(Q92755600)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31434679%20AND%20SRC:MED&resulttype=core&format=json

1 May 2020

title

Replication timing networks reveal a link between transcription regulatory circuits and replication timing control (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31434679%20AND%20SRC:MED&resulttype=core&format=json

1 May 2020

author

Juan Carlos Rivera-Mulia

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31434679%20AND%20SRC:MED&resulttype=core&format=json

1 May 2020

Sebo Kim

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31434679%20AND%20SRC:MED&resulttype=core&format=json

1 May 2020

Haitham Gabr

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31434679%20AND%20SRC:MED&resulttype=core&format=json

1 May 2020

Abhijit Chakraborty

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31434679%20AND%20SRC:MED&resulttype=core&format=json

1 May 2020

Ferhat Ay

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31434679%20AND%20SRC:MED&resulttype=core&format=json

1 May 2020

Tamer Kahveci

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31434679%20AND%20SRC:MED&resulttype=core&format=json

1 May 2020

David M Gilbert

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31434679%20AND%20SRC:MED&resulttype=core&format=json

1 May 2020

publication date

21 August 2019

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31434679%20AND%20SRC:MED&resulttype=core&format=json

1 May 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31434679%20AND%20SRC:MED&resulttype=core&format=json

1 May 2020

volume

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31434679%20AND%20SRC:MED&resulttype=core&format=json

1 May 2020

issue

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31434679%20AND%20SRC:MED&resulttype=core&format=json

1 May 2020

page(s)

1415-1428

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31434679%20AND%20SRC:MED&resulttype=core&format=json

describes a project that uses

1 May 2020

Cytoscape

1 reference

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

based on heuristic

inferred from PubMed Central ID database lookup

cites work

Transcription-dependent regulation of replication dynamics modulates genome stability

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Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication

11 February 2021

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11 February 2021

1 reference

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Cellular senescence induces replication stress with almost no affect on DNA replication timing

11 February 2021

1 reference

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

11 February 2021

1 reference

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Genome-wide analysis of PDX1 target genes in human pancreatic progenitors

11 February 2021

1 reference

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11 February 2021

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DNA replication timing alterations identify common markers between distinct progeroid diseases.

11 February 2021

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11 February 2021

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Macrophage-released ADAMTS1 promotes muscle stem cell activation

11 February 2021

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Stability of patient-specific features of altered DNA replication timing in xenografts of primary human acute lymphoblastic leukemia

11 February 2021

1 reference

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Conserved forkhead dimerization motif controls DNA replication timing and spatial organization of chromosomes in S. cerevisiae.

11 February 2021

1 reference

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Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis.

11 February 2021

1 reference

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Identification of large disjoint motifs in biological networks

11 February 2021

1 reference

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A global genetic interaction network maps a wiring diagram of cellular function

11 February 2021

1 reference

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Replicating Large Genomes: Divide and Conquer

11 February 2021

1 reference

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Systematic Functional Annotation and Visualization of Biological Networks

11 February 2021

1 reference

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Replication timing and transcriptional control: beyond cause and effect-part III.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

How to rule the nucleus: divide et impera

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Dissection of transcriptional and cis-regulatory control of differentiation in human pancreatic cancer

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Large-Scale Chromatin Structure-Function Relationships during the Cell Cycle and Development: Insights from Replication Timing.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Computing interaction probabilities in signaling networks.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Gene Network Analysis of Glucose Linked Signaling Pathways and Their Role in Human Hepatocellular Carcinoma Cell Growth and Survival in HuH7 and HepG2 Cell Lines

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

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

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Transcription factor binding dynamics during human ES cell differentiation

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Integrative analysis of 111 reference human epigenomes

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Chromatin decondensation is sufficient to alter nuclear organization in embryonic stem cells.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Gene Ontology Consortium: going forward

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Topologically associating domains are stable units of replication-timing regulation

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

The contribution of dormant origins to genome stability: from cell biology to human genetics.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Deregulated origin licensing leads to chromosomal breaks by rereplication of a gapped DNA template

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

The DNA replication program is altered at the FMR1 locus in fragile X embryonic stem cells

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

MiR-490-3p modulates the proliferation of vascular smooth muscle cells induced by ox-LDL through targeting PAPP-A.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

The transcriptional architecture of early human hematopoiesis identifies multilevel control of lymphoid commitment

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Epigenomic analysis of multilineage differentiation of human embryonic stem cells

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Transcriptional and epigenetic dynamics during specification of human embryonic stem cells

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Asynchronous replication, mono-allelic expression, and long range Cis-effects of ASAR6.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Versican processing by a disintegrin-like and metalloproteinase domain with thrombospondin-1 repeats proteinases-5 and -15 facilitates myoblast fusion.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Induced transcription results in local changes in chromatin structure, replication timing, and DNA polytenization in a site of intercalary heterochromatin.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Circuitry and dynamics of human transcription factor regulatory networks

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

GENCODE: the reference human genome annotation for The ENCODE Project

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Architecture of the human regulatory network derived from ENCODE data

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Abnormal developmental control of replication-timing domains in pediatric acute lymphoblastic leukemia

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

USF binding sequences from the HS4 insulator element impose early replication timing on a vertebrate replicator.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Fast gapped-read alignment with Bowtie 2

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Replication timing: a fingerprint for cell identity and pluripotency

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Interactome networks and human disease

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

A WNT/β-Catenin Signaling Activator, R-spondin, Plays Positive Regulatory Roles during Skeletal Myogenesis

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Densely interconnected transcriptional circuits control cell states in human hematopoiesis

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

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

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

BEDTools: a flexible suite of utilities for comparing genomic features

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Shifts in replication timing actively affect histone acetylation during nucleosome reassembly

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

WGCNA: an R package for weighted correlation network analysis

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Global reorganization of replication domains during embryonic stem cell differentiation

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Model-based analysis of ChIP-Seq (MACS)

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Geometric interpretation of gene coexpression network analysis

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

DNA replication timing of the human beta-globin domain is controlled by histone modification at the origin

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Network motifs: theory and experimental approaches

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Pathway recognition and augmentation by computational analysis of microarray expression data

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Quantifying the relationship between co-expression, co-regulation and gene function

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Cytoscape: a software environment for integrated models of biomolecular interaction networks

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Genome-wide coexpression dynamics: theory and application

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Network motifs: simple building blocks of complex networks

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Genetic network inference: from co-expression clustering to reverse engineering

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Gene ontology: tool for the unification of biology

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Replicon clusters are stable units of chromosome structure: evidence that nuclear organization contributes to the efficient activation and propagation of S phase in human cells

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Human hepatocellular carcinoma cell lines secrete the major plasma proteins and hepatitis B surface antigen

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

Neuronal cell differentiation of human neuroblastoma cells by retinoic acid plus herbimycin A.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6724675

11 February 2021

Identifiers

DOI

10.1101/GR.247049.118

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31434679%20AND%20SRC:MED&resulttype=core&format=json

1 May 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31434679%20AND%20SRC:MED&resulttype=core&format=json

1 May 2020

PubMed publication ID

31434679

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31434679%20AND%20SRC:MED&resulttype=core&format=json