Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Selective nanopore sequencing of human BRCA1 by Cas9-assisted targeting of chromosome segments (CATCH)

(2018) Tslil Gabrieli et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Vishnu Dileep et al.   Nature Communications

BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files

(2018) Alexander Payne et al.   BIOINFORMATICS

Dbf4 recruitment by forkhead transcription factors defines an upstream rate-limiting step in determining origin firing timing

(2017) Dingqiang Fang et al.   GENES & DEVELOPMENT

DNA replication timing influences gene expression level

(2017) Carolin A. Müller et al.   JOURNAL OF CELL BIOLOGY

Detecting DNA cytosine methylation using nanopore sequencing

(2017) Jared T Simpson et al.   NATURE METHODS

Mapping DNA methylation with high-throughput nanopore sequencing

(2017) Arthur C Rand et al.   NATURE METHODS

Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI)

(2017) Chongyi Chen et al.   SCIENCE

dUTPase inhibition augments replication defects of 5-Fluorouracil

(2017) Anna Hagenkort et al.   Oncotarget

Quantitative BrdU immunoprecipitation method demonstrates that Fkh1 and Fkh2 are rate-limiting activators of replication origins that reprogram replication timing in G1 phase

(2016) Jared M. Peace et al.   GENOME RESEARCH

Nuclear Architecture Organized by Rif1 Underpins the Replication-Timing Program

(2016) Rossana Foti et al.   MOLECULAR CELL

Unreplicated DNA remaining from unperturbed S phases passes through mitosis for resolution in daughter cells

(2016) Alberto Moreno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of DNA Replication by Optical Mapping in Nanochannels

(2016) Joris Lacroix et al.   Small

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

Cas9-Assisted Targeting of CHromosome segments CATCH enables one-step targeted cloning of large gene clusters

(2015) Wenjun Jiang et al.   Nature Communications

Origin plasticity during budding yeast DNA replication in vitro

(2014) J. Gros et al.   EMBO JOURNAL

Prereplicative complexes assembled in vitro support origin-dependent and independent DNA replication

(2014) K. F. On et al.   EMBO JOURNAL

DNA replication and spindle checkpoints cooperate during S phase to delay mitosis and preserve genome integrity

(2014) Maria M. Magiera et al.   JOURNAL OF CELL BIOLOGY

Kinetochores Coordinate Pericentromeric Cohesion and Early DNA Replication by Cdc7-Dbf4 Kinase Recruitment

(2013) Toyoaki Natsume et al.   MOLECULAR CELL

Migrating bubble during break-induced replication drives conservative DNA synthesis

(2013) Natalie Saini et al.   NATURE

The dynamics of genome replication using deep sequencing

(2013) Carolin A. Müller et al.   NUCLEIC ACIDS RESEARCH

Break-induced replication occurs by conservative DNA synthesis

(2013) R. A. Donnianni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Resolution Replication Profiles Define the Stochastic Nature of Genome Replication Initiation and Termination

(2013) Michelle Hawkins et al.   Cell Reports

dNTP pools determine fork progression and origin usage under replication stress

(2012) Jérôme Poli et al.   EMBO JOURNAL

Unraveling cell type–specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs

(2012) Emilie Besnard et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Regulation of DNA Replication within the Immunoglobulin Heavy-Chain Locus During B Cell Commitment

(2012) Agnieszka Demczuk et al.   PLOS BIOLOGY

Thymidine Analogues for Tracking DNA Synthesis

(2011) Brenton L. Cavanagh et al.   MOLECULES

Monitoring DNA replication in fission yeast by incorporation of 5-ethynyl-2′-deoxyuridine

(2011) Hui Hua et al.   NUCLEIC ACIDS RESEARCH

OriDB, the DNA replication origin database updated and extended

(2011) C. C. Siow et al.   NUCLEIC ACIDS RESEARCH

Chk1 inhibits replication factory activation but allows dormant origin firing in existing factories

(2010) Xin Quan Ge et al.   JOURNAL OF CELL BIOLOGY

GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome

(2010) Matthew D Sekedat et al.   Molecular Systems Biology

Evaluating genome-scale approaches to eukaryotic DNA replication

(2010) David M. Gilbert   NATURE REVIEWS GENETICS

Eukaryotic DNA replication origins: many choices for appropriate answers

(2010) Marcel Méchali   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Defining replication origin efficiency using DNA fiber assays

(2009) Sandie Tuduri et al.   CHROMOSOME RESEARCH

Cell type specific applicability of 5-ethynyl-2′-deoxyuridine (EdU) for dynamic proliferation assessment in flow cytometry

(2009) Simone Diermeier-Daucher et al.   CYTOMETRY PART A

Excess MCM proteins protect human cells from replicative stress by licensing backup origins of replication

(2008) Arkaitz Ibarra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay

(2008) L. Dolken et al.   RNA