Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis

Peak shape clustering reveals biological insights

(2015) Marzia A. Cremona et al.   BMC BIOINFORMATICS

Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells

(2015) Edward J. Grow et al.   NATURE

Structural basis for retroviral integration into nucleosomes

(2015) Daniel P. Maskell et al.   NATURE

The effects of chromatin organization on variation in mutation rates in the genome

(2015) Kateryna D. Makova et al.   NATURE REVIEWS GENETICS

Key determinants of target DNA recognition by retroviral intasomes

(2015) Erik Serrao et al.   Retrovirology

Arrested replication forks guide retrotransposon integration

(2015) J. Z. Jacobs et al.   SCIENCE

Statistical Computing in Functional Data Analysis: TheRPackagefda.usc

(2015) Manuel Febrero-Bande et al.   Journal of Statistical Software

A functional data analysis approach for genetic association studies

(2014) Matthew Reimherr et al.   Annals of Applied Statistics

Setdb1is required for germline development and silencing of H3K9me3-marked endogenous retroviruses in primordial germ cells

(2014) Sheng Liu et al.   GENES & DEVELOPMENT

Epistasis analysis for quantitative traits by functional regression model

(2014) F. Zhang et al.   GENOME RESEARCH

The dynamics of DNA methylation fidelity during mouse embryonic stem cell self-renewal and differentiation

(2014) Lei Zhao et al.   GENOME RESEARCH

Genomic Landscape of Human, Bat, and Ex Vivo DNA Transposon Integrations

(2014) Rebeca Campos-Sánchez et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular mechanisms of retroviral integration site selection

(2014) Mamuka Kvaratskhelia et al.   NUCLEIC ACIDS RESEARCH

DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data

(2014) Ayako Suzuki et al.   NUCLEIC ACIDS RESEARCH

Functional Analysis of Variance for Association Studies

(2014) Olga A. Vsevolozhskaya et al.   PLoS One

Chromatin Landscapes of Retroviral and Transposon Integration Profiles

(2014) Johann de Jong et al.   PLoS Genetics

Applications of functional data analysis: A systematic review

(2013) Shahid Ullah et al.   BMC Medical Research Methodology

Genetic and epigenetic determinants of DNA replication origins, position and activation

(2013) Marcel Méchali et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

HIV infection reveals widespread expansion of novel centromeric human endogenous retroviruses

(2013) R. Contreras-Galindo et al.   GENOME RESEARCH

Recruitment and Biological Consequences of Histone Modification of H3K27me3 and H3K9me3

(2013) J. Kim et al.   ILAR JOURNAL

DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape

(2013) Mingchao Xie et al.   NATURE GENETICS

Human-Specific HERV-K Insertion Causes Genomic Variations in the Human Genome

(2013) Wonseok Shin et al.   PLoS One

An introduction with medical applications to functional data analysis

(2013) Helle Sørensen et al.   STATISTICS IN MEDICINE

Inference for the mean of large $p$ small $n$ data: A finite-sample high-dimensional generalization of Hotelling’s theorem

(2013) Piercesare Secchi et al.   Electronic Journal of Statistics

Transposable Elements Re-Wire and Fine-Tune the Transcriptome

(2013) Michael Cowley et al.   PLoS Genetics

Transposable Elements: An Abundant and Natural Source of Regulatory Sequences for Host Genes

(2012) Rita Rebollo et al.   Annual Review of Genetics

Fine-Scale Maps of Recombination Rates and Hotspots in the Mouse Genome

(2012) Hadassa Brunschwig et al.   GENETICS

Distinct Mutational Behaviors Differentiate Short Tandem Repeats from Microsatellites in the Human Genome

(2012) Guruprasad Ananda et al.   Genome Biology and Evolution

A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?

(2012) Arkarachai Fungtammasan et al.   GENOME RESEARCH

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

ENCODE Data in the UCSC Genome Browser: year 5 update

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

From ancestral infectious retroviruses to bona fide cellular genes: Role of the captured syncytins in placentation

(2012) A. Dupressoir et al.   PLACENTA

Env-less endogenous retroviruses are genomic superspreaders

(2012) G. Magiorkinis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rescuing Alu: Recovery of New Inserts Shows LINE-1 Preserves Alu Activity through A-Tail Expansion

(2012) Bradley J. Wagstaff et al.   PLoS Genetics

The genomic landscape shaped by selection on transposable elements across 18 mouse strains

(2012) Christoffer Nellåker et al.   GENOME BIOLOGY

Sperm Methylation Profiles Reveal Features of Epigenetic Inheritance and Evolution in Primates

(2011) Antoine Molaro et al.   CELL

Association studies for next-generation sequencing

(2011) L. Luo et al.   GENOME RESEARCH

Pluripotency-related, Valproic Acid (VPA)-induced Genome-wide Histone H3 Lysine 9 (H3K9) Acetylation Patterns in Embryonic Stem Cells

(2011) Hadas Hezroni et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Polymorphic Integrations of an Endogenous Gammaretrovirus in the Mule Deer Genome

(2011) D. Elleder et al.   JOURNAL OF VIROLOGY

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retroviruses

(2011) Ravi P Subramanian et al.   Retrovirology

Distributions of Transposable Elements Reveal Hazardous Zones in Mammalian Introns

(2011) Ying Zhang et al.   PLoS Computational Biology

Retrotransposon-Induced Heterochromatin Spreading in the Mouse Revealed by Insertional Polymorphisms

(2011) Rita Rebollo et al.   PLoS Genetics

The (r)evolution of SINE versus LINE distributions in primate genomes: Sex chromosomes are important

(2010) E. M. Kvikstad et al.   GENOME RESEARCH

Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types

(2010) T. Ryba et al.   GENOME RESEARCH

Fine-scale recombination rate differences between sexes, populations and individuals

(2010) Augustine Kong et al.   NATURE

Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes

(2010) R. Z. Cer et al.   NUCLEIC ACIDS RESEARCH

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Estimating enrichment of repetitive elements from high-throughput sequence data

(2010) Daniel S Day et al.   GENOME BIOLOGY

Non-B DNA structure-induced genetic instability and evolution

(2009) Junhua Zhao et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Classification and nomenclature of endogenous retroviral sequences (ERVs)

(2009) Jonas Blomberg et al.   GENE

Integration target site selection by a resurrected human endogenous retrovirus

(2009) T. Brady et al.   GENES & DEVELOPMENT

A New Standard Genetic Map for the Laboratory Mouse

(2009) Allison Cox et al.   GENETICS

A Case Study in Exploratory Functional Data Analysis: Geometrical Features of the Internal Carotid Artery

(2009) Laura M. Sangalli et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

The role of DNA shape in protein–DNA recognition

(2009) Remo Rohs et al.   NATURE

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Revealing the History of Sheep Domestication Using Retrovirus Integrations

(2009) B. Chessa et al.   SCIENCE

Chromodomains direct integration of retrotransposons to heterochromatin

(2008) X. Gao et al.   GENOME RESEARCH

A common sequence motif associated with recombination hot spots and genome instability in humans

(2008) Simon Myers et al.   NATURE GENETICS

Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation

(2008) Ichiro Hiratani et al.   PLOS BIOLOGY

Genome-Wide Assessments Reveal Extremely High Levels of Polymorphism of Two Active Families of Mouse Endogenous Retroviral Elements

(2008) Ying Zhang et al.   PLoS Genetics