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1
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Universal patterns of stem cell fate in cycling adult tissues
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1 Klein, A.M., Simons, B.D., Universal patterns of stem cell fate in cycling adult tissues. Development 138 (2011), 3103–3111.
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Klein, A.M.1
Simons, B.D.2
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2
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84926339975
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Dynamic stem cell heterogeneity
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This paper provides a comprehensive review of recent findings on several non-hematopoietic stem cell dynamics made with in vivo live imaging (mammalian spermatogenesis, intestinal maintenance and the hair cycle), stressing quantitative aspects such as the neutral drift dynamics of stem-cell clones.
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2•• Krieger, T., Simons, B.D., Dynamic stem cell heterogeneity. Development 142 (2015), 1396–1406 This paper provides a comprehensive review of recent findings on several non-hematopoietic stem cell dynamics made with in vivo live imaging (mammalian spermatogenesis, intestinal maintenance and the hair cycle), stressing quantitative aspects such as the neutral drift dynamics of stem-cell clones.
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Development
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Krieger, T.1
Simons, B.D.2
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3
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84887983173
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An estimation of the number of cells in the human body
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3 Bianconi, E., Piovesan, A., Facchin, F., Beraudi, A., Casadei, R., Frabetti, F., Vitale, L., Pelleri, M.C., Tassani, S., Piva, F., et al. An estimation of the number of cells in the human body. Ann Hum Biol 40 (2013), 463–471.
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Pelleri, M.C.8
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Piva, F.10
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4
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84873619402
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Dynamical modelling of haematopoiesis: an integrated view over the system in homeostasis and under perturbation
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4 Manesso, E., Teles, J., Bryder, D., Peterson, C., Dynamical modelling of haematopoiesis: an integrated view over the system in homeostasis and under perturbation. J R Soc Interface, 10, 2013, 20120817.
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Manesso, E.1
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5
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84930647470
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Understanding, treating and avoiding hematological disease: better medicine through mathematics?
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This paper reviews the joint experimental, clinical and mathematical modeling efforts led by the two authors over almost four decades to understand a periodic hematological disease — cyclical neutropenia — and improve its treatment.
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5•• Dale, D.C., Mackey, M.C., Understanding, treating and avoiding hematological disease: better medicine through mathematics?. Bull Math Biol 77 (2015), 739–757 This paper reviews the joint experimental, clinical and mathematical modeling efforts led by the two authors over almost four decades to understand a periodic hematological disease — cyclical neutropenia — and improve its treatment.
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Dale, D.C.1
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Unravelling stem cell dynamics by lineage tracing
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6 Blanpain, C., Simons, B.D., Unravelling stem cell dynamics by lineage tracing. Nat Rev Mol Cell Biol 14 (2013), 489–502.
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Blanpain, C.1
Simons, B.D.2
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7
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Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding
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7 Lu, R., Neff, N.F., Quake, S.R., Weissman, I.L., Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding. Nat Biotechnol 29 (2011), 928–933.
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Lu, R.1
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8
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84876297531
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Diverse and heritable lineage imprinting of early haematopoietic progenitors
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8 Naik, S.H., Perié, L., Swart, E., Gerlach, C., van Rooij, N., de Boer, R.J., Schumacher, T.N., Diverse and heritable lineage imprinting of early haematopoietic progenitors. Nature 496 (2013), 229–232.
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Naik, S.H.1
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van Rooij, N.5
de Boer, R.J.6
Schumacher, T.N.7
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9
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84877601429
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Heterogeneous differentiation patterns of individual CD8+ T cells
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9 Gerlach, C., Rohr, J.C., Perié, L., van Rooij, N., van Heijst, J.W.J., Velds, A., Urbanus, J., Naik, S.H., Jacobs, H., Beltman, J.B., et al. Heterogeneous differentiation patterns of individual CD8+ T cells. Science 340 (2013), 635–639.
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Gerlach, C.1
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Urbanus, J.7
Naik, S.H.8
Jacobs, H.9
Beltman, J.B.10
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10
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84886924368
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Heterogeneity of young and aged murine hematopoietic stem cells revealed by quantitative clonal analysis using cellular barcoding
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10 Verovskaya, E., Broekhuis, M.J.C., Zwart, E., Ritsema, M., van Os, R., de Haan, G., Bystrykh, L.V., Heterogeneity of young and aged murine hematopoietic stem cells revealed by quantitative clonal analysis using cellular barcoding. Blood 122 (2013), 523–532.
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Verovskaya, E.1
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van Os, R.5
de Haan, G.6
Bystrykh, L.V.7
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11
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84877625807
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Disparate individual fates compose robust CD8+ T cell immunity
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The authors map the fate of individual naïve T cells during an immune response and use a stochastic framework for modeling the dynamics of T cell differentiation and proliferation. Thus they identify both model parameters and model topology from single-cell progeny data.
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11•• Buchholz, V.R., Flossdorf, M., Hensel, I., Kretschmer, L., Weissbrich, B., Gräf, P., Verschoor, A., Schiemann, M., Höfer, T., Busch, D.H., Disparate individual fates compose robust CD8+ T cell immunity. Science 340 (2013), 630–635 The authors map the fate of individual naïve T cells during an immune response and use a stochastic framework for modeling the dynamics of T cell differentiation and proliferation. Thus they identify both model parameters and model topology from single-cell progeny data.
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Science
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Buchholz, V.R.1
Flossdorf, M.2
Hensel, I.3
Kretschmer, L.4
Weissbrich, B.5
Gräf, P.6
Verschoor, A.7
Schiemann, M.8
Höfer, T.9
Busch, D.H.10
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12
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84877710866
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Single naive CD4+ T cells from a diverse repertoire produce different effector cell types during infection
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12 Tubo, N.J., Pagán, A.J., Taylor, J.J., Nelson, R.W., Linehan, J.L., Ertelt, J.M., Huseby, E.S., Way, S.S., Jenkins, M.K., Single naive CD4+ T cells from a diverse repertoire produce different effector cell types during infection. Cell 153 (2013), 785–796.
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Cell
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Tubo, N.J.1
Pagán, A.J.2
Taylor, J.J.3
Nelson, R.W.4
Linehan, J.L.5
Ertelt, J.M.6
Huseby, E.S.7
Way, S.S.8
Jenkins, M.K.9
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13
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84922949971
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Humoral immunity. Apoptosis and antigen affinity limit effector cell differentiation of a single naïve B cell
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13 Taylor, J.J., Pape, K.A., Steach, H.R., Jenkins, M.K., Humoral immunity. Apoptosis and antigen affinity limit effector cell differentiation of a single naïve B cell. Science 347 (2015), 784–787.
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Science
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Taylor, J.J.1
Pape, K.A.2
Steach, H.R.3
Jenkins, M.K.4
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14
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84908125658
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Clonal dynamics of native haematopoiesis
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14 Sun, J., Ramos, A., Chapman, B., Johnnidis, J.B., Le, L., Ho, Y.-J., Klein, A., Hofmann, O., Camargo, F.D., Clonal dynamics of native haematopoiesis. Nature 514 (2014), 322–327.
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Nature
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Sun, J.1
Ramos, A.2
Chapman, B.3
Johnnidis, J.B.4
Le, L.5
Ho, Y.-J.6
Klein, A.7
Hofmann, O.8
Camargo, F.D.9
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15
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84924038121
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Fundamental properties of unperturbed haematopoiesis from stem cells in vivo
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This paper combines the fate mapping of HSC in vivo with mathematical modeling. The authors find that self-renewal capacity gradually declines along the myeloid differentiation pathway and uncover a strong myeloid versus lymphoid flux bias already in young mice. Differentiation and net proliferation rates have been quantified for the hematopoietic stem and progenitor cell compartments in the adult bone marrow.
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15•• Busch, K., Klapproth, K., Barile, M., Flossdorf, M., Holland-Letz, T., Schlenner, S.M., Reth, M., Höfer, T., Rodewald, H.-R., Fundamental properties of unperturbed haematopoiesis from stem cells in vivo. Nature 518 (2015), 542–546 This paper combines the fate mapping of HSC in vivo with mathematical modeling. The authors find that self-renewal capacity gradually declines along the myeloid differentiation pathway and uncover a strong myeloid versus lymphoid flux bias already in young mice. Differentiation and net proliferation rates have been quantified for the hematopoietic stem and progenitor cell compartments in the adult bone marrow.
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(2015)
Nature
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Busch, K.1
Klapproth, K.2
Barile, M.3
Flossdorf, M.4
Holland-Letz, T.5
Schlenner, S.M.6
Reth, M.7
Höfer, T.8
Rodewald, H.-R.9
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16
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84903790194
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Fgd5 identifies hematopoietic stem cells in the murine bone marrow
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16 Gazit, R., Mandal, P.K., Ebina, W., Ben-Zvi, A., Nombela-Arrieta, C., Silberstein, L.E., Rossi, D.J., Fgd5 identifies hematopoietic stem cells in the murine bone marrow. J Exp Med 211 (2014), 1315–1331.
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J Exp Med
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Gazit, R.1
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Ben-Zvi, A.4
Nombela-Arrieta, C.5
Silberstein, L.E.6
Rossi, D.J.7
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17
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84896712623
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Determining lineage pathways from cellular barcoding experiments
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The authors develop a rigorous mathematical analysis of the development of barcoded hematopoietic progenitor cells after transplantation, finding that the data require additional paths beyond those found in the classical differentiation model especially for dendritic cells.
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17•• Perié, L., Hodgkin, P.D., Naik, S.H., Schumacher, T.N., de Boer, R.J., Duffy, K.R., Determining lineage pathways from cellular barcoding experiments. Cell Rep 6 (2014), 617–624 The authors develop a rigorous mathematical analysis of the development of barcoded hematopoietic progenitor cells after transplantation, finding that the data require additional paths beyond those found in the classical differentiation model especially for dendritic cells.
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Cell Rep
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Perié, L.1
Hodgkin, P.D.2
Naik, S.H.3
Schumacher, T.N.4
de Boer, R.J.5
Duffy, K.R.6
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18
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84876093634
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Quantifying T lymphocyte turnover
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The paper is a comprehensive review article on the mathematical analysis of experimental data acquired with proliferation-dependent labels, such as BrdU, CFSE, deuterium and others.
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18•• de Boer, R.J., Perelson, A.S., Quantifying T lymphocyte turnover. J Theor Biol 327 (2013), 45–87 The paper is a comprehensive review article on the mathematical analysis of experimental data acquired with proliferation-dependent labels, such as BrdU, CFSE, deuterium and others.
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J Theor Biol
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de Boer, R.J.1
Perelson, A.S.2
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19
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84946095465
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Reconciling estimates of cell proliferation from stable isotope labeling experiments
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19 Ahmed, R., Westera, L., Drylewicz, J., Elemans, M., Zhang, Y., Kelly, E., Reljic, R., Tesselaar, K., de Boer, R.J., Macallan, D.C., et al. Reconciling estimates of cell proliferation from stable isotope labeling experiments. PLoS Comput Biol, 11, 2015, e1004355.
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Ahmed, R.1
Westera, L.2
Drylewicz, J.3
Elemans, M.4
Zhang, Y.5
Kelly, E.6
Reljic, R.7
Tesselaar, K.8
de Boer, R.J.9
Macallan, D.C.10
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20
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34548601610
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Haematopoietic stem cells do not asymmetrically segregate chromosomes or retain BrdU
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20 Kiel, M.J., He, S., Ashkenazi, R., Gentry, S.N., Teta, M., Kushner, J.A., Jackson, T.L., Morrison, S.J., Haematopoietic stem cells do not asymmetrically segregate chromosomes or retain BrdU. Nature 449 (2007), 238–242.
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Kiel, M.J.1
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Ashkenazi, R.3
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Kushner, J.A.6
Jackson, T.L.7
Morrison, S.J.8
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21
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56549128268
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Hematopoietic stem cells reversibly switch from dormancy to self-renewal during homeostasis and repair
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21 Wilson, A., Laurenti, E., Oser, G., van der Wath, R.C., Blanco-Bose, W., Jaworski, M., Offner, S., Dunant, C.F., Eshkind, L., Bockamp, E., et al. Hematopoietic stem cells reversibly switch from dormancy to self-renewal during homeostasis and repair. Cell 135 (2008), 1118–1129.
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Wilson, A.1
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van der Wath, R.C.4
Blanco-Bose, W.5
Jaworski, M.6
Offner, S.7
Dunant, C.F.8
Eshkind, L.9
Bockamp, E.10
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22
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70349611262
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Estimating dormant and active hematopoietic stem cell kinetics through extensive modeling of bromodeoxyuridine label-retaining cell dynamics
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22 van der Wath, R.C., Wilson, A., Laurenti, E., Trumpp, A., Liò, P., Estimating dormant and active hematopoietic stem cell kinetics through extensive modeling of bromodeoxyuridine label-retaining cell dynamics. PLoS ONE, 4, 2009, e6972.
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PLoS ONE
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van der Wath, R.C.1
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23
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79951698622
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Dynamic variation in cycling of hematopoietic stem cells in steady state and inflammation
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23 Takizawa, H., Regoes, R.R., Boddupalli, C.S., Bonhoeffer, S., Manz, M.G., Dynamic variation in cycling of hematopoietic stem cells in steady state and inflammation. J Exp Med 208 (2011), 273–284.
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Takizawa, H.1
Regoes, R.R.2
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Bonhoeffer, S.4
Manz, M.G.5
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24
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84889568419
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SLAM family markers resolve functionally distinct subpopulations of hematopoietic stem cells and multipotent progenitors
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This paper presents detailed quantitative data on the proliferation of stem and progenitor cell compartments in native hematopoiesis that are suitable for mathematical modeling.
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24• Oguro, H., Ding, L., Morrison, S.J., SLAM family markers resolve functionally distinct subpopulations of hematopoietic stem cells and multipotent progenitors. Cell Stem Cell 13 (2013), 102–116 This paper presents detailed quantitative data on the proliferation of stem and progenitor cell compartments in native hematopoiesis that are suitable for mathematical modeling.
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Cell Stem Cell
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Oguro, H.1
Ding, L.2
Morrison, S.J.3
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25
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84964696936
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CCND1-CDK4-mediated cell cycle progression provides a competitive advantage for human hematopoietic stem cells in vivo
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Experiments show that cyclin D/CDK4 controls the output of hematopoietic stem cells; includes mathematical inference from combined measurements of BrdU and DNA content.
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25• Mende, N., Kuchen, E.E., Lesche, M., Grinenko, T., Kokkaliaris, K.D., Hanenberg, H., Lindemann, D., Dahl, A., Platz, A., Höfer, T., et al. CCND1-CDK4-mediated cell cycle progression provides a competitive advantage for human hematopoietic stem cells in vivo. J Exp Med 212 (2015), 1171–1183 Experiments show that cyclin D/CDK4 controls the output of hematopoietic stem cells; includes mathematical inference from combined measurements of BrdU and DNA content.
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J Exp Med
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Mende, N.1
Kuchen, E.E.2
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Grinenko, T.4
Kokkaliaris, K.D.5
Hanenberg, H.6
Lindemann, D.7
Dahl, A.8
Platz, A.9
Höfer, T.10
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26
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84857416171
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Maintenance of peripheral naive T cells is sustained by thymus output in mice but not humans
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26 den Braber, I., Mugwagwa, T., Vrisekoop, N., Westera, L., Mögling, R., de Boer, A.B., Willems, N., Schrijver, E.H.R., Spierenburg, G., Gaiser, K., et al. Maintenance of peripheral naive T cells is sustained by thymus output in mice but not humans. Immunity 36 (2012), 288–297.
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den Braber, I.1
Mugwagwa, T.2
Vrisekoop, N.3
Westera, L.4
Mögling, R.5
de Boer, A.B.6
Willems, N.7
Schrijver, E.H.R.8
Spierenburg, G.9
Gaiser, K.10
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27
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84924266729
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Lymphocyte maintenance during healthy aging requires no substantial alterations in cellular turnover
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This paper addresses the topical issue of age-related changes in the hematopoietic system. Using in vivo labeling of T lymphocytes with deuterated water, the authors find similar dynamics of most T cell subsets between young adult and elderly healthy individuals, arguing against changes in T cell homeostasis with age.
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27• Westera, L., van Hoeven, V., Drylewicz, J., Spierenburg, G., van Velzen, J.F., de Boer, R.J., Tesselaar, K., Borghans, J.A.M., Lymphocyte maintenance during healthy aging requires no substantial alterations in cellular turnover. Aging Cell 14 (2015), 219–227 This paper addresses the topical issue of age-related changes in the hematopoietic system. Using in vivo labeling of T lymphocytes with deuterated water, the authors find similar dynamics of most T cell subsets between young adult and elderly healthy individuals, arguing against changes in T cell homeostasis with age.
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Aging Cell
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Westera, L.1
van Hoeven, V.2
Drylewicz, J.3
Spierenburg, G.4
van Velzen, J.F.5
de Boer, R.J.6
Tesselaar, K.7
Borghans, J.A.M.8
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28
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60149104597
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Analysis of histone 2B-GFP retention reveals slowly cycling hematopoietic stem cells
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28 Foudi, A., Hochedlinger, K., Van Buren, D., Schindler, J.W., Jaenisch, R., Carey, V., Hock, H., Analysis of histone 2B-GFP retention reveals slowly cycling hematopoietic stem cells. Nat Biotechnol 27 (2009), 84–90.
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Foudi, A.1
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Jaenisch, R.5
Carey, V.6
Hock, H.7
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29
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84899619056
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Stretched cell cycle model for proliferating lymphocytes
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This paper further develops the Cyton model for B and T cell proliferation using quantitative in vitro data on the G1 and S/G2/M phase durations in individual cells. In contrast to the classical Smith-Martin model, which posits that the G1-S transition controls cell-cycle length, the new data also show an appreciable impact of a variable S/G2/M length.
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29• Dowling, M.R., Kan, A., Heinzel, S., Zhou, J.H.S., Marchingo, J.M., Wellard, C.J., Markham, J.F., Hodgkin, P.D., Stretched cell cycle model for proliferating lymphocytes. Proc Natl Acad Sci U S A 111 (2014), 6377–6382 This paper further develops the Cyton model for B and T cell proliferation using quantitative in vitro data on the G1 and S/G2/M phase durations in individual cells. In contrast to the classical Smith-Martin model, which posits that the G1-S transition controls cell-cycle length, the new data also show an appreciable impact of a variable S/G2/M length.
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Proc Natl Acad Sci U S A
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Dowling, M.R.1
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Marchingo, J.M.5
Wellard, C.J.6
Markham, J.F.7
Hodgkin, P.D.8
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30
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84914690072
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T cell signaling. Antigen affinity, costimulation, and cytokine inputs sum linearly to amplify T cell expansion
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This paper shows that the T cell receptor stimulus and costimulatory signals, including cytokines, imprint a cell-intrinsic division destiny, whereby T cells effectively count through generations before returning to a quiescent state. Moreover, the authors provide a quantitative framework for stimulus integration, finding that the contributions of individual stimuli to division destiny sum up linearly.
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30•• Marchingo, J.M., Kan, A., Sutherland, R.M., Duffy, K.R., Wellard, C.J., Belz, G.T., Lew, A.M., Dowling, M.R., Heinzel, S., Hodgkin, P.D., T cell signaling. Antigen affinity, costimulation, and cytokine inputs sum linearly to amplify T cell expansion. Science 346 (2014), 1123–1127 This paper shows that the T cell receptor stimulus and costimulatory signals, including cytokines, imprint a cell-intrinsic division destiny, whereby T cells effectively count through generations before returning to a quiescent state. Moreover, the authors provide a quantitative framework for stimulus integration, finding that the contributions of individual stimuli to division destiny sum up linearly.
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(2014)
Science
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Marchingo, J.M.1
Kan, A.2
Sutherland, R.M.3
Duffy, K.R.4
Wellard, C.J.5
Belz, G.T.6
Lew, A.M.7
Dowling, M.R.8
Heinzel, S.9
Hodgkin, P.D.10
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31
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84925860801
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T160-phosphorylated CDK2 defines threshold for HGF-dependent proliferation in primary hepatocytes
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31 Mueller, S., Huard, J., Waldow, K., Huang, X., D'Alessandro, L.A., Bohl, S., Börner, K., Grimm, D., Klamt, S., Klingmüller, U., et al. T160-phosphorylated CDK2 defines threshold for HGF-dependent proliferation in primary hepatocytes. Mol Syst Biol, 11, 2015, 795.
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Mol Syst Biol
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Mueller, S.1
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Huang, X.4
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Bohl, S.6
Börner, K.7
Grimm, D.8
Klamt, S.9
Klingmüller, U.10
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32
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84856762359
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Optimality in the development of intestinal crypts
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Itzkovitz, S.1
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33
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Cell lineages and the logic of proliferative control
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33 Lander, A.D., Gokoffski, K.K., Wan, F.Y.M., Nie, Q., Calof, A.L., Cell lineages and the logic of proliferative control. PLoS Biol, 7, 2009, e15.
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Lander, A.D.1
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34
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84856072934
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