Jasmine and Iris: population-scale structural variant comparison and analysis

Long-read mapping to repetitive reference sequences using Winnowmap2

(2022) Chirag Jain et al.   NATURE METHODS

A complete reference genome improves analysis of human genetic variation

(2022) Sergey Aganezov et al.   SCIENCE

The complete sequence of a human genome

(2022) Sergey Nurk et al.   SCIENCE

High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

(2022) Marta Byrska-Bishop et al.   CELL

Macrophage Migration Inhibitory Factor (MIF) and Its Homologue D-Dopachrome Tautomerase (DDT) Inversely Correlate with Inflammation in Discoid Lupus Erythematosus

(2021) Rosario Caltabiano et al.   MOLECULES

De novo structural mutation rates and gamete-of-origin biases revealed through genome sequencing of 2,396 families

(2021) Jonathan R. Belyeu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2021) Peter Ebert et al.   SCIENCE

Optimized sample selection for cost-efficient long-read population sequencing

(2021) T. Rhyker Ranallo-Benavidez et al.   GENOME RESEARCH

Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits

(2021) Doruk Beyter et al.   NATURE GENETICS

Structural variants are a major source of gene expression differences in humans and often affect multiple nearby genes

(2021) Alexandra J Scott et al.   GENOME RESEARCH

Pangenomics enables genotyping of known structural variants in 5202 diverse genomes

(2021) Jouni Sirén et al.   SCIENCE

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

(2020) Haley J. Abel et al.   NATURE

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update

(2020) Vahid Jalili et al.   NUCLEIC ACIDS RESEARCH

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

(2020) Michael Alonge et al.   CELL

A robust benchmark for detection of germline large deletions and insertions

(2020) Justin M. Zook et al.   NATURE BIOTECHNOLOGY

Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing

(2020) Sergey Aganezov et al.   GENOME RESEARCH

The GTEx Consortium atlas of genetic regulatory effects across human tissues

(2020)   SCIENCE

The UCSC Genome Browser database: 2021 update

(2020) Jairo Navarro Gonzalez et al.   NUCLEIC ACIDS RESEARCH

Characterizing the Major Structural Variant Alleles of the Human Genome

(2019) Peter A. Audano et al.   CELL

svtools: population-scale analysis of structural variation

(2019) David E Larson et al.   BIOINFORMATICS

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

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

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

(2019) Aaron M. Wenger et al.   NATURE BIOTECHNOLOGY

GraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs

(2019) Hannes P. Eggertsson et al.   Nature Communications

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line

(2018) Maria Nattestad et al.   GENOME RESEARCH

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

Piercing the dark matter: bioinformatics of long-range sequencing and mapping

(2018) Fritz J. Sedlazeck et al.   NATURE REVIEWS GENETICS

Paternally inherited cis-regulatory structural variants are associated with autism

(2018) William M. Brandler et al.   SCIENCE

CADD: predicting the deleteriousness of variants throughout the human genome

(2018) Philipp Rentzsch et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Contribution of de novo and mosaicTP53mutations to Li-Fraumeni syndrome

(2017) Mariette Renaux-Petel et al.   JOURNAL OF MEDICAL GENETICS

Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data

(2017) Yi-Fei Huang et al.   NATURE GENETICS

The impact of structural variation on human gene expression

(2017) Colby Chiang et al.   NATURE GENETICS

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

(2017) Daniel C. Jeffares et al.   Nature Communications

A Frameshift in CSF2RB Predominant Among Ashkenazi Jews Increases Risk for Crohn's Disease and Reduces Monocyte Signaling via GM-CSF

(2016) Ling-Shiang Chuang et al.   GASTROENTEROLOGY

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

The Ensembl Regulatory Build

(2015) Daniel R Zerbino et al.   GENOME BIOLOGY

Identifying Causal Variants at Loci with Multiple Signals of Association

(2014) F. Hormozdiari et al.   GENETICS

The contribution of de novo coding mutations to autism spectrum disorder

(2014) Ivan Iossifov et al.   NATURE

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

Accurate de novo and transmitted indel detection in exome-capture data using microassembly

(2014) Giuseppe Narzisi et al.   NATURE METHODS

Malignant Melanotic Schwannian Tumor

(2013) Jorge Torres-Mora et al.   AMERICAN JOURNAL OF SURGICAL PATHOLOGY

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

De novo mutations in human genetic disease

(2012) Joris A. Veltman et al.   NATURE REVIEWS GENETICS

A copy number variation morbidity map of developmental delay

(2011) Gregory M Cooper et al.   NATURE GENETICS

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

PHAST and RPHAST: phylogenetic analysis with space/time models

(2010) M. J. Hubisz et al.   BRIEFINGS IN BIOINFORMATICS