 1996; 58(1):267-88.
    • (1996) J R Stat Soc Ser B , vol.58 , Issue.1 , pp. 267-288
    • Tibshirani, R.1
  • 25
    • 84857466151 scopus 로고    scopus 로고
    • Machine Learning: a Probabilistic Perspective
    • Cambridge, Massachusetts: The MIT Press
    • Murphy KP. Machine Learning: a Probabilistic Perspective. Cambridge, Massachusetts: The MIT Press; 2012.
    • (2012)
    • Murphy, K.P.1
  • 26
    • 0003684449 scopus 로고    scopus 로고
    • The Elements of Statistical Learning
    • New York: Springer;
    • Hastie T, Tibshirani R, Friedman J. The Elements of Statistical Learning. New York: Springer; 2009.
    • (2009)
    • Hastie, T.1    Tibshirani, R.2    Friedman, J.3
  • 27
    • 68549133155 scopus 로고    scopus 로고
    • Learning from Imbalanced Data
    • He H, Garcia E. Learning from Imbalanced Data. IEEE Trans Knowl Data Eng. 2009; 21(9):1263-84.
    • (2009) IEEE Trans Knowl Data Eng , vol.21 , Issue.9 , pp. 1263-1284
    • He, H.1    Garcia, E.2
  • 28
    • 84863336952 scopus 로고    scopus 로고
    • Logistic regression applied to natural hazards: rare event logistic regression with replications
    • Guns M, Vanacker V, Glade T. Logistic regression applied to natural hazards: rare event logistic regression with replications. Nat Hazards Earth Syst Sci. 2012; 12:1937-47.
    • (2012) Nat Hazards Earth Syst Sci , vol.12 , pp. 1937-1947
    • Guns, M.1    Vanacker, V.2    Glade, T.3
  • 29
    • 56449120785 scopus 로고    scopus 로고
    • Bolasso: model consistent lasso estimation through the bootstrap
    • Madison, Wisconsin: Omnipress
    • Bach F. Bolasso: model consistent lasso estimation through the bootstrap. In: Proceedings of the 25th International Conference on Machine Learning. Madison, Wisconsin: Omnipress: 2008. p. 33-40.
    • (2008) Proceedings of the 25th International Conference on Machine Learning , pp. 33-40
    • Bach, F.1
  • 31
    • 70349466529 scopus 로고    scopus 로고
    • Population context determines cell-to-cell variability in endocytosis and virus infection
    • Snijder B, Sacher R, Rämö P, Damm EM, Liberali P, Pelkmans L. Population context determines cell-to-cell variability in endocytosis and virus infection. Nature. 2009; 461(7263):520-3.
    • (2009) Nature , vol.461 , Issue.7263 , pp. 520-523
    • Snijder, B.1    Sacher, R.2    Rämö, P.3    Damm, E.M.4    Liberali, P.5    Pelkmans, L.6
  • 32
    • 83655181439 scopus 로고    scopus 로고
    • Normalizing for individual cell population context in the analysis of high-content cellular screens
    • Knapp B, Rebhan I, Kumar A, Matula P, Kiani NA, Binder M, et al.Normalizing for individual cell population context in the analysis of high-content cellular screens. BMC Bioinformatics. 2011; 12(1):485.
    • (2011) BMC Bioinformatics , vol.12 , Issue.1 , pp. 485
    • Knapp, B.1    Rebhan, I.2    Kumar, A.3    Matula, P.4    Kiani, N.A.5    Binder, M.6
  • 33
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman L. Random forests. Mach Learn. 2001; 45:5-32.
    • (2001) Mach Learn , vol.45 , pp. 5-32
    • Breiman, L.1
  • 34
    • 83455164706 scopus 로고    scopus 로고
    • Temporal competition between differentiation programs determines cell fate choice
    • Kuchina A, Espinar L, Çagatay T, Balbin AO, Zhang F, Alvarado A, et al.Temporal competition between differentiation programs determines cell fate choice. Mol Syst Biol. 2011; 7(557):1-11.
    • (2011) Mol Syst Biol. , vol.7 , Issue.557 , pp. 1-11
    • Kuchina, A.1    Espinar, L.2    Çagatay, T.3    Balbin, A.O.4    Zhang, F.5    Alvarado, A.6
  • 35
    • 79955480292 scopus 로고    scopus 로고
    • Finite Mixtures of Generalized Linear Regression Models
    • Heidelberg, Germany: Physica Verlag
    • Grün B, Leisch F. Finite Mixtures of Generalized Linear Regression Models. In: Recent Advances in Linear Models and Related Areas SE - 11. Heidelberg, Germany: Physica Verlag: 2008. p. 205-30.
    • (2008) Recent Advances in Linear Models and Related Areas SE - 11. , pp. 205-230
    • Grün, B.1    Leisch, F.2
  • 36
    • 0000336139 scopus 로고
    • Regression models and life tables
    • Cox D. Regression models and life tables. JR stat soc B. 1972; 34(2):187-220.
    • (1972) JR stat soc B , vol.34 , Issue.2 , pp. 187-220
    • Cox, D.1
  • 37
    • 0001646484 scopus 로고
    • Cox's Regression Model for Counting Processes:A Large Sample Study
    • Andersen PK, Gill RD. Cox's Regression Model for Counting Processes:A Large Sample Study. Ann Stat. 1982; 10:1100-20.
    • (1982) Ann Stat , vol.10 , pp. 1100-1120
    • Andersen, P.K.1    Gill, R.D.2
  • 38
    • 0000351727 scopus 로고
    • Investigating Causal Relations by Econometric Models and Cross-spectral Methods
    • Granger CWJ. Investigating Causal Relations by Econometric Models and Cross-spectral Methods. Econometrica. 1969; 37(3):424-38.
    • (1969) Econometrica , vol.37 , Issue.3 , pp. 424-438
    • Granger, C.W.J.1
  • 40
    • 3042841912 scopus 로고    scopus 로고
    • Delta-Notch signaling and lateral inhibition in zebrafish spinal cord development
    • Appel B, Givan LA, Eisen JS. Delta-Notch signaling and lateral inhibition in zebrafish spinal cord development. BMC Dev Biol. 2001; 1:13.
    • (2001) BMC Dev Biol , vol.1 , pp. 13
    • Appel, B.1    Givan, L.A.2    Eisen, J.S.3
  • 41
    • 38349157811 scopus 로고    scopus 로고
    • Hematopoietic cytokines
    • Metcalf D. Hematopoietic cytokines. Blood. 2008; 111(2):485-91.
    • (2008) Blood , vol.111 , Issue.2 , pp. 485-491
    • Metcalf, D.1
  • 42
    • 34648821257 scopus 로고    scopus 로고
    • Molecular heterogeneity of breast carcinomas and the cancer stem cell hypothesis
    • Stingl J, Caldas C. Molecular heterogeneity of breast carcinomas and the cancer stem cell hypothesis. Nat Revi Cancer. 2007; 7(10):791-9.
    • (2007) Nat Revi Cancer , vol.7 , Issue.10 , pp. 791-799
    • Stingl, J.1    Caldas, C.2
  • 43
    • 84881236410 scopus 로고    scopus 로고
    • Positive Feedback Between PU.1 and the Cell Cycle Controls Myeloid Differentiation
    • Kueh HY, Champhekhar A, Nutt SL, Elowitz MB, Rothenberg EV. Positive Feedback Between PU.1 and the Cell Cycle Controls Myeloid Differentiation. Science. 2013; 341(6146):670-3.
    • (2013) Science , vol.341 , Issue.6146 , pp. 670-673
    • Kueh, H.Y.1    Champhekhar, A.2    Nutt, S.L.3    Elowitz, M.B.4    Rothenberg, E.V.5
  • 44
    • 80051505603 scopus 로고    scopus 로고
    • Hierarchical differentiation of Myeloid Progenitors is encoded in the transcription factor network
    • Krumsiek J, Marr C, Schroeder T, Theis FJ. Hierarchical differentiation of Myeloid Progenitors is encoded in the transcription factor network. PLoS ONE. 2011; 6(8):22649.
    • (2011) PLoS ONE , vol.6 , Issue.8 , pp. 22649
    • Krumsiek, J.1    Marr, C.2    Schroeder, T.3    Theis, F.J.4
  • 45
    • 84855447444 scopus 로고    scopus 로고
    • Stability and multiattractor dynamics of a toggle switch based on a two-stage model of stochastic gene expression
    • Strasser M, Theis FJ, Marr C. Stability and multiattractor dynamics of a toggle switch based on a two-stage model of stochastic gene expression. Biophys J. 2012; 102(1):19-29.
    • (2012) Biophys J , vol.102 , Issue.1 , pp. 19-29
    • Strasser, M.1    Theis, F.J.2    Marr, C.3
  • 47
    • 77649263847 scopus 로고    scopus 로고
    • Computational prediction of neural progenitor cell fates
    • Cohen AR, Gomes FLAF, Roysam B, Cayouette M. Computational prediction of neural progenitor cell fates. Nat Methods. 2010; 7(3):213-8.
    • (2010) Nat Methods , vol.7 , Issue.3 , pp. 213-218
    • Cohen, A.R.1    Gomes, F.L.A.F.2    Roysam, B.3    Cayouette, M.4
  • 49
    • 84898619040 scopus 로고    scopus 로고
    • A model-based analysis of culture-dependent phenotypes of mESCs
    • Herberg M, Kalkan T, Glauche I, Smith A, Roeder I. A model-based analysis of culture-dependent phenotypes of mESCs. PloS ONE. 2014; 9(3):92496.
    • (2014) PloS ONE , vol.9 , Issue.3 , pp. 92496
    • Herberg, M.1    Kalkan, T.2    Glauche, I.3    Smith, A.4    Roeder, I.5
  • 50
    • 84944925116 scopus 로고    scopus 로고
    • FGF/MAPK signaling sets the switching threshold of a bistable circuit controlling cell fate decisions in ES cells
    • Schröter C, Rué P, Mackenzie JP, Martinez Arias A. FGF/MAPK signaling sets the switching threshold of a bistable circuit controlling cell fate decisions in ES cells. bioRxiv. 2015. http://biorxiv.org/content/early/2015/04/21/015404.
    • (2015) bioRxiv.
    • Schröter, C.1    Rué, P.2    Mackenzie, J.P.3    Martinez Arias, A.4
  • 51
    • 80051967505 scopus 로고    scopus 로고
    • Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells
    • Gupta PB, Fillmore CM, Jiang G, Shapira SD, Tao K, Kuperwasser C, Lander ES. Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells. Cell. 2011; 146(4):633-44.
    • (2011) Cell , vol.146 , Issue.4 , pp. 633-644
    • Gupta, P.B.1    Fillmore, C.M.2    Jiang, G.3    Shapira, S.D.4    Tao, K.5    Kuperwasser, C.6    Lander, E.S.7
  • 52
    • 84858608410 scopus 로고    scopus 로고
    • Cancer stem cells: impact, heterogeneity, and uncertainty
    • Magee JA, Piskounova E, Morrison SJ. Cancer stem cells: impact, heterogeneity, and uncertainty. Cancer Cell. 2012; 21(3):283-96.
    • (2012) Cancer Cell , vol.21 , Issue.3 , pp. 283-296
    • Magee, J.A.1    Piskounova, E.2    Morrison, S.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.