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

Cellular senescence induces replication stress without affecting DNA replication timing

(2018) Juan Carlos Rivera-Mulia et al.   CELL CYCLE

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

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

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

(2018) Xianming Wang et al.   Molecular Metabolism

Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication

(2018) Jiao Sima et al.   CELL

Transcription-dependent regulation of replication dynamics modulates genome stability

(2018) Marion Blin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Takayo Sasaki et al.   EXPERIMENTAL HEMATOLOGY

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

(2017) Yan Guo et al.   GENOMICS

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

DNA replication timing alterations identify common markers between distinct progeroid diseases

(2017) Juan Carlos Rivera-Mulia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2017) A. Zachary Ostrow et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Macrophage-released ADAMTS1 promotes muscle stem cell activation

(2017) Hongqing Du et al.   Nature Communications

Identification of large disjoint motifs in biological networks

(2016) Rasha Elhesha et al.   BMC BIOINFORMATICS

How to rule the nucleus: divide et impera

(2016) Irina Solovei et al.   CURRENT OPINION IN CELL BIOLOGY

Replication timing and transcriptional control: beyond cause and effect — part III

(2016) Juan Carlos Rivera-Mulia et al.   CURRENT OPINION IN CELL BIOLOGY

Dissection of transcriptional andcis‐regulatory control of differentiation in human pancreatic cancer

(2016) Giuseppe R Diaferia et al.   EMBO JOURNAL

Replicating Large Genomes: Divide and Conquer

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

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

(2016) M. Costanzo et al.   SCIENCE

Systematic Functional Annotation and Visualization of Biological Networks

(2016) Anastasia Baryshnikova   Cell Systems

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

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Transcription factor binding dynamics during human ES cell differentiation

(2015) Alexander M. Tsankov et al.   NATURE

Motifs in the assembly of food web networks

(2015) Benjamin Baiser et al.   OIKOS

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

(2015) Emmanuelle Berger et al.   Biomed Research International

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

(2014) Robert C. Alver et al.   DNA REPAIR

Topologically associating domains are stable units of replication-timing regulation

(2014) Benjamin D. Pope et al.   NATURE

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

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

(2014) Pierre Therizols et al.   SCIENCE

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

(2013) Yufa Sun et al.   CARDIOVASCULAR RESEARCH

Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells

(2013) Casey A. Gifford et al.   CELL

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

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

(2013) K. J. Neelsen et al.   GENES & DEVELOPMENT

The DNA Replication Program Is Altered at the FMR1 Locus in Fragile X Embryonic Stem Cells

(2013) Jeannine Gerhardt et al.   MOLECULAR CELL

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

(2013) Elisa Laurenti et al.   NATURE IMMUNOLOGY

Asynchronous Replication, Mono-Allelic Expression, and Long Range Cis-Effects of ASAR6

(2013) Nathan Donley et al.   PLoS Genetics

Circuitry and Dynamics of Human Transcription Factor Regulatory Networks

(2012) Shane Neph et al.   CELL

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

(2012) Dmitry E. Koryakov et al.   CHROMOSOMA

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

(2012) T. Ryba et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Versican Processing by a Disintegrin-like and Metalloproteinase Domain with Thrombospondin-1 Repeats Proteinases-5 and -15 Facilitates Myoblast Fusion

(2012) Nicole Stupka et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

USF Binding Sequences from the HS4 Insulator Element Impose Early Replication Timing on a Vertebrate Replicator

(2012) Vahideh Hassan-Zadeh et al.   PLOS BIOLOGY

Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis

(2011) Noa Novershtern et al.   CELL

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

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

(2011) Xiang Hua Han et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Replication Timing: A Fingerprint for Cell Identity and Pluripotency

(2011) Tyrone Ryba et al.   PLoS Computational Biology

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) T. Ryba et al.   GENOME RESEARCH

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

(2009) I. Hiratani et al.   GENOME RESEARCH

Shifts in Replication Timing Actively Affect Histone Acetylation during Nucleosome Reassembly

(2009) Laura Lande-Diner et al.   MOLECULAR CELL

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

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

(2008) A. Goren et al.   GENES & DEVELOPMENT

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation

(2008) Ichiro Hiratani et al.   PLOS BIOLOGY

Geometric Interpretation of Gene Coexpression Network Analysis

(2008) Steve Horvath et al.   PLoS Computational Biology

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY