Integrating networks and comparative genomics reveals retroelement proliferation dynamics in hominid genomes

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Regulatory activities of transposable elements: from conflicts to benefits

(2016) Edward B. Chuong et al.   NATURE REVIEWS GENETICS

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Percolation transition in dynamical traffic network with evolving critical bottlenecks

(2015) Daqing Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing

(2014) E. Helman et al.   GENOME RESEARCH

Hominoid Composite Non-LTR Retrotransposons—Variety, Assembly, Evolution, and Structural Determinants of Mobilization

(2014) Bianca Ianc et al.   MOLECULAR BIOLOGY AND EVOLUTION

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons

(2014) Frank M. J. Jacobs et al.   NATURE

DNA methylation dynamics of the human preimplantation embryo

(2014) Zachary D. Smith et al.   NATURE

The DNA methylation landscape of human early embryos

(2014) Hongshan Guo et al.   NATURE

Gibbon genome and the fast karyotype evolution of small apes

(2014) Lucia Carbone et al.   NATURE

Inference of Transposable Element Ancestry

(2014) Aaron C. Wacholder et al.   PLoS Genetics

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Great ape genetic diversity and population history

(2013) Javier Prado-Martinez et al.   NATURE

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

Human Transposon Tectonics

(2012) Kathleen H. Burns et al.   CELL

Active human retrotransposons: variation and disease

(2012) Dustin C Hancks et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

A small world of weak ties provides optimal global integration of self-similar modules in functional brain networks

(2012) L. K. Gallos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Landscape of Somatic Retrotransposition in Human Cancers

(2012) E. Lee et al.   SCIENCE

Mobile elements in the human genome: implications for disease

(2012) Szilvia Solyom et al.   Genome Medicine

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

(2012) Christoffer Nellåker et al.   GENOME BIOLOGY

Ultra-fast sequence clustering from similarity networks with SiLiX

(2011) Vincent Miele et al.   BMC BIOINFORMATICS

Detecting Network Communities: An Application to Phylogenetic Analysis

(2011) Roberto F. S. Andrade et al.   PLoS Computational Biology

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

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

Sequence embedding for fast construction of guide trees for multiple sequence alignment

(2010) Gordon Blackshields et al.   Algorithms for Molecular Biology

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

SVA retrotransposons: Evolution and genetic instability

(2010) Dustin C. Hancks et al.   SEMINARS IN CANCER BIOLOGY

The backbone of the climate network

(2009) J. F. Donges et al.   EPL

Exon-trapping mediated by the human retrotransposon SVA

(2009) D. C. Hancks et al.   GENOME RESEARCH

5'-Transducing SVA retrotransposon groups spread efficiently throughout the human genome

(2009) A. Damert et al.   GENOME RESEARCH

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Climate Networks around the Globe are Significantly Affected by El Niño

(2008) K. Yamasaki et al.   PHYSICAL REVIEW LETTERS