Related references
Note: Only part of the references are listed.Twelve years of SAMtools and BCFtools
Petr Danecek et al.
GIGASCIENCE (2021)
H3K27ac bookmarking promotes rapid post-mitotic activation of the pluripotent stem cell program without impacting 3D chromatin reorganization
Bobbie Pelham-Webb et al.
MOLECULAR CELL (2021)
Replication timing maintains the global epigenetic state in human cells
Kyle N. Klein et al.
SCIENCE (2021)
Genome-wide mapping of human DNA replication by optical replication mapping supports a stochastic model of eukaryotic replication
Weitao Wang et al.
MOLECULAR CELL (2021)
H2A.Z facilitates licensing and activation of early replication origins
Haizhen Long et al.
NATURE (2020)
SciPy 1.0: fundamental algorithms for scientific computing in Python
Pauli Virtanen et al.
NATURE METHODS (2020)
Histone variant H3.3 residue S31 is essential for Xenopus gastrulation regardless of the deposition pathway
David Sitbon et al.
NATURE COMMUNICATIONS (2020)
Chromatin replication and epigenetic cell memory
Kathleen R. Stewart-Morgan et al.
NATURE CELL BIOLOGY (2020)
The roles of histone variants in fine-tuning chromatin organization and function
Sara Martire et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2020)
Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites
Alexy Promonet et al.
NATURE COMMUNICATIONS (2020)
Array programming with NumPy
Charles R. Harris et al.
NATURE (2020)
Two HIRA-dependent pathways mediate H3.3 de novo deposition and recycling during transcription
Julia Torne et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2020)
Histone deposition pathways determine the chromatin landscapes of H3.1 and H3.3 K27M oncohistones
Jay F. Sarthy et al.
ELIFE (2020)
Developmental differences in genome replication program and origin activation
Cathia Rausch et al.
NUCLEIC ACIDS RESEARCH (2020)
Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans
Maude Strobino et al.
GENOME RESEARCH (2020)
The expanding landscape of 'oncohistone' mutations in human cancers
Benjamin A. Nacev et al.
NATURE (2019)
Phosphorylation of histone H3.3 at serine 31 promotes p300 activity and enhancer acetylation
Sara Martire et al.
NATURE GENETICS (2019)
Dynamic Incorporation of Histone H3 Variants into Chromatin Is Essential for Acquisition of Aggressive Traits and Metastatic Colonization
Ana P. Gomes et al.
CANCER CELL (2019)
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
Daehwan Kim et al.
NATURE BIOTECHNOLOGY (2019)
Control of DNA replication timing in the 3D genome
Claire Marchal et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2019)
Active and Repressed Chromatin Domains Exhibit Distinct Nucleosome Segregation during DNA Replication
Thelma M. Escobar et al.
CELL (2019)
Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication
Jiao Sima et al.
CELL (2019)
Transcription shapes DNA replication initiation and termination in human cells
Yu-Hung Chen et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2019)
The Encyclopedia of DNA elements (ENCODE): data portal update
Carrie A. Davis et al.
NUCLEIC ACIDS RESEARCH (2018)
Chromatin domains rich in inheritance
Danny Reinberg et al.
SCIENCE (2018)
Intragenic origins due to short G1 phases underlie oncogene-induced DNA replication stress
Morgane Macheret et al.
NATURE (2018)
High-resolution visualization of H3 variants during replication reveals their controlled recycling
Camille Clement et al.
NATURE COMMUNICATIONS (2018)
Functional activity of the H3.3 histone chaperone complex HIRA requires trimerization of the HIRA subunit
Dominique Ray-Gallet et al.
NATURE COMMUNICATIONS (2018)
Chromatin plasticity: A versatile landscape that underlies cell fate and identity
Tejas Yadav et al.
SCIENCE (2018)
H3K9me3 demethylase Kdm4d facilitates the formation of pre-initiative complex and regulates DNA replication
Rentian Wu et al.
NUCLEIC ACIDS RESEARCH (2017)
DNA replication timing during development anticipates transcriptional programs and parallels enhancer activation
Joseph C. Siefert et al.
GENOME RESEARCH (2017)
Variants of core histones and their roles in cell fate decisions, development and cancer
Marcus Buschbeck et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2017)
H3K4 Methylation-Dependent Memory of Somatic Cell Identity Inhibits Reprogramming and Development of Nuclear Transfer Embryos
Eva Hormanseder et al.
CELL STEM CELL (2017)
DNA replication origins-where do we begin?
Marie-Noelle Prioleau et al.
GENES & DEVELOPMENT (2016)
deepTools2: a next generation web server for deep-sequencing data analysis
Fidel Ramirez et al.
NUCLEIC ACIDS RESEARCH (2016)
Selectivity of ORC binding sites and the relation to replication timing, fragile sites, and deletions in cancers
Benoit Miotto et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Maintenance of Epigenetic Information
Genevieve Almouzni et al.
COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2016)
Replication landscape of the human genome
Nataliya Petryk et al.
NATURE COMMUNICATIONS (2016)
The Histone Variant H3.3 Is Enriched at Drosophila Amplicon Origins but Does Not Mark Them for Activation
Neha P. Paranjape et al.
G3-GENES GENOMES GENETICS (2016)
The chromatin environment shapes DNA replication origin organization and defines origin classes
Christelle Cayrou et al.
GENOME RESEARCH (2015)
Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells
Juan Carlos Rivera-Mulia et al.
GENOME RESEARCH (2015)
Mitotic Transcriptional Activation: Clearance of Actively Engaged Pol II via Transcriptional Elongation Control in Mitosis
Kaiwei Liang et al.
MOLECULAR CELL (2015)
Epigenomics Roadmap for regulation
Casey E. Romanoski et al.
NATURE (2015)
The histone chaperone CAF-1 safeguards somatic cell identity
Sihem Cheloufi et al.
NATURE (2015)
DNA replication origin activation in space and time
Michalis Fragkos et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2015)
Histone H3 Variants and Their Chaperones During Development and Disease: Contributing to Epigenetic Control
Dan Filipescu et al.
ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY, VOL 30 (2014)
Hira-Mediated H3.3 Incorporation Is Required for DNA Replication and Ribosomal RNA Transcription in the Mouse Zygote
Chih-Jen Lin et al.
DEVELOPMENTAL CELL (2014)
Transcription Recovery after DNA Damage Requires Chromatin Priming by the H3.3 Histone Chaperone HIRA
Salome Adam et al.
CELL (2013)
Genome-wide mapping of human DNA-replication origins: Levels of transcription at ORC1 sites regulate origin selection and replication timing
Gaetano Ivan Dellino et al.
GENOME RESEARCH (2013)
Controlling DNA replication origins in response to DNA damage - inhibit globally, activate locally
Mona Yekezare et al.
JOURNAL OF CELL SCIENCE (2013)
Evolution of histone H3: emergence of variants and conservation of post-translational modification sites
Jakob H. Waterborg
BIOCHEMISTRY AND CELL BIOLOGY (2012)
Interference Between DNA Replication and Transcription as a Cause of Genomic Instability
Yea-Lih Lin et al.
CURRENT GENOMICS (2012)
Fast gapped-read alignment with Bowtie 2
Ben Langmead et al.
NATURE METHODS (2012)
Unraveling cell type-specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs
Emilie Besnard et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2012)
Analysis of DNA replication profiles in budding yeast and mammalian cells using DNA combing
Julien N. Bianco et al.
METHODS (2012)
Dynamics of Histone H3 Deposition In Vivo Reveal a Nucleosome Gap-Filling Mechanism for H3.3 to Maintain Chromatin Integrity
Dominique Ray-Gallet et al.
MOLECULAR CELL (2011)
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan et al.
BIOINFORMATICS (2010)
Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions
Aaron D. Goldberg et al.
CELL (2010)
Quantitative Interaction Proteomics and Genome-wide Profiling of Epigenetic Histone Marks and Their Readers
Michiel Vermeulen et al.
CELL (2010)
Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis
Ichiro Hiratani et al.
GENOME RESEARCH (2010)
Sequencing newly replicated DNA reveals widespread plasticity in human replication timing
R. Scott Hansen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Mixing or Not Mixing
Dominique Ray-Gallet et al.
SCIENCE (2010)
Genome-Wide Kinetics of Nucleosome Turnover Determined by Metabolic Labeling of Histones
Roger B. Deal et al.
SCIENCE (2010)
Epigenetic inheritance during the cell cycle
Aline V. Probst et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2009)
Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation
Ichiro Hiratani et al.
PLOS BIOLOGY (2008)
Epigenetic memory of an active gene state depends on histone H3.3 incorporation into chromatin in the absence of transcription
Ray Kit Ng et al.
NATURE CELL BIOLOGY (2008)
Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis
H Tagami et al.
CELL (2004)