I. Dodd

发表

Theoretical Analysis of Epigenetic Cell Memory by Nucleosome Modification

K. Sneppen, I. Dodd, M. A. Micheelsen, 2007, Cell.

Modeling Bistable Chromatin States

K. Sneppen, I. Dodd, 2017 .

Nucleosome dynamics and maintenance of epigenetic states of CpG islands.

K. Sneppen, I. Dodd, 2016, Physical review. E.

Nucleosome dynamics and maintenance of epigenetic states of CpG islands

K. Sneppen, I. Dodd, 2016, bioRxiv.

Minimal Gene Regulatory Circuits for a Lysis-Lysogeny Choice in the Presence of Noise

K. Sneppen, S. Krishna, I. Dodd, 2010, PloS one.

Barriers and silencers: a theoretical toolkit for control and containment of nucleosome-based epigenetic states.

Kim Sneppen, K. Sneppen, I. Dodd, 2011, Journal of molecular biology.

Programmable DNA looping using engineered bivalent dCas9 complexes

I. Dodd, Nan Hao, K. Shearwin, 2017, Nature Communications.

Action at a distance in CI repressor regulation of the bacteriophage 186 genetic switch

I. Dodd, J. Egan, 2002, Molecular microbiology.

Improved detection of helix-turn-helix DNA-binding motifs in protein sequences.

I. Dodd, J. Egan, Egan Jb, 1990, Nucleic acids research.

Control of gene expression in the P2-related template coliphages. III. DNA sequence of the major control region of phage 186.

I. Dodd, J. Egan, B. Kalionis, 1986, Journal of molecular biology.

Cro’s role in the CI–Cro bistable switch is critical for λ’s transition from lysogeny to lytic development

Ian B. Dodd, Keith E. Shearwin, J. Barry Egan, 2007 .

The Helix-Turn-Helix Motif of the Coliphage 186 Immunity Repressor Binds to Two Distinct Recognition Sequences*

I. Dodd, K. Shearwin, J. Egan, 2002, The Journal of Biological Chemistry.

The late-expressed region of the temperate coliphage 186 genome.

I. Dodd, J. Egan, R. Portelli, 1998, Virology.

DNA Binding by the Coliphage 186 Repressor Protein CI (*)

I. Dodd, J. Egan, 1996, The Journal of Biological Chemistry.

The Cro‐like Apl repressor of coliphage 186 is required for prophage excision and binds near the phage attachment site

I. Dodd, J. Egan, Michael R. Reed, 1993, Molecular microbiology.

Control of gene expression in the temperate coliphage 186. VIII. Control of lysis and lysogeny by a transcriptional switch involving face-to-face promoters.

I. Dodd, J. Egan, B. Kalionis, 1990, Journal of molecular biology.

Systematic method for the detection of potential λ Cro-like DNA-binding regions in proteins

Ian B. Dodd, I. Dodd, Egan Jb, 1987 .

Identification of residues in the N-terminal PAS domains important for dimerization of Arnt and AhR

Ian B. Dodd, Keith E. Shearwin, Nan Hao, 2011, Nucleic acids research.

Bacteriophage P4 Vis protein is needed for prophage excision.

I. Dodd, F. Forti, D. Ghisotti, 2004, Virology.

Minimal gene regulatory circuits that can count like bacteriophage lambda.

K. Sneppen, S. Krishna, I. Dodd, 2009, Journal of molecular biology.

Promoter Activation by CII, a Potent Transcriptional Activator from Bacteriophage 186*

I. Dodd, D. Priest, K. Shearwin, 2014, The Journal of Biological Chemistry.

RNA polymerase pausing at a protein roadblock can enhance transcriptional interference by promoter occlusion

Michael T. Crooks, I. Dodd, Nan Hao, 2019, FEBS letters.

Road rules for traffic on DNA—systematic analysis of transcriptional roadblocking in vivo

Sandeep Krishna, Ian B. Dodd, Keith E. Shearwin, 2014, Nucleic acids research.

Enhancer-like long-range transcriptional activation by λ CI-mediated DNA looping

Lun Cui, I. Dodd, K. Shearwin, 2013, Proceedings of the National Academy of Sciences.

Modelling transcriptional interference and DNA looping in gene regulation.

K. Sneppen, I. Dodd, K. Shearwin, 2007, Journal of molecular biology.

Potent transcriptional interference by pausing of RNA polymerases over a downstream promoter.

Ian B. Dodd, Keith E. Shearwin, J. Barry Egan, 2009, Molecular cell.

DNA methylation in human epigenomes depends on local topology of CpG sites

Kim Sneppen, Ian B. Dodd, Jan O. Haerter, 2016, Nucleic acids research.

Cooperative stabilization of the SIR complex provides robust epigenetic memory in a model of SIR silencing in Saccharomyces cerevisiae

K. Sneppen, I. Dodd, 2015, Epigenetics.

Quantitation of interactions between two DNA loops demonstrates loop domain insulation in E. coli cells

D. Dunlap, I. Dodd, D. Priest, 2014, Proceedings of the National Academy of Sciences.

Collaboration between CpG sites is needed for stable somatic inheritance of DNA methylation states

Kim Sneppen, Ian B. Dodd, Jan O. Haerter, 2013, Nucleic acids research.

Programmable DNA looping using engineered bivalent dCas9 complexes

I. Dodd, Nan Hao, K. Shearwin, 2017, Nature Communications.

Theory for the stability and regulation of epigenetic landscapes

Kim Sneppen, Namiko Mitarai, K. Sneppen, 2010, Physical biology.

Ultrasensitive gene regulation by positive feedback loops in nucleosome modification

Kim Sneppen, K. Sneppen, I. Dodd, 2008, Molecular systems biology.

One-step cloning and chromosomal integration of DNA.

D. Endy, I. Dodd, D. Priest, 2013, ACS synthetic biology.

The prediction of helix-turn-helix DNA-binding regions in proteins. A reply to Yudkin.

I. Dodd, J. Egan, I B Dodd, 1988, Protein engineering.

from lysogeny to lytic development Cro s role in the CI Cro bistable switch is critical for » s transition Material Supplemental

I. Dodd, J. Egan, Rachel A. Schubert, 2016 .

Octamerization of lambda CI repressor is needed for effective repression of P(RM) and efficient switching from lysogeny.

I. Dodd, J. Egan, I B Dodd, 2001, Genes & development.

A Simple Histone Code Opens Many Paths to Epigenetics

Kim Sneppen, Ian B. Dodd, K. Sneppen, 2012, PLoS Comput. Biol..

Cooperativity in long-range gene regulation by the λ CI repressor

Ian B. Dodd, Keith E. Shearwin, J. Barry Egan, 2004 .

Revisited gene regulation in bacteriophage λ

Ian B. Dodd, Keith E. Shearwin, J. Barry Egan, 2005 .

Positive and Negative Control of Enhancer-Promoter Interactions by Other DNA Loops Generates Specificity and Tunability.

I. Dodd, Nan Hao, K. Shearwin, 2019, Cell reports.

Cooperativity in long-range gene regulation by the lambda CI repressor.

I. Dodd, K. Shearwin, A. Hochschild, 2004, Genes & development.

The Escherichia coli retrons Ec67 and Ec86 replace DNA between the cos site and a transcription terminator of a 186-related prophage.

I. Dodd, J. Egan, 1996, Virology.

Economy of Operon Formation: Cotranscription Minimizes Shortfall in Protein Complexes

K. Sneppen, S. Krishna, I. Dodd, 2010, mBio.

Analysis of Infection Time Courses Shows CII Levels Determine the Frequency of Lysogeny in Phage 186

S. Krishna, I. Dodd, Nan Hao, 2021, Pharmaceuticals.

Instability of CII is needed for efficient switching between lytic and lysogenic development in bacteriophage 186

I. Dodd, K. Shearwin, A. Ahlgren-Berg, 2020, Nucleic acids research.

Why Do Phage Play Dice?

Kim Sneppen, Sandeep Krishna, Ian B. Dodd, 2009, Journal of Virology.

Why Do Phage Play Dice? (cid:1)

K. Sneppen, S. Krishna, I. Dodd, 2009 .

Revisited gene regulation in bacteriophage lambda.

I. Dodd, K. Shearwin, J. Egan, 2005, Current opinion in genetics & development.

A mathematical model for transcriptional interference by RNA polymerase traffic in Escherichia coli.

Kim Sneppen, K. Sneppen, I. Dodd, 2005, Journal of molecular biology.

Directing traffic on DNA—How transcription factors relieve or induce transcriptional interference

I. Dodd, Nan Hao, K. Shearwin, 2017, Transcription.

The Generation of Promoter-Mediated Transcriptional Noise in Bacteria

Kim Sneppen, Ian B. Dodd, Namiko Mitarai, 2008, PLoS Comput. Biol..

Quantitation of the DNA tethering effect in long-range DNA looping in vivo and in vitro using the Lac and lambda repressors

D. Dunlap, I. Dodd, D. Priest, 2022 .

Bacteriophage lambda repressor mediates the formation of a complex enhancer-like structure

I. Dodd, K. Shearwin, Lun Cui, 2013, Transcription.

The loopometer: a quantitative in vivo assay for DNA-looping proteins

I. Dodd, Nan Hao, K. Shearwin, 2021, Nucleic acids research.

The structural basis of cooperative regulation at an alternate genetic switch.

I. Dodd, M. Lewis, K. Shearwin, 2006, Molecular cell.

Defining the SOS operon of coliphage 186.

I. Dodd, J. Egan, I. Lamont, 1996, Virology.

A quantitative binding model for the Apl protein, the dual purpose recombination-directionality factor and lysis-lysogeny regulator of bacteriophage 186

I. Dodd, K. Shearwin, J. Egan, 2019, bioRxiv.

The role of repressor kinetics in relief of transcriptional interference between convergent promoters

I. Dodd, Nan Hao, K. Shearwin, 2016, Nucleic acids research.

Single molecule analysis of DNA wrapping and looping by a circular 14mer wheel of the bacteriophage 186 CI repressor

D. Dunlap, L. Finzi, I. Dodd, 2013, Nucleic acids research.

Systematic method for the detection of potential lambda Cro-like DNA-binding regions in proteins.

I. Dodd, J. Egan, I B Dodd, 1987, Journal of molecular biology.

Efficient chromosomal-scale DNA looping in Escherichia coli using multiple DNA-looping elements

K. Sneppen, I. Dodd, Nan Hao, 2017, Nucleic acids research.

Network models of phage-bacteria coevolution.

K. Sneppen, M. Rosvall, S. Krishna, 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

Identification of residues in the N-terminal PAS domains important for dimerization of Arnt and AhR

I. Dodd, A. Chapman-Smith, Nan Hao, 2011, Nucleic Acids Research.

When push comes to shove - RNA polymerase and DNA-bound protein roadblocks

I. Dodd, Nan Hao, K. Shearwin, 2023, Biophysical Reviews.

Cro's role in the CI Cro bistable switch is critical for {lambda}'s transition from lysogeny to lytic development.

I. Dodd, K. Shearwin, J. Egan, 2007, Genes & Development.

Quantitation of the DNA tethering effect in long-range DNA looping in vivo and in vitro using the Lac and λ repressors

I. Dodd, K. Shearwin, Sandip Kumar, 2013, Proceedings of the National Academy of Sciences.