Transposable Elements and DNA Methylation Create in Embryonic Stem Cells Human-Specific Regulatory Sequences Associated with Distal Enhancers and Noncoding RNAs

Energetically Biased DNA Motor Containing a Thermodynamically Stable Partial Strand Displacement State

(2014) Preston B. Landon et al.   LANGMUIR

DNA methylation dynamics of the human preimplantation embryo

(2014) Zachary D. Smith et al.   NATURE

Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance

(2014) Alexandre Fort et al.   NATURE GENETICS

The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity

(2014) Xinyi Lu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Dynamic regulation of human endogenous retroviruses mediates factor-induced reprogramming and differentiation potential

(2014) M. Ohnuki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types

(2013) J. Ernst et al.   GENOME RESEARCH

RNA-guided diagnostics and therapeutics for next-generation individualized nanomedicine

(2013) Gennadi V. Glinsky   JOURNAL OF CLINICAL INVESTIGATION

An on-demand four-way junction DNAzyme nanoswitch driven by inosine-based partial strand displacement

(2013) Alexander H. Mo et al.   Nanoscale

Differential L1 regulation in pluripotent stem cells of humans and apes

(2013) Maria C. N. Marchetto et al.   NATURE

Differentiation-defective phenotypes revealed by large-scale analyses of human pluripotent stem cells

(2013) M. Koyanagi-Aoi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The human placenta methylome

(2013) D. I. Schroeder et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Epigenomic Reconfiguration During Mammalian Brain Development

(2013) R. Lister et al.   SCIENCE

The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements

(2013) Pierre-Étienne Jacques et al.   PLoS Genetics

Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

(2013) Aurélie Kapusta et al.   PLoS Genetics

Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome

(2012) Miao Yu et al.   CELL

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

(2012) Dominic Schmidt et al.   CELL

Nanog-like Regulates Endoderm Formation through the Mxtx2-Nodal Pathway

(2012) Cong Xu et al.   DEVELOPMENTAL CELL

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

ENCODE Data in the UCSC Genome Browser: year 5 update

(2012) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Functional and Molecular Characterization of the Role of CTCF in Human Embryonic Stem Cell Biology

(2012) Sri Kripa Balakrishnan et al.   PLoS One

Complexity of chromatin folding is captured by the strings and binders switch model

(2012) M. Barbieri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency

(2012) Federico A Santoni et al.   Retrovirology

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

Human-Specific Histone Methylation Signatures at Transcription Start Sites in Prefrontal Neurons

(2012) Hennady P. Shulha et al.   PLOS BIOLOGY

Transposable elements reveal a stem cell-specific class of long noncoding RNAs

(2012) David Kelley et al.   GENOME BIOLOGY

CpG Deamination Creates Transcription Factor–Binding Sites with High Efficiency

(2011) Tomasz Żemojtel et al.   Genome Biology and Evolution

Reprogramming somatic cells into iPS cells activates LINE-1 retroelement mobility

(2011) Silke Wissing et al.   HUMAN MOLECULAR GENETICS

Somatic retrotransposition alters the genetic landscape of the human brain

(2011) J. Kenneth Baillie et al.   NATURE

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Accelerated Recruitment of New Brain Development Genes into the Human Genome

(2011) Yong E. Zhang et al.   PLOS BIOLOGY

MicroRNA-Driven Developmental Remodeling in the Brain Distinguishes Humans from Other Primates

(2011) Mehmet Somel et al.   PLOS BIOLOGY

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

(2011) A. P. Jason de Koning et al.   PLoS Genetics

Epigenetic Control of Retrotransposon Expression in Human Embryonic Stem Cells

(2010) A. Macia et al.   MOLECULAR AND CELLULAR BIOLOGY

Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation

(2010) Daan Peric-Hupkes et al.   MOLECULAR CELL

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Genetic history of an archaic hominin group from Denisova Cave in Siberia

(2010) David Reich et al.   NATURE

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

(2010) Galih Kunarso et al.   NATURE GENETICS

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Global discovery of primate-specific genes in the human genome

(2009) S.-K. Tay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

Origin of Primate Orphan Genes: A Comparative Genomics Approach

(2008) M. Toll-Riera et al.   MOLECULAR BIOLOGY AND EVOLUTION

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

(2008) Lars Guelen et al.   NATURE

Methylation and deamination of CpGs generate p53-binding sites on a genomic scale

(2008) Tomasz Zemojtel et al.   TRENDS IN GENETICS