Systematic Search for Recipes to Generate Induced Pluripotent Stem Cells

Recipes and mechanisms of cellular reprogramming: a case study on budding yeast Saccharomyces cerevisiae

(2011) Shengchao Ding et al.   BMC Systems Biology

A Novel Knowledge-Driven Systems Biology Approach for Phenotype Prediction upon Genetic Intervention

(2011) Rui Chang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Somatic coding mutations in human induced pluripotent stem cells

(2011) Athurva Gore et al.   NATURE

Copy number variation and selection during reprogramming to pluripotency

(2011) Samer M. Hussein et al.   NATURE

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

(2011) Ryan Lister et al.   NATURE

Immunogenicity of induced pluripotent stem cells

(2011) Tongbiao Zhao et al.   NATURE

Quantifying the Waddington landscape and biological paths for development and differentiation

(2011) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Potential Landscape of Genetic Circuits Imposes the Arrow of Time in Stem Cell Differentiation

(2010) Jin Wang et al.   BIOPHYSICAL JOURNAL

Prediction of quantitative phenotypes based on genetic networks: a case study in yeast sporulation

(2010) Li Shen et al.   BMC Systems Biology

Direct Reprogramming of Fibroblasts into Functional Cardiomyocytes by Defined Factors

(2010) Masaki Ieda et al.   CELL

Identification and Classification of Chromosomal Aberrations in Human Induced Pluripotent Stem Cells

(2010) Yoav Mayshar et al.   Cell Stem Cell

A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity

(2010) Na-Yu Chia et al.   NATURE

Nuclear reprogramming to a pluripotent state by three approaches

(2010) Shinya Yamanaka et al.   NATURE

Direct conversion of fibroblasts to functional neurons by defined factors

(2010) Thomas Vierbuchen et al.   NATURE

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

Disease candidate gene identification and prioritization using protein interaction networks

(2009) Jing Chen et al.   BMC BIOINFORMATICS

Stem Cell States, Fates, and the Rules of Attraction

(2009) Tariq Enver et al.   Cell Stem Cell

Technical Challenges in Using Human Induced Pluripotent Stem Cells to Model Disease

(2009) Krishanu Saha et al.   Cell Stem Cell

Exploring the human genome with functional maps

(2009) C. Huttenhower et al.   GENOME RESEARCH

A Network-Based Method for Predicting Disease-Causing Genes

(2009) Shaul Karni et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Elite and stochastic models for induced pluripotent stem cell generation

(2009) Shinya Yamanaka   NATURE

Combinatorial binding predicts spatio-temporal cis-regulatory activity

(2009) Robert P. Zinzen et al.   NATURE

Forcing cells to change lineages

(2009) Thomas Graf et al.   NATURE

ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells

(2009) Z. Ouyang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stem Cells, the Molecular Circuitry of Pluripotency and Nuclear Reprogramming

(2008) Rudolf Jaenisch et al.   CELL

Extreme Makeover: Converting One Cell into Another

(2008) Qiao Zhou et al.   Cell Stem Cell

Quantitative Inference by Qualitative Semantic Knowledge Mining with Bayesian Model Averaging

(2008) Rui Chang et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

In vivo reprogramming of adult pancreatic exocrine cells to β-cells

(2008) Qiao Zhou et al.   NATURE

Predicting expression patterns from regulatory sequence in Drosophila segmentation

(2008) Eran Segal et al.   NATURE

Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks

(2008) Jun Zhu et al.   NATURE GENETICS

A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans

(2008) Insuk Lee et al.   NATURE GENETICS

Modeling semantics of inconsistent qualitative knowledge for quantitative Bayesian network inference

(2008) Rui Chang et al.   NEURAL NETWORKS

A Computational Model for Understanding Stem Cell, Trophectoderm and Endoderm Lineage Determination

(2008) Vijay Chickarmane et al.   PLoS One

Potential landscape and flux framework of nonequilibrium networks: Robustness, dissipation, and coherence of biochemical oscillations

(2008) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy

(2008) Wan Kim et al.   GENOME BIOLOGY