Literature DB >> 19738627

Systems biology of stem cell fate and cellular reprogramming.

Ben D Macarthur1, Avi Ma'ayan, Ihor R Lemischka.   

Abstract

Stem cell differentiation and the maintenance of self-renewal are intrinsically complex processes requiring the coordinated dynamic expression of hundreds of genes and proteins in precise response to external signalling cues. Numerous recent reports have used both experimental and computational techniques to dissect this complexity. These reports suggest that the control of cell fate has both deterministic and stochastic elements: complex underlying regulatory networks define stable molecular 'attractor' states towards which individual cells are drawn over time, whereas stochastic fluctuations in gene and protein expression levels drive transitions between coexisting attractors, ensuring robustness at the population level.

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Year:  2009        PMID: 19738627      PMCID: PMC2928569          DOI: 10.1038/nrm2766

Source DB:  PubMed          Journal:  Nat Rev Mol Cell Biol        ISSN: 1471-0072            Impact factor:   94.444


  116 in total

1.  Towards a proteome-scale map of the human protein-protein interaction network.

Authors:  Jean-François Rual; Kavitha Venkatesan; Tong Hao; Tomoko Hirozane-Kishikawa; Amélie Dricot; Ning Li; Gabriel F Berriz; Francis D Gibbons; Matija Dreze; Nono Ayivi-Guedehoussou; Niels Klitgord; Christophe Simon; Mike Boxem; Stuart Milstein; Jennifer Rosenberg; Debra S Goldberg; Lan V Zhang; Sharyl L Wong; Giovanni Franklin; Siming Li; Joanna S Albala; Janghoo Lim; Carlene Fraughton; Estelle Llamosas; Sebiha Cevik; Camille Bex; Philippe Lamesch; Robert S Sikorski; Jean Vandenhaute; Huda Y Zoghbi; Alex Smolyar; Stephanie Bosak; Reynaldo Sequerra; Lynn Doucette-Stamm; Michael E Cusick; David E Hill; Frederick P Roth; Marc Vidal
Journal:  Nature       Date:  2005-09-28       Impact factor: 49.962

Review 2.  Filtering transcriptional noise during development: concepts and mechanisms.

Authors:  Alfonso Martinez Arias; Penelope Hayward
Journal:  Nat Rev Genet       Date:  2006-01       Impact factor: 53.242

3.  Dissecting self-renewal in stem cells with RNA interference.

Authors:  Natalia Ivanova; Radu Dobrin; Rong Lu; Iulia Kotenko; John Levorse; Christina DeCoste; Xenia Schafer; Yi Lun; Ihor R Lemischka
Journal:  Nature       Date:  2006-06-11       Impact factor: 49.962

4.  Polycomb complexes repress developmental regulators in murine embryonic stem cells.

Authors:  Laurie A Boyer; Kathrin Plath; Julia Zeitlinger; Tobias Brambrink; Lea A Medeiros; Tong Ihn Lee; Stuart S Levine; Marius Wernig; Adriana Tajonar; Mridula K Ray; George W Bell; Arie P Otte; Miguel Vidal; David K Gifford; Richard A Young; Rudolf Jaenisch
Journal:  Nature       Date:  2006-04-19       Impact factor: 49.962

5.  The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells.

Authors:  Yuin-Han Loh; Qiang Wu; Joon-Lin Chew; Vinsensius B Vega; Weiwei Zhang; Xi Chen; Guillaume Bourque; Joshy George; Bernard Leong; Jun Liu; Kee-Yew Wong; Ken W Sung; Charlie W H Lee; Xiao-Dong Zhao; Kuo-Ping Chiu; Leonard Lipovich; Vladimir A Kuznetsov; Paul Robson; Lawrence W Stanton; Chia-Lin Wei; Yijun Ruan; Bing Lim; Huck-Hui Ng
Journal:  Nat Genet       Date:  2006-03-05       Impact factor: 38.330

6.  Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.

Authors:  Aravind Subramanian; Pablo Tamayo; Vamsi K Mootha; Sayan Mukherjee; Benjamin L Ebert; Michael A Gillette; Amanda Paulovich; Scott L Pomeroy; Todd R Golub; Eric S Lander; Jill P Mesirov
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-30       Impact factor: 11.205

7.  Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise.

Authors:  John R S Newman; Sina Ghaemmaghami; Jan Ihmels; David K Breslow; Matthew Noble; Joseph L DeRisi; Jonathan S Weissman
Journal:  Nature       Date:  2006-05-14       Impact factor: 49.962

8.  Gene network shaping of inherent noise spectra.

Authors:  D W Austin; M S Allen; J M McCollum; R D Dar; J R Wilgus; G S Sayler; N F Samatova; C D Cox; M L Simpson
Journal:  Nature       Date:  2006-02-02       Impact factor: 49.962

9.  Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors.

Authors:  Kazutoshi Takahashi; Shinya Yamanaka
Journal:  Cell       Date:  2006-08-10       Impact factor: 41.582

10.  Multistable and multistep dynamics in neutrophil differentiation.

Authors:  Hannah H Chang; Philmo Y Oh; Donald E Ingber; Sui Huang
Journal:  BMC Cell Biol       Date:  2006-02-28       Impact factor: 4.241

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  156 in total

1.  5-Aminoimidazole-4-carboxyamide ribonucleoside induces G(1)/S arrest and Nanog downregulation via p53 and enhances erythroid differentiation.

Authors:  Hee-Don Chae; Man-Ryul Lee; Hal E Broxmeyer
Journal:  Stem Cells       Date:  2012-02       Impact factor: 6.277

2.  Stability and multiattractor dynamics of a toggle switch based on a two-stage model of stochastic gene expression.

Authors:  Michael Strasser; Fabian J Theis; Carsten Marr
Journal:  Biophys J       Date:  2012-01-03       Impact factor: 4.033

Review 3.  Epigenetic memories: structural marks or active circuits?

Authors:  Floriane Nicol-Benoît; Pascale Le-Goff; Yves Le-Dréan; Florence Demay; Farzad Pakdel; Gilles Flouriot; Denis Michel
Journal:  Cell Mol Life Sci       Date:  2012-02-14       Impact factor: 9.261

4.  Combining competition assays with genetic complementation strategies to dissect mouse embryonic stem cell self-renewal and pluripotency.

Authors:  Dung-Fang Lee; Jie Su; Ana Sevilla; Julian Gingold; Christoph Schaniel; Ihor R Lemischka
Journal:  Nat Protoc       Date:  2012-03-22       Impact factor: 13.491

5.  The potential landscape of genetic circuits imposes the arrow of time in stem cell differentiation.

Authors:  Jin Wang; Li Xu; Erkang Wang; Sui Huang
Journal:  Biophys J       Date:  2010-07-07       Impact factor: 4.033

6.  Network plasticity of pluripotency transcription factors in embryonic stem cells.

Authors:  Adam Filipczyk; Carsten Marr; Simon Hastreiter; Justin Feigelman; Michael Schwarzfischer; Philipp S Hoppe; Dirk Loeffler; Konstantinos D Kokkaliaris; Max Endele; Bernhard Schauberger; Oliver Hilsenbeck; Stavroula Skylaki; Jan Hasenauer; Konstantinos Anastassiadis; Fabian J Theis; Timm Schroeder
Journal:  Nat Cell Biol       Date:  2015-09-21       Impact factor: 28.824

7.  Nanog dynamics in single embryonic stem cells.

Authors:  Simon Hastreiter; Timm Schroeder
Journal:  Cell Cycle       Date:  2016       Impact factor: 4.534

Review 8.  Toward a complete in silico, multi-layered embryonic stem cell regulatory network.

Authors:  Huilei Xu; Christoph Schaniel; Ihor R Lemischka; Avi Ma'ayan
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2010 Nov-Dec

9.  Inhibition of master transcription factors in pluripotent cells induces early stage differentiation.

Authors:  Debojyoti De; Myong-Ho Jeong; Young-Eun Leem; Dmitri I Svergun; David E Wemmer; Jong-Sun Kang; Kyeong Kyu Kim; Sung-Hou Kim
Journal:  Proc Natl Acad Sci U S A       Date:  2014-01-16       Impact factor: 11.205

10.  Oct4 and the small molecule inhibitor, SC1, regulates Tet2 expression in mouse embryonic stem cells.

Authors:  Yongyan Wu; Zekun Guo; Ye Liu; Bo Tang; Yi Wang; Liping Yang; Juan Du; Yong Zhang
Journal:  Mol Biol Rep       Date:  2012-12-20       Impact factor: 2.316

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