A complete reference genome improves analysis of human genetic variation

Failure to Detect Mutations in U2AF1 due to Changes in the GRCh38 Reference Sequence

(2022) Christopher A. Miller et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Curated variation benchmarks for challenging medically relevant autosomal genes

(2022) Justin Wagner et al.   NATURE BIOTECHNOLOGY

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

(2021) Daniel Taliun et al.   NATURE

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

(2021) Haoyu Cheng et al.   NATURE METHODS

CADD-Splice—improving genome-wide variant effect prediction using deep learning-derived splice scores

(2021) Philipp Rentzsch et al.   Genome Medicine

HTSlib: C library for reading/writing high-throughput sequencing data

(2021) James K Bonfield et al.   GigaScience

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

The Need for a Human Pangenome Reference Sequence

(2021) Karen H. Miga et al.   Annual Review of Genomics and Human Genetics

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

Local adaptation and archaic introgression shape global diversity at human structural variant loci

(2021) Stephanie M Yan et al.   eLife

Detecting Selection in Multiple Populations by Modeling Ancestral Admixture Components

(2021) Jade Yu Cheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads

(2021) Kishwar Shafin et al.   NATURE METHODS

Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals

(2020) Lu Chen et al.   CELL

Progress, Challenges, and Surprises in Annotating the Human Genome

(2020) Daniel R. Zerbino et al.   Annual Review of Genomics and Human Genetics

Pangenome Graphs

(2020) Jordan M. Eizenga et al.   Annual Review of Genomics and Human Genetics

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski 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

Weighted minimizer sampling improves long read mapping

(2020) Chirag Jain et al.   BIOINFORMATICS

Expanded encyclopaedias of DNA elements in the human and mouse genomes

(2020) Jill E. Moore et al.   NATURE

A robust benchmark for detection of germline large deletions and insertions

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

Whole exome sequencing identifies the novel putative gene variants related with type 2 diabetes in Mizo population, northeast India

(2020) Freda Lalrohlui et al.   GENE

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

Predicting Splicing from Primary Sequence with Deep Learning

(2019) Kishore Jaganathan et al.   CELL

Characterizing the Major Structural Variant Alleles of the Human Genome

(2019) Peter A. Audano et al.   CELL

Best practices for benchmarking germline small-variant calls in human genomes

(2019) Peter Krusche et al.   NATURE BIOTECHNOLOGY

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

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

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

Haplotypes spanning centromeric regions reveal persistence of large blocks of archaic DNA

(2019) Sasha A Langley et al.   eLife

Improved assembly and variant detection of a haploid human genome using single‐molecule, high‐fidelity long reads

(2019) Mitchell R. Vollger et al.   ANNALS OF HUMAN GENETICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Physiological and Genetic Adaptations to Diving in Sea Nomads

(2018) Melissa A. Ilardo et al.   CELL

A synthetic-diploid benchmark for accurate variant-calling evaluation

(2018) Heng Li et al.   NATURE METHODS

Accurate detection of complex structural variations using single-molecule sequencing

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

Familial Esophageal Squamous Cell Carcinoma with damaging rare/germline mutations in KCNJ12/KCNJ18 and GPRIN2 genes

(2018) Narjes Khalilipour et al.   Cancer Genetics

Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects

(2018) Allison A. Regier et al.   Nature Communications

Effect of Collapsed Duplications on Diversity Estimates: What to Expect

(2018) Diego A Hartasánchez et al.   Genome Biology and Evolution

Assembly of a pan-genome from deep sequencing of 910 humans of African descent

(2018) Rachel M. Sherman et al.   NATURE GENETICS

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

(2018) Annalisa Buniello et al.   NUCLEIC ACIDS RESEARCH

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

(2017) Valerie A. Schneider et al.   GENOME RESEARCH

ClinVar: improving access to variant interpretations and supporting evidence

(2017) Melissa J Landrum et al.   NUCLEIC ACIDS RESEARCH

A high-coverage Neandertal genome from Vindija Cave in Croatia

(2017) Kay Prüfer et al.   SCIENCE

The evolution and population diversity of human-specific segmental duplications

(2017) Megan Y. Dennis et al.   Nature Ecology & Evolution

TNNI1, TNNI2 and TNNI3: Evolution, regulation, and protein structure–function relationships

(2016) Juan-Juan Sheng et al.   GENE

De novo assembly and phasing of a Korean human genome

(2016) Jeong-Sun Seo et al.   NATURE

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

(2016) Swapan Mallick et al.   NATURE

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

A method for calculating probabilities of fitness consequences for point mutations across the human genome

(2015) Brad Gulko et al.   NATURE GENETICS

Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics

(2015) Sarah Munchel et al.   Oncotarget

Big Data: Astronomical or Genomical?

(2015) Zachary D. Stephens et al.   PLOS BIOLOGY

Extending reference assembly models

(2015) Deanna M Church et al.   GENOME BIOLOGY

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

Finished sequence and assembly of the DUF1220-rich 1q21 region using a haploid human genome

(2014) Majesta O’Bleness et al.   BMC GENOMICS

Single haplotype assembly of the human genome from a hydatidiform mole

(2014) Karyn Meltz Steinberg et al.   GENOME RESEARCH

Centromere reference models for human chromosomes X and Y satellite arrays

(2014) K. H. Miga et al.   GENOME RESEARCH

Reconstructing complex regions of genomes using long-read sequencing technology

(2014) J. Huddleston et al.   GENOME RESEARCH

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

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

The contribution of de novo coding mutations to autism spectrum disorder

(2014) Ivan Iossifov et al.   NATURE

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

The phosphatase JKAP/DUSP22 inhibits T-cell receptor signalling and autoimmunity by inactivating Lck

(2014) Ju-Pi Li et al.   Nature Communications

RFMix: A Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference

(2013) Brian K. Maples et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

A public resource facilitating clinical use of genomes

(2012) Madeleine P. Ball et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

(2012) D. G. MacArthur et al.   SCIENCE

A probabilistic disease-gene finder for personal genomes

(2011) M. Yandell et al.   GENOME RESEARCH

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Mutations in Potassium Channel Kir2.6 Cause Susceptibility to Thyrotoxic Hypokalemic Periodic Paralysis

(2010) Devon P. Ryan et al.   CELL

Diversity of Human Copy Number Variation and Multicopy Genes

(2010) Peter H. Sudmant et al.   SCIENCE

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE