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

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

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

(2020) Anders Bergström et al.   SCIENCE

TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats

(2020) Alla Mikheenko et al.   BIOINFORMATICS

The string decomposition problem and its applications to centromere analysis and assembly

(2020) Tatiana Dvorkina et al.   BIOINFORMATICS

Weighted minimizer sampling improves long read mapping

(2020) Chirag Jain et al.   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

A high-coverage Neandertal genome from Chagyrskaya Cave

(2020) Fabrizio Mafessoni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Liftoff: accurate mapping of gene annotations

(2020) Alaina Shumate et al.   BIOINFORMATICS

Chromosome-scale, haplotype-resolved assembly of human genomes

(2020) Shilpa Garg et al.   NATURE BIOTECHNOLOGY

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads

(2020) David Porubsky et al.   NATURE BIOTECHNOLOGY

Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing

(2020) Isac Lee et al.   NATURE METHODS

Human Artificial Chromosomes that Bypass Centromeric DNA

(2019) Glennis A. Logsdon et al.   CELL

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

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

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

Parallelization of MAFFT for large-scale multiple sequence alignments

(2018) Tsukasa Nakamura et al.   BIOINFORMATICS

Strand-seq enables reliable separation of long reads by chromosome via expectation maximization

(2018) Maryam Ghareghani et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Alpha satellite DNA biology: finding function in the recesses of the genome

(2018) Shannon M. McNulty et al.   CHROMOSOME RESEARCH

Linear assembly of a human centromere on the Y chromosome

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Transcriptional fates of human-specific segmental duplications in brain

(2018) Max L. Dougherty et al.   GENOME RESEARCH

Detecting DNA cytosine methylation using nanopore sequencing

(2017) Jared T Simpson et al.   NATURE METHODS

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

(2017) Ashley D Sanders et al.   Nature Protocols

A high-coverage Neandertal genome from Vindija Cave in Croatia

(2017) Kay Prüfer et al.   SCIENCE

Diversity and distribution of alpha satellite DNA in the genome of an Old World monkey: Cercopithecus solatus

(2016) Lauriane Cacheux et al.   BMC GENOMICS

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

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

(2016) Swapan Mallick et al.   NATURE

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

Evolutionary Origin of Higher-Order Repeat Structure in Alpha-Satellite DNA of Primate Centromeres

(2014) A. Koga et al.   DNA RESEARCH

Reconstructing complex regions of genomes using long-read sequencing technology

(2014) J. Huddleston et al.   GENOME RESEARCH

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Y. Liao et al.   BIOINFORMATICS

Expansion of a 12-kb VNTR containing the REXO1L1 gene cluster underlies the microscopically visible euchromatic variant of 8q21.2

(2013) Christine Tyson et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Great ape genetic diversity and population history

(2013) Javier Prado-Martinez et al.   NATURE

The octamer is the major form of CENP-A nucleosomes at human centromeres

(2013) Dan Hasson et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Strand-seq: A unifying tool for studies of chromosome segregation

(2013) Ester Falconer et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

The Genomic and Transcriptomic Landscape of a HeLa Cell Line

(2013) Jonathan J. M. Landry et al.   G3-Genes Genomes Genetics

lobSTR: A short tandem repeat profiler for personal genomes

(2012) Melissa Gymrek et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Correlating Multiallelic Copy Number Polymorphisms with Disease Susceptibility

(2012) Stuart Cantsilieris et al.   HUMAN MUTATION

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

Formation of novel CENP-A domains on tandem repetitive DNA and across chromosome breakpoints on human chromosome 8q21 neocentromeres

(2011) Dan Hasson et al.   CHROMOSOMA

Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee

(2011) M. Ventura et al.   GENOME RESEARCH

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

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

(2010) Heng Li et al.   BIOINFORMATICS

Genome-wide characterization of centromeric satellites from multiple mammalian genomes

(2010) C. Alkan et al.   GENOME RESEARCH

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

(2010) Faraz Hach et al.   NATURE METHODS

Diversity of Human Copy Number Variation and Multicopy Genes

(2010) Peter H. Sudmant et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The Evolutionary Origin of Man Can Be Traced in the Layers of Defunct Ancestral Alpha Satellites Flanking the Active Centromeres of Human Chromosomes

(2009) Valery A. Shepelev et al.   PLoS Genetics

Analysis of the largest tandemly repeated DNA families in the human genome

(2008) Peter E Warburton et al.   BMC GENOMICS