From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps

(2022) Mitchell R Vollger et al.   BIOINFORMATICS

Complete genomic and epigenetic maps of human centromeres

(2022) Nicolas Altemose et al.   SCIENCE

Epigenetic patterns in a complete human genome

(2022) Ariel Gershman et al.   SCIENCE

The complete sequence of a human genome

(2022) Sergey Nurk et al.   SCIENCE

Segmental duplications and their variation in a complete human genome

(2022) Mitchell R. Vollger et al.   SCIENCE

The Dfam community resource of transposable element families, sequence models, and genome annotations

(2021) Jessica Storer et al.   Mobile DNA

Transposable element subfamily annotation has a reproducibility problem

(2021) Kaitlin M. Carey et al.   Mobile DNA

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

(2021) Peter Ebert et al.   SCIENCE

Comparative analyses of gibbon centromeres reveal dynamic genus specific shifts in repeat composition

(2021) Gabrielle A Hartley et al.   MOLECULAR BIOLOGY AND EVOLUTION

The structure, function and evolution of a complete human chromosome 8

(2021) Glennis A. Logsdon et al.   NATURE

A common 1.6 mb Y-chromosomal inversion predisposes to subsequent deletions and severe spermatogenic failure in humans

(2021) Pille Hallast et al.   eLife

Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome

(2021) Wilfried M. Guiblet et al.   GENOME RESEARCH

Somatic Hypomethylation of Pericentromeric SST1 Repeats and Tetraploidization in Human Colorectal Cancer Cells

(2021) Beatriz González et al.   Cancers

Molecular Evolutionary Genetics Analysis (MEGA) for macOS

(2020) Glen Stecher et al.   MOLECULAR BIOLOGY AND EVOLUTION

An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data

(2020) Vasanthan Jayakumar et al.   BMC GENOMICS

RepeatModeler2 for automated genomic discovery of transposable element families

(2020) Jullien M. Flynn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The UCSC repeat browser allows discovery and visualization of evolutionary conflict across repeat families

(2020) Jason D. Fernandes et al.   Mobile DNA

Telomere-to-telomere assembly of a complete human X chromosome

(2020) Karen H. Miga et al.   NATURE

RNA contributions to the form and function of biomolecular condensates

(2020) Christine Roden et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Loss of X Chromosome Inactivation in Androgenetic Complete Hydatidiform Moles With 46, XX Karyotype

(2020) Xiaojing Chen et al.   INTERNATIONAL JOURNAL OF GYNECOLOGICAL PATHOLOGY

Chromatin regulatory dynamics of early human small intestinal development using a directed differentiation model

(2020) Yu-Han Hung et al.   NUCLEIC ACIDS RESEARCH

G4Hunter web application: a web server for G-quadruplex prediction

(2019) Václav Brázda et al.   BIOINFORMATICS

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

(2019) Alexey M Kozlov et al.   BIOINFORMATICS

Hominoid-Specific Transposable Elements and KZFPs Facilitate Human Embryonic Genome Activation and Control Transcription in Naive Human ESCs

(2019) Julien Pontis et al.   Cell Stem Cell

The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist

(2019) Joke G. van Bemmel et al.   NATURE GENETICS

Independent amylase gene copy number bursts correlate with dietary preferences in mammals

(2019) Petar Pajic et al.   eLife

Nascent RNA analyses: tracking transcription and its regulation

(2019) Erin M. Wissink et al.   NATURE REVIEWS GENETICS

A high-quality genome assembly for the endangered golden snub-nosed monkey (Rhinopithecus roxellana)

(2019) Lu Wang et al.   GigaScience

Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants

(2019) Yaoxi He et al.   Nature Communications

FlexiDot: Highly customizable, ambiguity-aware dotplots for visual sequence analyses

(2018) Kathrin M Seibt et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Transposable elements: genome innovation, chromosome diversity, and centromere conflict

(2018) Savannah J. Klein et al.   CHROMOSOME RESEARCH

Centromere transcription allows CENP-A to transit from chromatin association to stable incorporation

(2018) Georg O.M. Bobkov et al.   JOURNAL OF CELL BIOLOGY

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

A novel long non-coding RNA from NBL2 pericentromeric macrosatellite forms a perinucleolar aggregate structure in colon cancer

(2018) Gabrijela Dumbović et al.   NUCLEIC ACIDS RESEARCH

Earth BioGenome Project: Sequencing life for the future of life

(2018) Harris A. Lewin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-resolution comparative analysis of great ape genomes

(2018) Zev N. Kronenberg et al.   SCIENCE

Shifting the limits in wheat research and breeding using a fully annotated reference genome

(2018) et al.   SCIENCE

Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs

(2018) Joana Carlevaro-Fita et al.   GENOME RESEARCH

Co-Opted Megasatellite DNA Drives Evolution of Secondary Night Vision in Azara's Owl Monkey

(2017) Akihiko Koga et al.   Genome Biology and Evolution

The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology

(2017) Eugene J. Gardner et al.   GENOME RESEARCH

Truncated ORF1 proteins can suppress LINE-1 retrotransposition in trans

(2017) Mark Sokolowski et al.   NUCLEIC ACIDS RESEARCH

ALU ternative Regulation for Gene Expression

(2017) Ling-Ling Chen et al.   TRENDS IN CELL BIOLOGY

RNA-dependent stabilization of SUV39H1 at constitutive heterochromatin

(2017) Whitney L Johnson et al.   eLife

Detection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing

(2017) Barun Pradhan et al.   Scientific Reports

Next-generation sequencing-based detection of germline L1-mediated transductions

(2016) Jelena Tica et al.   BMC GENOMICS

Long Terminal Repeats: From Parasitic Elements to Building Blocks of the Transcriptional Regulatory Repertoire

(2016) Peter J. Thompson et al.   MOLECULAR CELL

Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)

(2016) Dig Bijay Mahat et al.   Nature Protocols

Regulatory activities of transposable elements: from conflicts to benefits

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

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Viruses and mobile elements as drivers of evolutionary transitions

(2016) Eugene V. Koonin   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Long-read sequence assembly of the gorilla genome

(2016) D. Gordon et al.   SCIENCE

Roles for retrotransposon insertions in human disease

(2016) Dustin C. Hancks et al.   Mobile DNA

Establishment of Centromeric Chromatin by the CENP-A Assembly Factor CAL1 Requires FACT-Mediated Transcription

(2015) Chin-Chi Chen et al.   DEVELOPMENTAL CELL

A survey of transposable element classification systems – A call for a fundamental update to meet the challenge of their diversity and complexity

(2015) Benoît Piégu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Dfam database of repetitive DNA families

(2015) Robert Hubley et al.   NUCLEIC ACIDS RESEARCH

Sequence Features and Transcriptional Stalling within Centromere DNA Promote Establishment of CENP-A Chromatin

(2015) Sandra Catania et al.   PLoS Genetics

High variability of genomic instability and gene expression profiling in different HeLa clones

(2015) Annalisa Frattini et al.   Scientific Reports

Repetitive centromeric satellite RNA is essential for kinetochore formation and cell division

(2014) Silvana Rošić et al.   JOURNAL OF CELL BIOLOGY

Resolving the complexity of the human genome using single-molecule sequencing

(2014) Mark J. P. Chaisson et al.   NATURE

Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes

(2014) J. M. C. Tubio et al.   SCIENCE

Hypermorphic expression of centromeric retroelement-encoded small RNAs impairs CENP-A loading

(2013) Dawn M. Carone et al.   CHROMOSOME RESEARCH

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

(2013) H. Kwak et al.   SCIENCE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Dfam: a database of repetitive DNA based on profile hidden Markov models

(2012) Travis J. Wheeler et al.   NUCLEIC ACIDS RESEARCH

LINE-1 Elements in Structural Variation and Disease

(2011) Christine R. Beck et al.   Annual Review of Genomics and Human Genetics

Retrotransposition of marked SVA elements by human L1s in cultured cells

(2011) Dustin C. Hancks et al.   HUMAN MOLECULAR GENETICS

The non-autonomous retrotransposon SVA is trans -mobilized by the human LINE-1 protein machinery

(2011) Julija Raiz et al.   NUCLEIC ACIDS RESEARCH

Human Endogenous Retrovirus K106 (HERV-K106) Was Infectious after the Emergence of Anatomically Modern Humans

(2011) Aashish R. Jha et al.   PLoS One

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Expression, tandem repeat copy number variation and stability of four macrosatellite arrays in the human genome

(2010) Deanna C Tremblay et al.   BMC GENOMICS

LINE-1 Activity in Facultative Heterochromatin Formation during X Chromosome Inactivation

(2010) Jennifer C. Chow et al.   CELL

A Novel Correlation between LINE-1 Hypomethylation and the Malignancy of Gastrointestinal Stromal Tumors

(2010) S. Igarashi et al.   CLINICAL CANCER RESEARCH

SVA retrotransposons: Evolution and genetic instability

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

Mobile elements create structural variation: Analysis of a complete human genome

(2009) J. Xing et al.   GENOME RESEARCH

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

(2009) A. Damert et al.   GENOME RESEARCH

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells

(2009) Madeleine P Ball et al.   NATURE BIOTECHNOLOGY

Stabilization of quadruplex DNA perturbs telomere replication leading to the activation of an ATR-dependent ATM signaling pathway

(2009) Angela Rizzo et al.   NUCLEIC ACIDS RESEARCH

LINE Retrotransposon RNA Is an Essential Structural and Functional Epigenetic Component of a Core Neocentromeric Chromatin

(2009) Anderly C. Chueh et al.   PLoS Genetics

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Analysis of the largest tandemly repeated DNA families in the human genome

(2008) Peter E Warburton et al.   BMC GENOMICS

A universal classification of eukaryotic transposable elements implemented in Repbase

(2008) Vladimir V. Kapitonov et al.   NATURE REVIEWS GENETICS