Concise review: erythroid versus myeloid lineage commitment: regulating the master regulators, Stem Cells, vol.31, issue.7, p.23559316, 2013. ,
Transcription factor heterogeneity in pluripotent stem cells: a stochastic advantage, Development, vol.141, issue.11, pp.2173-81, 2014. ,
Stochastic mRNA synthesis in mammalian cells, PLoS Biol, vol.4, issue.10, p.309, 2006. ,
On the spontaneous stochastic dynamics of a single gene: complexity of the molecular interplay at the promoter, BMC Syst Biol, vol.4, issue.4, p.2, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00542455
Chance at the heart of the cell, Prog Biophys Mol Biol, vol.110, pp.1-4, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00720052
Every cell is special: genome-wide studies add a new dimension to single-cell biology, Cell, vol.157, issue.1, pp.8-11, 2014. ,
Intrinsic and extrinsic contributions to stochasticity in gene expression, Proc Natl Acad Sci USA, vol.99, issue.20, pp.12795-800, 2002. ,
Stochastic gene expression in a single cell, Science, vol.297, issue.5584, pp.1183-1189, 2002. ,
Noise in gene expression: origins, consequences, and control, Science, vol.309, issue.5743, pp.2010-2013, 2005. ,
DOI : 10.1126/science.1105891
URL : http://europepmc.org/articles/pmc1360161?pdf=render
Effects of macromolecular crowding on genetic networks, Biophys J, vol.101, issue.12, pp.2882-91, 2011. ,
DOI : 10.1016/j.bpj.2011.10.053
URL : https://doi.org/10.1016/j.bpj.2011.10.053
Decomposing noise in biochemical signaling systems highlights the role of protein degradation, Biophys J, vol.104, issue.8, pp.1783-93, 2013. ,
Cell-cycle control of developmentally regulated transcription factors accounts for heterogeneity in human pluripotent cells, Stem Cell Rep, vol.1, pp.532-576, 2013. ,
Single mammalian cells compensate for differences in cellular volume and dna copy number through independent global transcriptional mechanisms, Mol Cell, vol.58, issue.2, pp.339-52, 2015. ,
Computational analysis of cell-tocell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells, Nat Biotechnol, vol.33, issue.2, pp.155-60, 2015. ,
A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages, Nat Commun, vol.7, p.10220, 2016. ,
Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise, Nature, vol.441, issue.7095, pp.840-846, 2006. ,
We are all individuals: causes and consequences of non-genetic heterogeneity in mammalian cells, Curr Opin Genet Dev, vol.21, issue.6, pp.753-761, 2011. ,
Modeling bi-modality improves characterization of cell cycle on gene expression in single cells, PLoS Comput Biol, vol.10, issue.7, p.1003696, 2014. ,
Transcriptomewide noise controls lineage choice in mammalian progenitor cells, Nature, vol.453, issue.7194, pp.544-551, 2008. ,
Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells, Cell, vol.161, issue.5, pp.1187-201, 2015. ,
Single-cell-based analysis highlights a surge in cell-to-cell molecular variability preceding irreversible commitment in a differentiation process, PLoS Biol, vol.14, issue.12, p.1002585, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01934489
Stochastic gene expression in fluctuating environments, Print) Journal Article Research Support, vol.167, issue.1, 2004. ,
Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 tat fluctuations drive phenotypic diversity, Cell, vol.122, issue.2, pp.169-82, 2005. ,
Architecturedependent noise discriminates functionally analogous differentiation circuits, Cell, vol.139, issue.3, pp.512-534, 2009. ,
Cell fate-decision as high-dimensional critical state transition, BioRvix, 2016. ,
Visualizing spatiotemporal dynamics of multicellular cell-cycle progressions with fucci technology, Cold Spring Harb Protoc, vol.132, issue.3, pp.487-498, 2014. ,
Computational assignment of cell-cycle stage from single-cell transcriptome data, Methods, vol.85, pp.54-61, 2015. ,
Bayesian analysis of singlecell sequencing data, PLoS Comput Biol, vol.11, issue.6, p.1004333, 2015. ,
Molecular biology of the cell, 2002. ,
TGF-beta cooperates with TGF-alpha to induce the self-renewal of normal erythrocytic progenitors: evidence for an autocrine mechanism, Embo J, vol.18, issue.10, 1999. ,
URL : https://hal.archives-ouvertes.fr/hal-00194310
Automatic cell counting with ImageJ, Anal Biochem, vol.473, pp.63-68, 2015. ,
Large-scale analysis by SAGE reveals new mechanisms of v-erbA oncogene action, BMC Genomics, vol.8, p.390, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00193775
R: a language and environment for statistical computing, 2008. ,
The ade4 package: implementing the duality diagram for ecologists, J Stat Softw, vol.22, pp.1-20, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00434575
The pharmacological characterization of a novel selective 5-hydroxytryptamine1a receptor antagonist, NAD-299, J Pharmacol Exp Ther, vol.283, issue.1, pp.216-241, 1997. ,
Label-free cell cycle analysis for highthroughput imaging flow cytometry, Nat Commun, vol.7, p.10256, 2016. ,
Reconstructing cell cycle pseudo time-series via single-cell transcriptome data, Nat Commun, vol.8, issue.1, p.22, 2017. ,
Cell cycle and cell size dependent gene expression reveals distinct subpopulations at single-cell level, Front Genet, vol.8, p.1, 2017. ,
A new paradigm for hematopoietic cell lineages: revision of the classical concept of the myeloid-lymphoid dichotomy, Trends in immunology, vol.30, issue.5, pp.193-200, 2009. ,
A clonogenic common myeloid progenitor that gives rise to all myeloid lineages, Nature, vol.404, issue.6774, pp.193-200, 2000. ,
Distinctive and indispensable roles of PU.1 in maintenance of hematopoietic stem cells and their differentiation, Blood, vol.106, issue.5, p.1895212, 2005. ,
URL : https://hal.archives-ouvertes.fr/hal-00080082
Identification of clonogenic common lymphoid progenitors in mouse bone marrow, Cell, vol.91, issue.5, p.9393859, 1997. ,
Dynamic regulation of PU.1 expression in multipotent hematopoietic progenitors. The Journal of experimental medicine, vol.201, p.2212785, 2005. ,
Prospective isolation and global gene expression analysis of the erythrocyte colony-forming unit (CFU-E), PLOS Biology, vol.105, issue.5, pp.1937-1982, 2005. ,
Modification of hematopoietic stem cell fate by 5aza 2'deoxycytidine and trichostatin A, Blood, vol.103, issue.11, p.14976039, 2004. ,
Primed and ready: understanding lineage commitment through single cell analysis, Trends in cell biology, vol.25, issue.8, p.26004869, 2015. ,
Inferring rules of lineage commitment in haematopoiesis, Nature cell biology, vol.14, issue.3, pp.287-94, 2012. ,
Single-cell analysis of mixed-lineage states leading to a binary cell fate choice, Nature, 2016. ,
Transcriptome-wide noise controls lineage choice in mammalian progenitor cells, Nature, vol.453, issue.7194, pp.544-551, 2008. ,
Gene expression fluctuations in murine hematopoietic stem cells with cell cycle progression, Journal of cellular physiology, vol.214, issue.3, p.4286177, 2008. ,
Cell-cycle-dependent oscillation of GATA2 expression in hematopoietic cells, Blood, vol.109, issue.10, pp.4200-4208, 2007. ,
Metabolic circuits in neural stem cells, Cellular and Molecular Life Sciences, vol.71, issue.21, pp.4221-4241, 2014. ,
Differential dependence on aerobic glycolysis in normal and malignant hematopoietic stem and progenitor cells to sustain daughter cell production, Blood, vol.122, issue.21, pp.793-793, 2013. ,
Energy metabolism in mesenchymal stem cells during osteogenic differentiation, Stem Cells and Development, vol.25, issue.2, pp.114-122, 2015. ,
Metabolic reprogramming during neuronal differentiation from aerobic glycolysis to neuronal oxidative phosphorylation. eLife, vol.5, p.13374, 2016. ,
DOI : 10.7554/elife.13374
URL : https://doi.org/10.7554/elife.13374
A metabolic switch controls intestinal differentiation downstream of Adenomatous polyposis coli (apc). eLife, vol.6, p.22706, 2017. ,
Metabolic determinants of embryonic development and stem cell fate, Reproduction, Fertility and Development, vol.27, issue.1, pp.82-88, 2014. ,
The embryonic origins of erythropoiesis in mammals, Blood, vol.119, issue.21, pp.4828-4865, 2012. ,
Variability of intracellular lactate dehydrogenase isoenzymes in single human erythrocytes, Anal Chem, vol.66, issue.7, pp.1175-1183, 1994. ,
Lactate-dehydrogenase isoenzymes of human erythrocyte-membranes, Clinica Chimica Acta, vol.79, issue.1, pp.15-19, 1977. ,
DOI : 10.1016/0009-8981(77)90454-5
Essential role for nix in autophagic maturation of erythroid cells, Nature, issue.7201, pp.232-66, 2008. ,
Avian erythrocytes have functional mitochondria, opening novel perspectives for birds as animal models in the study of ageing, Frontiers in Zoology, vol.10, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00838062
Single-cell-based analysis highlights a surge in cell-to-cell 23 molecular variability preceding irreversible commitment in a differentiation process, PLoS Biol, vol.14, issue.12, p.1002585, 2016. ,
Single-lineage transcriptome analysis reveals key regulatory pathways in primitive erythroid progenitors in the mouse embryo, Blood, vol.117, issue.18, pp.4924-4958, 2011. ,
Comprehensive proteomic analysis of human erythropoiesis, Cell Rep, vol.16, issue.5, pp.1470-84, 2016. ,
URL : https://hal.archives-ouvertes.fr/inserm-01356018
Tgf-? cooperates with tgf-? to induce the self-renewal of normal erythrocytic progenitors: evidence for an autocrine mechanism, The EMBO Journal, vol.18, issue.10, pp.2764-2781, 1999. ,
URL : https://hal.archives-ouvertes.fr/hal-00194310
Role of the different rar isoforms in controlling the erythrocytic differentiation sequence. interference with the v-erba and p135gag-myb-ets nuclear oncogenes, Oncogene, vol.16, issue.5, pp.563-74, 1998. ,
URL : https://hal.archives-ouvertes.fr/hal-00194313
, R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, 2013.
High cleavage efficiency of a 2a peptide derived from porcine teschovirus-1 in human cell lines, zebrafish and mice, PLoS One, vol.6, issue.4, p.18556, 2011. ,
Integration of pcr fragments at any specific site within cloning vectors without the use of restriction enzymes and dna ligase, Biotechniques, vol.31, issue.1, p.88, 2001. ,
Isozymes of mammalian hexokinase: structure, subcellular localization and metabolic function, Journal of Experimental Biology, vol.206, issue.12, pp.2049-2057, 2003. ,
ontrol of glycolysis through regulation of pfk1: old friends and recent additions, Cold Spring Harb. Symp. Quant. Biol, vol.76, pp.211-216, 2011. ,
The allosteric regulation of pyruvate kinase by fructose-1,6-bisphosphate, Structure, vol.6, issue.2, pp.195-210, 1998. ,
Molecular biology and biochemistry of pyruvate dehydrogenase complexes, FASEB J, vol.4, issue.14, pp.3224-3257, 1990. ,
Recent advances in mechanisms regulating glucose oxidation at the level of the pyruvate dehydrogenase complex by pdks, American Journal of Physiology-Endocrinology and Metabolism, vol.284, issue.5, pp.855-862, 2003. ,
Amino acid sequence of chicken heart cytochrome c, J Biol Chem, vol.241, issue.2, pp.507-522, 1966. ,
The primary structure of human rieske iron-sulfur protein of mitochondrial cytochrome bc1 complex deduced from cdna analysis, Biochemistry International, vol.20, issue.1, pp.155-160, 1990. ,
Mitochondrial variability as a source of extrinsic cellular noise, Plos Computational Biology, vol.8, issue.3, 2012. ,
Galloflavin (cas 568-80-9): a novel inhibitor of lactate dehydrogenase, ChemMedChem, vol.7, issue.2, pp.311-318, 2012. ,
,
Selective inhibitors of human lactate dehydrogenases and lactate dehydrogenase from the malarial parasite plasmodium falciparum, Journal of Medicinal Chemistry, vol.41, issue.20, pp.3879-3887, 1998. ,
Inhibition of lactate dehydrogenase a induces oxidative stress and inhibits tumor progression, Proc Natl Acad Sci U S A, vol.107, issue.5, pp.2037-2079, 2010. ,
Metabolic targets for cancer therapy, Nature Reviews Drug Discovery, vol.12, issue.12, pp.965-965, 2013. ,
Inhibition of ldh-a by lentivirus-mediated small interfering rna suppresses intestinal-type gastric cancer tumorigenicity through the downregulation of oct4, Cancer Letters, vol.321, issue.1, pp.45-54, 2012. ,
Fx11 inhibits aerobic glycolysis and growth of neuroblastoma cells, Surgery, vol.161, issue.3, pp.747-752, 2017. ,
Glucose and glutamine metabolism regulate human hematopoietic stem cell lineage specification, Cell Stem Cell, vol.15, issue.2, pp.169-84, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-02191586
Cholesterol synthesis-related enzyme oxidosqualene cyclase is required to maintain self-renewal in primary erythroid progenitors, Cell Proliferation, vol.44, issue.5, pp.441-452, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00652350
Aerobic glycolysis: beyond proliferation, Front Immunol, vol.6, p.227, 2015. ,
Cell-state-specific metabolic dependency in hematopoiesis and leukemogenesis, Cell, vol.158, issue.6, pp.1309-1323, 2014. ,
The metabolic programming of stem cells, Genes Development, vol.31, issue.4, pp.336-346, 2017. ,
Regulation of t lymphocyte metabolism, Journal of Immunology, vol.172, issue.8, pp.4661-4665, 2004. ,
The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogramming, Cell Res, vol.22, issue.1, pp.168-77, 2012. ,
Interplay between metabolic identities in the intestinal crypt supports stem cell function, Nature, vol.543, issue.7645, p.424, 2017. ,
Measuring dissolved oxygen to track erythroid differentiation of hematopoietic progenitor cells in culture, Journal of Biotechnology, vol.187, pp.135-138, 2014. ,
Cell cycle regulation and erythroid differentiation, Curr Top Microbiol Immunol, vol.212, pp.175-94, 1996. ,
Integrated time-lapse and single-cell transcription studies highlight the variable and dynamic nature of human hematopoietic cell fate commitment, Plos Biology, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01934491
Glycolysis-mediated changes in acetyl-coa and histone acetylation control the early differentiation of embryonic stem cells, Cell Metab, vol.21, issue.3, pp.392-402, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01256018
The impact of cellular metabolism on chromatin dynamics and epigenetics, Nat Cell Biol, vol.19, issue.11, pp.1298-1306, 2017. ,
Sir2: an nad-dependent histone deacetylase that connects chromatin silencing, metabolism, and aging, Cold Spring Harb Symp Quant Biol, vol.65, pp.297-302, 2000. ,
Atp-dependent chromatin remodeling during mammalian development, Development, vol.143, issue.16, pp.2882-97, 2016. ,
Energy metabolism in the acquisition and maintenance of stemness, Seminars in Cell Developmental Biology, vol.52, pp.68-75, 2016. ,
, fonction des signaux provenant de l'environnement extra-cellulaire (nutriments, cytokines, O2, ou autre), pour permettre aux cellules de choisir entre la voie de l'auto-renouvellement
The genetics of myelodysplastic syndrome : from clonal haematopoiesis to secondary leukaemia, Nature Reviews Cancer, vol.17, issue.5, 2017. ,
Congenital differences of the upper extremity : classification and treatment principles, Clin Orthop Surg, vol.3, issue.3, pp.172-179, 2011. ,
The role of symmetric stem cell divisions in tissue homeostasis, PLoS Comput Biol, vol.11, issue.12, p.1004629, 2015. ,
Mechanisms of asymmetric stem cell division, Cell, vol.132, issue.4, pp.583-97, 2008. ,
The scl gene product is required for the generation of all hematopoietic lineages in the adult mouse, Embo Journal, vol.15, issue.16, pp.4123-4129, 1996. ,
A novel transcription factor, t-bet, directs th1 lineage commitment, Cell, vol.100, issue.6, pp.655-669, 2000. ,
Higher-order orchestration of hematopoiesis : is cohesin a new player, Exp Hematol, vol.40, issue.12, pp.967-73, 2012. ,
Pax5 : a master regulator of b cell development and leukemogenesis, Adv Immunol, vol.111, pp.179-206, 2011. ,
What is a master regulator ?, J Stem Cell Res Ther, vol.3, 2013. ,
Expulsion of erythroid nucleus and its phagocytosis, Anatomical Record, vol.173, issue.1, p.123, 1972. ,
Developmental regulation of erythropoietin and erythropoiesis, American Journal of Physiology-Regulatory Integrative and Comparative Physiology, vol.273, issue.6, pp.1829-1844, 1997. ,
Mitochondrial clearance by autophagy in developing erythrocytes clearly important, but just how much so ?, Cell Cycle, vol.9, issue.10, pp.1901-1906, 2010. ,
Chromatin compaction in terminally differentiated avian blood cells : the role of linker histone h5 and non-histone protein ment, Chromosome Research, vol.19, issue.5, pp.579-590, 2011. ,
Avian erythrocytes have functional mitochondria, opening novel perspectives for birds as animal models in the study of ageing, Frontiers in Zoology, vol.10, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00838062
, Biology of erythropoietin. Haematologica, vol.83, issue.8, pp.724-732, 1998.
Stem cell antigen 2 : a new gene involved in the self-renewal of erythroid progenitors, Cell Proliferation, vol.41, issue.5, pp.726-738, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00425132
Cholesterol synthesis-related enzyme oxidosqualene cyclase is required to maintain self-renewal in primary erythroid progenitors, Cell Proliferation, vol.44, issue.5, pp.441-452, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00652350
Regulated expression of human alpha-globin and beta-globin genes in transient heterokaryons, Molecular and Cellular Biology, vol.11, issue.3, pp.1239-1247, 1991. ,
The molecular and mathematical basis of waddington's epigenetic landscape : a framework for post-darwinian biology ?, Bioessays, vol.34, issue.2, pp.149-57, 2012. ,
Leveling waddington : the emergence of direct programming and the loss of cell fate hierarchies, Nat Rev Mol Cell Biol, vol.14, issue.4, pp.225-261, 2013. ,
Stochastic gene expression in a single cell, Science, vol.297, issue.5584, p.39, 2002. ,
particle genetics' : treating every cell as unique, Trends Genet, vol.30, issue.2, p.39, 2014. ,
URL : https://hal.archives-ouvertes.fr/ensl-00944571
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells, Nature, vol.498, issue.7453, p.40, 2013. ,
A darwinian theory for the origin of cellular differentiation, Molecular and General Genetics MGG, vol.255, issue.2, pp.201-208, 1997. ,
Stochasticity in gene expression : from theories to phenotypes, 1997. ,
Systems biology of stem cells : three useful perspectives to help overcome the paradigm of linear pathways, Philosophical Transactions of the Royal Society of London B : Biological Sciences, vol.366, pp.2247-2259, 1575. ,
Inside a living cell, Trends in Biochemical Sciences, vol.16, issue.6, pp.203-206, 1991. ,
Crick, F Historical Article England Nature Nature, Nature, vol.227, issue.5258, pp.561-564, 1970. ,
On regulation of gene activity, Cold Spring Harbor Symposia on Quantitative Biology, vol.26, p.193, 1961. ,
A model for the statistical fluctuations of protein numbers in a microbial population, J Theor Biol, vol.71, issue.4, p.39, 1978. ,
Expression noise and acetylation profiles distinguish hdac functions, Molecular Cell, vol.47, issue.2, pp.193-202, 2012. ,
Quantifying the contribution of chromatin dynamics to stochastic gene expression reveals long, locus-dependent periods between transcriptional bursts, BMC Biology, vol.11, issue.1, p.15, 2013. ,
Regulated noise in the epigenetic landscape of development and disease, Cell, vol.148, issue.6, pp.1123-1154, 2012. ,
Real-time kinetics of gene activity in individual bacteria, Cell, vol.123, issue.6, p.39, 2005. ,
Effects of molecular memory and bursting on fluctuations in gene expression, Science, vol.319, issue.5861, p.39, 2008. ,
Mammalian genes are transcribed with widely different bursting kinetics, Science, vol.332, issue.6028, p.39, 2011. ,
Translation dynamics of single mrnas in live cells and neurons, Science, vol.352, issue.6292, pp.1430-1435, 2016. ,
Visualization of single endogenous polysomes reveals the dynamics of translation in live human cells, J Cell Biol, vol.214, issue.6, pp.769-81, 2016. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01622667
Single-molecule imaging of transcription factor binding to dna in live mammalian cells, Nat Methods, vol.10, issue.5, pp.421-427, 2013. ,
Measurement of gene regulation in individual cells reveals rapid switching between promoter states, Science, vol.351, issue.6278, pp.1218-1222, 2016. ,
Single-molecule dynamics of enhanceosome assembly in embryonic stem cells, Cell, vol.156, issue.6, pp.1274-1285, 2014. ,
Long-lived binding of sox2 to dna predicts cell fate in the four-cell mouse embryo, Cell, vol.165, issue.1, pp.75-87, 2016. ,
Two dna-encoded strategies for increasing expression with opposing effects on promoter dynamics and transcriptional noise, Genome Res, vol.23, issue.6, p.39, 2013. ,
Dynamics and heterogeneity of a fate determinant during transition towards cell differentiation. Elife, 4, 2015. Pelaez, Nicolas Gavalda-Miralles, Arnau Wang, Bao Navarro, Heliodoro Tejedor Gudjonson, Herman Rebay, Ilaria Dinner ,
,
, , p.8924, 2015.
Epigenetic and conventional regulation is distributed among activators of flo11 allowing tuning of population-level heterogeneity in its expression, PLoS Genet, vol.5, issue.10, p.1000673, 2009. ,
Transcription factors modulate c-fos transcriptional bursts, Cell Rep, vol.8, issue.1, p.39, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01312884
Shaping development by stochasticity and dynamics in gene regulation, Open Biology, vol.7, issue.5, 2017. ,
Mechanism of transcriptional bursting in bacteria, Biophysical Journal, vol.106, issue.2, pp.484-485, 2014. ,
Stochastic model of supercoiling-dependent transcription, Phys. Rev. Lett, vol.117, p.18101, 2016. ,
Effects of transcriptional pausing on gene expression dynamics, PLoS Comput Biol, vol.6, issue.3, p.1000704, 2010. ,
Transcriptional bursting is intrinsically caused by interplay between rna polymerases on dna, Nature Communications, vol.7, 2016. ,
Linking stochastic fluctuations in chromatin structure and gene expression, PLoS Biol, vol.11, issue.8, p.39, 2013. ,
Toward experimental manipulation of stochasticity in gene expression, Progress in Biophysics Molecular Biology, vol.110, pp.44-53, 2012. ,
,
Transcriptional burst frequency and burst size are equally modulated across the human genome, Proc Natl Acad Sci U S A, vol.109, issue.43, pp.17454-17463, 2012. ,
, Leor S OD006677/OD/NIH HHS/United States P50 GM085764/GM/NIGMS NIH HHS/United States P50GM081879/GM/NIGMS
, United States Proceedings of the National Academy of Sciences of the United States of America Proc Natl Acad Sci, vol.109, pp.17454-17463, 2012.
Dynamic heterogeneity and dna methylation in embryonic stem cells, Mol Cell, vol.55, issue.2, p.39, 2014. ,
Interplay between gene expression noise and regulatory network architecture, Trends Genet, vol.28, p.39, 2012. ,
The complex transcription regulatory landscape of our genome : control in three dimensions, EMBO J, vol.30, issue.21, pp.4345-55, 2011. ,
Variability in gene expression underlies incomplete penetrance, Nature, vol.463, issue.7283, p.39, 2010. ,
Models of stochastic gene expression, Phys. Life Rev, vol.2, p.39, 2005. ,
Mitochondria and the non-genetic origins of cell-to-cell variability : More is different, Bioessays, vol.38, issue.1, pp.64-76, 2016. ,
A probabilistic theory for cell differentiation, embryonic mortality and dna c-value paradox, Speculations in Science and Technology, vol.6, issue.5, pp.471-478, 1983. ,
Non-genetic heterogeneity of cells in development : more than just noise. Development, vol.136, p.39, 2009. ,
Altan-Bonnet. Variability and robustness in t cell activation from regulated heterogeneity in protein levels, Science, vol.321, issue.5892, p.37, 2008. ,
Noise facilitates transcriptional control under dynamic inputs, Cell, vol.160, issue.3, p.39, 2015. ,
Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase, Cell, vol.150, issue.6, p.40, 2012. ,
Stochastic spineless expression creates the retinal mosaic for colour vision, Nature, vol.440, issue.7081, pp.174-80, 2006. ,
Blastocyst lineage formation, early embryonic asymmetries and axis patterning in the mouse, Journal Article Research Support, Non-U.S. Gov't Review, vol.136, issue.5, pp.950-1991, 2009. ,
Transcriptional heterogeneity and lineage commitment in myeloid progenitors, Cell, vol.163, issue.7, pp.1663-1677, 2015. ,
Screening for noise in gene expression identifies drug synergies, Science, vol.344, issue.6190, pp.1392-1396, 2014. ,
Cellular noise regulons underlie fluctuations in saccharomyces cerevisiae, Mol Cell, vol.45, issue.4, p.39, 2012. ,
Non-genetic origins of cell-to-cell variability in trail-induced apoptosis, Nature, vol.459, issue.7245, p.39, 2009. ,
Modeling dynamics of cell-to-cell variability in trail-induced apoptosis explains fractional killing and predicts reversible resistance, PLoS Comput Biol, vol.10, issue.10, p.1003893, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-00942885
, Oct, vol.23, issue.10, p.1003893, 2014.
Conflict between noise and plasticity in yeast, PLoS Genet, vol.6, issue.11, p.1001185, 2010. ,
Cell-cycle control of developmentally regulated transcription factors accounts for heterogeneity in human pluripotent cells, Stem cell reports, vol.1, pp.532-576, 2013. ,
Developmental mechanisms underlying variable, invariant and plastic phenotypes, Annals of Botany, vol.117, issue.5, pp.733-748, 2016. ,
Bacterial persistence as a phenotypic switch, Electronic) Journal Article Research Support, vol.305, issue.5690, pp.1095-9203, 2004. ,
A chance at survival : gene expression noise and phenotypic diversification strategies, Electronic) Journal Article Research Support, Non-U.S. Gov't Review, vol.71, issue.6, pp.1365-2958, 2009. ,
An animated landscape representation of cd4(+) t-cell differentiation, variability, and plasticity : Insights into the behavior of populations versus cells, Eur J Immunol, vol.44, issue.8, pp.2216-2245, 2014. ,
An excitable gene regulatory circuit induces transient cellular differentiation, Nature, vol.440, issue.7083, pp.545-550, 2006. ,
Regulation of noise in the expression of a single gene, Nat Genet, vol.31, issue.1, pp.69-73, 2002. ,
Using gene expression noise to understand gene regulation, Science, vol.336, issue.6078, p.39, 2012. ,
Transcription factor profiling in individual hematopoietic progenitors by digital rt-pcr, Proc Natl Acad Sci U S A, vol.103, issue.47, pp.17807-17819, 2006. ,
The technology and biology of single-cell rna sequencing, Mol Cell, vol.58, issue.4, pp.610-630, 2015. ,
Single-cell epigenomics : powerful new methods for understanding gene regulation and cell identity, Genome Biology, vol.17, 2016. ,
Simultaneous epitope and transcriptome measurement in single cells, Nat Methods, vol.14, issue.9, pp.865-868, 2017. ,
Basics : Bayesian analysis of single-cell sequencing data, PLoS Comput Biol, vol.11, issue.6, p.1004333, 2015. ,
Single-cell insights into transcriptomic diversity in immunity, Current Opinion in Systems Biology, vol.5, pp.63-71, 2017. ,
,
Stem cell differentiation as a non-markov stochastic proces, Cell Systems, vol.5, issue.3, pp.268-282, 2017. ,
What population reveals about individual cell identity : Single-cell parameter estimation of models of gene expression in yeast, PLoS Comput Biol, vol.12, issue.2, p.1004706, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01248298
Gene regulatory network inference from single-cell data using multivariate information measures, Cell Syst, vol.5, issue.3, pp.251-267, 2017. ,
Inferring gene regulatory networks from single-cell data : a mechanistic approach, Bmc Systems Biology, p.11, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01646910
Translation of ludwig boltzmann's paper "on the relationship between the second fundamental theorem of the mechanical theory of heat and probability calculations regarding the conditions for thermal equilibrium" sitzungberichte der kaiserlichen akademie der wissenschaften. mathematisch-naturwissen classe. abt. ii, lxxvi 1877, Entropy, vol.76, issue.4, pp.1971-2009, 1909. ,
The second law : Energy, chaos and form, Scientific American Book, 1994. ,
A mathematical theory of communication, Bell System Technical Journal, vol.27, pp.623-656, 1948. ,
Single-cell-based analysis highlights a surge in cell-to-cell molecular variability preceding irreversible commitment in a differentiation process, PLoS Biol, vol.14, issue.12, p.1002585, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01934489
The strategy of the genes, 1957. ,
Approche endodarwinienne de la variabilité intercellulaire de l'expression génétique, 2004. ,
, Institut national d'agronomie de Paris Grignon, 2004.
The genetic basis of phenotypic heterogeneity in myelodysplastic syndromes, Nat Rev Cancer, vol.12, issue.12, pp.849-59, 2012. ,
Carbohydrates as a source of energy, American Journal of Clinical Nutrition, vol.59, issue.3, pp.682-685, 1994. ,
The double life of atp, Sci Am, vol.301, issue.6, pp.84-90, 2009. ,
Nad+/nadh and nadp+/nadph in cellular functions and cell death : Regulation and biological consequences, Antioxidants Redox Signaling, vol.10, issue.2, p.206, 2007. ,
Otto fritz meyerhof and the elucidation of the glycolytic pathway, J Biol Chem, vol.280, issue.4, p.3, 2005. ,
The glycolytic pathway is tightly controlled. Biochemistry, 2002. ,
Histone deacetylase sirt1 negatively regulates the differentiation of interleukin-9-producing cd4+ t cells, Immunity, vol.44, issue.6, pp.1337-1349, 2016. ,
Hexokinase 2 is a determinant of neuroblastoma metastasis, British Journal of Cancer, vol.114, issue.7, pp.759-766, 2016. ,
Regulation of hexokinase i : crystal structure of recombinant human brain hexokinase complexed with glucose and phosphate11edited by i. a. wilson, Journal of Molecular Biology, vol.282, issue.2, pp.345-357, 1998. ,
ontrol of glycolysis through regulation of pfk1 : old friends and recent additions, Cold Spring Harb. Symp. Quant. Biol, vol.76, pp.211-216, 2011. ,
Fructose 2,6-bisphosphate 2 years after its discovery, Biochemical Journal, vol.206, issue.1, pp.1-12, 1982. ,
Role of fructose 2,6-bisphosphate in the control of glycolysis in mammalian-tissues, Biochemical Journal, vol.245, issue.2, pp.313-324, 1987. ,
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase : Head-to-head with a bifunctional enzyme that controls glycolysis, Biochemical Journal, vol.381, pp.561-579, 2004. ,
The allosteric regulation of pyruvate kinase by fructose-1,6-bisphosphate, Structure, vol.6, issue.2, pp.195-210, 1998. ,
The hematopoietic stem cell niche : Low in oxygen but a nice place to be, Journal of Cellular Physiology, vol.222, issue.1, pp.17-22, 2010. ,
Control of respiration and atp synthesis in mammalian mitochondria and cells, Biochemical Journal, vol.284, pp.1-13, 1992. ,
Aerobic glycolysis : beyond proliferation, Front Immunol, vol.6, p.227, 2015. ,
The metabolism of tumors in the body, Journal of General Physiology, vol.8, issue.6, pp.519-530, 1927. ,
Principles of biochemistry second edition ,
Inhibition of lactate dehydrogenase a (ldha) using sodium oxamate leads to metabolic changes, decreased growth and migration in medulloblastoma cell lines, Neuro-Oncology, vol.17, pp.10-10, 2015. ,
Evolution of a gene, Science, vol.189, issue.4197, pp.102-114, 1975. ,
,
Cell-state-specific metabolic dependency in hematopoiesis and leukemogenesis, Cell, vol.158, issue.6, pp.1309-1323, 2014. ,
Lactate dehydrogenase-a inhibition induces human glioblastoma multiforme stem cell differentiation and death, Scientific Reports, vol.5, 2015. ,
Metabolic reprogramming during neuronal differentiation from aerobic glycolysis to neuronal oxidative phosphorylation. eLife, vol.5, p.13374, 2016. ,
Lactate dehydrogenase a promotes the invasion and proliferation of pituitary adenoma, Scientific Reports, vol.7, 2017. ,
Inhibition of ldh-a by lentivirus-mediated small interfering rna suppresses intestinal-type gastric cancer tumorigenicity through the downregulation of oct4, Cancer Letters, vol.321, issue.1, pp.45-54, 2012. ,
Fx11 inhibits aerobic glycolysis and growth of neuroblastoma cells, Surgery, vol.161, issue.3, pp.747-752, 2017. ,
Mechanisms regulating stemness and differentiation in embryonal carcinoma cells, Stem Cells International, p.20, 2017. ,
Hypoxic regulation of lactate dehydrogenase a : Interaction between hypoxia-inducible factor 1 and camp response elements, vol.270, pp.21021-21027, 1995. ,
Hif-1 : upstream and downstream of cancer metabolism. Current Opinion in Genetics Development, vol.20, pp.51-56, 2010. ,
Lamp-1 is upregulated in human glioblastoma cell lines induced to undergo apoptosis, J Biomed Sci, vol.8, issue.4, p.20, 2001. ,
Hif-1-mediated expression of pyruvate dehydrogenase kinase : A metabolic switch required for cellular adaptation to hypoxia, Cell Metabolism, vol.3, issue.3, pp.177-185, 2006. ,
,
The distinct metabolic profile of hematopoietic stem cells reflects their location in a hypoxic niche, Cell Stem Cell, vol.7, issue.3, pp.380-390, 2010. ,
Bougioukas Georgios, and Sivridis Efthimios. Lung cancer : An organized cellular and metabolic domain, Cancer Biology & Therapy, vol.6, issue.9, pp.1472-1475, 2007. ,
Savvas Mendrinos, and Efthimios Sivridis. The metabolic interactions between tumor cells and tumorassociated stroma (tas) in prostatic cancer, Cancer Biol Ther, vol.13, issue.13, pp.1284-1289, 2012. ,
The monocarboxylate transporter family-structure and functional characterization, IUBMB Life, vol.64, issue.1, pp.1-9, 2012. ,
Ldha is a feedback activator of hypoxia inducible factor 1-alpha in ovarian cancer, Int J Clin Exp Pathol, vol.9, issue.10, pp.10437-10443, 2016. ,
Targeting the lactate transporter mct1 in endothelial cells inhibits lactateinduced hif-1 activation and tumor angiogenesis, Plos One, vol.7, issue.3, 2012. ,
Lactic acid : No longer an inert and end-product of glycolysis, Physiology, vol.32, issue.6, pp.453-463, 2017. ,
The mechanism of epinephrine action, American Journal of Physiology-Legacy Content, vol.93, issue.1, pp.273-283, 1930. ,
Studies in carbohydrate metabolism. i. a glucose-lactic acid cycle involving muscle and liver, Journal of Biological Chemistry, vol.85, issue.2, pp.571-584, 1930. ,
Cdna cloning of the human monocarboxylate transporter-1 and chromosomal localization of the slc16a1 locus to 1p13.2-p12, Genomics, vol.23, issue.2, pp.500-503, 1994. ,
A mitochondrial mystery, solved, Science, vol.337, issue.6090, pp.41-43, 2012. ,
The oxidative phosphorylation system in mammalian mitochondria, Advances in Mitochondrial Medicine, vol.942, pp.3-37, 2012. ,
Chapter 25 analysis of electron transfer and superoxide generation in the cytochrome bc1 complex, Methods Enzymol, vol.456, pp.459-73, 2009. ,
The protonmotive q cycle : A general formulation, FEBS Letters, vol.59, issue.2, pp.137-139, 1975. ,
A mitochondrial factor conferring oligomycin sensitivity on soluble mitochondrial atpase, Biochem Biophys Res Commun, vol.10, pp.435-444, 1963. ,
A reconstituted system of oxidative phosphorylation, Biochemical and Biophysical Research Communications, vol.14, issue.1, p.75, 1963. ,
Mammalian mitochondrial complex i : Biogenesis, regulation, and reactive oxygen species generation, Biochemical and Biophysical Research Communications, vol.12, issue.12, pp.1431-1470, 2009. ,
Enhancement of human embryonic stem cell pluripotency through inhibition of the mitochondrial respiratory chain, Stem Cell Research, vol.3, issue.2-3, pp.142-156, 2009. ,
Antibiotics as tools for metabolic studies .1. a survey of toxic antibiotics in respiratory, phosphorylative and glycolytic systems, Archives of Biochemistry and Biophysics, vol.78, issue.2, pp.587-597, 1958. ,
Molecular biology and biochemistry of pyruvate dehydrogenase complexes, FASEB J, vol.4, issue.14, pp.3224-3257, 1990. ,
,
,
Single-cell rna-seq highlights intratumoral heterogeneity in primary glioblastoma, Science, vol.344, issue.6190, p.40, 2014. ,
Metabolic networks : enzyme function and metabolite structure, Current Opinion in Structural Biology, vol.14, issue.3, pp.300-306, 2004. ,
Low o2 tensions and the prevention of differentiation of hes cells, Proc Natl Acad Sci U S A, vol.102, issue.13, pp.4783-4791, 2005. ,
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells, Cell, vol.133, issue.6, p.30, 2008. ,
Hypoxic metabolism in human hematopoietic stem cells, Cell Biosci, vol.5, p.39, 2015. ,
Aerobic glycolysis : meeting the metabolic requirements of cell proliferation, Annu Rev Cell Dev Biol, vol.27, pp.441-64, 2011. ,
Interaction among skeletal muscle metabolic energy systems during intense exercise, J Nutr Metab, p.905612, 2010. ,
The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogramming, Cell Res, vol.22, issue.1, pp.168-77, 2012. ,
,
Interplay between metabolic identities in the intestinal crypt supports stem cell function, Nature, vol.543, issue.7645, p.424, 2017. ,
Single-lineage transcriptome analysis reveals key regulatory pathways in primitive erythroid progenitors in the mouse embryo, Blood, vol.117, issue.18, pp.4924-4958, 2011. ,
The embryonic origins of erythropoiesis in mammals, Blood, vol.119, issue.21, pp.4828-4865, 2012. ,
Metabolic targets for cancer therapy, Nature Reviews Drug Discovery, vol.12, issue.11, pp.829-846, 2013. ,
, Metabolic regulation of hematopoietic stem cell commitment and erythroid differentiation, Current Opinion in Hematology, vol.23, issue.3, 2016.
Concise review : Energy metabolites : Key mediators of the epigenetic state of pluripotency, Stem Cells, vol.33, issue.8, pp.2374-2380, 2015. ,
Glycolysis-mediated changes in acetyl-coa and histone acetylation control the early differentiation of embryonic stem cells, Cell Metab, vol.21, issue.3, pp.392-402, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01256018
Aerobic glycolysis promotes t helper 1 cell differentiation through an epigenetic mechanism, Science, vol.354, issue.6311, pp.481-484, 2016. ,
Mitochondrial oxidative metabolism is required for the cardiac differentiation of stem cells, Nature Clinical Practice Cardiovascular Medicine, vol.4, p.60, 2007. ,
Mitochondrial function controls proliferation and early differentiation potential of embryonic stem cells, Stem Cells, vol.29, issue.3, pp.486-495, 2011. ,
The impact of cellular metabolism on chromatin dynamics and epigenetics, Nat Cell Biol, vol.19, issue.11, p.202, 2017. ,
Inhibition of -kg-dependent histone and dna demethylases by fumarate and succinate that are accumulated in mutations of fh and sdh tumor suppressors, Genes Dev, vol.26, issue.12, pp.1326-1338, 2012. ,
Serum-based culture conditions provoke gene expression variability in mouse embryonic stem cells as revealed by single-cell analysis, Cell Reports, vol.14, issue.4, pp.956-965, 2016. ,
Metabolic regulation of epigenetics, Cell Metabolism, vol.16, issue.1, pp.9-17, 2012. ,
Sir2 : an nad-dependent histone deacetylase that connects chromatin silencing, metabolism, and aging, Cold Spring Harb Symp Quant Biol, vol.65, pp.297-302, 2000. ,
,
Sirtuin 1 regulation of developmental genes during differentiation of stem cells, vol.107, pp.13736-13741, 2010. ,
Sirt1 contributes critically to the redox-dependent fate of neural progenitors, Nature Cell Biology, vol.10, p.385, 2008. ,
Nicotinamide overcomes pluripotency deficits and reprogramming barriers, Stem Cells, vol.31, issue.6, pp.1121-1135, 2013. ,
Metabolic reprogramming of stem cell epigenetics, Cell Stem Cell, vol.17, issue.6, pp.651-662, 2015. ,
,
,
Sirt1 regulates dna methylation and differentiation potential of embryonic stem cells by antagonizing dnmt3l, Cell Reports, vol.18, issue.8, pp.1930-1945, 2017. ,
Metabolic plasticity in stem cell homeostasis and differentiation, Cell Stem Cell, vol.11, issue.5, pp.596-606, 2012. ,
Tgf-cooperates with tgf-to induce the self-renewal of normal erythrocytic progenitors : evidence for an autocrine mechanism, The EMBO Journal, vol.18, issue.10, pp.2764-2781, 1999. ,
URL : https://hal.archives-ouvertes.fr/hal-00194310
Intrinsic and extrinsic contributions to stochasticity in gene expression, Proc Natl Acad Sci U S A, vol.99, issue.20, p.39, 2002. ,
Single mammalian cells compensate for differences in cellular volume and dna copy number through independent global transcriptional mechanisms, Mol Cell, vol.58, issue.2, p.40, 2015. ,
Automated cell cycle and cell size measurements for single-cell gene expression studies, BMC Research Notes, vol.11, issue.1, p.92, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01934493
Integrated time-lapse and single-cell transcription studies highlight the variable and dynamic nature of human hematopoietic cell fate commitment, PLOS Biology, vol.15, issue.7, pp.1-23, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01934491
Visualizing data using t-sne, Journal of Machine Learning Research, vol.9, pp.2579-2605, 2008. ,
Cell fate decision as high-dimensional critical state transition, PLOS Biology, vol.14, issue.12, pp.1-28, 2016. ,
Dynamics of lineage commitment revealed by single-cell transcriptomics of differentiating embryonic stem cells, Nature Communications, vol.8, issue.1, p.1096, 2017. ,
Characterization of directed differentiation by high-throughput single-cell rna-seq. bioRxiv, 2014. ,
Identifying early-warning signals of critical transitions with strong noise by dynamical network markers, vol.5, p.17501, 2009. ,
Stochastic expression of a multiple antibiotic resistance activator confers transient resistance in single cells, Scientific Reports, vol.6, 2016. ,
The unforeseen challenge : from genotype-to-phenotype in cell populations, Reports on Progress in Physics, vol.78, issue.3, p.36602, 2015. ,
An update on therapeutic opportunities offered by cancer glycolytic metabolism, Bioorganic Medicinal Chemistry Letters, vol.24, issue.21, pp.4915-4925, 2014. ,
The regulation and function of lactate dehydrogenase a : Therapeutic potential in brain tumor, Brain Pathology, vol.26, issue.1, pp.3-17, 2016. ,
Glucose and glutamine metabolism regulate human hematopoietic stem cell lineage specification, Cell Stem Cell, vol.15, issue.2, pp.169-84, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-02191586
What makes the cell differentiate ?, Progress in Biophysics and Molecular Biology, vol.110, issue.1, pp.41-43, 2012. ,
Distinct metabolic states can support selfrenewal and lipogenesis in human pluripotent stem cells under different culture conditions, Cell Reports, vol.16, issue.6, pp.1536-1547, 2016. ,
Metabolic regulation of hematopoietic and leukemic stem/progenitor cells under homeostatic and stress conditions, International Journal of Hematology, vol.106, issue.1, pp.18-26, 2017. ,
A metabolic core model elucidates how enhanced utilization of glucose and glutamine, with enhanced glutamine-dependent lactate production, promotes cancer cell growth : The warburq effect, PLOS Computational Biology, vol.13, issue.9, pp.1-29, 2017. ,
Chromatin remodelling in mammalian differentiation : lessons from atp-dependent remodellers, Nature Reviews Genetics, vol.7, p.461 ,
Chromatin remodeling in neural stem cell differentiation, Current Opinion in Neurobiology, vol.20, issue.4, pp.408-415, 2010. ,
,
Chromatin remodeling enzyme snf2h regulates embryonic lens differentiation and denucleation, Tomas Stopka, and Ales Cvekl, vol.143, pp.1937-1947, 2016. ,
Atp-dependent chromatin remodeling during mammalian development, Development, vol.143, issue.16, pp.2882-97, 2016. ,
Serial analysis of gene expression (sage) in the silkworm, bombyx mori, Genomics, vol.86, pp.233-241, 2005. ,
URL : https://hal.archives-ouvertes.fr/hal-00124092
Atp-dependent chromatin remodeling : going mobile, FEBS Letters, vol.476, issue.1-2, pp.68-72, 2000. ,
Sirtuins : Nad+-dependent deacetylase mechanism and regulation, Mechanisms? Aesthetics? Molecular imaging, vol.16, issue.5, pp.535-543, 2012. ,
Srebp-regulated lipid metabolism : convergent physiology -divergent pathophysiology, Nature Reviews Endocrinology, vol.13, p.710, 2017. ,
Hif-1-regulated glucose metabolism : A key to apoptosis resistance ?, Cell Cycle, vol.6, issue.7, p.17404504, 2007. ,
Srebp activity is regulated by mtorc1 and contributes to aktdependent cell growth, Cell Metab, vol.8, issue.3-3, pp.224-236, 2008. ,
,
mtor-and hif-1-mediated aerobic glycolysis as metabolic basis for trained immunity, vol.345, 2014. ,
Proliferation, survival and metabolism : the role of pi3k/akt/mtor signalling in pluripotency and cell fate determination, Development, vol.143, issue.17, pp.3050-3060, 2016. ,
,
, Akt-directed glucose metabolism can prevent bax conformation change and promote growth factor-independent survival, Mol Cell Biol, vol.23, issue.20, pp.7315-7328, 2003.
Myc and tumor metabolism : chicken and egg, The EMBO Journal, vol.36, issue.23, pp.3409-3420, 2017. ,