TY - JOUR AU - Enver, T. AU - Pera, M. AU - Peterson, C. AU - Andrews, P. W. PY - 2009 DA - 2009// TI - Stem cell states, fates, and the rules of attraction JO - Cell Stem Cell VL - 4 UR - https://doi.org/10.1016/j.stem.2009.04.011 DO - 10.1016/j.stem.2009.04.011 ID - Enver2009 ER - TY - JOUR AU - Hubbard, E. J. PY - 2007 DA - 2007// TI - Caenorhabditis elegans germ line: a model for stem cell biology JO - Dev Dyn VL - 236 UR - https://doi.org/10.1002/dvdy.21335 DO - 10.1002/dvdy.21335 ID - Hubbard2007 ER - TY - JOUR AU - Robert, J. S. PY - 2004 DA - 2004// TI - Model systems in stem cell biology JO - Bioessays VL - 26 UR - https://doi.org/10.1002/bies.20100 DO - 10.1002/bies.20100 ID - Robert2004 ER - TY - JOUR AU - Brenner, S. PY - 2010 DA - 2010// TI - Sequences and consequences JO - Philos Trans R Soc Lond B Biol Sci VL - 365 UR - https://doi.org/10.1098/rstb.2009.0221 DO - 10.1098/rstb.2009.0221 ID - Brenner2010 ER - TY - JOUR AU - Regev, A. AU - Shapiro, E. PY - 2002 DA - 2002// TI - Cells as computation JO - Nature VL - 419 UR - https://doi.org/10.1038/419343a DO - 10.1038/419343a ID - Regev2002 ER - TY - JOUR AU - Jensen, J. PY - 2004 DA - 2004// TI - Gene regulatory factors in pancreatic development JO - Dev Dyn VL - 229 UR - https://doi.org/10.1002/dvdy.10460 DO - 10.1002/dvdy.10460 ID - Jensen2004 ER - TY - JOUR AU - Ebben, J. D. AU - Treisman, D. M. AU - Zorniak, M. AU - Kutty, R. G. AU - Clark, P. A. AU - Kuo, J. S. PY - 2010 DA - 2010// TI - The cancer stem cell paradigm: a new understanding of tumor development and treatment JO - Expert Opin Ther Targets VL - 14 UR - https://doi.org/10.1517/14712598.2010.485186 DO - 10.1517/14712598.2010.485186 ID - Ebben2010 ER - TY - JOUR AU - Perin, L. AU - Giuliani, S. AU - Sedrakyan, S. AU - DAS, S. AU - De Filippo, R. E. PY - 2008 DA - 2008// TI - Stem cell and regenerative science applications in the development of bioengineering of renal tissue JO - Pediatr Res VL - 63 UR - https://doi.org/10.1203/PDR.0b013e3181660653 DO - 10.1203/PDR.0b013e3181660653 ID - Perin2008 ER - TY - JOUR AU - Tilly, J. L. AU - Rueda, B. R. PY - 2008 DA - 2008// TI - Minireview: stem cell contribution to ovarian development, function, and disease JO - Endocrinology VL - 149 UR - https://doi.org/10.1210/en.2008-0458 DO - 10.1210/en.2008-0458 ID - Tilly2008 ER - TY - JOUR AU - Rubin, L. L. AU - Haston, K. M. PY - 2011 DA - 2011// TI - Stem cell biology and drug discovery JO - BMC Biol VL - 9 UR - https://doi.org/10.1186/1741-7007-9-42 DO - 10.1186/1741-7007-9-42 ID - Rubin2011 ER - TY - JOUR AU - Zhang, X. Z. AU - Li, X. J. AU - Ji, H. F. AU - Zhang, H. Y. PY - 2009 DA - 2009// TI - Impact of drug discovery on stem cell biology JO - Biochem Biophys Res Commun VL - 383 UR - https://doi.org/10.1016/j.bbrc.2009.04.026 DO - 10.1016/j.bbrc.2009.04.026 ID - Zhang2009 ER - TY - JOUR AU - Hubbard, E. J. AU - Greenstein, D. PY - 2000 DA - 2000// TI - The Caenorhabditis elegans gonad: a test tube for cell and developmental biology JO - Dev Dyn VL - 218 UR - https://doi.org/3.0.CO;2-W DO - 3.0.CO;2-W ID - Hubbard2000 ER - TY - JOUR AU - Palsson, B. PY - 2000 DA - 2000// TI - The challenges of in silico biology JO - Nat Biotechnol VL - 18 UR - https://doi.org/10.1038/81125 DO - 10.1038/81125 ID - Palsson2000 ER - TY - JOUR AU - Noble, D. PY - 2002 DA - 2002// TI - Modeling the heart–from genes to cells to the whole organ JO - Science VL - 295 UR - https://doi.org/10.1126/science.1069881 DO - 10.1126/science.1069881 ID - Noble2002 ER - TY - JOUR AU - Sample, C. AU - Shvartsman, S. Y. PY - 2010 DA - 2010// TI - Multiscale modeling of diffusion in the early Drosophila embryo JO - Proc Natl Acad Sci USA VL - 107 UR - https://doi.org/10.1073/pnas.1001139107 DO - 10.1073/pnas.1001139107 ID - Sample2010 ER - TY - JOUR AU - Caicedo-Carvajal, C. E. AU - Shinbrot, T. PY - 2008 DA - 2008// TI - In silico zebrafish pattern formation JO - Dev Biol VL - 315 UR - https://doi.org/10.1016/j.ydbio.2007.12.036 DO - 10.1016/j.ydbio.2007.12.036 ID - Caicedo-Carvajal2008 ER - TY - JOUR AU - Jamshidi, N. AU - Palsson, B. O. PY - 2009 DA - 2009// TI - Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes JO - BMC Syst Biol VL - 3 UR - https://doi.org/10.1186/1752-0509-3-44 DO - 10.1186/1752-0509-3-44 ID - Jamshidi2009 ER - TY - JOUR AU - Edelman, L. B. AU - Chandrasekaran, S. AU - Price, N. D. PY - 2010 DA - 2010// TI - Systems biology of embryogenesis JO - Reprod Fertil Dev VL - 22 UR - https://doi.org/10.1071/RD09215 DO - 10.1071/RD09215 ID - Edelman2010 ER - TY - JOUR AU - Roeder, I. AU - Radtke, F. PY - 2009 DA - 2009// TI - Stem cell biology meets systems biology JO - Development VL - 136 UR - https://doi.org/10.1242/dev.040758 DO - 10.1242/dev.040758 ID - Roeder2009 ER - TY - JOUR AU - Meier-Schellersheim, M. AU - Fraser, I. D. AU - Klauschen, F. PY - 2009 DA - 2009// TI - Multiscale modeling for biologists JO - Wiley Interdiscip Rev Syst Biol Med VL - 1 UR - https://doi.org/10.1002/wsbm.33 DO - 10.1002/wsbm.33 ID - Meier-Schellersheim2009 ER - TY - JOUR AU - Efroni, S. AU - Harel, D. AU - Cohen, I. R. PY - 2007 DA - 2007// TI - Emergent dynamics of thymocyte development and lineage determination JO - PLoS Comput Biol VL - 3 UR - https://doi.org/10.1371/journal.pcbi.0030013 DO - 10.1371/journal.pcbi.0030013 ID - Efroni2007 ER - TY - JOUR AU - Kam, N. AU - Kugler, H. AU - Marelly, R. AU - Appleby, L. AU - Fisher, J. AU - Pnueli, A. AU - Harel, D. AU - Stern, M. J. AU - Hubbard, E. J. PY - 2008 DA - 2008// TI - A scenario-based approach to modeling development: a prototype model of C. elegans vulval fate specification JO - Dev Biol VL - 323 UR - https://doi.org/10.1016/j.ydbio.2008.07.030 DO - 10.1016/j.ydbio.2008.07.030 ID - Kam2008 ER - TY - JOUR AU - Meier-Schellersheim, M. AU - Xu, X. AU - Angermann, B. AU - Kunkel, E. J. AU - Jin, T. AU - Germain, R. N. PY - 2006 DA - 2006// TI - Key role of local regulation in chemosensing revealed by a new molecular interaction-based modeling method JO - PLoS Comput Biol VL - 2 UR - https://doi.org/10.1371/journal.pcbi.0020082 DO - 10.1371/journal.pcbi.0020082 ID - Meier-Schellersheim2006 ER - TY - JOUR AU - Shvartsman, S. Y. AU - Muratov, C. B. AU - Lauffenburger, D. A. PY - 2002 DA - 2002// TI - Modeling and computational analysis of EGF receptor-mediated cell communication in Drosophila oogenesis JO - Development VL - 129 ID - Shvartsman2002 ER - TY - JOUR AU - Slepchenko, B. M. AU - Schaff, J. C. AU - Macara, I. AU - Loew, L. M. PY - 2003 DA - 2003// TI - Quantitative cell biology with the Virtual Cell JO - Trends Cell Biol VL - 13 UR - https://doi.org/10.1016/j.tcb.2003.09.002 DO - 10.1016/j.tcb.2003.09.002 ID - Slepchenko2003 ER - TY - JOUR AU - Shapiro, B. E. AU - Levchenko, A. AU - Meyerowitz, E. M. AU - Wold, B. J. AU - Mjolsness, E. D. PY - 2003 DA - 2003// TI - Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg042 DO - 10.1093/bioinformatics/btg042 ID - Shapiro2003 ER - TY - JOUR AU - Yener, B. AU - Acar, E. AU - Aguis, P. AU - Bennett, K. AU - Vandenberg, S. L. AU - Plopper, G. E. PY - 2008 DA - 2008// TI - Multiway modeling and analysis in stem cell systems biology JO - BMC Syst Biol VL - 2 UR - https://doi.org/10.1186/1752-0509-2-63 DO - 10.1186/1752-0509-2-63 ID - Yener2008 ER - TY - JOUR AU - Wang, Z. AU - Matsudaira, P. AU - Gong, Z. PY - 2010 DA - 2010// TI - STORM: a general model to determine the number and adaptive changes of epithelial stem cells in teleost, murine and human intestinal tracts JO - PLoS One VL - 5 UR - https://doi.org/10.1371/journal.pone.0014063 DO - 10.1371/journal.pone.0014063 ID - Wang2010 ER - TY - JOUR AU - Clayton, E. AU - Doupe, D. P. AU - Klein, A. M. AU - Winton, D. J. AU - Simons, B. D. AU - Jones, P. H. PY - 2007 DA - 2007// TI - A single type of progenitor cell maintains normal epidermis JO - Nature VL - 446 UR - https://doi.org/10.1038/nature05574 DO - 10.1038/nature05574 ID - Clayton2007 ER - TY - JOUR AU - Lopez-Garcia, C. AU - Klein, A. M. AU - Simons, B. D. AU - Winton, D. J. PY - 2010 DA - 2010// TI - Intestinal stem cell replacement follows a pattern of neutral drift JO - Science VL - 330 UR - https://doi.org/10.1126/science.1196236 DO - 10.1126/science.1196236 ID - Lopez-Garcia2010 ER - TY - JOUR AU - Gerike, T. G. AU - Paulus, U. AU - Potten, C. S. AU - Loeffler, M. PY - 1998 DA - 1998// TI - A dynamic model of proliferation and differentiation in the intestinal crypt based on a hypothetical intraepithelial growth factor JO - Cell Prolif VL - 31 UR - https://doi.org/10.1046/j.1365-2184.1998.00113.x DO - 10.1046/j.1365-2184.1998.00113.x ID - Gerike1998 ER - TY - JOUR AU - Meineke, F. A. AU - Potten, C. S. AU - Loeffler, M. PY - 2001 DA - 2001// TI - Cell migration and organization in the intestinal crypt using a lattice-free model JO - Cell Prolif VL - 34 UR - https://doi.org/10.1046/j.0960-7722.2001.00216.x DO - 10.1046/j.0960-7722.2001.00216.x ID - Meineke2001 ER - TY - JOUR AU - Buske, P. AU - Galle, J. AU - Barker, N. AU - Aust, G. AU - Clevers, H. AU - Loeffler, M. PY - 2011 DA - 2011// TI - A comprehensive model of the spatio-temporal stem cell and tissue organisation in the intestinal crypt JO - PLoS Comput Biol VL - 7 UR - https://doi.org/10.1371/journal.pcbi.1001045 DO - 10.1371/journal.pcbi.1001045 ID - Buske2011 ER - TY - JOUR AU - Elliott, C. M. AU - Stinner, B. AU - Venkataraman, C. PY - 2012 DA - 2012// TI - Modelling cell motility and chemotaxis with evolving surface finite elements JO - J R Soc Interface VL - 9 UR - https://doi.org/10.1098/rsif.2012.0276 DO - 10.1098/rsif.2012.0276 ID - Elliott2012 ER - TY - JOUR AU - Nguyen, T. T. AU - Calvano, S. E. AU - Lowry, S. F. AU - Androulakis, I. P. PY - 2013 DA - 2013// TI - An agent-based model of cellular dynamics and circadian variability in human endotoxemia JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0055550 DO - 10.1371/journal.pone.0055550 ID - Nguyen2013 ER - TY - JOUR AU - Kempf, H. AU - Hatzikirou, H. AU - Bleicher, M. AU - Meyer-Hermann, M. PY - 2013 DA - 2013// TI - In silico analysis of cell cycle synchronisation effects in radiotherapy of tumour spheroids JO - PLoS Comput Biol VL - 9 UR - https://doi.org/10.1371/journal.pcbi.1003295 DO - 10.1371/journal.pcbi.1003295 ID - Kempf2013 ER - TY - JOUR AU - Narvaez-Tovar, C. A. AU - Garzon-Alvarado, D. A. PY - 2012 DA - 2012// TI - Computational modeling of the mechanical modulation of the growth plate by sustained loading JO - Theor Biol Med Model VL - 9 UR - https://doi.org/10.1186/1742-4682-9-41 DO - 10.1186/1742-4682-9-41 ID - Narvaez-Tovar2012 ER - TY - JOUR AU - Mansurov, A. N. AU - Stein, A. A. AU - Beloussov, L. V. PY - 2012 DA - 2012// TI - A simple model for estimating the active reactions of embryonic tissues to a deforming mechanical force JO - Biomech Model Mechanobiol VL - 11 UR - https://doi.org/10.1007/s10237-012-0439-y DO - 10.1007/s10237-012-0439-y ID - Mansurov2012 ER - TY - JOUR AU - Cohen, I. R. AU - Harel, D. PY - 2007 DA - 2007// TI - Explaining a complex living system: dynamics, multi-scaling and emergence JO - J R Soc Interface VL - 4 UR - https://doi.org/10.1098/rsif.2006.0173 DO - 10.1098/rsif.2006.0173 ID - Cohen2007 ER - TY - JOUR AU - Harel, D. PY - 2005 DA - 2005// TI - A Turing-like test for biological modeling JO - Nat Biotechnol VL - 23 UR - https://doi.org/10.1038/nbt0405-495 DO - 10.1038/nbt0405-495 ID - Harel2005 ER - TY - JOUR AU - Fisher, J. AU - Harel, D. AU - Henzinger, T. A. PY - 2011 DA - 2011// TI - Biology as reactivity JO - Commun Acm VL - 54 UR - https://doi.org/10.1145/2001269.2001289 DO - 10.1145/2001269.2001289 ID - Fisher2011 ER - TY - JOUR AU - Fisher, J. AU - Henzinger, T. A. PY - 2007 DA - 2007// TI - Executable cell biology JO - Nat Biotechnol VL - 25 UR - https://doi.org/10.1038/nbt1356 DO - 10.1038/nbt1356 ID - Fisher2007 ER - TY - JOUR AU - Setty, Y. PY - 2012 DA - 2012// TI - Multi-scale computational modeling of developmental biology JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts307 DO - 10.1093/bioinformatics/bts307 ID - Setty2012 ER - TY - JOUR AU - Setty, Y. AU - Cohen, I. R. AU - Dor, Y. AU - Harel, D. PY - 2008 DA - 2008// TI - Four-dimensional realistic modeling of pancreatic organogenesis JO - Proc Natl Acad Sci USA VL - 105 UR - https://doi.org/10.1073/pnas.0808725105 DO - 10.1073/pnas.0808725105 ID - Setty2008 ER - TY - JOUR AU - Setty, Y. AU - Dalfo, D. AU - Korta, D. Z. AU - Hubbard, E. J. AU - Kugler, H. PY - 2012 DA - 2012// TI - A model of stem cell population dynamics: in silico analysis and in vivo validation JO - Development VL - 139 UR - https://doi.org/10.1242/dev.067512 DO - 10.1242/dev.067512 ID - Setty2012 ER - TY - JOUR AU - Setty, Y. AU - Chen, C. C. AU - Secrier, M. AU - Skoblov, N. AU - Kalamatianos, D. AU - Emmott, S. PY - 2011 DA - 2011// TI - How neurons migrate: a dynamic in-silico model of neuronal migration in the developing cortex JO - BMC Syst Biol VL - 5 UR - https://doi.org/10.1186/1752-0509-5-154 DO - 10.1186/1752-0509-5-154 ID - Setty2011 ER - TY - JOUR AU - Puri, S. AU - Hebrok, M. PY - 2010 DA - 2010// TI - Cellular plasticity within the pancreas–lessons learned from development JO - Dev Cell VL - 18 UR - https://doi.org/10.1016/j.devcel.2010.02.005 DO - 10.1016/j.devcel.2010.02.005 ID - Puri2010 ER - TY - JOUR AU - Ahlgren, U. AU - Pfaff, S. L. AU - Jessell, T. M. AU - Edlund, T. AU - Edlund, H. PY - 1997 DA - 1997// TI - Independent requirement for ISL1 in formation of pancreatic mesenchyme and islet cells JO - Nature VL - 385 UR - https://doi.org/10.1038/385257a0 DO - 10.1038/385257a0 ID - Ahlgren1997 ER - TY - JOUR AU - Chu, K. AU - Nemoz-Gaillard, E. AU - Tsai, M. J. PY - 2001 DA - 2001// TI - BETA2 and pancreatic islet development JO - Recent Prog Horm Res VL - 56 UR - https://doi.org/10.1210/rp.56.1.23 DO - 10.1210/rp.56.1.23 ID - Chu2001 ER - TY - JOUR AU - Yesil, P. AU - Lammert, E. PY - 2008 DA - 2008// TI - Islet dynamics: a glimpse at beta cell proliferation JO - Histol Histopathol VL - 23 ID - Yesil2008 ER - TY - JOUR AU - Herrera, P. L. AU - Nepote, V. AU - Delacour, A. PY - 2002 DA - 2002// TI - Pancreatic cell lineage analyses in mice JO - Endocrine VL - 19 UR - https://doi.org/10.1385/ENDO:19:3:267 DO - 10.1385/ENDO:19:3:267 ID - Herrera2002 ER - TY - JOUR AU - Ahlgren, U. AU - Jonsson, J. AU - Edlund, H. PY - 1996 DA - 1996// TI - The morphogenesis of the pancreatic mesenchyme is uncoupled from that of the pancreatic epithelium in IPF1/PDX1-deficient mice JO - Development VL - 122 ID - Ahlgren1996 ER - TY - JOUR AU - Sand, F. W. AU - Hornblad, A. AU - Johansson, J. K. AU - Loren, C. AU - Edsbagge, J. AU - Stahlberg, A. AU - Magenheim, J. AU - Ilovich, O. AU - Mishani, E. AU - Dor, Y. PY - 2011 DA - 2011// TI - Growth-limiting role of endothelial cells in endoderm development JO - Dev Biol VL - 352 UR - https://doi.org/10.1016/j.ydbio.2011.01.026 DO - 10.1016/j.ydbio.2011.01.026 ID - Sand2011 ER - TY - JOUR AU - Pierreux, C. E. AU - Cordi, S. AU - Hick, A. C. AU - Achouri, Y. AU - Ruiz de Almodovar, C. AU - Prevot, P. P. AU - Courtoy, P. J. AU - Carmeliet, P. AU - Lemaigre, F. P. PY - 2010 DA - 2010// TI - Epithelial: Endothelial cross-talk regulates exocrine differentiation in developing pancreas JO - Dev Biol VL - 347 UR - https://doi.org/10.1016/j.ydbio.2010.08.024 DO - 10.1016/j.ydbio.2010.08.024 ID - Pierreux2010 ER - TY - JOUR AU - Magenheim, J. AU - Ilovich, O. AU - Lazarus, A. AU - Klochendler, A. AU - Ziv, O. AU - Werman, R. AU - Hija, A. AU - Cleaver, O. AU - Mishani, E. AU - Keshet, E. PY - 2011 DA - 2011// TI - Blood vessels restrain pancreas branching, differentiation and growth JO - Development VL - 138 UR - https://doi.org/10.1242/dev.066548 DO - 10.1242/dev.066548 ID - Magenheim2011 ER - TY - JOUR AU - Byrd, D. T. AU - Kimble, J. PY - 2009 DA - 2009// TI - Scratching the niche that controls Caenorhabditis elegans germline stem cells JO - Semin Cell Dev Biol VL - 20 UR - https://doi.org/10.1016/j.semcdb.2009.09.005 DO - 10.1016/j.semcdb.2009.09.005 ID - Byrd2009 ER - TY - JOUR AU - Hansen, D. AU - Schedl, T. PY - 2006 DA - 2006// TI - The regulatory network controlling the proliferation-meiotic entry decision in the Caenorhabditis elegans germ line JO - Curr Top Dev Biol VL - 76 UR - https://doi.org/10.1016/S0070-2153(06)76006-9 DO - 10.1016/S0070-2153(06)76006-9 ID - Hansen2006 ER - TY - JOUR AU - Kimble, J. AU - Crittenden, S. L. PY - 2007 DA - 2007// TI - Controls of germline stem cells, entry into meiosis, and the sperm/oocyte decision in Caenorhabditis elegans JO - Annu Rev Cell Dev Biol VL - 23 UR - https://doi.org/10.1146/annurev.cellbio.23.090506.123326 DO - 10.1146/annurev.cellbio.23.090506.123326 ID - Kimble2007 ER - TY - JOUR AU - Ayala, R. AU - Shu, T. AU - Tsai, L. H. PY - 2007 DA - 2007// TI - Trekking across the brain: the journey of neuronal migration JO - Cell VL - 128 UR - https://doi.org/10.1016/j.cell.2006.12.021 DO - 10.1016/j.cell.2006.12.021 ID - Ayala2007 ER - TY - JOUR AU - LoTurco, J. J. AU - Bai, J. PY - 2006 DA - 2006// TI - The multipolar stage and disruptions in neuronal migration JO - Trends Neurosci VL - 29 UR - https://doi.org/10.1016/j.tins.2006.05.006 DO - 10.1016/j.tins.2006.05.006 ID - LoTurco2006 ER - TY - JOUR AU - Tsai, J. W. AU - Chen, Y. AU - Kriegstein, A. R. AU - Vallee, R. B. PY - 2005 DA - 2005// TI - LIS1 RNA interference blocks neural stem cell division, morphogenesis, and motility at multiple stages JO - J Cell Biol VL - 170 UR - https://doi.org/10.1083/jcb.200505166 DO - 10.1083/jcb.200505166 ID - Tsai2005 ER - TY - JOUR AU - Ramos, R. L. AU - Bai, J. AU - LoTurco, J. J. PY - 2006 DA - 2006// TI - Heterotopia formation in rat but not mouse neocortex after RNA interference knockdown of DCX JO - Cereb Cortex VL - 16 UR - https://doi.org/10.1093/cercor/bhj074 DO - 10.1093/cercor/bhj074 ID - Ramos2006 ER -