Accurate Identification of DNA Replication Origin by Fusing Epigenomics and Chromatin Interaction Information

ORI-Deep: improving the accuracy for predicting origin of replication sites by using a blend of features and long short-term memory network

(2022) Mahwish Shahid et al.   BRIEFINGS IN BIOINFORMATICS

Mammalian DNA Replication Timing

(2021) Athanasios E. Vouzas et al.   Cold Spring Harbor Perspectives in Biology

iORI-ENST: identifying origin of replication sites based on elastic net and stacking learning

(2021) Y. Yao et al.   SAR AND QSAR IN ENVIRONMENTAL RESEARCH

Chromatin loop anchors predict transcript and exon usage

(2021) Yu Zhang et al.   BRIEFINGS IN BIOINFORMATICS

Expression and Prognostic Value of MCM Family Genes in Osteosarcoma

(2021) Jian Zhou et al.   Frontiers in Molecular Biosciences

The Emerging Roles of Fox Family Transcription Factors in Chromosome Replication, Organization, and Genome Stability

(2020) Yue Jin et al.   Cells

Superresolution imaging reveals spatiotemporal propagation of human replication foci mediated by CTCF-organized chromatin structures

(2020) Qian Peter Su et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ori-Finder 3: a web server for genome-wide prediction of replication origins in Saccharomyces cerevisiae

(2020) Dan Wang et al.   BRIEFINGS IN BIOINFORMATICS

Computational prediction of species-specific yeast DNA replication origin via iterative feature representation

(2020) Balachandran Manavalan et al.   BRIEFINGS IN BIOINFORMATICS

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

(2019) Qian Du et al.   Nature Communications

H2A.Z facilitates licensing and activation of early replication origins

(2019) Haizhen Long et al.   NATURE

iRO-3wPseKNC: identify DNA replication origins by three-window-based PseKNC

(2018) Bin Liu et al.   BIOINFORMATICS

The mechanism of eukaryotic CMG helicase activation

(2018) Max E. Douglas et al.   NATURE

Eukaryotic core promoters and the functional basis of transcription initiation

(2018) Vanja Haberle et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Using recursive feature elimination in random forest to account for correlated variables in high dimensional data

(2018) Burcu F. Darst et al.   BMC GENETICS

Transfer learning for classification of cardiovascular tissues in histological images

(2018) Claudia Mazo et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

Regulation of the initiation of DNA replication in human cells

(2018) Tatiana N. Moiseeva et al.   DNA REPAIR

RT States: systematic annotation of the human genome using cell type-specific replication timing programs

(2018) Axel Poulet et al.   BIOINFORMATICS

Identify origin of replication in Saccharomyces cerevisiae using two-step feature selection technique

(2018) Fu-Ying Dao et al.   BIOINFORMATICS

Transcription shapes DNA replication initiation and termination in human cells

(2018) Yu-Hung Chen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Mechanisms for initiating cellular DNA replication

(2017) Franziska Bleichert et al.   SCIENCE

Dynamic regulation of histone H3K9 is linked to the switch between replication and transcription at the Dbf4 origin-promoter locus

(2016) Kathleen Kylie et al.   CELL CYCLE

Replication origins: determinants or consequences of nuclear organization?

(2016) Anna B Marks et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Replicating Large Genomes: Divide and Conquer

(2016) Juan Carlos Rivera-Mulia et al.   MOLECULAR CELL

Selectivity of ORC binding sites and the relation to replication timing, fragile sites, and deletions in cancers

(2016) Benoit Miotto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Replication landscape of the human genome

(2016) Nataliya Petryk et al.   Nature Communications

iOri-Human: identify human origin of replication by incorporating dinucleotide physicochemical properties into pseudo nucleotide composition

(2016) Chang-Jian Zhang et al.   Oncotarget

iROS-gPseKNC: Predicting replication origin sites in DNA by incorporating dinucleotide position-specific propensity into general pseudo nucleotide composition

(2016) Xuan Xiao et al.   Oncotarget

c-ETS transcription factors play an essential role in the licensing of human MCM4 origin of replication

(2015) Kaveri Sidhu et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The core promoter: At the heart of gene expression

(2015) Yehuda M. Danino et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The chromatin environment shapes DNA replication origin organization and defines origin classes

(2015) Christelle Cayrou et al.   GENOME RESEARCH

A widespread role of the motif environment in transcription factor binding across diverse protein families

(2015) Iris Dror et al.   GENOME RESEARCH

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Replication stress is a potent driver of functional decline in ageing haematopoietic stem cells

(2014) Johanna Flach et al.   NATURE

iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition

(2014) Hao Lin et al.   NUCLEIC ACIDS RESEARCH

The Spatiotemporal Program of DNA Replication Is Associated with Specific Combinations of Chromatin Marks in Human Cells

(2014) Franck Picard et al.   PLoS Genetics

Chromatin and DNA Replication

(2013) D. M. MacAlpine et al.   Cold Spring Harbor Perspectives in Biology

DNA Replication Timing

(2013) N. Rhind et al.   Cold Spring Harbor Perspectives in Biology

Genomic Instability in Cancer

(2013) T. Abbas et al.   Cold Spring Harbor Perspectives in Biology

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Genome-wide depletion of replication initiation events in highly transcribed regions

(2011) M. M. Martin et al.   GENOME RESEARCH

Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features

(2011) C. Cayrou et al.   GENOME RESEARCH

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Spi-1/PU.1 Oncogene Accelerates DNA Replication Fork Elongation and Promotes Genetic Instability in the Absence of DNA Breakage

(2010) P. Rimmele et al.   CANCER RESEARCH

Chromatin signatures of the Drosophila replication program

(2010) M. L. Eaton et al.   GENOME RESEARCH

HBO1 Histone Acetylase Activity Is Essential for DNA Replication Licensing and Inhibited by Geminin

(2010) Benoit Miotto et al.   MOLECULAR CELL

Eukaryotic DNA replication origins: many choices for appropriate answers

(2010) Marcel Méchali   NATURE REVIEWS MOLECULAR CELL BIOLOGY

ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data

(2008) Nodin Weddington et al.   BMC BIOINFORMATICS

Replication fork movement sets chromatin loop size and origin choice in mammalian cells

(2008) Sylvain Courbet et al.   NATURE