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List of works by Orkun S Soyer

A Philosophical Perspective on Evolutionary Systems Biology

scientific article published in March 2015

A Single Community Dominates Structure and Function of a Mixture of Multiple Methanogenic Communities

scientific article

A stable genetic polymorphism underpinning microbial syntrophy

scientific article published on 3 June 2016

Adaptive dynamics with a single two-state protein

scientific article published on August 2008

An integrated computational-experimental approach reveals Yersinia pestis genes essential across a narrow or a broad range of environmental conditions

scientific article published on 21 July 2017

Bacterial drug tolerance under clinical conditions is governed by anaerobic adaptation but not anaerobic respiration

scientific article published on 21 July 2014

BioJazz: in silico evolution of cellular networks with unbounded complexity using rule-based modeling

scientific article published on 22 June 2015

Biodiversity-function relationships in methanogenic communities

scientific article published on 22 November 2018

Bistability in feedback circuits as a byproduct of evolution of evolvability

scientific article published on 17 January 2012

Challenges in microbial ecology: building predictive understanding of community function and dynamics ⬇️

scientific article published on 29 March 2016

ChemChaste: Simulating spatially inhomogeneous biochemical reaction–diffusion systems for modeling cell–environment feedbacks

scientific article published in 2022

Cooperation in microbial communities and their biotechnological applications.

scientific article

Core signalling motif displaying multistability through multi-state enzymes

scientific article published on October 2016

Depicting a protein's two faces: GPCR classification by phylogenetic tree-based HMMs

scientific article published on 01 November 2003

Dimerization in Aminergic G-Protein-Coupled Receptors: Application of a Hidden-Site Class Model of Evolution†

article

Duplicate retention in signalling proteins and constraints from network dynamics.

scientific article published on 6 September 2010

Emergence and maintenance of functional modules in signaling pathways

scientific article

Engineering and Biology: Counsel for a Continued Relationship

scientific article

Engineering microbial communities using thermodynamic principles and electrical interfaces

scientific article published on 18 December 2017

Enzyme Sequestration as a Tuning Point in Controlling Response Dynamics of Signalling Networks

scientific article

Evolution of complexity in signaling pathways

scholarly article

Evolution of response dynamics underlying bacterial chemotaxis ⬇️

scientific article (publication date: 16 August 2011)

Evolution of taxis responses in virtual bacteria: non-adaptive dynamics

scientific article

Evolution under fluctuating environments explains observed robustness in metabolic networks

scientific article

Evolutionary principles underlying structure and response dynamics of cellular networks

scientific article published on January 2012

Evolutionary systems biology: what it is and why it matters

scientific article published on 16 May 2013

Impact of spatial organization on a novel auxotrophic interaction among soil microbes

scientific article published on 23 March 2018

Increasing sulfate levels show a differential impact on synthetic communities comprising different methanogens and a sulfate reducer

scientific article published on 01 May 2019

Inhibiting the reproduction of SARS-CoV-2 through perturbations in human lung cell metabolic network

scientific article published on 24 November 2020

Integrated Human-Virus Metabolic Modelling Predicts Host-Based Antiviral Targets Against Chikungunya, Dengue and Zika Viruses

scholarly article published 19 July 2017

Integrated human-virus metabolic stoichiometric modelling predicts host-based antiviral targets against Chikungunya, Dengue and Zika viruses

scholarly article by Sean Aller et al published 12 September 2018 in Journal of the Royal Society Interface

Interrogating metabolism as an electron flow system

scientific article published on 01 February 2019

Manganese oxide biomineralization provides protection against nitrite toxicity in a cell density dependent manner

article

Mapping epigenetic changes to the host cell genome induced by Burkholderia pseudomallei reveals pathogen-specific and pathogen-generic signatures of infection

scientific article published on 3 August 2016

MetQy-an R package to query metabolic functions of genes and genomes

article

Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment

scientific article published on 20 August 2016

Metabolic tinker: an online tool for guiding the design of synthetic metabolic pathways

scientific article published on 10 April 2013

Microbial diversity arising from thermodynamic constraints

scientific article published on April 2016

Modelling and Analysis of Feedback Control Mechanisms Underlying Osmoregulation in Yeast

NMR structure of the second intracellular loop of the alpha 2A adrenergic receptor: evidence for a novel cytoplasmic helix

scientific article

Nonlinear Dynamics in Gene Regulation Promote Robustness and Evolvability of Gene Expression Levels

scientific article

Parasites lead to evolution of robustness against gene loss in host signaling networks

scientific article published on 15 July 2008

Phosphate sink containing two-component signaling systems as tunable threshold devices

scientific article

Phosphorelays provide tunable signal processing capabilities for the cell

scientific article (publication date: 2013)

Predicting functional sites in proteins: site-specific evolutionary models and their application to neurotransmitter transporters

scientific article

Probing conformational changes in neurotransmitter transporters: a structural context

scientific article published on October 2003

Regulating the total level of a signaling protein can vary its dynamics in a range from switch like ultrasensitivity to adaptive responses.

scientific article

Response dynamics of phosphorelays suggest their potential utility in cell signalling.

scientific article published on 11 August 2010

Signal transduction networks: topology, response and biochemical processes

scientific article

Simulating the evolution of signal transduction pathways

Split histidine kinases enable ultrasensitivity and bistability in two-component signaling networks

scientific article

Synthetic microbial communities

scientific article

Systems and synthetic biology underpinning biotechnology

scientific article published on 27 June 2013

The evolution of connectivity in metabolic networks

scientific article

The promise of evolutionary systems biology: lessons from bacterial chemotaxis

scientific article published on 29 June 2010

The roles of integration in molecular systems biology ⬇️

scientific article published on November 1, 2011

Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis

scientific article published on 06 May 2020

Ultrasensitive Negative Feedback Control: A Natural Approach for the Design of Synthetic Controllers

scientific article

Unlimited multistability and Boolean logic in microbial signalling

scientific article published on July 2015

Using evolutionary methods to study G-protein coupled receptors.

scientific article

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