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1. Full Text Regulation of Cell Cycle to Stimulate Adult Cardiomyocyte Proliferation and Cardiac Regeneration
by Mohamed, Tamer M.A and Ang, Yen-Sin and Radzinsky, Ethan and Zhou, Ping and Huang, Yu and Elfenbein, Arye and Foley, Amy and Magnitsky, Sergey and Srivastava, Deepak
Cell, ISSN 0092-8674, 03/2018, Volume 173, Issue 1, pp. 104 - 116.e12
Human diseases are often caused by loss of somatic cells that are incapable of re-entering the cell cycle for regenerative repair. Here, we report a... 
heart failure | cyclin | proliferation | cell cycle | regeneration | cytokinesis | cardiomyocyte | cell division | CDK | heart | HYPERTROPHY | INFARCTION | EXPRESSION ANALYSIS | AMPLIFICATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | MICE | ZEBRAFISH HEART REGENERATION | FAILURE | CANCER | FIBROBLASTS | PROGRAM | CELL BIOLOGY | Cyclin D1 - metabolism | Cell Proliferation | Protein-Tyrosine Kinases - metabolism | Cyclin-Dependent Kinase 4 - genetics | Heart - physiology | Humans | Myosin Heavy Chains - genetics | Cyclin B1 - metabolism | CDC2 Protein Kinase - metabolism | Cell Cycle Proteins - antagonists & inhibitors | Myocardial Infarction - pathology | Transforming Growth Factor beta - antagonists & inhibitors | Myocardial Infarction - veterinary | Induced Pluripotent Stem Cells - cytology | Induced Pluripotent Stem Cells - metabolism | CDC2 Protein Kinase - genetics | Myocytes, Cardiac - cytology | Mice, Inbred C57BL | Cell Cycle Proteins - metabolism | Cyclin B1 - genetics | Rats | Mice, Transgenic | Nuclear Proteins - metabolism | Myocardial Infarction - metabolism | Cyclin-Dependent Kinase 4 - metabolism | Cytokinesis | Regeneration | Animals | Cyclin D1 - genetics | Nuclear Proteins - antagonists & inhibitors | Myocytes, Cardiac - metabolism | Mice | Transforming Growth Factor beta - metabolism | Protein-Tyrosine Kinases - antagonists & inhibitors | Heart | Bone morphogenetic proteins | Transforming growth factors | Cell cycle | Stem cells | Cell Cycle | Cardiomyocyte | Cell Division | Cyclin
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2. Full Text A Pattern-Based Method for the Identification of MicroRNA Binding Sites and Their Corresponding Heteroduplexes
by Miranda, Kevin C and Huynh, Tien and Tay, Yvonne and Ang, Yen-Sin and Tam, Wai-Leong and Thomson, Andrew M and Lim, Bing and Rigoutsos, Isidore
Cell, ISSN 0092-8674, 2006, Volume 126, Issue 6, pp. 1203 - 1217
We present , a method for identifying microRNA binding sites and their corresponding heteroduplexes. does not rely upon cross-species conservation, is... 
RNA INTERFERENCE | CAENORHABDITIS-ELEGANS | FAMILIES | BIOCHEMISTRY & MOLECULAR BIOLOGY | INSULIN-SECRETION | GENES | NETWORKS | DISCOVERY | TARGET PREDICTIONS | CELL BIOLOGY | Cell Line | Computational Biology - methods | Nucleic Acid Heteroduplexes - genetics | Humans | RNA, Messenger - genetics | Genome - genetics | MicroRNAs - metabolism | Binding Sites - genetics | Open Reading Frames - genetics | RNA, Messenger - metabolism | Molecular Biology - methods | Nucleic Acid Heteroduplexes - metabolism | Heteroduplex Analysis - methods | Algorithms | Animals | Caenorhabditis - genetics | Mice | MicroRNAs - genetics | Protein Biosynthesis - genetics | Software Design | Untranslated Regions - genetics | Drosophila - genetics | Amino acids | Research | RNA | Protein binding | Animal genetics | Stem cell research | Developmental biology | Analysis | Stem cells | Chemical properties | Methods
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3. Full Text Wdr5 Mediates Self-Renewal and Reprogramming via the Embryonic Stem Cell Core Transcriptional Network
by Ang, Yen-Sin and Tsai, Su-Yi and Lee, Dung-Fang and Monk, Jonathan and Su, Jie and Ratnakumar, Kajan and Ding, Junjun and Ge, Yongchao and Darr, Henia and Chang, Betty and Wang, Jianlong and Rendl, Michael and Bernstein, Emily and Schaniel, Christoph and Lemischka, Ihor R
Cell, ISSN 0092-8674, 2011, Volume 145, Issue 2, pp. 183 - 197
The embryonic stem (ES) cell transcriptional and chromatin-modifying networks are critical for self-renewal maintenance. However, it remains unclear whether... 
METHYLATION | DEVELOPMENTAL REGULATORS | CHROMATIN-STRUCTURE | RECOGNITION | HISTONE H3 | BIOCHEMISTRY & MOLECULAR BIOLOGY | GENES | POLYCOMB | BINDING | GENOME | PLURIPOTENT | CELL BIOLOGY | Embryonic Stem Cells - metabolism | Myeloid-Lymphoid Leukemia Protein - metabolism | Embryonic Stem Cells - cytology | Histone-Lysine N-Methyltransferase | Transcriptional Activation | Gene Regulatory Networks | Sequence Analysis, DNA | Animals | Proteins - metabolism | Chromatin Immunoprecipitation | Octamer Transcription Factor-3 - metabolism | Mice | Histones - metabolism | Methylation | Medical colleges | Genetic aspects | Embryonic stem cells | Genomics | Analysis | reprogramming | embryonic stem | histone methylation | Oct4 | wdr5 | transcriptional network | induced pluripotent stem | chromatin | trithorax
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4. Full Text Contractility of single cardiomyocytes differentiated from pluripotent stem cells depends on physiological shape and substrate stiffness
by Alexandre J. S. Ribeiro and Yen-Sin Ang and Ji-Dong Fu and Renee N. Rivas and Tamer M. A. Mohamed and Gadryn C. Higgs and Deepak Srivastava and Beth L. Pruitt
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 10/2015, Volume 112, Issue 41, pp. 12705 - 12710
Single cardiomyocytes contain myofibrils that harbor the sarcomerebased contractile machinery of the myocardium. Cardiomyocytes differentiated from human... 
Single cell | Cardiomyocyte | Stem cell | Sarcomeres | Contractility | MATRIX | ISOFORMS | MYOSIN | contractility | MULTIDISCIPLINARY SCIENCES | TENSION | MYOCYTE SHAPE | sarcomeres | CULTURE | ADULT CARDIOMYOCYTES | STRESS FIBERS | single cell | stem cell | CARDIAC TROPONIN-T | cardiomyocyte | CALCIUM | Myocardial Contraction | Pluripotent Stem Cells - metabolism | Pluripotent Stem Cells - cytology | Myocytes, Cardiac - cytology | Models, Biological | Cell Shape | Humans | Cells, Cultured | Mitochondria, Heart | Myocytes, Cardiac - metabolism | Cell Differentiation | Calcium Signaling | Genotype | Genetic aspects | Muscle contraction | Identification and classification | Heart cells | Biological Sciences
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5. Full Text Chemical Enhancement of In Vitro and In Vivo Direct Cardiac Reprogramming
by Mohamed, Tamer M A and Stone, Nicole R and Berry, Emily C and Radzinsky, Ethan and Huang, Yu and Pratt, Karishma and Ang, Yen-Sin and Yu, Pengzhi and Wang, Haixia and Tang, Shibing and Magnitsky, Sergey and Ding, Sheng and Ivey, Kathryn N and Srivastava, Deepak
Circulation, ISSN 0009-7322, 03/2017, Volume 135, Issue 10, pp. 978 - 995
BACKGROUND:Reprogramming of cardiac fibroblasts into induced cardiomyocyte-like cells in situ represents a promising strategy for cardiac regeneration. A... 
Heart | Regeneration | Transcription factors | Cell differentiation | MOUSE FIBROBLASTS | cell differentiation | DEXAMETHASONE | CARDIAC & CARDIOVASCULAR SYSTEMS | EXPRESSION ANALYSIS | regeneration | transcription factors | HEART-FAILURE | CATENIN | heart | PLURIPOTENT STEM-CELLS | GROWTH-FACTOR-BETA | INHIBITION | AMPLIFICATION | FUNCTIONAL CARDIOMYOCYTES | PERIPHERAL VASCULAR DISEASE | Dioxoles - therapeutic use | MEF2 Transcription Factors - genetics | Heterocyclic Compounds, 3-Ring - pharmacology | Humans | Wnt Proteins - metabolism | Benzamides - therapeutic use | Dioxoles - pharmacology | Transforming Growth Factor beta - antagonists & inhibitors | Benzamides - pharmacology | Fibroblasts - metabolism | GATA4 Transcription Factor - metabolism | Myocytes, Cardiac - cytology | Cells, Cultured | GATA4 Transcription Factor - genetics | Myocardium - pathology | Transcription Factors - genetics | T-Box Domain Proteins - genetics | T-Box Domain Proteins - metabolism | Heart - diagnostic imaging | Cellular Reprogramming - drug effects | Transcription Factors - metabolism | Magnetic Resonance Imaging | Animals | Myocardial Infarction - drug therapy | Fibroblasts - drug effects | Heterocyclic Compounds, 3-Ring - therapeutic use | MEF2 Transcription Factors - metabolism | Myocytes, Cardiac - metabolism | Fibroblasts - cytology | Mice | Wnt Proteins - antagonists & inhibitors | Transforming Growth Factor beta - metabolism | Care and treatment | Heart cells | Dosage and administration | Research | Transforming growth factors | Heart diseases | reprogramming | cardiac differentiation | calcium | heart regeneration
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6. Full Text Patient-specific induced pluripotent stem-cell-derived models of LEOPARD syndrome
by Carvajal-Vergara, Xonia and Sevilla, Ana and Dsouza, Sunita L and Ang, Yen-Sin and Schaniel, Christoph and Lee, Dung-Fang and Yang, Lei and Kaplan, Aaron D and Adler, Eric D and Rozov, Roye and Ge, Yongchao and Cohen, Ninette and Edelmann, Lisa J and Chang, Betty and Waghray, Avinash and Su, Jie and Pardo, Sherly and Lichtenbelt, Klaske D and Tartaglia, Marco and Gelb, Bruce D and Lemischka, Ihor R
Nature, ISSN 0028-0836, 06/2010, Volume 465, Issue 7299, pp. 808 - 812
The generation of reprogrammed induced pluripotent stem cells (iPSCs) from patients with defined genetic disorders holds the promise of increased understanding... 
SOMATIC PTPN11 MUTATIONS | SHP2 MUTATIONS | HUMAN ES | HEMATOPOIESIS | MULTIDISCIPLINARY SCIENCES | CARDIAC-HYPERTROPHY | DISEASE | LEUKEMOGENESIS | DIFFERENTIATION | LEUKEMIA | FIBROBLASTS | Protein Tyrosine Phosphatase, Non-Receptor Type 11 - metabolism | Embryonic Stem Cells - metabolism | Humans | Male | Gene Expression Profiling | LEOPARD Syndrome - drug therapy | Octamer Transcription Factor-3 - genetics | Phosphoproteins - analysis | SOXB1 Transcription Factors - genetics | Polymerase Chain Reaction | Adult | Female | Cell Differentiation | Fibroblasts - metabolism | Induced Pluripotent Stem Cells - metabolism | Precision Medicine | Induced Pluripotent Stem Cells - pathology | Cell Line | Induced Pluripotent Stem Cells - enzymology | Nanog Homeobox Protein | LEOPARD Syndrome - metabolism | NFATC Transcription Factors - metabolism | Cells, Cultured | Fibroblasts - pathology | Homeodomain Proteins - genetics | Cell Lineage | Myocytes, Cardiac - pathology | Models, Biological | LEOPARD Syndrome - pathology | Myocytes, Cardiac - metabolism | Enzyme Activation | Protein Tyrosine Phosphatase, Non-Receptor Type 11 - genetics | Mitogen-Activated Protein Kinases - metabolism | NFATC Transcription Factors - genetics | Proteins | Signal transduction | Insects | Genes | Cardiomyocytes | Mutation | Kinases
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7. Full Text The long noncoding RNA Chaer defines an epigenetic checkpoint in cardiac hypertrophy
by Wang, Zhihua and Zhang, Xiao-Jing and Ji, Yan-Xiao and Zhang, Peng and Deng, Ke-Qiong and Gong, Jun and Ren, Shuxun and Wang, Xinghua and Chen, Iris and Wang, He and Gao, Chen and Yokota, Tomohiro and Ang, Yen Sin and Li, Shen and Cass, Ashley and Vondriska, Thomas M and Li, Guangping and Deb, Arjun and Srivastava, Deepak and Yang, Huang-Tian and Xiao, Xinshu and Li, Hongliang and Wang, Yibin
Nature Medicine, ISSN 1078-8956, 10/2016, Volume 22, Issue 10, pp. 1131 - 1139
Epigenetic reprogramming is a critical process of pathological gene induction during cardiac hypertrophy and remodeling, but the underlying regulatory... 
MEDICINE, RESEARCH & EXPERIMENTAL | CARDIOMYOCYTE HYPERTROPHY | PRESSURE-OVERLOAD | PATHOLOGICAL HYPERTROPHY | BIOCHEMISTRY & MOLECULAR BIOLOGY | HEART-FAILURE | HISTONE METHYLATION | MTOR | CELL BIOLOGY | RAPTOR | GENE-EXPRESSION | BINDING | EZH2 | TOR Serine-Threonine Kinases - metabolism | Humans | Immunoblotting | Gene Expression Profiling | Gene Knockdown Techniques | Mechanistic Target of Rapamycin Complex 1 | Multiprotein Complexes - metabolism | Chromatin Immunoprecipitation | Computer Simulation | Myocardium - metabolism | Real-Time Polymerase Chain Reaction | Echocardiography | Rats | In Situ Hybridization, Fluorescence | RNA, Long Noncoding - genetics | Reverse Transcriptase Polymerase Chain Reaction | Heart - diagnostic imaging | Mice, Knockout | Blotting, Northern | Animals | Epigenesis, Genetic - genetics | Myocytes, Cardiac - metabolism | Mice | Cardiomegaly - genetics | In Vitro Techniques | Methylation | Polycomb Repressive Complex 2 - metabolism | Induced Pluripotent Stem Cells | Histone Code - genetics | Cardiomegaly - metabolism | Genetic aspects | Research | RNA | Heart enlargement | Heart | Epigenetic inheritance | Antisense RNA | Genes | TOR protein | Chromatin | Rapamycin | Gene expression | Ribonucleic acid--RNA | Polycomb group proteins | Lysine | Regulatory mechanisms (biology) | DNA methylation | Epigenetics | Catalysis | Inhibition | Histone H3 | Hypertrophy
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8. Full Text Oxygen: Double-Edged Sword in Cardiac Function and Repair
by Ang, Yen-Sin and Srivastava, Deepak
Circulation Research, ISSN 0009-7330, 10/2014, Volume 115, Issue 10, pp. 824 - 825
HEART | STEM-CELLS | COMPLEX | CARDIAC & CARDIOVASCULAR SYSTEMS | MYOCYTES | REGENERATION | PERIPHERAL VASCULAR DISEASE | CELL-CYCLE ARREST | CARDIOMYOCYTES | HYPOXIA | HEMATOLOGY | Cell Cycle Checkpoints | Animals | Reactive Oxygen Species - metabolism | Myocytes, Cardiac - cytology
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9. Full Text Disease Model of GATA4 Mutation Reveals Transcription Factor Cooperativity in Human Cardiogenesis
by Ang, Yen-Sin and Rivas, Renee N and Ribeiro, Alexandre J.S and Srivas, Rohith and Rivera, Janell and Stone, Nicole R and Pratt, Karishma and Mohamed, Tamer M.A and Fu, Ji-Dong and Spencer, C. Ian and Tippens, Nathaniel D and Li, Molong and Narasimha, Anil and Radzinsky, Ethan and Moon-Grady, Anita J and Yu, Haiyuan and Pruitt, Beth L and Snyder, Michael P and Srivastava, Deepak
Cell, ISSN 0092-8674, 12/2016, Volume 167, Issue 7, pp. 1734 - 1749.e22
Mutation of highly conserved residues in transcription factors may affect protein-protein or protein-DNA interactions, leading to gene network dysregulation... 
systems biology | heart development | gene regulation | disease modeling | birth defect | GATA4 | TBX5 | cardiomyopathy | epigenetics | congenital heart defects | PLURIPOTENT STEM-CELLS | VENTRAL MORPHOGENESIS | CHROMATIN | BIOCHEMISTRY & MOLECULAR BIOLOGY | ATRIAL SEPTATION | HEART TUBE FORMATION | GENE-EXPRESSION | CARDIOMYOCYTES | DIFFERENTIATION | CARDIAC DEVELOPMENT | CELL BIOLOGY | Chromatin | Signal Transduction | Heart - growth & development | Humans | Heart Defects, Congenital - pathology | GATA4 Transcription Factor - genetics | Male | Phosphatidylinositol 3-Kinases - metabolism | Mutation, Missense | T-Box Domain Proteins - genetics | Heart Defects, Congenital - genetics | Myocytes, Cardiac - pathology | Enhancer Elements, Genetic | Myocytes, Cardiac - metabolism | Female | Induced Pluripotent Stem Cells | Pharmacogenetics | Genes | Stem cells | Genetic aspects | Models | DNA binding proteins | Mechanical engineering | Epigenetic inheritance | Genetic disorders | Developmental biology | Congenital heart disease | Anopheles | Analysis | birth defects
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10. Full Text Construction and Validation of a Regulatory Network for Pluripotency and Self-Renewal of Mouse Embryonic Stem Cells
by Xu, Huilei and Ang, Yen-Sin and Sevilla, Ana and Lemischka, Ihor R and Ma'ayan, Avi
PLoS Computational Biology, ISSN 1553-734X, 08/2014, Volume 10, Issue 8, p. e1003777
A 30-node signed and directed network responsible for self-renewal and pluripotency of mouse embryonic stem cells (mESCs) was extracted from several ChIP-Seq... 
OCT4 | CIRCUITRY | GENES | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | STATE | NANOG | DIFFERENTIATION | TCF3 | FATE | EXPRESSION | OCT-3/4 | Cell Line | Reproducibility of Results | Animals | Gene Regulatory Networks - genetics | Computer Simulation | Pluripotent Stem Cells - physiology | Gene Expression Profiling | Mice | Gene Regulatory Networks - physiology | Systems Biology | Embryonic Stem Cells - physiology | Gene Knockdown Techniques | Stem cell research | Genetic research | Genetic aspects | Research | Nucleotide sequencing | Embryonic stem cells | Gene expression | DNA sequencing | Studies | Datasets | Stem cells | Ordinary differential equations | Agreements | Experiments | Binding sites
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11. Full Text Function follows form: shape and substrate stiffness drive maturity in human cardiomyocytes differentiated from pluripotent stem cells
by Ribeiro, Alexandre and Ang, Yen-Sin and Fu, Jidong and Rivas, Renee and Srivastava, Deepak and Pruitt, Beth L
Circulation, ISSN 0009-7322, 11/2014, Volume 130, Issue 22
Usage | Analysis | Stem cells | Heart cells | Electrophysiology | Cell physiology | Research | Heart muscle
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12. Full Text Oct4 and Klf4 Reprogram Dermal Papilla Cells into Induced Pluripotent Stem Cells
by Tsai, Su‐Yi and Clavel, Carlos and Kim, Soo and Ang, Yen‐Sin and Grisanti, Laura and Lee, Dung‐Fang and Kelley, Kevin and Rendl, Michael
STEM CELLS, ISSN 1066-5099, 02/2010, Volume 28, Issue 2, pp. 221 - 228
Direct reprogramming of somatic cells into induced pluripotent stem (iPS) cells by only four transcription factors (Oct4, Sox2, Klf4, and c‐Myc) has great... 
Hair follicle | Reprogramming | Dermal papilla | Cell fate | Induced pluripotent stem cells | MOUSE | INDUCTION | CELL & TISSUE ENGINEERING | CELL BIOLOGY | ONCOLOGY | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | MYC | HUMAN FIBROBLASTS | GENERATION | HEMATOLOGY | Dermis - metabolism | Humans | Cells, Cultured | Male | Mice, Transgenic | Reverse Transcriptase Polymerase Chain Reaction | Octamer Transcription Factor-3 - genetics | Animals | Kruppel-Like Transcription Factors - metabolism | Mice, Mutant Strains | Octamer Transcription Factor-3 - metabolism | Female | Fibroblasts - cytology | Mice | Dermis - cytology | Induced Pluripotent Stem Cells - cytology | SOXB1 Transcription Factors | Cellular Reprogramming - genetics | Gonadotropins, Equine | Kruppel-Like Transcription Factors - genetics | Cellular Reprogramming - physiology
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13. Full Text Stem cells and reprogramming: breaking the epigenetic barrier?
by Ang, Yen-Sin and Gaspar-Maia, Alexandre and Lemischka, Ihor R and Bernstein, Emily
Trends in Pharmacological Sciences, ISSN 0165-6147, 2011, Volume 32, Issue 7, pp. 394 - 401
Increasing evidence suggests that epigenetic regulation is key to the maintenance of the stem cell state. Chromatin is the physiological form of eukaryotic... 
Advanced Basic Science | LINEAGE COMMITMENT | DEFINED FACTORS | X-CHROMOSOME | CHROMATIN-STRUCTURE | TRANSCRIPTIONAL NETWORK | SELF-RENEWAL | PHARMACOLOGY & PHARMACY | PLURIPOTENCY | EARLY EMBRYOGENESIS | ES CELLS | RNAI SCREEN | Embryonic Stem Cells - metabolism | Animals | Epigenomics | Gene Expression Regulation, Developmental | Humans | Embryonic Development - genetics | Chromatin - genetics | Embryonic Stem Cells - physiology | Histones | Chromatin | DNA binding proteins | Embryonic stem cells | Methylation | Analysis
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