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List of works by Ian B. Dodd

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

scientific article published on 23 December 2004

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

scientific article published on 13 August 2020

A simple histone code opens many paths to epigenetics

scientific article

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

scientific article published on August 2002

Bacteriophage P4 Vis protein is needed for prophage excision

scientific article published in April 2004

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

scientific article

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

scientific article published on 20 October 2011

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

scientific article

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

scientific article published in July 1990

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

scientific article

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

scientific article published on February 2004

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

scientific article

DNA binding by the coliphage 186 repressor protein CI.

scientific article

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

scientific article published on 29 February 2016

Defining the SOS operon of coliphage 186.

scientific article published on May 1996

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

scientific article published on 27 January 2017

Economy of operon formation: cotranscription minimizes shortfall in protein complexes

scientific article

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

scientific article

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

scientific article published on 4 February 2013

Functional alignment of regulatory networks: a study of temperate phages

scientific article

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

scientific article

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

scientific article published on 19 November 2020

Minimal gene regulatory circuits for a lysis-lysogeny choice in the presence of noise

scientific article

Minimal gene regulatory circuits that can count like bacteriophage lambda

scientific article published on 28 September 2009

Modelling transcriptional interference and DNA looping in gene regulation.

scientific article

Network models of phage-bacteria coevolution.

scientific article published on 8 December 2006

Nucleosome dynamics and maintenance of epigenetic states of CpG islands

scientific article published on 28 June 2016

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

scientific article published in November 2001

One-step cloning and chromosomal integration of DNA.

scientific article

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

scientific article published on 01 February 2019

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

scientific article published on June 2009

Programmable DNA looping using engineered bivalent dCas9 complexes

scientific article published on 20 November 2017

Promoter activation by CII, a potent transcriptional activator from bacteriophage 186.

scientific article

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

scientific article

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

scientific article published on 16 December 2013

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

scientific article published on 29 March 2019

Revisited gene regulation in bacteriophage lambda.

scientific article

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

scientific article

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

scientific article published on 24 April 2013

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

scientific article published in April 1987

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

scientific article published on 01 December 1993

The generation of promoter-mediated transcriptional noise in bacteria

scientific article

The helix-turn-helix motif of the coliphage 186 immunity repressor binds to two distinct recognition sequences

scientific article

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

scientific article published on 19 April 2021

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

scientific article published on 01 September 1988

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

scientific article published on 4 July 2016

The structural basis of cooperative regulation at an alternate genetic switch

scientific article published on 01 March 2006

Theoretical analysis of epigenetic cell memory by nucleosome modification.

scientific article

Theory for the stability and regulation of epigenetic landscapes.

scientific article published on 4 June 2010

Ultrasensitive gene regulation by positive feedback loops in nucleosome modification

scientific article

Why Do Phage Play Dice?

scientific article

Why do phage play dice?

scientific article published on 09 September 2009

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