DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Replication timing maintains the global epigenetic state in human cells

(2021) Kyle N. Klein et al.   SCIENCE

Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer

(2020) Joanna Achinger-Kawecka et al.   Nature Communications

4D Genome Rewiring during Oncogene-Induced and Replicative Senescence

(2020) Satish Sati et al.   MOLECULAR CELL

Recurrence-Associated Long Non-coding RNA LNAPPCC Facilitates Colon Cancer Progression via Forming a Positive Feedback Loop with PCDH7

(2020) Ting Li et al.   Molecular Therapy-Nucleic Acids

Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer

(2020) Sarah E. Johnstone et al.   CELL

Replication timing and epigenome remodelling are associated with the nature of chromosomal rearrangements in cancer

(2019) Qian Du et al.   Nature Communications

Attenuated chromatin compartmentalization in meiosis and its maturation in sperm development

(2019) Kris G. Alavattam et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genome-wide stability of the DNA replication program in single mammalian cells

(2019) Saori Takahashi et al.   NATURE GENETICS

Heterochromatin drives compartmentalization of inverted and conventional nuclei

(2019) Martin Falk et al.   NATURE

Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization

(2019) Hisashi Miura et al.   NATURE GENETICS

The influence of DNA methylation on monoallelic expression

(2019) Simão Teixeira da Rocha et al.   Essays in Biochemistry

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Allele-specific control of replication timing and genome organization during development

(2018) Juan Carlos Rivera-Mulia et al.   GENOME RESEARCH

Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming

(2018) Ralph Stadhouders et al.   NATURE GENETICS

Accurate detection of complex structural variations using single-molecule sequencing

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

MLL2 conveys transcription-independent H3K4 trimethylation in oocytes

(2018) Courtney W. Hanna et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten

(2018) Shalima S. Nair et al.   Epigenetics & Chromatin

Single-cell replication profiling to measure stochastic variation in mammalian replication timing

(2018) Vishnu Dileep et al.   Nature Communications

MLL2 conveys transcription-independent H3K4 trimethylation in oocytes

(2018) Courtney W. Hanna et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Bottom–up modeling of chromatin segregation due to epigenetic modifications

(2018) Quinn MacPherson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Genome-Wide Study of Allele-Specific Expression in Colorectal Cancer

(2018) Zhi Liu et al.   Frontiers in Genetics

Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin

(2017) Adam G. Larson et al.   NATURE

DNA methylation signatures follow preformed chromatin compartments in cardiac myocytes

(2017) Stephan Nothjunge et al.   Nature Communications

Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression

(2017) Petko Fiziev et al.   Cell Reports

Structural Modeling of Chromatin Integrates Genome Features and Reveals Chromosome Folding Principle

(2017) Wen Jun Xie et al.   Scientific Reports

TADtool: visual parameter identification for TAD-calling algorithms

(2016) Kai Kruse et al.   BIOINFORMATICS

Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations

(2016) Phillippa C. Taberlay et al.   GENOME RESEARCH

Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos

(2016) Xiaoyu Liu et al.   NATURE

Allelic reprogramming of the histone modification H3K4me3 in early mammalian development

(2016) Bingjie Zhang et al.   NATURE

Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition

(2016) John Arne Dahl et al.   NATURE

Genes with monoallelic expression contribute disproportionately to genetic diversity in humans

(2016) Virginia Savova et al.   NATURE GENETICS

Spliced synthetic genes as internal controls in RNA sequencing experiments

(2016) Simon A Hardwick et al.   NATURE METHODS

H3K9me3 demethylase Kdm4d facilitates the formation of pre-initiative complex and regulates DNA replication

(2016) Rentian Wu et al.   NUCLEIC ACIDS RESEARCH

Epigenetic Determinants of Cancer

(2016) Stephen B. Baylin et al.   Cold Spring Harbor Perspectives in Biology

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor

(2015) Nathan C. Sheffield et al.   BIOINFORMATICS

Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells

(2015) Juan Carlos Rivera-Mulia et al.   GENOME RESEARCH

The role of DNA methylation in directing the functional organization of the cancer epigenome

(2015) Fides D. Lay et al.   GENOME RESEARCH

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer

(2014) Phillippa C. Taberlay et al.   GENOME RESEARCH

Redundant Mechanisms to Form Silent Chromatin at Pericentromeric Regions Rely on BEND3 and DNA Methylation

(2014) Nehmé Saksouk et al.   MOLECULAR CELL

The Candidate Cancer Gene Database: a database of cancer driver genes from forward genetic screens in mice

(2014) Kenneth L. Abbott et al.   NUCLEIC ACIDS RESEARCH

Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations

(2014) Eivind Lund et al.   NUCLEIC ACIDS RESEARCH

Interplay between the Cancer Genome and Epigenome

(2013) Hui Shen et al.   CELL

Lamin B1 depletion in senescent cells triggers large-scale changes in gene expression and the chromatin landscape

(2013) P. P. Shah et al.   GENES & DEVELOPMENT

Functional DNA demethylation is accompanied by chromatin accessibility

(2013) Kurinji Pandiyan et al.   NUCLEIC ACIDS RESEARCH

A Reference Methylome Database and Analysis Pipeline to Facilitate Integrative and Comparative Epigenomics

(2013) Qiang Song et al.   PLoS One

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes

(2013) James P Reddington et al.   GENOME BIOLOGY

Bpipe: a tool for running and managing bioinformatics pipelines

(2012) Simon P. Sadedin et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The aberrant asynchronous replication — characterizing lymphocytes of cancer patients — is erased following stem cell transplantation

(2012) Arnon Nagler et al.   BMC CANCER

Regional Activation of the Cancer Genome by Long-Range Epigenetic Remodeling

(2012) Saul A. Bert et al.   CANCER CELL

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Downregulation ofDLC-1Gene by Promoter Methylation during Primary Colorectal Cancer Progression

(2012) Haixia Peng et al.   Biomed Research International

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

PeakRanger: A cloud-enabled peak caller for ChIP-seq data

(2011) Xin Feng et al.   BMC BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Monoallelic Expression Determines Oncogenic Progression and Outcome in Benign and Malignant Brain Tumors

(2011) E. J. Walker et al.   CANCER RESEARCH

Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer

(2011) G. C. Hon et al.   GENOME RESEARCH

Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina–associated domains

(2011) Benjamin P Berman et al.   NATURE GENETICS

Histone hypoacetylation is required to maintain late replication timing of constitutive heterochromatin

(2011) Corella S. Casas-Delucchi et al.   NUCLEIC ACIDS RESEARCH

Allelic Skewing of DNA Methylation Is Widespread across the Genome

(2010) Leonard C. Schalkwyk et al.   AMERICAN JOURNAL OF HUMAN GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Nucleosome-Interacting Proteins Regulated by DNA and Histone Methylation

(2010) Till Bartke et al.   CELL

Heterochromatin protein 1 (HP1) modulates replication timing of the Drosophila genome

(2010) M. Schwaiger et al.   GENOME RESEARCH

Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types

(2010) T. Ryba et al.   GENOME RESEARCH

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Concerted Loading of Mcm2–7 Double Hexamers around DNA during DNA Replication Origin Licensing

(2009) Dirk Remus et al.   CELL

Sequencing newly replicated DNA reveals widespread plasticity in human replication timing

(2009) R. S. Hansen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Aberrant allele-specific replication, independent of parental origin, in blood cells of cancer patients

(2008) Zohar A Dotan et al.   BMC CANCER