Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders

Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes

(2022) Jana Ebler et al.   NATURE GENETICS

The complete sequence of a human genome

(2022) Sergey Nurk et al.   SCIENCE

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

(2021) Haoyu Cheng et al.   NATURE METHODS

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

(2021) Peter Ebert et al.   SCIENCE

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

(2021) Glennis A. Logsdon et al.   NATURE

Polθ reverse transcribes RNA and promotes RNA-templated DNA repair

(2021) Gurushankar Chandramouly et al.   Science Advances

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

A new 1p36.13‐1p36.12 microdeletion syndrome characterized by learning disability, behavioral abnormalities, and ptosis

(2020) Line Aagaard Nolting et al.   CLINICAL GENETICS

Determining the impact of uncharacterized inversions in the human genome by droplet digital PCR

(2020) Marta Puig et al.   GENOME RESEARCH

A structural variation reference for medical and population genetics

(2020) Ryan L. Collins et al.   NATURE

Mapping and characterization of structural variation in 17,795 human genomes

(2020) Haley J. Abel et al.   NATURE

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

(2020) Kishwar Shafin et al.   NATURE BIOTECHNOLOGY

Insights into human genetic variation and population history from 929 diverse genomes

(2020) Anders Bergström et al.   SCIENCE

Recurrent inversion toggling and great ape genome evolution

(2020) David Porubsky et al.   NATURE GENETICS

Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution

(2020) Flavia Angela Maria Maggiolini et al.   GENOME RESEARCH

Characterizing the Major Structural Variant Alleles of the Human Genome

(2019) Peter A. Audano et al.   CELL

Transition from a meiotic to a somatic-like DNA damage response during the pachytene stage in mouse meiosis

(2019) Andrea Enguita-Marruedo et al.   PLoS Genetics

Genomic inversions and GOLGA core duplicons underlie disease instability at the 15q25 locus

(2019) Flavia A. M. Maggiolini et al.   PLoS Genetics

Evolutionary and functional analysis of RBMY1 gene copy number variation on the human Y chromosome

(2019) Wentao Shi et al.   HUMAN MOLECULAR GENETICS

Multi-platform discovery of haplotype-resolved structural variation in human genomes

(2019) Mark J. P. Chaisson et al.   Nature Communications

A method for genome-wide genealogy estimation for thousands of samples

(2019) Leo Speidel et al.   NATURE GENETICS

Evolutionary and functional impact of common polymorphic inversions in the human genome

(2019) Carla Giner-Delgado et al.   Nature Communications

Single-cell analysis of structural variations and complex rearrangements with tri-channel processing

(2019) Ashley D. Sanders et al.   NATURE BIOTECHNOLOGY

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Comparison of village dog and wolf genomes highlights the role of the neural crest in dog domestication

(2018) Amanda L. Pendleton et al.   BMC BIOLOGY

Inversion variants in human and primate genomes

(2018) Claudia Rita Catacchio et al.   GENOME RESEARCH

Predicting human genes susceptible to genomic instability associated withAlu/Alu-mediated rearrangements

(2018) Xiaofei Song et al.   GENOME RESEARCH

High-resolution comparative analysis of great ape genomes

(2018) Zev N. Kronenberg et al.   SCIENCE

Long-read sequence and assembly of segmental duplications

(2018) Mitchell R. Vollger et al.   NATURE METHODS

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

Single-cell template strand sequencing by Strand-seq enables the characterization of individual homologs

(2017) Ashley D Sanders et al.   Nature Protocols

Dense and accurate whole-chromosome haplotyping of individual genomes

(2017) David Porubsky et al.   Nature Communications

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

(2016) Heng Li   BIOINFORMATICS

The Landscape of Mouse Meiotic Double-Strand Break Formation, Processing, and Repair

(2016) Julian Lange et al.   CELL

Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region

(2016) Kiana Mohajeri et al.   GENOME RESEARCH

Characterizing polymorphic inversions in human genomes by single-cell sequencing

(2016) Ashley D. Sanders et al.   GENOME RESEARCH

Direct chromosome-length haplotyping by single-cell sequencing

(2016) David Porubský et al.   GENOME RESEARCH

Mechanisms underlying structural variant formation in genomic disorders

(2016) Claudia M. B. Carvalho et al.   NATURE REVIEWS GENETICS

Local Ancestry Inference in a Large US-Based Hispanic/Latino Study: Hispanic Community Health Study/Study of Latinos (HCHS/SOL)

(2016) Sharon R. Browning et al.   G3-Genes Genomes Genetics

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

Human inversions and their functional consequences

(2015) Marta Puig et al.   Briefings in Functional Genomics

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

Phylogenetic Analysis Supports a Link between DUF1220 Domain Number and Primate Brain Expansion

(2015) Fabian Zimmer et al.   Genome Biology and Evolution

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

(2015) Peter H. Sudmant et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Large multiallelic copy number variations in humans

(2015) Robert E Handsaker et al.   NATURE GENETICS

WASP: allele-specific software for robust molecular quantitative trait locus discovery

(2015) Bryce van de Geijn et al.   NATURE METHODS

The Contribution of Alu Elements to Mutagenic DNA Double-Strand Break Repair

(2015) Maria E. Morales et al.   PLoS Genetics

Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates

(2015) Bo Yuan et al.   PLoS Genetics

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Evidence for Increased Levels of Positive and Negative Selection on the X Chromosome versus Autosomes in Humans

(2014) Krishna R. Veeramah et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome sequence of a 45,000-year-old modern human from western Siberia

(2014) Qiaomei Fu et al.   NATURE

Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability

(2014) Francesca Antonacci et al.   NATURE GENETICS

Refining analyses of copy number variation identifies specific genes associated with developmental delay

(2014) Bradley P Coe et al.   NATURE GENETICS

Integrated mechanism for the generation of the 5′ junctions of LINE inserts

(2014) Katsumi Yamaguchi et al.   NUCLEIC ACIDS RESEARCH

Duplication of the NPHP1 gene in patients with autism spectrum disorder and normal intellectual ability: a case series

(2014) Yuka Yasuda et al.   Annals of General Psychiatry

Validation and Genotyping of Multiple Human Polymorphic Inversions Mediated by Inverted Repeats Reveals a High Degree of Recurrence

(2014) Cristina Aguado et al.   PLoS Genetics

Large Inverted Duplications in the Human Genome Form via a Fold-Back Mechanism

(2014) Karen E. Hermetz et al.   PLoS Genetics

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

(2013) Y. Liao et al.   BIOINFORMATICS

DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation

(2013) Eugene Bragin et al.   NUCLEIC ACIDS RESEARCH

Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males Versus Females

(2013) G. D. Poznik et al.   SCIENCE

Evolutionary History and Genome Organization of DUF1220 Protein Domains

(2013) Majesta S. O’Bleness et al.   G3-Genes Genomes Genetics

Recombination Dynamics of a Human Y-Chromosomal Palindrome: Rapid GC-Biased Gene Conversion, Multi-kilobase Conversion Tracts, and Rare Inversions

(2013) Pille Hallast et al.   PLoS Genetics

The Specificity and Flexibility of L1 Reverse Transcription Priming at Imperfect T-Tracts

(2013) Clément Monot et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The origin, global distribution, and functional impact of the human 8p23 inversion polymorphism

(2012) Maximilian P.A. Salm et al.   GENOME RESEARCH

Recombination-restarted replication makes inverted chromosome fusions at inverted repeats

(2012) Ken’Ichi Mizuno et al.   NATURE

Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly

(2012) Ernest T Lam et al.   NATURE BIOTECHNOLOGY

Structural diversity and African origin of the 17q21.31 inversion polymorphism

(2012) Karyn Meltz Steinberg et al.   NATURE GENETICS

DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution

(2012) Ester Falconer et al.   NATURE METHODS

A copy number variation morbidity map of developmental delay

(2011) Gregory M Cooper et al.   NATURE GENETICS

Genome-Wide Signatures of ‘Rearrangement Hotspots’ within Segmental Duplications in Humans

(2011) Mohammed Uddin et al.   PLoS One

Ataxia telangiectasia mutated (ATM) modulates long interspersed element-1 (L1) retrotransposition in human neural stem cells

(2011) N. G. Coufal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

A Human Genome Structural Variation Sequencing Resource Reveals Insights into Mutational Mechanisms

(2010) Jeffrey M. Kidd et al.   CELL

mrsFAST: a cache-oblivious algorithm for short-read mapping

(2010) Faraz Hach et al.   NATURE METHODS

Different integration site structures between L1 protein-mediated retrotransposition in cis and retrotransposition in trans

(2010) Kenji K Kojima   Mobile DNA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Isodicentric Y Chromosomes and Sex Disorders as Byproducts of Homologous Recombination that Maintains Palindromes

(2009) Julian Lange et al.   CELL

Duplication hotspots, rare genomic disorders, and common disease

(2009) Heather C Mefford et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Characterization of six human disease-associated inversion polymorphisms

(2009) Francesca Antonacci et al.   HUMAN MOLECULAR GENETICS

A burst of segmental duplications in the genome of the African great ape ancestor

(2009) Tomas Marques-Bonet et al.   NATURE

Genetic Evidence That the Non-Homologous End-Joining Repair Pathway Is Involved in LINE Retrotransposition

(2009) Jun Suzuki et al.   PLoS Genetics

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

Mapping and sequencing of structural variation from eight human genomes

(2008) Jeffrey M. Kidd et al.   NATURE

Evolutionary toggling of the MAPT 17q21.31 inversion region

(2008) Michael C Zody et al.   NATURE GENETICS

Expanding the clinical phenotype of the 3q29 microdeletion syndrome and characterization of the reciprocal microduplication

(2008) Blake C Ballif et al.   Molecular Cytogenetics