Systematic Search for Recipes to Generate Induced Pluripotent Stem Cells

被引：49

作者：

Chang, Rui ^{[1
]}

Shoemaker, Robert ^{[1
]}

Wang, Wei ^{[1
]}

机构：

[1] Univ Calif San Diego, Dept Chem & Biochem, La Jolla, CA 92093 USA

来源：

PLOS COMPUTATIONAL BIOLOGY | 2011年 / 7卷 / 12期

关键词：

POTENTIAL LANDSCAPE; NETWORK; MODEL; FIBROBLASTS; ROBUSTNESS; EXPRESSION; IDENTIFICATION; DISSIPATION; KNOWLEDGE; INFERENCE;

D O I：

10.1371/journal.pcbi.1002300

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Generation of induced pluripotent stem cells (iPSCs) opens a new avenue in regenerative medicine. One of the major hurdles for therapeutic applications is to improve the efficiency of generating iPSCs and also to avoid the tumorigenicity, which requires searching for new reprogramming recipes. We present a systems biology approach to efficiently evaluate a large number of possible recipes and find those that are most effective at generating iPSCs. We not only recovered several experimentally confirmed recipes but we also suggested new ones that may improve reprogramming efficiency and quality. In addition, our approach allows one to estimate the cell-state landscape, monitor the progress of reprogramming, identify important regulatory transition states, and ultimately understand the mechanisms of iPSC generation.

引用

页数：13

共 52 条

[1]

Alok Aggarwal RJA, 1987, P 19 ANN ACM C THEOR

[2]

[Anonymous], 2014, The strategy of the genes

[3] A predictive model for transcriptional control of physiology in a free living cell [J].

Bonneau, Richard ;

Facciotti, Marc T. ;

Reiss, David J. ;

Schmid, Amy K. ;

Pan, Min ;

Kaur, Amardeep ;

Thorsson, Vesteinn ;

Shannon, Paul ;

Johnson, Michael H. ;

Bare, J. Christopher ;

Longabaugh, William ;

Vuthoori, Madhavi ;

Whitehead, Kenia ;

Madar, Aviv ;

Suzuki, Lena ;

Mori, Tetsuya ;

Chang, Dong-Eun ;

DiRuggiero, Jocelyne ;

Johnson, Carl H. ;

Hood, Leroy ;

Baliga, Nitin S. .

CELL, 2007, 131 (07) :1354-1365

[4] Quantitative Inference by Qualitative Semantic Knowledge Mining with Bayesian Model Averaging [J].

Chang, Rui ;

Stetter, Martin ;

Brauer, Wilfried .

IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING, 2008, 20 (12) :1587-1600

[5] Modeling semantics of inconsistent qualitative knowledge for quantitative Bayesian network inference [J].

Chang, Rui ;

Brauer, Wilfried ;

Stetter, Martin .

NEURAL NETWORKS, 2008, 21 (2-3) :182-192

[6] A Novel Knowledge-Driven Systems Biology Approach for Phenotype Prediction upon Genetic Intervention [J].

Chang, Rui ;

Shoemaker, Robert ;

Wang, Wei .

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2011, 8 (05) :1170-1182

[7] Disease candidate gene identification and prioritization using protein interaction networks [J].

Chen, Jing ;

Aronow, Bruce J. ;

Jegga, Anil G. .

BMC BIOINFORMATICS, 2009, 10

[8] A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity [J].

Chia, Na-Yu ;

Chan, Yun-Shen ;

Feng, Bo ;

Lu, Xinyi ;

Orlov, Yuriy L. ;

Moreau, Dimitri ;

Kumar, Pankaj ;

Yang, Lin ;

Jiang, Jianming ;

Lau, Mei-Sheng ;

Huss, Mikael ;

Soh, Boon-Seng ;

Kraus, Petra ;

Li, Pin ;

Lufkin, Thomas ;

Lim, Bing ;

Clarke, Neil D. ;

Bard, Frederic ;

Ng, Huck-Hui .

NATURE, 2010, 468 (7321) :316-U207

[9] Transcriptional dynamics of the embryonic stem cell switch [J].

Chickarmane, Vijay ;

Troein, Carl ;

Nuber, Ulrike A. ;

Sauro, Herbert M. ;

Peterson, Carsten .

PLOS COMPUTATIONAL BIOLOGY, 2006, 2 (09) :1080-1092

[10] A Computational Model for Understanding Stem Cell, Trophectoderm and Endoderm Lineage Determination [J].

Chickarmane, Vijay ;

Peterson, Carsten .

PLOS ONE, 2008, 3 (10)

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