T2T-YAO: A Telomere-to-telomere Assembled Diploid Reference Genome for Han Chinese

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

(2023) Melanie Kirsche et al.   NATURE METHODS

Regulation of ribosomal RNA gene copy number, transcription and nucleolus organization in eukaryotes

(2023) Yutaro Hori et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual

(2023) Kuan-Hao Chao et al.   G3-Genes Genomes Genetics

Recombination between heterologous human acrocentric chromosomes

(2023) Andrea Guarracino et al.   NATURE

A pangenome reference of 36 Chinese populations

(2023) Yang Gao et al.   NATURE

A draft human pangenome reference

(2023) Wen-Wei Liao et al.   NATURE

Increased mutation and gene conversion within human segmental duplications

(2023) Mitchell R. Vollger et al.   NATURE

Telomere-to-telomere assembly of diploid chromosomes with Verkko

(2023) Mikko Rautiainen et al.   NATURE BIOTECHNOLOGY

Repetitive elements in aging and neurodegeneration

(2023) Katie E. Copley et al.   TRENDS IN GENETICS

Fast characterization of segmental duplication structure in multiple genome assemblies

(2022) Hamza Išerić et al.   Algorithms for Molecular Biology

Multiplex de Bruijn graphs enable genome assembly from long, high-fidelity reads

(2022) Anton Bankevich et al.   NATURE BIOTECHNOLOGY

Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation

(2022) Giulio Formenti et al.   NATURE METHODS

Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies

(2022) Ann M. Mc Cartney et al.   NATURE METHODS

Long-read mapping to repetitive reference sequences using Winnowmap2

(2022) Chirag Jain et al.   NATURE METHODS

Complete genomic and epigenetic maps of human centromeres

(2022) Nicolas Altemose et al.   SCIENCE

Epigenetic patterns in a complete human genome

(2022) Ariel Gershman et al.   SCIENCE

From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

(2022) Savannah J. Hoyt et al.   SCIENCE

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

A next-generation human genome sequence

(2022) Deanna M. Church   SCIENCE

Segmental duplications and their variation in a complete human genome

(2022) Mitchell R. Vollger et al.   SCIENCE

Semi-automated assembly of high-quality diploid human reference genomes

(2022) Erich D. Jarvis et al.   NATURE

GENCODE: reference annotation for the human and mouse genomes in 2023

(2022) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

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

(2021) Glennis A. Logsdon et al.   NATURE

The human ribosomal DNA array is composed of highly homogenized tandem clusters

(2021) Yutaro Hori et al.   GENOME RESEARCH

The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types

(2021) Tingting Chen et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Genome Warehouse: A Public Repository Housing Genome-scale Data

(2021) Meili Chen et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

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

(2021) Kishwar Shafin et al.   NATURE METHODS

Ancient genomes from northern China suggest links between subsistence changes and human migration

(2020) Chao Ning et al.   Nature Communications

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

(2020) Sergey Nurk et al.   GENOME RESEARCH

Liftoff: accurate mapping of gene annotations

(2020) Alaina Shumate et al.   BIOINFORMATICS

SVIM-asm: structural variant detection from haploid and diploid genome assemblies

(2020) David Heller et al.   BIOINFORMATICS

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

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

Integrating Hi-C links with assembly graphs for chromosome-scale assembly

(2019) Jay Ghurye et al.   PLoS Computational Biology

Whole Genome Analyses of Chinese Population and De Novo Assembly of A Northern Han Genome

(2019) Zhenglin Du et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Mechanisms of rDNA Copy Number Maintenance

(2019) Jonathan O. Nelson et al.   TRENDS IN GENETICS

Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation

(2018) Ian T. Fiddes et al.   GENOME RESEARCH

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

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

A universal SNP and small-indel variant caller using deep neural networks

(2018) Ryan Poplin et al.   NATURE BIOTECHNOLOGY

Long-read sequence and assembly of segmental duplications

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

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Genetic History of Xinjiang’s Uyghurs Suggests Bronze Age Multiple-Way Contacts in Eurasia

(2017) Qidi Feng et al.   MOLECULAR BIOLOGY AND EVOLUTION

A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y

(2016) Marta Tomaszkiewicz et al.   GENOME RESEARCH

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Narrowing the localization of the region breakpoint in most frequent Robertsonian translocations

(2014) Malgorzata Jarmuz-Szymczak et al.   CHROMOSOME RESEARCH

Single haplotype assembly of the human genome from a hydatidiform mole

(2014) Karyn Meltz Steinberg et al.   GENOME RESEARCH

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

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

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

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

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

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

(2012) Ernest T Lam et al.   NATURE BIOTECHNOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS