Modeling the dynamic epigenome: from histone modifications towards self-organizing chromatin

A Structural Perspective on the Where, How, Why, and What of Nucleosome Positioning

(2012) Gaurav Arya et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Progressive methylation of ageing histones by Dot1 functions as a timer

(2011) Dirk De Vos et al.   EMBO REPORTS

Manifestations and mechanisms of stem cell aging

(2011) Ling Liu et al.   JOURNAL OF CELL BIOLOGY

A Polycomb-based switch underlying quantitative epigenetic memory

(2011) Andrew Angel et al.   NATURE

Cancer epigenetics reaches mainstream oncology

(2011) Manuel Rodríguez-Paredes et al.   NATURE MEDICINE

Transcription factories in the context of the nuclear and genome organization

(2011) S. V. Razin et al.   NUCLEIC ACIDS RESEARCH

Epigenetic regulation of aging stem cells

(2011) E A Pollina et al.   ONCOGENE

Timescales of human adaptation: the role of epigenetic processes

(2011) Christopher W Kuzawa et al.   Epigenomics

Locus dependence in epigenetic chromatin silencing

(2010) Swagatam Mukhopadhyay et al.   BIOSYSTEMS

Do chromatin loops provide epigenetic gene expression states?

(2010) Wulan Deng et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer

(2010) A. E. Teschendorff et al.   GENOME RESEARCH

Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains

(2010) V. K. Rakyan et al.   GENOME RESEARCH

Gene expression density profiles characterize modes of genomic regulation: Theory and experiment

(2010) Hans Binder et al.   JOURNAL OF BIOTECHNOLOGY

Innovation in gene regulation: The case of chromatin computation

(2010) Sonja J. Prohaska et al.   JOURNAL OF THEORETICAL BIOLOGY

A three-dimensional model of the yeast genome

(2010) Zhijun Duan et al.   NATURE

CpG islands influence chromatin structure via the CpG-binding protein Cfp1

(2010) John P. Thomson et al.   NATURE

Epigenetics and cardiovascular disease

(2010) José M. Ordovás et al.   Nature Reviews Cardiology

Age-related changes in Arc transcription and DNA methylation within the hippocampus

(2010) M.R. Penner et al.   NEUROBIOLOGY OF AGING

Computational Micromodel for Epigenetic Mechanisms

(2010) Karthika Raghavan et al.   PLoS One

Molecular coupling of DNA methylation and histone methylation

(2010) Hideharu Hashimoto et al.   Epigenomics

Spatial and Topological Organization of DNA Chains Induced by Gene Co-localization

(2010) Ivan Junier et al.   PLoS Computational Biology

Chromatin Signatures in Multipotent Human Hematopoietic Stem Cells Indicate the Fate of Bivalent Genes during Differentiation

(2009) Kairong Cui et al.   Cell Stem Cell

Theoretical framework for the histone modification network: modifications in the unstructured histone tails form a robust scale-free network

(2009) Yohei Hayashi et al.   GENES TO CELLS

Inheritance of epigenetic chromatin silencing

(2009) Diana David-Rus et al.   JOURNAL OF THEORETICAL BIOLOGY

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Epigenetic inheritance during the cell cycle

(2009) Aline V. Probst et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

What controls nucleosome positions?

(2009) Eran Segal et al.   TRENDS IN GENETICS

Implications of a life-long dynamic epigenome

(2009) Moshe Szyf   Epigenomics

Chromatin domains in higher eukaryotes: insights from genome-wide mapping studies

(2008) Elzo de Wit et al.   CHROMOSOMA

From single cells to tissue architecture—a bottom-up approach to modelling the spatio-temporal organisation of complex multi-cellular systems

(2008) J. Galle et al.   JOURNAL OF MATHEMATICAL BIOLOGY

Chromatin Insulators: Regulatory Mechanisms and Epigenetic Inheritance

(2008) Ashley M. Bushey et al.   MOLECULAR CELL

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS

Modelling and analysis of gene regulatory networks

(2008) Guy Karlebach et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY