D. Gilbert

发表

Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression

William Stafford Noble, Maxwell W. Libbrecht, J. Bilmes, 2014, bioRxiv.

Expanded encyclopaedias of DNA elements in the human and mouse genomes

Michael J. Purcaro, Gene W. Yeo, M. Gerstein, 2020, Nature.

Defining functional DNA elements in the human genome

Morgan C. Giddings, E. Birney, M. Gerstein, 2014, Proceedings of the National Academy of Sciences.

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

S. Dalton, Jinfeng Zhang, D. Gilbert, 2010, Genome research.

SPIN reveals genome-wide landscape of nuclear compartmentalization

D. Gilbert, B. van Steensel, A. Belmont, 2021, Genome biology.

Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program

William Stafford Noble, Daniel L. Vera, William S Noble, 2015, Genome research.

Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq

Daniel L. Vera, Juan Carlos Rivera-Mulia, D. Gilbert, 2018, Nature Protocols.

Integrative detection and analysis of structural variation in cancer genomes

William Stafford Noble, Jesse R. Dixon, Royden A. Clark, 2018, Nature Genetics.

SPIN reveals genome-wide landscape of nuclear compartmentalization

D. Gilbert, B. van Steensel, A. Belmont, 2020, Genome Biology.

An encyclopedia of mouse DNA elements (Mouse ENCODE)

Philip Cayting, Katrina Learned, Daniel Blankenberg, 2012, Genome Biology.

A comparative encyclopedia of DNA elements in the mouse genome

Shane J. Neph, Dmitri D. Pervouchine, Matthew D. Rasmussen, 2014, Nature.

The many faces of the origin recognition complex.

D. Gilbert, Takayo Sasaki, 2007, Current opinion in cell biology.

Maintenance of Stable Heterochromatin Domains by Dynamic HP1 Binding

Tom Misteli, T. Misteli, T. Jenuwein, 2003, Science.

Local rewiring of genome–nuclear lamina interactions by transcription

Peiyao A. Zhao, D. Gilbert, B. van Steensel, 2020, The EMBO journal.

Local rewiring of genome–nuclear lamina interactions by transcription

Peiyao A. Zhao, D. Gilbert, B. van Steensel, 2019, bioRxiv.

Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell type-specific expression

William Stafford Noble, Maxwell W. Libbrecht, J. Bilmes, 2014, bioRxiv.

Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation.

Hiroshi Kimura, Rory Stark, Michael D. Wilson, 2012, Molecular cell.

Replication timing and transcriptional control: beyond cause and effect.

D. Gilbert, David M Gilbert, 2009, Current opinion in cell biology.

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

D. Gilbert, I. Hiratani, Junjie Lu, 2002, Current Opinion in Genetics and Development.

Highly stable loading of Mcm proteins onto chromatin in living cells requires replication to unload

Michael W. Davidson, James G. McNally, David M. Gilbert, 2011, The Journal of cell biology.

In search of the holy replicator

David M. Gilbert, D. Gilbert, 2004, Nature Reviews Molecular Cell Biology.

Replicating Chromatin in the Eukaryotic Genome

D. Gilbert, M. Gordon, D. Bartlett, 2018 .

Evaluating genome-scale approaches to eukaryotic DNA replication

David M. Gilbert, D. Gilbert, 2010, Nature Reviews Genetics.

Overexpression of ORC subunits and increased ORC‐chromatin association in transformed mammalian cells

D. Gilbert, A. Mcnairn, Adrian J. McNairn, 2005, Journal of cellular biochemistry.

Site-specific initiation of DNA replication in Xenopus egg extract requires nuclear structure

M. DePamphilis, D. Gilbert, H. Miyazawa, 1995, Molecular and cellular biology.

Stability, chromatin association and functional activity of mammalian pre‐replication complex proteins during the cell cycle

J. Pines, N. den Elzen, D. Gilbert, 2001, The EMBO journal.

Making Sense of Eukaryotic DNA Replication Origins

David M. Gilbert, D. Gilbert, 2001, Science.

Replicating Large Genomes: Divide and Conquer.

Juan Carlos Rivera-Mulia, D. Gilbert, J. Rivera-Mulia, 2016, Molecular cell.

DNA replication timing.

N. Rhind, D. Gilbert, 2013, Cold Spring Harbor perspectives in biology.

Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation

Dirk Schübeler, Mari Itoh, Tyrone Ryba, 2008, PLoS biology.

Control of DNA replication timing in the 3D genome

D. Gilbert, Jiao Sima, Claire Marchal, 2019, Nature Reviews Molecular Cell Biology.

Identification of cis Elements for Spatio-temporal Control of DNA Replication

Daniel L. Vera, Kyle N. Klein, S. Mundlos, 2018 .

Identification of cis elements for spatio-temporal control of DNA replication

Daniel L. Vera, Kyle N. Klein, S. Mundlos, 2018, bioRxiv.

Epigenetic Control of Hundreds of Chromosome-Associated lncRNA Genes Essential for Replication and Stability

P. Spellman, D. Gilbert, E. Bouhassira, 2022, bioRxiv.

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

Daniel L. Vera, P. Fraser, D. Gilbert, 2017, bioRxiv.

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

Daniel L. Vera, P. Fraser, D. Gilbert, 2017, bioRxiv.

Activation of mammalian Chk1 during DNA replication arrest

C. Smythe, D. Gilbert, C. Feijóo, 2001, The Journal of cell biology.

DNA Replication Timing Is Maintained Genome-Wide in Primary Human Myoblasts Independent of D4Z4 Contraction in FSH Muscular Dystrophy

David M. Gilbert, Tyrone Ryba, Dana Battaglia, 2011, PloS one.

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

Zhaohui S. Qin, Z. Qin, D. Gilbert, 2018, bioRxiv.

Genome-wide analysis of replication timing in mammalian cells: troubleshooting problems encountered when comparing different cell types.

D. Gilbert, V. Dileep, Ruth A. Didier, 2012, Methods.

Epigenetic vs. Sequence-Dependent Control of Eukaryotic Replication Timing

Kyle N. Klein, D. Gilbert, 2016 .

Replication origins run (ultra) deep

D. Gilbert, 2012, Nature Structural &Molecular Biology.

Cohesin depleted cells pass through mitosis and reconstitute a functional nuclear architecture

Erez Lieberman Aiden, Volker J Schmid, Kyle N. Klein, 2019 .

The replication origin decision point is a mitogen-independent, 2-aminopurine-sensitive, G1-phase event that precedes restriction point control

D. Gilbert, J. R. Wu, 1997, Molecular and cellular biology.

Spatial distribution and specification of mammalian replication origins during G 1 phase

D. Gilbert, E. Solessio, Feng Li, 2003 .

Spatial distribution and specification of mammalian replication origins during G1 phase

D. Gilbert, E. Solessio, Feng Li, 2003, The Journal of cell biology.

Replication origins in yeast versus metazoa: separation of the haves and the have nots.

D. Gilbert, D. Gilbert, 1998, Current opinion in genetics & development.

Regulation of mammalian replication origin usage in Xenopus egg extract.

D. Gilbert, D. Dimitrova, 1998, Journal of cell science.

Development of a single-cell array for large-scale DNA fluorescence in situ hybridization.

Steven Lenhert, Jingjiao Guan, James W. Shirley, 2013, Lab on a chip.

Evidence for a mammalian late-G1 phase inhibitor of replication licensing distinct from geminin or Cdk activity

D. Gilbert, J. Blow, Takayo Sasaki, 2011, Nucleus.

Temporally coordinated assembly and disassembly of replication factories in the absence of DNA synthesis

D. Gilbert, D. Dimitrova, 2000, Nature Cell Biology.

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

Tamer Kahveci, F. Ay, D. Gilbert, 2019, Genome research.

Replication Timing Networks: a novel class of gene regulatory networks

Tamer Kahveci, D. Gilbert, J. Rivera-Mulia, 2017, bioRxiv.

Replication Timing Networks: a novel class of gene regulatory networks

Tamer Kahveci, D. Gilbert, J. Rivera-Mulia, 2017, bioRxiv.

Origin-specific initiation of mammalian nuclear DNA replication in a Xenopus cell-free system.

D. Gilbert, G. Yu, J. R. Wu, 1997, Methods.

Replication Labeling with Halogenated Thymidine Analogs

D. Gilbert, T. Yokochi, D. Gilbert, 2007, Current protocols in cell biology.

Mimosine Arrests DNA Synthesis at Replication Forks by Inhibiting Deoxyribonucleotide Metabolism (*)

M. DePamphilis, D. Gilbert, W. Burhans, 1995, The Journal of Biological Chemistry.

Replication timing of DNA sequences associated with human centromeres and telomeres

H. Willard, D. Gilbert, S. Cohen, 1990, Molecular and cellular biology.

Head and/or CaaX domain deletions of lamin proteins disrupt preformed lamin A and C but not lamin B structure in mammalian cells.

D. Gilbert, C. Hutchison, M. Izumi, 2000, Molecular Biology of the Cell.

Bovine papilloma virus plasmids replicate randomly in mouse fibroblasts throughout S phase of the cell cycle

Stanley N Cohen, D. Gilbert, 1987, Cell.

Chromosome architecture can dictate site-specific initiation of DNA replication in Xenopus egg extracts

D. Gilbert, J. R. Wu, S. Keezer, 1996, The Journal of cell biology.

Lovastatin arrests CHO cells between the origin decision point and the restriction point

D. Gilbert, Jia-Rui Wu, Jia-rui Wu, 2000, FEBS letters.

Genome-Wide Identification of Early-Firing Human Replication Origins by Optical Replication Mapping [preprint]

Kyle N. Klein, N. Rhind, Z. Weng, 2020 .

Genome-Wide Identification of Early-Firing Human Replication Origins by Optical Replication Mapping

Kyle N. Klein, N. Rhind, Z. Weng, 2017, bioRxiv.

Site-specific initiation of DNA replication in metazoan chromosomes and the role of nuclear organization.

M. DePamphilis, D. Gilbert, J. Blow, 1993, Cold Spring Harbor symposia on quantitative biology.

Ligand dependence of estrogen receptor induced changes in chromatin structure.

P. Chambon, R. Losson, D. Gilbert, 1992, Nucleic acids research.

The distribution of genomic variations in human iPSCs is related to replication-timing reorganization during reprogramming.

Jun S. Liu, J. Collins, Hu Li, 2014, Cell reports.

Dynamic chromosomal interactions and control of heterochromatin positioning by Ki‐67

D. Gilbert, B. van Steensel, Elzo de Wit, 2021, bioRxiv.

Analysis of mammalian origin specification in ORC-depleted Xenopus egg extracts.

D. Gilbert, G. Yu, J. R. Wu, 1998, Genes to cells : devoted to molecular & cellular mechanisms.

Epigenetic control of chromosome-associated lncRNA genes essential for replication and stability

P. Spellman, D. Gilbert, E. Bouhassira, 2022, Nature Communications.

Stability and nuclear distribution of mammalian replication protein A heterotrimeric complex.

D. Gilbert, D. Dimitrova, 2000, Experimental cell research.

Heterochromatin and tri-methylated lysine 20 of histone H4 in animals

D. Gilbert, W. Shi, L. Fanti, 2004, Journal of Cell Science.

Topologically associating domains are stable units of replication-timing regulation

Yanli Wang, Tamer Kahveci, Yong Cheng, 2014, Nature.

Genome-scale analysis of replication timing: from bench to bioinformatics

Tyrone Ryba, Dana Battaglia, Ichiro Hiratani, 2011, Nature Protocols.

Productive Hepatitis C Virus Infection of Stem Cell-Derived Hepatocytes Reveals a Critical Transition to Viral Permissiveness during Differentiation

David M. Gilbert, Norman M. Kneteman, Stephen Dalton, 2012, PLoS pathogens.

Copy Number Variation Is a Fundamental Aspect of the Placental Genome

David M. Gilbert, Anton Valouev, Juan Carlos Rivera-Mulia, 2014, PLoS genetics.

Replication Timing: A Fingerprint for Cell Identity and Pluripotency

Ichiro Hiratani, Jinfeng Zhang, Michael Kulik, 2011, PLoS Comput. Biol..

Heterochromatin, HP1 and methylation at lysine 9 of histone H3 in animals

D. Gilbert, Harris Morrison, N. Huskisson, 2002, Chromosoma.

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

D. Gilbert, I. Hiratani, Junjie Lu, 2002, Current opinion in genetics & development.

The replication timing program of the Chinese hamster β-globin locus is established coincident with its repositioning near peripheral heterochromatin in early G1 phase

M. C. Butler, D. Gilbert, S. Keezer, 2001, The Journal of cell biology.

Nuclear Position Leaves Its Mark on Replication Timing

D. Gilbert, 2001, The Journal of cell biology.

The spatial position and replication timing of chromosomal domains are both established in early G1 phase.

D. Gilbert, D. Dimitrova, D S Dimitrova, 1999, Molecular cell.

Replication timing maintains the global epigenetic state in human cells

Kyle N. Klein, Peiyao A. Zhao, S. Dalton, 2019, bioRxiv.

Random-choice replication of extrachromosomal bovine papillomavirus (BPV) molecules in heterogeneous, clonally derived BPV-infected cell lines

D. Gilbert, S. Cohen, J. B. Ravnan, 1992, Journal of virology.

Position effects on the timing of replication of chromosomally integrated simian virus 40 molecules in Chinese hamster cells

D. Gilbert, S. Cohen, David M. GILBERTt, 1990 .

Position effects on the timing of replication of chromosomally integrated simian virus 40 molecules in Chinese hamster cells.

D. Gilbert, S. Cohen, Stanley N. Cohen, 1990, Molecular and cellular biology.

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

D. Gilbert, J. Rivera-Mulia, 2016, Current opinion in cell biology.

Three Dimensional Organization of the Nucleus: adding DNA sequences to the big picture

P. Fraser, D. Gilbert, 2015, Genome Biology.

Complex correlations: replication timing and mutational landscapes during cancer and genome evolution.

D. Gilbert, Jiao Sima, David M Gilbert, 2014, Current opinion in genetics & development.

Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication

Stefan Mundlos, Peter Fraser, Elphège P. Nora, 2019, Cell.

High-throughput single-cell epigenomic profiling by targeted insertion of promoters (TIP-seq)

S. Henikoff, H. Kimura, D. Gilbert, 2021, The Journal of cell biology.

Replication Domains: Genome Compartmentalization into Functional Replication Units.

Juan Carlos Rivera-Mulia, Peiyao A. Zhao, D. Gilbert, 2017, Advances in experimental medicine and biology.

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

Tamer Kahveci, Haitham Gabr, Juan Carlos Rivera-Mulia, 2015, Genome research.

Cohesin depleted cells rebuild functional nuclear compartments after endomitosis

Erez Lieberman Aiden, Volker J Schmid, Kyle N. Klein, 2019, Nature Communications.

Estradiol-inducible squelching and cell growth arrest by a chimeric VP16-estrogen receptor expressed in Saccharomyces cerevisiae: suppression by an allele of PDR1

P Chambon, P. Chambon, R. Losson, 1993, Molecular and cellular biology.

Rapid Irreversible Transcriptional Reprogramming in Human Stem Cells Accompanied by Discordance between Replication Timing and Chromatin Compartment

Rachel Patton McCord, Zhaohui S. Qin, David M. Gilbert, 2019, Stem cell reports.

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

Juan Carlos Rivera-Mulia, Vishnu Dileep, D. Gilbert, 2015, Cold Spring Harbor symposia on quantitative biology.

The replication domain model: regulating replicon firing in the context of large-scale chromosome architecture.

D. Gilbert, B. Pope, David M Gilbert, 2013, Journal of molecular biology.

Replication-timing boundaries facilitate cell-type and species-specific regulation of a rearranged human chromosome in mouse.

Michael D. Wilson, Tyrone Ryba, Duncan T Odom, 2012, Human molecular genetics.

Space and time in the nucleus: developmental control of replication timing and chromosome architecture.

Benjamin D. Pope, D. Gilbert, T. Ryba, 2010, Cold Spring Harbor symposia on quantitative biology.

Autosomal lyonization of replication domains during early Mammalian development.

D. Gilbert, I. Hiratani, 2010, Advances in experimental medicine and biology.

G9a selectively represses a class of late-replicating genes at the nuclear periphery

Yoichi Shinkai, Junjie Lu, Tyrone Ryba, 2009, Proceedings of the National Academy of Sciences.

Replication timing as an epigenetic mark

D. Gilbert, I. Hiratani, 2009, Epigenetics.

Domain-wide regulation of DNA replication timing during mammalian development

David M. Gilbert, Ichiro Hiratani, Benjamin D. Pope, 2009, Chromosome Research.

Uncoupling global and fine-tuning replication timing determinants for mouse pericentric heterochromatin

D. Gilbert, Prim B. Singh, Rong Wu, 2006, The Journal of cell biology.

Origins go plastic.

D. Gilbert, 2005, Molecular cell.

Low-cost fabrication of centimetre-scale periodic arrays of single plasmid DNA molecules.

D. Gilbert, S. Takebayashi, S. Lenhert, 2013, Lab on a chip.

Differential subnuclear localization and replication timing of histone H3 lysine 9 methylation states.

D. Gilbert, Prim B. Singh, David M Gilbert, 2005, Molecular biology of the cell.

Control of DNA replication timing in the 3D genome

D. Gilbert, Jiao Sima, Claire Marchal, 2019, Nature Reviews Molecular Cell Biology.

4D Genome Rewiring during Oncogene-Induced and Replicative Senescence

Daniel Jost, Modesto Orozco, Marc A Marti-Renom, 2020, Molecular cell.

Integrative detection and analysis of structural variation in cancer genomes

William Stafford Noble, Jesse R. Dixon, Royden A. Clark, 2018, Nature Genetics.

An Integrative Framework for Detecting Structural Variations in Cancer Genomes

William Stafford Noble, Feng Yue, Jesse R. Dixon, 2017, bioRxiv.

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

Bernadett Papp, Michael Kulik, Mari Itoh, 2010, Genome research.

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

Ichiro Hiratani, David M. Gilbert, Nodin Weddington, 2008, BMC Bioinformatics.

Actin up in the nucleus

D. Gilbert, D. Amberg, David C. Amberg, 2004, Nature Reviews Molecular Cell Biology.

Mouse Rif1 is a key regulator of the replication‐timing programme in mammalian cells

Vishnu Dileep, Claude Antony, D. Gilbert, 2012, The EMBO journal.

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

D. Gilbert, J. Rivera-Mulia, J. Lemaître, 2018, Cell cycle.

An integrative ENCODE resource for cancer genomics

Jie Xu, Lucas Lochovsky, Donghoon Lee, 2019, Nature Communications.

Cell cycle regulated transcription of heterochromatin in mammals vs. fission yeast: Functional conservation or coincidence?

D. Gilbert, Junjie Lu, 2008, Cell cycle.

RB Reversibly Inhibits DNA Replication via Two Temporally Distinct Mechanisms

Steven P. Angus, M. C. Cardoso, D. Gilbert, 2004, Molecular and Cellular Biology.

Mcm2, but Not Rpa, Is a Component of the Mammalian Early G1-Phase Prereplication Complex

D. Gilbert, I. Todorov, D. Dimitrova, 1999, The Journal of cell biology.

Mapping Replication Timing in Single Mammalian Cells

D. Gilbert, V. Dileep, T. Baslan, 2022, Current protocols.

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

D. Gilbert, V. Dileep, 2018, Nature Communications.

Single-cell replication profiling reveals stochastic regulation of the mammalian replication-timing program

D. Gilbert, V. Dileep, 2017, bioRxiv.

3D genome organization contributes to genome instability at fragile sites

B. Kerem, D. Gilbert, J. Rivera-Mulia, 2020, Nature Communications.

Replication timing alterations in leukemia reflect stable clinically-relevant changes in genome architecture

Kyle N. Klein, A. Koren, C. Eaves, 2019, bioRxiv.

Proliferation-dependent and cell cycle–regulated transcription of mouse pericentric heterochromatin

D. Gilbert, Junjie Lu, 2007, The Journal of cell biology.

Perspectives on ENCODE

Xintao Wei, Christopher B. Burge, Jason Liu, 2020, Nature.

Chromatin-interaction compartment switch at developmentally regulated chromosomal domains reveals an unusual principle of chromatin folding

Tyrone Ryba, Vishnu Dileep, Shin-ichiro Takebayashi, 2012, Proceedings of the National Academy of Sciences.

Bacterial artificial chromosomes establish replication timing and sub-nuclear compartment de novo as extra-chromosomal vectors

D. Gilbert, Jiao Sima, M. Gordon, 2017, Nucleic acids research.

Many paths lead chromatin to the nuclear periphery

Benjamin D. Pope, D. Gilbert, Jiao Sima, 2015, BioEssays : news and reviews in molecular, cellular and developmental biology.

Genetics: Up and down in Down's syndrome

D. Gilbert, B. Pope, 2014, Nature.

Continuous-trait probabilistic model for comparing multi-species functional genomic data

Quanquan Gu, R. O’Neill, D. Gilbert, 2018, bioRxiv.

Spatio-temporal re-organization of replication foci accompanies replication domain consolidation during human pluripotent stem cell lineage specification

E. Stanley, D. Gilbert, K. Wilson, 2016, Cell cycle.

Nuclear Architecture Organized by Rif1 Underpins the Replication-Timing Program

Wolfgang Huber, Thomas Manke, Remco Loos, 2016, Molecular cell.

Nuclear Architecture Organized by Rif1 Underpins the Replication-Timing Program

W. Huber, Paul Bertone, T. Jenuwein, 2016, Molecular cell.

Developmental control of replication timing defines a new breed of chromosomal domains with a novel mechanism of chromatin unfolding

David M. Gilbert, Tyrone Ryba, Shin-ichiro Takebayashi, 2012, Nucleus.

Cell fate transitions and the replication timing decision point

D. Gilbert, 2010, The Journal of cell biology.

Cohesin-mediated loop anchors confine the locations of human replication origins

Jennifer E. Phillips-Cremins, Kyle N. Klein, Peiyao A. Zhao, 2021, bioRxiv.

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

Tyrone Ryba, Dana Battaglia, Benjamin D. Pope, 2012, Genome research.

Autonomous replication in mouse cells: A correction

Stanley N Cohen, D. Gilbert, 1989, Cell.

Replication timing alterations in leukemia affect clinically relevant chromosome domains.

Kyle N. Klein, A. Koren, C. Eaves, 2019, Blood advances.

Replication timing alterations in leukemia reflect stable clinically-relevant changes in genome architecture

Kyle N. Klein, A. Koren, C. Eaves, 2019, bioRxiv.

Murine esBAF chromatin remodeling complex subunits BAF 250 a and Brg

G. Crabtree, D. Gilbert, T. Ryba, 2014 .

Murine esBAF chromatin remodeling complex subunits BAF250a and Brg1 are necessary to maintain and reprogram pluripotency-specific replication timing of select replication domains

Yong Fan, Miguel A Esteban, Tyrone Ryba, 2013, Epigenetics & Chromatin.

G2 phase chromatin lacks determinants of replication timing

Michael W. Davidson, David M. Gilbert, Junjie Lu, 2010, The Journal of cell biology.

Epigenomic replication: linking epigenetics to DNA replication.

D. Gilbert, David M Gilbert, Adrian J McNairn, 2003, BioEssays : news and reviews in molecular, cellular and developmental biology.

Temporal order of replication of Xenopus laevis 5S ribosomal RNA genes in somatic cells.

D. Gilbert, 1986, Proceedings of the National Academy of Sciences of the United States of America.

Mammalian nuclei become licensed for DNA replication during late telophase.

D. Gilbert, J. Blow, T. Prokhorova, 2002, Journal of cell science.

Spatio‐temporal organization of DNA replication in murine embryonic stem, primary, and immortalized cells

D. Gilbert, Margaret M. Panning, 2005, Journal of cellular biochemistry.

Differentiation-induced replication-timing changes are restricted to AT-rich/long interspersed nuclear element (LINE)-rich isochores.

Ichiro Hiratani, D. Gilbert, I. Hiratani, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Proliferation-dependent and cell cycle–regulated transcription of mouse pericentric heterochromatin

D. Gilbert, Junjie Lu, 2007, The Journal of Cell Biology.

Structure of a palindromic amplicon junction implicates microhomology-mediated end joining as a mechanism of sister chromatid fusion during gene amplification.

D. Gilbert, Y. Okuno, P. Hahn, 2004, Nucleic acids research.

DNA replication and nuclear organization: prospects for a soluble in vitro system.

D. Gilbert, D. Dimitrova, 1999, Critical reviews in eukaryotic gene expression.

Nuclear organisation and replication timing are coupled through RIF1–PP1 interaction

M. Cristina Cardoso, Alexander Rapp, David M. Gilbert, 2019, Nature Communications.

Pre-replication complex proteins assemble at regions of low nucleosome occupancy within the Chinese hamster dihydrofolate reductase initiation zone

M. L. Le Beau, D. Gilbert, J. Dennis, 2010, Nucleic acids research.

Observing S-phase dynamics of histone modifications with fluorescently labeled antibodies.

D. Gilbert, Anna V Terry, Rong Wu, 2006, Methods in molecular biology.

Chinese hamster ORC subunits dynamically associate with chromatin throughout the cell-cycle.

T. Misteli, D. Gilbert, Y. Okuno, 2005, Experimental cell research.

A Distinct G1 Step Required to Specify the Chinese Hamster DHFR Replication Origin

D. Gilbert, Jiarui Wu, 1996, Science.

Replication timing and metazoan evolution

D. Gilbert, 2002, Nature Genetics.

Replication origin plasticity, Taylor-made: inhibition vs recruitment of origins under conditions of replication stress

D. Gilbert, 2007, Chromosoma.

High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells

Peiyao A. Zhao, D. Gilbert, Takayo Sasaki, 2020, Genome Biology.

Genome-Wide Mapping of Human DNA Replication by Optical Replication Mapping Supports a Stochastic Model of Eukaryotic Replication

Kyle N. Klein, N. Rhind, Z. Weng, 2020, bioRxiv.

Replication Timing and Transcription Identifies a Novel Fragility Signature Under Replication Stress

B. Kerem, D. Gilbert, J. Rivera-Mulia, 2019, bioRxiv.

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

Daniel L. Vera, Sunny Das, Juan Carlos Rivera-Mulia, 2017, Experimental hematology.

Human Papillomavirus Infections : Warts or

K. Makarova, B. Edgar, D. MacAlpine, 2013 .

High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells

Peiyao A. Zhao, D. Gilbert, Takayo Sasaki, 2019, Genome Biology.

Repli-seq: genome-wide analysis of replication timing by next-generation sequencing

Daniel L. Vera, David M. Gilbert, Juan Carlos Rivera-Mulia, 2017, bioRxiv.

The Chinese Hamster Dihydrofolate Reductase Replication Origin Decision Point Follows Activation of Transcription and Suppresses Initiation of Replication within Transcription Units

D. Gilbert, Takayo Sasaki, Y. Okuno, 2006, Molecular and Cellular Biology.

Genome-Wide Mapping of Human DNA Replication by Optical Replication Mapping Supports a Stochastic Model of Eukaryotic Replication Timing [preprint]

Kyle N. Klein, N. Rhind, Z. Weng, 2020 .

Genome-Wide Mapping of Human DNA Replication by Optical Replication Mapping Supports a Stochastic Model of Eukaryotic Replication Timing

Kyle N. Klein, N. Rhind, Z. Weng, 2020 .

Computing interaction probabilities in signaling networks

Tamer Kahveci, Haitham Gabr, David M. Gilbert, 2015, BCB.

Microfluidic extraction and stretching of chromosomal DNA from single cell nuclei for DNA fluorescence in situ hybridization

D. Gilbert, S. Takebayashi, J. Guan, 2012, Biomedical Microdevices.

Catalytically Enhanced Cas9 through Directed Protein Evolution

Kyle N. Klein, D. Gilbert, Hong Li, 2020, bioRxiv.

The future of human embryonic stem cell research: addressing ethical conflict with responsible scientific research.

D. Gilbert, 2004, Medical science monitor : international medical journal of experimental and clinical research.

Zika Virus Infection Induces DNA Damage Response in Human Neural Progenitors That Enhances Viral Replication

Hongjun Song, D. Gilbert, A. Gunjan, 2019, Journal of Virology.

Sensitivity of the origin decision point to specific inhibitors of cellular signaling and metabolism.

D. Gilbert, S. Keezer, Susan M. Keezer, 2002, Experimental cell research.

Precise repair of mPing excision sites is facilitated by target site duplication derived microhomology

D. Gilbert, C. N. Hancock, J. Burnette, 2015, Mobile DNA.

Influence of ATM-Mediated DNA Damage Response on Genomic Variation in Human Induced Pluripotent Stem Cells.

Hu Li, D. Gilbert, Junjie Lu, 2016, Stem cells and development.

High throughput genome-wide single cell protein:DNA binding site mapping by targeted insertion of promoters (TIP-seq)

S. Henikoff, D. Gilbert, V. Dileep, 2021, bioRxiv.

DNA Replication Timing.

N. Rhind, D. Gilbert, 2020, Cold Spring Harbor perspectives in medicine.

Initiation of DNA replication in Saccharomyces cerevisiae G1‐phase nuclei by Xenopus egg extract

D. Gilbert, Jiarui Wu, Ji‐Wu Wang, 2000, Journal of cellular biochemistry.

Cohesin-mediated loop anchors confine the locations of human replication origins

Jennifer E. Phillips-Cremins, Kyle N. Klein, Peiyao A. Zhao, 2022, Nature.

Unearthing worm replication origins

D. Gilbert, Takayo Sasaki, 2017, Nature Structural &Molecular Biology.

Rapid DNA preparation for 2D gel analysis of replication intermediates.

D. Gilbert, J. R. Wu, 1995, Nucleic acids research.

Evidence for a pre‐restriction point Cdk3 activity

D. Gilbert, S. Keezer, 2002, Journal of cellular biochemistry.

9 DNA Replication and Nuclear Architecture

D. Gilbert, S. Gasser, 2006 .

DNA replication timing alterations identify common markers between distinct progeroid diseases

Juan Carlos Rivera-Mulia, Claudia Trevilla-Garcia, D. Gilbert, 2017, Proceedings of the National Academy of Sciences.

Homogeneous tetracycline‐regulatable gene expression in mammalian fibroblasts

D. Gilbert, M. Izumi, 2000, Journal of cellular biochemistry.

Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes

M. Gerstein, Z. Weng, Manolis Kellis, 2022, Nature.

Microfluidic extraction and stretching of chromosomal DNA from single cell nuclei for DNA fluorescence in situ hybridization

D. Gilbert, R. Chella, S. Takebayashi, 2012, Biomedical microdevices.

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

D. Gilbert, V. Dileep, 2018, Nature Communications.

Continuous-trait probabilistic model for comparing multi-species functional genomic data

Rachel J. O'Neill, Quanquan Gu, Yang Zhang, 2018, bioRxiv.

Mammalian DNA Replication Timing.

D. Gilbert, Athanasios E. Vouzas, 2021, Cold Spring Harbor Perspectives in Biology.

FISH Finder: a high-throughput tool for analyzing FISH images

James W. Shirley, Xiuwen Liu, D. Gilbert, 2011, Bioinform..

G9a selectively represses a class of late-replicating genes at the nuclear periphery

D. Gilbert, T. Ryba, I. Hiratani, 2009, Proceedings of the National Academy of Sciences.

A comparative encyclopedia of DNA elements in the mouse genome

Mukul S. Bansal, Shane J. Neph, Dmitri D. Pervouchine, 2014, Nature.

Defining functional DNA elements in the human genome

Morgan C. Giddings, E. Birney, M. Gerstein, 2014, Proceedings of the National Academy of Sciences.

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

S. Dalton, K. Plath, D. Gilbert, 2010, Genome research.

Uncoupling global and fine-tuning replication timing determinants for mouse pericentric heterochromatin

D. Gilbert, Prim B. Singh, Rong Wu, 2006, The Journal of cell biology.

Replication timing maintains the global epigenetic state in human cells

Kyle N. Klein, Peiyao A. Zhao, S. Dalton, 2019, Science.

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease

Morgan C. Giddings, E. Birney, M. Gerstein, 2014, Proceedings of the National Academy of Sciences.

Many paths lead chromatin to the nuclear periphery

Benjamin D. Pope, D. Gilbert, Jiao Sima, 2015, Bioessays.