Systems biology of cell differentiation – We follow three complementary approaches to address the regulation of cell proliferation and differentiation. In a first approach, we start from a fecund, simple model organ whose regulation has been extensively characterized at the genetic and biochemical levels: the C. elegans germ line. We ask how the current knowledge of regulatory parts all fits together to explain organ-level behavior. We perform experiments that target organ-level behavior of the germ line, rather than individual genes in the regulatory network. Guided by these experiments, and building on knowledge generated by many labs over the past 30 years, we use mathematical and computational methods to analyze how the regulatory network accounts for organ-level control of cell proliferation and differentiation. Read the rest at cinquin.org.uk

Taylor P.H., Cinquin A., Cinquin O. (2016) Quantification of in vivo progenitor mutation accrual with ultra-low error rate and minimal input DNA using SIP-HAVA-seq. Genome Research. Cinquin A., Chiang M., Paz A., Hallman S., Yuan O., Vysniauskaite I., Fowlkes C.C., Cinquin O. (2016) Intermittent Stem Cell Cycling Balances Self-Renewal and Senescence of the C. elegans Germ Line. PLOS Genetics 12(4) Cinquin A., Zheng L., Taylor P.H., Paz A., Zhang L., Chiang M., Snow J.J., Nie Q., Cinquin O. (2015) Semi-permeable diffusion barriers enhance patterning robustness in the C. elegans germ line. Dev Cell 35(4) Chiang M., Hallman S., Cinquin A., Reyes de Mochel N., Paz A., Kawauchi S., Calof A.L., Cho K.W., Fowlkes C.C., Cinquin O. (2015) Analysis of in vivo single cell behavior by high throughput, human-in-the-loop segmentation of three-dimensional images. BMC Bioinformatics 16:397 Chiang M., Cinquin A., Paz A., Meeds E., Price C.A., Welling M. & Cinquin O. (2015) Control of Caenorhabditis elegans germ-line stem-cell cycling speed meets requirements of design to minimize mutation accumulation. BMC Biology 13(1):51 Meeds E., Chiang M., Lee M., Cinquin O., Lowengrub J. & Welling M. (2015) POPE: post optimization posterior evaluation of likelihood free models. BMC Bioinformatics 16:264. Reyes de Mochel N.S., Luong M., Chiang M., Javier A.L., Luu E., Toshihiko F., MacGregor G.R., Cinquin O., Cho, KWY. (2015). BMP signaling regulates both cell proliferation and ICM lineage commitment in preimplantation-stage mouse embryos. Dev Biol 397(1), pp45-55. Wong B.*, Paz A.*, Corrado M., Ramos B., Cinquin A., Cinquin O.† & Hui E.† (2013) Live imaging reveals active infiltration of mitotic zone by its stem cell niche. Integr Biol (Camb) 5(7), pp976-82 Stringari C., Cinquin A., Cinquin O., Digman M.A., Donovan P.J. & Gratton E (2011). Phasor approach to fluorescence lifetime microscopy distinguishes different metabolic states of germ cells in a live tissue. P.N.A.S. 108(33), pp13582-87 Cinquin O., Crittenden S.L., Morgan D. & Kimble J. (2010) Progression from a stem cell-like state to early differentiation in the C. elegans germ line P.N.A.S. 107(5), pp2048-53