Epigenetic patterns in a complete human genome

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

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

(2021) Glennis A. Logsdon et al.   NATURE

Forged by DXZ4, FIRRE, and ICCE: How Tandem Repeats Shape the Active and Inactive X Chromosome

(2020) Prakhar Bansal et al.   Frontiers in Cell and Developmental Biology

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

(2020) Kishwar Shafin et al.   NATURE BIOTECHNOLOGY

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

Single-molecule regulatory architectures captured by chromatin fiber sequencing

(2020) Andrew B. Stergachis et al.   SCIENCE

Loss of X Chromosome Inactivation in Androgenetic Complete Hydatidiform Moles With 46, XX Karyotype

(2020) Xiaojing Chen et al.   INTERNATIONAL JOURNAL OF GYNECOLOGICAL PATHOLOGY

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

(2020) Isac Lee et al.   NATURE METHODS

HDAC Inhibition Increases HLA Class I Expression in Uveal Melanoma

(2020) Zahra Souri et al.   Cancers

Genomic inversions and GOLGA core duplicons underlie disease instability at the 15q25 locus

(2019) Flavia A. M. Maggiolini et al.   PLoS Genetics

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

(2019) Remco Bouckaert et al.   PLoS Computational Biology

Centromeric Satellite DNAs: Hidden Sequence Variation in the Human Population

(2019) Miga   Genes

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

(2019) Sasha A Langley et al.   eLife

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

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

The Human-Specific BOLA2 Duplication Modifies Iron Homeostasis and Anemia Predisposition in Chromosome 16p11.2 Autism Individuals

(2019) Giuliana Giannuzzi et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Human NORs, comprising rDNA arrays and functionally conserved distal elements, are located within dynamic chromosomal regions

(2019) Marjolein van Sluis et al.   GENES & DEVELOPMENT

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

(2018) Ikuo K. Suzuki et al.   CELL

Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis

(2018) Ian T. Fiddes et al.   CELL

Unexpected conformational variations of the human centromeric chromatin complex

(2018) Jitendra Thakur et al.   GENES & DEVELOPMENT

Cis D4Z4 repeat duplications associated with facioscapulohumeral muscular dystrophy type 2

(2018) Richard J L F Lemmers et al.   HUMAN MOLECULAR GENETICS

Epigenomics in 3D: importance of long-range spreading and specific interactions in epigenomic maintenance

(2018) Daniel Jost et al.   NUCLEIC ACIDS RESEARCH

DNA methylation reprogramming of functional elements during mammalian embryonic development

(2018) Congru Li et al.   Cell Discovery

Heterochromatin: Guardian of the Genome

(2018) Aniek Janssen et al.   Annual Review of Cell and Developmental Biology

Umap and Bismap: quantifying genome and methylome mappability

(2018) Mehran Karimzadeh et al.   NUCLEIC ACIDS RESEARCH

MadID, a Versatile Approach to Map Protein-DNA Interactions, Highlights Telomere-Nuclear Envelope Contact Sites in Human Cells

(2018) Michal Sobecki et al.   Cell Reports

The 4D nucleome project

(2017) Job Dekker et al.   NATURE

Detecting DNA cytosine methylation using nanopore sequencing

(2017) Jared T Simpson et al.   NATURE METHODS

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

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

Centromere evolution and CpG methylation during vertebrate speciation

(2017) Kazuki Ichikawa et al.   Nature Communications

Genomic variation within alpha satellite DNA influences centromere location on human chromosomes with metastable epialleles

(2016) Megan E. Aldrup-MacDonald et al.   GENOME RESEARCH

Schizophrenia risk from complex variation of complement component 4

(2016) Aswin Sekar et al.   NATURE

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Deletion ofDXZ4on the human inactive X chromosome alters higher-order genome architecture

(2016) Emily M. Darrow et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chimpanzee genomic diversity reveals ancient admixture with bonobos

(2016) M. de Manuel et al.   SCIENCE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

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

(2014) Allison M. Cotton et al.   HUMAN MOLECULAR GENETICS

Epigenetic resolution of the ‘curse of complexity’ in adaptive evolution of complex traits

(2014) Alexander V. Badyaev   JOURNAL OF PHYSIOLOGY-LONDON

The DNA methylation landscape of human early embryos

(2014) Hongshan Guo et al.   NATURE

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

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

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

(2012) Zhong Deng et al.   EMBO JOURNAL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Transposable Elements, Epigenetics, and Genome Evolution

(2012) N. V. Fedoroff   SCIENCE

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

(2012) Kasper D Hansen et al.   GENOME BIOLOGY

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

(2011) Felix Krueger et al.   BIOINFORMATICS

Distinct DNA methylation patterns associated with active and inactive centromeres of the maize B chromosome

(2011) D.-H. Koo et al.   GENOME RESEARCH

Aberrant Overexpression of Satellite Repeats in Pancreatic and Other Epithelial Cancers

(2011) D. T. Ting et al.   SCIENCE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

CpG Island Hypermethylation in Human Astrocytomas

(2010) Xiwei Wu et al.   CANCER RESEARCH

Perspectives and diagnostic considerations in spinal muscular atrophy

(2010) Thomas W Prior   GENETICS IN MEDICINE

Diversity of Human Copy Number Variation and Multicopy Genes

(2010) Peter H. Sudmant et al.   SCIENCE

Sequencing Primate Genomes: What Have We Learned?

(2009) Tomas Marques-Bonet et al.   Annual Review of Genomics and Human Genetics

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Long tandem repeats as a form of genomic copy number variation: structure and length polymorphism of a chromosome 5p repeat in control and schizophrenia populations

(2009) Heather A. Bruce et al.   PSYCHIATRIC GENETICS

Aggressive assembly of pyrosequencing reads with mates

(2008) Jason R. Miller et al.   BIOINFORMATICS

DXZ4 chromatin adopts an opposing conformation to that of the surrounding chromosome and acquires a novel inactive X-specific role involving CTCF and antisense transcripts

(2008) B. P. Chadwick   GENOME RESEARCH

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

(2008) Jan Hauke et al.   HUMAN MOLECULAR GENETICS

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

(2008) Robin C. Allshire et al.   NATURE REVIEWS GENETICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY