Lista de obras - Orkun S Soyer - Dominio Público Uruguay

A Philosophical Perspective on Evolutionary Systems Biology

artículo científico publicado en 2015

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

artículo científico publicado en 2017

A stable genetic polymorphism underpinning microbial syntrophy

artículo científico publicado en 2016

Adaptive dynamics with a single two-state protein

artículo científico publicado en 2008

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

artículo científico publicado en 2017

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

artículo científico publicado en 2014

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

artículo científico publicado en 2015

Biodiversity-function relationships in methanogenic communities

artículo científico publicado en 2018

Bistability in feedback circuits as a byproduct of evolution of evolvability

artículo científico publicado en 2012

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

artículo científico

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

artículo científico publicado en 2022

Cooperation in microbial communities and their biotechnological applications.

artículo científico publicado en 2017

Core signalling motif displaying multistability through multi-state enzymes

artículo científico publicado en 2016

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

artículo científico publicado en 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.

artículo científico publicado en 2010

Emergence and maintenance of functional modules in signaling pathways

artículo científico publicado en 2007

Engineering and Biology: Counsel for a Continued Relationship

artículo científico publicado en 2015

Engineering microbial communities using thermodynamic principles and electrical interfaces

artículo científico publicado en 2017

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

artículo científico publicado en 2016

Evolution of complexity in signaling pathways

artículo científico publicado en 2006

Evolution of response dynamics underlying bacterial chemotaxis ⬇️

artículo científico publicado el 16 de agosto de 2011

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

artículo científico publicado en 2008

Evolution under fluctuating environments explains observed robustness in metabolic networks

artículo científico publicado en 2010

Evolutionary principles underlying structure and response dynamics of cellular networks

artículo científico

Evolutionary systems biology: What it is and why it matters ⬇️

artículo científico publicado el 16 de mayo de 2013

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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 2016

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

artículo científico publicado en 2013

Microbial diversity arising from thermodynamic constraints

artículo científico publicado en 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

artículo científico publicado en 2002

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

artículo científico publicado en 2016

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

artículo científico publicado en 2008

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

artículo científico publicado en 2014

Phosphorelays provide tunable signal processing capabilities for the cell

artículo científico publicado en 2013

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

artículo científico publicado en 2004

Probing conformational changes in neurotransmitter transporters: a structural context

artículo científico publicado en 2003

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

artículo científico publicado en 2009

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

artículo científico publicado en 2010

Signal transduction networks: topology, response and biochemical processes

artículo científico publicado en 2005

Simulating the evolution of signal transduction pathways

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

artículo científico publicado en 2013

Synthetic microbial communities

artículo científico publicado en 2014

Systems and synthetic biology underpinning biotechnology ⬇️

artículo científico publicado el 27 de junio de 2013

The evolution of connectivity in metabolic networks

artículo científico publicado en 2005

The promise of evolutionary systems biology: lessons from bacterial chemotaxis

artículo científico publicado en 2010

The roles of integration in molecular systems biology ⬇️

artículo científico publicado el 1 de noviembre de 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

artículo científico publicado en 2016

Unlimited multistability and Boolean logic in microbial signalling

artículo científico publicado en 2015

Using evolutionary methods to study G-protein coupled receptors.

artículo científico publicado en 2002

Lista de obras de Orkun S Soyer

A Philosophical Perspective on Evolutionary Systems Biology

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

A stable genetic polymorphism underpinning microbial syntrophy

Adaptive dynamics with a single two-state protein

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

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

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

Biodiversity-function relationships in methanogenic communities

Bistability in feedback circuits as a byproduct of evolution of evolvability

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

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

Cooperation in microbial communities and their biotechnological applications.

Core signalling motif displaying multistability through multi-state enzymes

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

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

Duplicate retention in signalling proteins and constraints from network dynamics.

Emergence and maintenance of functional modules in signaling pathways

Engineering and Biology: Counsel for a Continued Relationship

Engineering microbial communities using thermodynamic principles and electrical interfaces

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

Evolution of complexity in signaling pathways

Evolution of response dynamics underlying bacterial chemotaxis ⬇️

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

Evolution under fluctuating environments explains observed robustness in metabolic networks

Evolutionary principles underlying structure and response dynamics of cellular networks

Evolutionary systems biology: What it is and why it matters ⬇️

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

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

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

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

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

Interrogating metabolism as an electron flow system

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

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

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

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

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

Microbial diversity arising from thermodynamic constraints

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

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

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

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

Phosphorelays provide tunable signal processing capabilities for the cell

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

Probing conformational changes in neurotransmitter transporters: a structural context

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

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

Signal transduction networks: topology, response and biochemical processes

Simulating the evolution of signal transduction pathways

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

Synthetic microbial communities

Systems and synthetic biology underpinning biotechnology ⬇️

The evolution of connectivity in metabolic networks

The promise of evolutionary systems biology: lessons from bacterial chemotaxis

The roles of integration in molecular systems biology ⬇️

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

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

Unlimited multistability and Boolean logic in microbial signalling

Using evolutionary methods to study G-protein coupled receptors.