msRepDB: a comprehensive repetitive sequence database of over 80 000 species

Repeat DNA expands our understanding of autism spectrum disorder

(2021) Anthony J. Hannan   NATURE

Patterns of de novo tandem repeat mutations and their role in autism

(2021) Ileena Mitra et al.   NATURE

A sensitive repeat identification framework based on short and long reads

(2021) Xingyu Liao et al.   NUCLEIC ACIDS RESEARCH

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

Genomic Repeats Categorize Genes with Distinct Functions for Orchestrated Regulation

(2020) J. Yuyang Lu et al.   Cell Reports

Genome-wide detection of tandem DNA repeats that are expanded in autism

(2020) Brett Trost et al.   NATURE

New Understanding of the Relevant Role of LINE-1 Retrotransposition in Human Disease and Immune Modulation

(2020) Xiao Zhang et al.   Frontiers in Cell and Developmental Biology

RepAHR: an improved approach for de novo repeat identification by assembly of the high-frequency reads

(2020) Xingyu Liao et al.   BMC BIOINFORMATICS

Dark Matter of Primate Genomes: Satellite DNA Repeats and Their Evolutionary Dynamics

(2020) Syed Farhan Ahmad et al.   Cells

An Efficient Trimming Algorithm based on Multi-Feature Fusion Scoring Model for NGS Data

(2019) Xingyu Liao et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

The effects of repeated whole genome duplication events on the evolution of cytokinin signaling pathway

(2018) Elisabeth Kaltenegger et al.   BMC EVOLUTIONARY BIOLOGY

Tandem repeats mediating genetic plasticity in health and disease

(2018) Anthony J. Hannan   NATURE REVIEWS GENETICS

Rapid and precise alignment of raw reads against redundant databases with KMA

(2018) Philip T. L. C. Clausen et al.   BMC BIOINFORMATICS

Improving de novo assembly based on read classification

(2018) xingyu Liao et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study

(2017) Qingyu Chen et al.   Database-The Journal of Biological Databases and Curation

Repetitive DNA loci and their modulation by the non-canonical nucleic acid structures R-loops and G-quadruplexes

(2017) Amanda C. Hall et al.   Nucleus

Repetitive DNA loci and their modulation by the non-canonical nucleic acid structures R-loops and G-quadruplexes

(2017) Amanda C. Hall et al.   Nucleus

A hot L1 retrotransposon evades somatic repression and initiates human colorectal cancer

(2016) Emma C. Scott et al.   GENOME RESEARCH

REPdenovo: Inferring De Novo Repeat Motifs from Short Sequence Reads

(2016) Chong Chu et al.   PLoS One

The Dfam database of repetitive DNA families

(2015) Robert Hubley et al.   NUCLEIC ACIDS RESEARCH

Short Inverted Repeats Are Hotspots for Genetic Instability: Relevance to Cancer Genomes

(2015) Steve Lu et al.   Cell Reports

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

RepARK—de novo creation of repeat libraries from whole-genome NGS reads

(2014) Philipp Koch et al.   NUCLEIC ACIDS RESEARCH

Repetitive Sequences in Plant Nuclear DNA: Types, Distribution, Evolution and Function

(2014) Shweta Mehrotra et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Multiple cellular mechanisms prevent chromosomal rearrangements involving repetitive DNA

(2012) Carolyn M. George et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Extensive somatic L1 retrotransposition in colorectal tumors

(2012) S. Solyom et al.   GENOME RESEARCH

LINE-1 Elements in Structural Variation and Disease

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

Expanded GGGGCC Hexanucleotide Repeat in Noncoding Region of C9ORF72 Causes Chromosome 9p-Linked FTD and ALS

(2011) Mariely DeJesus-Hernandez et al.   NEURON

A Hexanucleotide Repeat Expansion in C9ORF72 Is the Cause of Chromosome 9p21-Linked ALS-FTD

(2011) Alan E. Renton et al.   NEURON

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

All y’all need to know ‘bout retroelements in cancer

(2010) Victoria P. Belancio et al.   SEMINARS IN CANCER BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS