-
1
-
-
84867026349
-
Optimization of a GCaMP calcium indicator for neural activity imaging
-
Akerboom J, Chen TW, Wardill TJ, Tian L, Marvin JS, Mutlu S, Calderón NC, Esposti F, Borghuis BG, Sun XR, Gordus A (2012) Optimization of a GCaMP calcium indicator for neural activity imaging. J Neurosci 32: 13819–13840
-
(2012)
J Neurosci
, vol.32
, pp. 13819-13840
-
-
Akerboom, J.1
Chen, T.W.2
Wardill, T.J.3
Tian, L.4
Marvin, J.S.5
Mutlu, S.6
Calderón, N.C.7
Esposti, F.8
Borghuis, B.G.9
Sun, X.R.10
Gordus, A.11
-
2
-
-
78049290933
-
Variability in G-protein-coupled signaling studied with microfluidic devices
-
Bao XR, Fraser IDC, Wall EA, Quake SR, Simon MI (2010) Variability in G-protein-coupled signaling studied with microfluidic devices. Biophys J 99: 2414–2422
-
(2010)
Biophys J
, vol.99
, pp. 2414-2422
-
-
Bao, X.R.1
Fraser, I.D.C.2
Wall, E.A.3
Quake, S.R.4
Simon, M.I.5
-
3
-
-
84899574465
-
Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development
-
Bendall SC, Davis KL, Amir E-AD, Tadmor MD, Simonds EF, Chen TJ, Shenfeld DK, Nolan GP, Pe'er D (2014) Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development. Cell 157: 714–725
-
(2014)
Cell
, vol.157
, pp. 714-725
-
-
Bendall, S.C.1
Davis, K.L.2
Amir, E.-A.D.3
Tadmor, M.D.4
Simonds, E.F.5
Chen, T.J.6
Shenfeld, D.K.7
Nolan, G.P.8
Pe'er, D.9
-
4
-
-
84923292191
-
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
-
Buettner F, Natarajan KN, Casale FP, Proserpio V, Scialdone A, Theis FJ, Teichmann SA, Marioni JC, Stegle O (2015) Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nat Biotechnol 33: 155–160
-
(2015)
Nat Biotechnol
, vol.33
, pp. 155-160
-
-
Buettner, F.1
Natarajan, K.N.2
Casale, F.P.3
Proserpio, V.4
Scialdone, A.5
Theis, F.J.6
Teichmann, S.A.7
Marioni, J.C.8
Stegle, O.9
-
6
-
-
71149092283
-
Dynamics and variability of ERK2 response to EGF in individual living cells
-
Cohen-Saidon C, Cohen AA, Sigal A, Liron Y, Alon U (2009) Dynamics and variability of ERK2 response to EGF in individual living cells. Mol Cell 36: 885–893
-
(2009)
Mol Cell
, vol.36
, pp. 885-893
-
-
Cohen-Saidon, C.1
Cohen, A.A.2
Sigal, A.3
Liron, Y.4
Alon, U.5
-
7
-
-
0037603113
-
Morphogenesis and oncogenesis of MCF-10A mammary epithelial acini grown in three-dimensional basement membrane cultures
-
Debnath J, Muthuswamy SK, Brugge JS (2003) Morphogenesis and oncogenesis of MCF-10A mammary epithelial acini grown in three-dimensional basement membrane cultures. Methods 30: 256–268
-
(2003)
Methods
, vol.30
, pp. 256-268
-
-
Debnath, J.1
Muthuswamy, S.K.2
Brugge, J.S.3
-
8
-
-
84933676032
-
Applications for single cell trajectory analysis in inner ear development and regeneration
-
Durruthy-Durruthy R, Heller S (2015) Applications for single cell trajectory analysis in inner ear development and regeneration. Cell Tissue Res 361: 49–57
-
(2015)
Cell Tissue Res
, vol.361
, pp. 49-57
-
-
Durruthy-Durruthy, R.1
Heller, S.2
-
10
-
-
84873622581
-
Properties of cell death models calibrated and compared using Bayesian approaches
-
Eydgahi H, Chen WW, Muhlich JL, Vitkup D, Tsitsiklis JN, Sorger PK (2013) Properties of cell death models calibrated and compared using Bayesian approaches. Mol Syst Biol 9: 644
-
(2013)
Mol Syst Biol
, vol.9
, pp. 644
-
-
Eydgahi, H.1
Chen, W.W.2
Muhlich, J.L.3
Vitkup, D.4
Tsitsiklis, J.N.5
Sorger, P.K.6
-
11
-
-
84867303343
-
A dynamical-systems view of stem cell biology
-
Furusawa C, Kaneko K (2012) A dynamical-systems view of stem cell biology. Science 338: 215–217
-
(2012)
Science
, vol.338
, pp. 215-217
-
-
Furusawa, C.1
Kaneko, K.2
-
12
-
-
33745451921
-
Oscillations and variability in the p53 system
-
Geva-Zatorsky N, Rosenfeld N, Itzkovitz S, Milo R, Sigal A, Dekel E, Yarnitzky T, Liron Y, Polak P, Lahav G, Alon U (2006) Oscillations and variability in the p53 system. Mol Syst Biol 2: 2006.0033
-
(2006)
Mol Syst Biol
, vol.2
, pp. 2006.0033
-
-
Geva-Zatorsky, N.1
Rosenfeld, N.2
Itzkovitz, S.3
Milo, R.4
Sigal, A.5
Dekel, E.6
Yarnitzky, T.7
Liron, Y.8
Polak, P.9
Lahav, G.10
Alon, U.11
-
13
-
-
35748977901
-
Universally sloppy parameter sensitivities in systems biology models
-
Gutenkunst RN, Waterfall JJ, Casey FP, Brown KS, Myers CR, Sethna JP (2007) Universally sloppy parameter sensitivities in systems biology models. PLoS Comput Biol 3: 1871–1878
-
(2007)
PLoS Comput Biol
, vol.3
, pp. 1871-1878
-
-
Gutenkunst, R.N.1
Waterfall, J.J.2
Casey, F.P.3
Brown, K.S.4
Myers, C.R.5
Sethna, J.P.6
-
14
-
-
84949845518
-
Paracrine communication maximizes cellular response fidelity in wound signaling
-
Handly LN, Pilko A, Wollman R (2015) Paracrine communication maximizes cellular response fidelity in wound signaling. Elife 4: e09652
-
(2015)
Elife
, vol.4
-
-
Handly, L.N.1
Pilko, A.2
Wollman, R.3
-
15
-
-
0024391789
-
Photochemically generated cytosolic calcium pulses and their detection by fluo-3
-
Kao JP, Harootunian AT, Tsien RY (1989) Photochemically generated cytosolic calcium pulses and their detection by fluo-3. J Biol Chem 264: 8179–8184
-
(1989)
J Biol Chem
, vol.264
, pp. 8179-8184
-
-
Kao, J.P.1
Harootunian, A.T.2
Tsien, R.Y.3
-
16
-
-
84860527594
-
Noise in cellular signaling pathways: causes and effects
-
Ladbury JE, Arold ST (2012) Noise in cellular signaling pathways: causes and effects. Trends Biochem Sci 37: 173–178
-
(2012)
Trends Biochem Sci
, vol.37
, pp. 173-178
-
-
Ladbury, J.E.1
Arold, S.T.2
-
17
-
-
77951187551
-
A noisy paracrine signal determines the cellular NF-kappaB response to lipopolysaccharide
-
Lee TK, Denny EM, Sanghvi JC, Gaston JE, Maynard ND, Hughey JJ, Covert MW (2009) A noisy paracrine signal determines the cellular NF-kappaB response to lipopolysaccharide. Sci Signal 2: ra65
-
(2009)
Sci Signal
, vol.2
, pp. ra65
-
-
Lee, T.K.1
Denny, E.M.2
Sanghvi, J.C.3
Gaston, J.E.4
Maynard, N.D.5
Hughey, J.J.6
Covert, M.W.7
-
18
-
-
0038361339
-
Metabotropic receptor activation, desensitization and sequestration-I: modelling calcium and inositol 1,4,5-trisphosphate dynamics following receptor activation
-
Lemon G, Gibson WG, Bennett MR (2003) Metabotropic receptor activation, desensitization and sequestration-I: modelling calcium and inositol 1,4,5-trisphosphate dynamics following receptor activation. J Theor Biol 223: 93–111
-
(2003)
J Theor Biol
, vol.223
, pp. 93-111
-
-
Lemon, G.1
Gibson, W.G.2
Bennett, M.R.3
-
19
-
-
0028178965
-
i oscillations derived from a detailed kinetic model: a Hodgkin-Huxley like formalism
-
i oscillations derived from a detailed kinetic model: a Hodgkin-Huxley like formalism. J Theor Biol 166: 461–473
-
(1994)
J Theor Biol
, vol.166
, pp. 461-473
-
-
Li, Y.-X.1
Rinzel, J.2
-
20
-
-
84893308174
-
A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation
-
Liepe J, Kirk P, Filippi S, Toni T, Barnes CP, Stumpf MPH (2014) A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation. Nat Protoc 9: 439–456
-
(2014)
Nat Protoc
, vol.9
, pp. 439-456
-
-
Liepe, J.1
Kirk, P.2
Filippi, S.3
Toni, T.4
Barnes, C.P.5
Stumpf, M.P.H.6
-
21
-
-
84923132388
-
Highly multiplexed profiling of single-cell effector functions reveals deep functional heterogeneity in response to pathogenic ligands
-
Lu Y, Xue Q, Eisele MR, Sulistijo ES, Brower K, Han L, Amir E-AD, Pe'er D, Miller-Jensen K, Fan R (2015) Highly multiplexed profiling of single-cell effector functions reveals deep functional heterogeneity in response to pathogenic ligands. Proc Natl Acad Sci USA 112: E607–E615
-
(2015)
Proc Natl Acad Sci USA
, vol.112
, pp. E607-E615
-
-
Lu, Y.1
Xue, Q.2
Eisele, M.R.3
Sulistijo, E.S.4
Brower, K.5
Han, L.6
Amir, E.-A.D.7
Pe'er, D.8
Miller-Jensen, K.9
Fan, R.10
-
22
-
-
84924365758
-
Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape
-
Marco E, Karp RL, Guo G, Robson P, Hart AH, Trippa L, Yuan G-C (2014) Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape. Proc Natl Acad Sci USA 111: E5643–E5650
-
(2014)
Proc Natl Acad Sci USA
, vol.111
, pp. E5643-E5650
-
-
Marco, E.1
Karp, R.L.2
Guo, G.3
Robson, P.4
Hart, A.H.5
Trippa, L.6
Yuan, G.-C.7
-
23
-
-
0032555788
-
2+ stores has a key role in nonmuscle cell signaling and function
-
2+ stores has a key role in nonmuscle cell signaling and function. J Cell Biol 142: 1395–1398
-
(1998)
J Cell Biol
, vol.142
, pp. 1395-1398
-
-
Meldolesi, J.1
Pozzan, T.2
-
24
-
-
79951520820
-
What's all the noise about developmental stochasticity?
-
Oates AC (2011) What's all the noise about developmental stochasticity? Development 138: 601–607
-
(2011)
Development
, vol.138
, pp. 601-607
-
-
Oates, A.C.1
-
25
-
-
79952606233
-
Addressing parameter identifiability by model-based experimentation
-
Raue A, Kreutz C, Maiwald T, Klingmuller U, Timmer J (2011) Addressing parameter identifiability by model-based experimentation. IET Syst Biol 5: 120–130
-
(2011)
IET Syst Biol
, vol.5
, pp. 120-130
-
-
Raue, A.1
Kreutz, C.2
Maiwald, T.3
Klingmuller, U.4
Timmer, J.5
-
26
-
-
84914125325
-
Noise decomposition of intracellular biochemical signaling networks using nonequivalent reporters
-
Rhee A, Cheong R, Levchenko A (2014) Noise decomposition of intracellular biochemical signaling networks using nonequivalent reporters. Proc Natl Acad Sci USA 111: 17330–17335
-
(2014)
Proc Natl Acad Sci USA
, vol.111
, pp. 17330-17335
-
-
Rhee, A.1
Cheong, R.2
Levchenko, A.3
-
27
-
-
84918571678
-
Accurate information transmission through dynamic biochemical signaling networks
-
Selimkhanov J, Taylor B, Yao J, Pilko A, Albeck J, Hoffmann A, Tsimring L, Wollman R (2014) Accurate information transmission through dynamic biochemical signaling networks. Science 346: 1370–1373
-
(2014)
Science
, vol.346
, pp. 1370-1373
-
-
Selimkhanov, J.1
Taylor, B.2
Yao, J.3
Pilko, A.4
Albeck, J.5
Hoffmann, A.6
Tsimring, L.7
Wollman, R.8
-
28
-
-
84974587998
-
Wishbone identifies bifurcating developmental trajectories from singel-cell data
-
Setty M, Tadmor MD, Reich-Zeliger S, Angel O, Salame TM, Kathali P, Choi K, Bendall S, Friedman N, Pe'er D (2016) Wishbone identifies bifurcating developmental trajectories from singel-cell data. Nat Biotechnol 34: 637–645
-
(2016)
Nat Biotechnol
, vol.34
, pp. 637-645
-
-
Setty, M.1
Tadmor, M.D.2
Reich-Zeliger, S.3
Angel, O.4
Salame, T.M.5
Kathali, P.6
Choi, K.7
Bendall, S.8
Friedman, N.9
Pe'er, D.10
-
29
-
-
84883365868
-
The geometry of the Pareto front in biological phenotype space
-
Sheftel H, Shoval O, Mayo A, Alon U (2013) The geometry of the Pareto front in biological phenotype space. Ecol Evol 3: 1471–1483
-
(2013)
Ecol Evol
, vol.3
, pp. 1471-1483
-
-
Sheftel, H.1
Shoval, O.2
Mayo, A.3
Alon, U.4
-
30
-
-
12244257806
-
Noisy signal amplification in ultrasensitive signal transduction
-
Shibata T, Fujimoto K (2005) Noisy signal amplification in ultrasensitive signal transduction. Proc Natl Acad Sci USA 102: 331–336
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 331-336
-
-
Shibata, T.1
Fujimoto, K.2
-
31
-
-
70349466529
-
Population context determines cell-to-cell variability in endocytosis and virus infection
-
Snijder B, Sacher R, Rämö P, Damm E-M, Liberali P, Pelkmans L (2009) Population context determines cell-to-cell variability in endocytosis and virus infection. Nature 461: 520–523
-
(2009)
Nature
, vol.461
, pp. 520-523
-
-
Snijder, B.1
Sacher, R.2
Rämö, P.3
Damm, E.-M.4
Liberali, P.5
Pelkmans, L.6
-
32
-
-
80054019114
-
Wound repair: toward understanding and integration of single-cell and multicellular wound responses
-
Sonnemann KJ, Bement WM (2011) Wound repair: toward understanding and integration of single-cell and multicellular wound responses. Annu Rev Cell Dev Biol 27: 237–263
-
(2011)
Annu Rev Cell Dev Biol
, vol.27
, pp. 237-263
-
-
Sonnemann, K.J.1
Bement, W.M.2
-
33
-
-
84937604921
-
IMMUNOLOGY. An interactive reference framework for modeling a dynamic immune system
-
Spitzer MH, Gherardini PF, Fragiadakis GK, Bhattacharya N, Yuan RT, Hotson AN, Finck R, Carmi Y, Zunder ER, Fantl WJ, Bendall SC, Engleman EG, Nolan GP (2015) IMMUNOLOGY. An interactive reference framework for modeling a dynamic immune system. Science 349: 1259425
-
(2015)
Science
, vol.349
, pp. 1259425
-
-
Spitzer, M.H.1
Gherardini, P.F.2
Fragiadakis, G.K.3
Bhattacharya, N.4
Yuan, R.T.5
Hotson, A.N.6
Finck, R.7
Carmi, Y.8
Zunder, E.R.9
Fantl, W.J.10
Bendall, S.C.11
Engleman, E.G.12
Nolan, G.P.13
-
34
-
-
84887123973
-
Genetically encoded calcium indicator illuminates calcium dynamics in primary cilia
-
Su S, Phua SC, DeRose R, Chiba S, Narita K, Kalugin PN, Katada T, Kontani K, Takeda S, Inoue T (2013) Genetically encoded calcium indicator illuminates calcium dynamics in primary cilia. Nat Methods 10: 1105–1107
-
(2013)
Nat Methods
, vol.10
, pp. 1105-1107
-
-
Su, S.1
Phua, S.C.2
DeRose, R.3
Chiba, S.4
Narita, K.5
Kalugin, P.N.6
Katada, T.7
Kontani, K.8
Takeda, S.9
Inoue, T.10
-
35
-
-
77954541844
-
Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing
-
Tay S, Hughey JJ, Lee TK, Lipniacki T, Quake SR, Covert MW (2010) Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing. Nature 466: 267–271
-
(2010)
Nature
, vol.466
, pp. 267-271
-
-
Tay, S.1
Hughey, J.J.2
Lee, T.K.3
Lipniacki, T.4
Quake, S.R.5
Covert, M.W.6
-
36
-
-
84890036078
-
Using optogenetics to interrogate the dynamic control of signal transmission by the Ras/Erk module
-
Toettcher JE, Weiner OD, Lim WA (2013) Using optogenetics to interrogate the dynamic control of signal transmission by the Ras/Erk module. Cell 155: 1422–1434
-
(2013)
Cell
, vol.155
, pp. 1422-1434
-
-
Toettcher, J.E.1
Weiner, O.D.2
Lim, W.A.3
-
37
-
-
84942940566
-
Defining cell types and states with single-cell genomics
-
Trapnell C (2015) Defining cell types and states with single-cell genomics. Genome Res 25: 1491–1498
-
(2015)
Genome Res
, vol.25
, pp. 1491-1498
-
-
Trapnell, C.1
-
38
-
-
0029059239
-
Type I, II, and III inositol 1,4,5-trisphosphate receptors are unequally susceptible to down-regulation and are expressed in markedly different proportions in different cell types
-
Wojcikiewicz RJ (1995) Type I, II, and III inositol 1,4,5-trisphosphate receptors are unequally susceptible to down-regulation and are expressed in markedly different proportions in different cell types. J Biol Chem 270: 11678–11683
-
(1995)
J Biol Chem
, vol.270
, pp. 11678-11683
-
-
Wojcikiewicz, R.J.1
|