Epigenetic patterns in a complete human genome

The Sequence Alignment/Map format and SAMtools

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Fast gapped-read alignment with Bowtie 2

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

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BEDTools: a flexible suite of utilities for comparing genomic features

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Initial sequencing and analysis of the human genome

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Model-based Analysis of ChIP-Seq (MACS)

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A global reference for human genetic variation

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An integrated encyclopedia of DNA elements in the human genome

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Twelve years of SAMtools and BCFtools

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

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The sequence of the human genome

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EMBOSS: the European molecular biology open software suite.

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deepTools2: a next generation web server for deep-sequencing data analysis

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Integrative analysis of 111 reference human epigenomes

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Regulation of chromatin by histone modifications

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Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

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BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

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Histone H3K27ac separates active from poised enhancers and predicts developmental state

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Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome

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mclust 5: Clustering, Classification and Density Estimation Using Gaussian Finite Mixture Models

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Opportunities and challenges in long-read sequencing data analysis

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Schizophrenia risk from complex variation of complement component 4

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The ENCODE (ENCyclopedia Of DNA Elements) Project

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Transcriptome assembly from long-read RNA-seq alignments with StringTie2

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The Encyclopedia of DNA elements (ENCODE): data portal update

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Mesoporous silicon sponge as an anti-pulverization structure for high-performance lithium-ion battery anodes

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Role of transposable elements in heterochromatin and epigenetic control

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zoo : S3 Infrastructure for Regular and Irregular Time Series

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Long-read human genome sequencing and its applications

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

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Landscape of X chromosome inactivation across human tissues

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Detecting DNA cytosine methylation using nanopore sequencing

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The DNA methylation landscape of human early embryos

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BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions

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

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Transitions in Distinct Histone H3 Methylation Patterns at the Heterochromatin Domain Boundaries

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Gene Body-Specific Methylation on the Active X Chromosome

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The 4D nucleome project

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KMC 3: counting and manipulating k‐mer statistics

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Diversity of Human Copy Number Variation and Multicopy Genes

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Transposable Elements, Epigenetics, and Genome Evolution

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Complete genomic and epigenetic maps of human centromeres

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Aggressive assembly of pyrosequencing reads with mates

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Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis

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Epigenetic regulation of centromeric chromatin: old dogs, new tricks?

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Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

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Aberrant Overexpression of Satellite Repeats in Pancreatic and Other Epithelial Cancers

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Hierarchical order in chromosome-specific human alpha satellite DNA

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Heterochromatin: Guardian of the Genome

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Human-Specific NOTCH2NL Genes Expand Cortical Neurogenesis through Delta/Notch Regulation

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Heterochromatin, Satellite DNA, and Cell Function

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WhatsHap: fast and accurate read-based phasingPreprint

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Androgen responsive adult human prostatic epithelial cell lines immortalized by human papillomavirus 18

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

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Inappropriate Gene Activation in FSHD

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Insulators and Boundaries: Versatile Regulatory Elements in the Eukaryotic Genome

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The DNA sequence and comparative analysis of human chromosome 20

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Segmental duplications and their variation in a complete human genome

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

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The epigenetic basis of cellular heterogeneity

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Role of H3K9me3 heterochromatin in cell identity establishment and maintenance

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Specification of kinetochore-forming chromatin by the histone H3 variant CENP-A

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Chimpanzee genomic diversity reveals ancient admixture with bonobos

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Genome-wide allele-specific analysis: insights into regulatory variation

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Deletion of <i>DXZ4</i> on the human inactive X chromosome alters higher-order genome architecture

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Long-read mapping to repetitive reference sequences using Winnowmap2

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Landscape of DNA methylation on the X chromosome reflects CpG density, functional chromatin state and X-chromosome inactivation

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Single-molecule regulatory architectures captured by chromatin fiber sequencing

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Genome-Wide Analysis of DNA Methylation Dynamics during Early Human Development

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X Chromosome Inactivation Is Initiated in Human Preimplantation Embryos

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Common themes and cell type specific variations of higher order chromatin arrangements in the mouse

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CTCF: the protein, the binding partners, the binding sites and their chromatin loops

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Facioscapulohumeral muscular dystrophy in mice overexpressing FRG1

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Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution

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

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Characterization of neo-centromeres in marker chromosomes lacking detectable alpha-satellite DNA

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A role for CTCF and cohesin in subtelomere chromatin organization, TERRA transcription, and telomere end protection

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The complete sequence of a human genomePreprint

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Probing DNA shape and methylation state on a genomic scale with DNase I

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Long-range single-molecule mapping of chromatin accessibility in eukaryotes

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Prognostic significance of HLA class I expression in osteosarcoma defined by anti‐pan HLA class I monoclonal antibody, EMR8‐5

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A conserved function for pericentromeric satellite DNA

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Umap and Bismap: quantifying genome and methylome mappability

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Survival motor neuron gene 2 silencing by DNA methylation correlates with spinal muscular atrophy disease severity and can be bypassed by histone deacetylase inhibition

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CpG Island Hypermethylation in Human Astrocytomas

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A near‐complete assembly of asparagus bean provides insights into anthocyanin accumulation in pods

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The ICF syndrome protein CDCA7 harbors a unique DNA binding domain that recognizes a CpG dyad in the context of a non-B DNA

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The complete diploid reference genome of RPE-1 identifies human phased epigenetic landscapesPreprint

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Genome graphs detect human polymorphisms in active epigenomic state during influenza infection

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