The Human Pangenome Project: a global resource to map genomic diversity

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 Need for a Human Pangenome Reference Sequence

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

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

(2021) Glennis A. Logsdon et al.   NATURE

Towards complete and error-free genome assemblies of all vertebrate species

(2021) Arang Rhie et al.   NATURE

Operationalizing the CARE and FAIR Principles for Indigenous data futures

(2021) Stephanie Russo Carroll et al.   Scientific Data

Targeted long-read sequencing identifies missing disease-causing variation

(2021) Danny E. Miller et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A pneumonia outbreak associated with a new coronavirus of probable bat origin

(2020) Peng Zhou et al.   NATURE

Pan-genomics in the human genome era

(2020) Rachel M. Sherman et al.   NATURE REVIEWS GENETICS

Pangenome Graphs

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

The Architecture of SARS-CoV-2 Transcriptome

(2020) Dongwan Kim et al.   CELL

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

(2020) Haley J. Abel et al.   NATURE

Rights, interests and expectations: Indigenous perspectives on unrestricted access to genomic data

(2020) Maui Hudson et al.   NATURE REVIEWS GENETICS

Clinical Genetics Lacks Standard Definitions and Protocols for the Collection and Use of Diversity Measures

(2020) Alice B. Popejoy et al.   AMERICAN JOURNAL OF HUMAN GENETICS

SPAligner: alignment of long diverged molecular sequences to assembly graphs

(2020) Tatiana Dvorkina et al.   BMC BIOINFORMATICS

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

(2020) Karen H. Miga et al.   NATURE

Long-read human genome sequencing and its applications

(2020) Glennis A. Logsdon et al.   NATURE REVIEWS GENETICS

The Human Genome Project changed everything

(2020) Richard A. Gibbs   NATURE REVIEWS GENETICS

The Illusion of Inclusion — The “All of Us” Research Program and Indigenous Peoples’ DNA

(2020) Keolu Fox   NEW ENGLAND JOURNAL OF MEDICINE

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

(2020) Sergey Nurk et al.   GENOME RESEARCH

The major genetic risk factor for severe COVID-19 is inherited from Neanderthals

(2020) Hugo Zeberg et al.   NATURE

The UCSC Genome Browser database: 2021 update

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

The Missing Diversity in Human Genetic Studies

(2019) Giorgio Sirugo et al.   CELL

Assembly Graph Browser: interactive visualization of assembly graphs

(2019) Alla Mikheenko et al.   BIOINFORMATICS

Sequence tube maps: making graph genomes intuitive to commuters

(2019) Wolfgang Beyer et al.   BIOINFORMATICS

Fully-sensitive seed finding in sequence graphs using a hybrid index

(2019) Ali Ghaffaari et al.   BIOINFORMATICS

WashU Epigenome Browser update 2019

(2019) Daofeng Li et al.   NUCLEIC ACIDS RESEARCH

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

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

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

MoMI-G: modular multi-scale integrated genome graph browser

(2019) Toshiyuki T. Yokoyama et al.   BMC BIOINFORMATICS

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

Accurate genotyping across variant classes and lengths using variant graphs

(2018) Jonas Andreas Sibbesen et al.   NATURE GENETICS

Accurate detection of complex structural variations using single-molecule sequencing

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

BrownieAligner: accurate alignment of Illumina sequencing data to de Bruijn graphs

(2018) Mahdi Heydari et al.   BMC BIOINFORMATICS

Variation graph toolkit improves read mapping by representing genetic variation in the reference

(2018) Erik Garrison et al.   NATURE BIOTECHNOLOGY

GfaViz: flexible and interactive visualization of GFA sequence graphs

(2018) Giorgio Gonnella et al.   BIOINFORMATICS

SGTK: a toolkit for visualization and assessment of scaffold graphs

(2018) Olga Kunyavskaya et al.   BIOINFORMATICS

The clinical imperative for inclusivity: Race, ethnicity, and ancestry (REA) in genomics

(2018) Alice B. Popejoy et al.   HUMAN MUTATION

BioSamples database: an updated sample metadata hub

(2018) Mélanie Courtot et al.   NUCLEIC ACIDS RESEARCH

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

Haplosaurus computes protein haplotypes for use in precision drug design

(2018) William Spooner et al.   Nature Communications

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

deBGA: read alignment with de Bruijn graph-based seed and extension

(2016) Bo Liu et al.   BIOINFORMATICS

Read mapping on de Bruijn graphs

(2016) Antoine Limasset et al.   BMC BIOINFORMATICS

Genomics is failing on diversity

(2016) Alice B. Popejoy et al.   NATURE

The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data

(2016) Laura Clarke et al.   NUCLEIC ACIDS RESEARCH

The FAIR Guiding Principles for scientific data management and stewardship

(2016) Mark D. Wilkinson et al.   Scientific Data

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

(2015) Ryan R. Wick et al.   BIOINFORMATICS

Ten years of pan-genome analyses

(2015) George Vernikos et al.   CURRENT OPINION IN MICROBIOLOGY

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

ClinGen — The Clinical Genome Resource

(2015) Heidi L. Rehm et al.   NEW ENGLAND JOURNAL OF MEDICINE

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Identifying and Classifying Trait Linked Polymorphisms in Non-Reference Species by Walking Coloured de Bruijn Graphs

(2013) Richard M. Leggett et al.   PLoS One

The 1000 Genomes Project: data management and community access

(2012) Laura Clarke et al.   NATURE METHODS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Cactus: Algorithms for genome multiple sequence alignment

(2011) B. Paten et al.   GENOME RESEARCH

Genomics for the world

(2011) Carlos D. Bustamante et al.   NATURE

The Human Epigenome Browser at Washington University

(2011) Xin Zhou et al.   NATURE METHODS

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

DNA Returned to Tribe, Raising Questions About Consent

(2010) J. Couzin-Frankel   SCIENCE

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Physicians' attitudes toward race, genetics, and clinical medicine

(2009) Vence L Bonham et al.   GENETICS IN MEDICINE

Building the sequence map of the human pan-genome

(2009) Ruiqiang Li et al.   NATURE BIOTECHNOLOGY

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Next generation disparities in human genomics: concerns and remedies

(2009) Anna C. Need et al.   TRENDS IN GENETICS