### 2022

1. Generating Immune-aware SARS-CoV-2 Spike Proteins for Universal Vaccine Design
In Proceedings of the 1st Workshop on Healthcare AI and COVID-19, ICML 2022 , 184 , 2022
2. Modeling isogenic cancer cell response upon varying TRAIL stimulations to decipher the kinetic determinants of cell fate decision
In 9th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE) , 2022
3. Prediction of gene essentiality using machine learning and genome-scale metabolic models
In 9th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE) , 2022
4. Discovery of new senolytics using machine learning
bioRxiv , 2022
5. Trade-Offs in Biosensor Optimization for Dynamic Pathway Engineering
ACS Synthetic Biology , 11 , 2022
6. From sequence to yield : deep learning for protein production systems
bioRxiv , 2022
7. Stabilisation of Antithetic Control via Molecular Buffering
Journal of the Royal Society Interface , 2022

### 2021

1. Systems level profiling of chemotherapy-induced stress resolution in cancer cells reveals druggable trade-offs
PNAS , 118 , 2021
2. Epigenome and phenome study reveals circulating markers pertinent to brain health
medRxiv , 2021
3. Microbial polysaccharides: An emerging family of natural biomaterials for cancer therapy and diagnostics
Seminars in Cancer Biology , 2021
4. Prediction of cellular burden with host-circuit models
Synthetic Gene Circuits: Methods in Molecular Biology , 2021
5. Opportunities at the interface of network science and metabolic modelling
Frontiers in Bioengineering and Biotechnology , 9 , 2021

### 2020

1. Genotype-phenotype map of an RNA-ligand complex
bioRxiv , 2020
2. Computation of single-cell metabolite distributions using mixture models
Frontiers in Cell and Development Biology , 8 , 2020
3. Metabolite sequestration enables rapid recovery from fatty acid depletion in Escherichia coli
mBio , 11 , 2020
4. A stochastic model of gene expression with polymerase recruitment and pause release
Biophysical Journal , 2020

### 2019

1. Pathways to cellular supremacy in biocomputing
Nature Communications , 2019
2. Riboswitch identification using Ligase-Assisted Selection for the Enrichment of Responsive Ribozymes (LigASERR)
Synthetic Biology , 4 , 2019
3. Multiobjective optimization of gene circuits for metabolic engineering
In 8th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE) , 2019
4. Growth Defects and Loss-of-Function in Synthetic Gene Circuits
ACS Synthetic Biology , 8 , 2019
5. Stochastic modelling reveals mechanisms of metabolic heterogeneity
Communications Biology , 2 , 2019
6. Dynamics of complex feedback architectures in metabolic pathways
Automatica , 99 , 2019
7. Analysis of a genetic-metabolic oscillator with piecewise linear models
Journal of Theoretical Biology , 462 , 2019

### 2018

1. Host-circuit interactions explain unexpected behavior of a gene circuit .
In 7th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE) , 2018
2. The power of synthetic biology for bioproduction, remediation and pollution control
EMBO reports , 19 , 2018
3. Flux-dependent graphs for metabolic networks
npj Systems Biology and Applications , 4 , 2018
4. Dynamic metabolic control: towards precision engineering of metabolism
Journal of Industrial Microbiology & Biotechnology , 45 , 2018
5. Are We There Yet? How and When Specific Biotechnologies Will Improve Human Health
Biotechnology Journal , 2018

### 2017

1. Fundamental Design Principles for Transcription-Factor-Based Metabolite Biosensors
ACS Synthetic Biology , 6 , 2017

### 2016

1. Shaping pulses to control bistable systems: Analysis, computation and counterexamples
Automatica , 63 , 2016

### 2015

Proceedings of the National Academy of Sciences , 112 , 2015
2. Shaping pulses to control bistable biological systems
In Proceedings of the American Control Conference , 2015-July , 2015
3. Dynamic optimization of metabolic networks coupled with gene expression
Journal of Theoretical Biology , 365 , 2015
4. Noise propagation in synthetic gene circuits for metabolic control.
ACS Synthetic Biology , 4 , 2015
5. Design of a bistable switch to control cellular uptake
Journal of The Royal Society Interface , 12 , 2015

### 2014

1. Spatial Quantification of Cytosolic Ca2+ Accumulation in Nonexcitable Cells:An Analytical Study
IEEE/ACM Transactions on Computational Biology and Bioinformatics , 11 , 2014
2. Model Reduction of Genetic-Metabolic Networks via Time Scale Separation
, 2014
3. The EGFR demonstrates linear signal transmission.
Integrative biology , 8 , 2014

### 2013

1. Control of protein concentrations in heterogeneous cell populations
In Proceeding of the European Control Conference , 2013
2. Stochastic simulation of enzymatic reactions under transcriptional feedback regulation
In Proceeding of the European Control Conference , 2013
3. Cumulative Signal Transmission in Nonlinear Reaction-Diffusion Networks
PLoS ONE , 8 , 2013
4. Synthetic gene circuits for metabolic control: design trade-offs and constraints.
Journal of the Royal Society, Interface / the Royal Society , 10 , 2013

### 2012

1. Analytic computation of the integrated response in nonlinear reaction-diffusion systems
In 51st IEEE Conference on Decision and Control , 2012
2. Design constraints in an operon circuit for engineered control of metabolic networks
In 51st Conference on Decision and Control , 2012
3. Design tradeoffs in a synthetic gene control circuit for metabolic networks
In Proceedings of the American Control Conference , 2012
4. Predicting the F(ab)-mediated effect of monoclonal antibodies in vivo by combining cell-level kinetic and pharmacokinetic modelling.
Journal of pharmacokinetics and pharmacodynamics , 39 , 2012
5. Multistability and oscillations in genetic control of metabolism
Journal of theoretical biology , 295 , 2012

### 2011

1. Optimal control of metabolic networks with saturable enzyme kinetics.
IET systems biology , 5 , 2011
2. Optimal adaptation of metabolic networks in dynamic equilibrium
In Proceedings of the American Control Conference , 2011
3. Global gene regulation in metabolic networks
In Proceedings of the 18th IFAC World Congress , 2011

### 2010

1. Control structure and limitations of biochemical networks
In Proceedings of the American Control Conference , 2010

### 2009

1. Sequential activation of metabolic pathways: a dynamic optimization approach.
Bulletin of mathematical biology , 71 , 2009
2. Ligand accumulation counteracts therapeutic inhibition of receptor systems
In Foundations of Systems Biology and Engineering , 2009
3. An analytic characterization of all stabilizing feedbacks for LTI plants
In Proceeding of the European Control Conference , 2009

### 2008

1. Optimal metabolic pathway activation
In Proceedings of the IFAC World Congress , 2008
2. Cascaded Multilevel Inverter With Regeneration Capability and Reduced Number of Switches
IEEE Transactions on Industrial Electronics , 55 , 2008

### 2007

1. H\textlessinf\textgreater2\textless/inf\textgreater optimal ripple-free deadbeat controller design
Automatica , 43 , 2007
2. Optimal metabolic regulation by temporal variation of enzyme activities: a control theoretic approach
In Foundations of Systems Biology and Engineering , 2007
3. Effect of downstream feedback on the achievable performance of feedback control loops for serial processes
In Proceeding of the European Control Conference , 2007
4. Optimal triangular approximation for linear stable multivariable systems
In Proceedings of the American Control Conference , 2007
5. On structurally constrained H2 performance bounds for stable MIMO plant models
IET Control Theory & Applications , 1 , 2007
6. H2 Optimal ripple-free deadbeat controller design
Automatica , 43 , 2007
7. Double objective optimal multivariable ripple-free deadbeat control
International Journal of Control , 80 , 2007

### 2006

1. Suboptimal triangular controller design methodology for full MIMO stable systems
In Proceedings of the UKACC Conference , 2006
2. Basic integrated modelling: a case study
International Journal of Electrical Engineering Education , 43 , 2006

### 2005

1. MIMO interactions in sampled data systems
In Proceedings of the 16th IFAC World Congress , 2005
2. Novel cell based on reduced single-phase active front end for multicell converters
In 31st Annual Conference of IEEE Industrial Electronics Society, 2005. IECON 2005. , 2005
<!--

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</div> </li>

• Modeling isogenic cancer cell response upon varying TRAIL stimulations to decipher the kinetic determinants of cell fate decision
In 9th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE) , 2022
• Prediction of gene essentiality using machine learning and genome-scale metabolic models
In 9th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE) , 2022
• Discovery of new senolytics using machine learning
bioRxiv , 2022
• Trade-Offs in Biosensor Optimization for Dynamic Pathway Engineering
ACS Synthetic Biology , 11 , 2022
• From sequence to yield : deep learning for protein production systems
bioRxiv , 2022
• Stabilisation of Antithetic Control via Molecular Buffering
Journal of the Royal Society Interface , 2022
• </ol>

2021

1. Systems level profiling of chemotherapy-induced stress resolution in cancer cells reveals druggable trade-offs
PNAS , 118 , 2021
2. Epigenome and phenome study reveals circulating markers pertinent to brain health
medRxiv , 2021
3. Microbial polysaccharides: An emerging family of natural biomaterials for cancer therapy and diagnostics
Seminars in Cancer Biology , 2021
4. Prediction of cellular burden with host-circuit models
Synthetic Gene Circuits: Methods in Molecular Biology , 2021
5. Opportunities at the interface of network science and metabolic modelling
Frontiers in Bioengineering and Biotechnology , 9 , 2021

2020

1. Genotype-phenotype map of an RNA-ligand complex
bioRxiv , 2020
2. Computation of single-cell metabolite distributions using mixture models
Frontiers in Cell and Development Biology , 8 , 2020
3. Metabolite sequestration enables rapid recovery from fatty acid depletion in Escherichia coli
mBio , 11 , 2020
4. A stochastic model of gene expression with polymerase recruitment and pause release
Biophysical Journal , 2020

2019

1. Pathways to cellular supremacy in biocomputing
Nature Communications , 2019
2. Riboswitch identification using Ligase-Assisted Selection for the Enrichment of Responsive Ribozymes (LigASERR)
Synthetic Biology , 4 , 2019
3. Multiobjective optimization of gene circuits for metabolic engineering
In 8th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE) , 2019
4. Growth Defects and Loss-of-Function in Synthetic Gene Circuits
ACS Synthetic Biology , 8 , 2019
5. Stochastic modelling reveals mechanisms of metabolic heterogeneity
Communications Biology , 2 , 2019
6. Dynamics of complex feedback architectures in metabolic pathways
Automatica , 99 , 2019
7. Analysis of a genetic-metabolic oscillator with piecewise linear models
Journal of Theoretical Biology , 462 , 2019

2018

1. Host-circuit interactions explain unexpected behavior of a gene circuit .
In 7th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE) , 2018
2. The power of synthetic biology for bioproduction, remediation and pollution control
EMBO reports , 19 , 2018
3. Flux-dependent graphs for metabolic networks
npj Systems Biology and Applications , 4 , 2018
4. Dynamic metabolic control: towards precision engineering of metabolism
Journal of Industrial Microbiology & Biotechnology , 45 , 2018
5. Are We There Yet? How and When Specific Biotechnologies Will Improve Human Health
Biotechnology Journal , 2018

2017

1. Fundamental Design Principles for Transcription-Factor-Based Metabolite Biosensors
ACS Synthetic Biology , 6 , 2017

2016

1. Shaping pulses to control bistable systems: Analysis, computation and counterexamples
Automatica , 63 , 2016

2015

Proceedings of the National Academy of Sciences , 112 , 2015
2. Shaping pulses to control bistable biological systems
In Proceedings of the American Control Conference , 2015-July , 2015
3. Dynamic optimization of metabolic networks coupled with gene expression
Journal of Theoretical Biology , 365 , 2015
4. Noise propagation in synthetic gene circuits for metabolic control.
ACS Synthetic Biology , 4 , 2015
5. Design of a bistable switch to control cellular uptake
Journal of The Royal Society Interface , 12 , 2015

2014

1. Spatial Quantification of Cytosolic Ca2+ Accumulation in Nonexcitable Cells:An Analytical Study
IEEE/ACM Transactions on Computational Biology and Bioinformatics , 11 , 2014
2. Model Reduction of Genetic-Metabolic Networks via Time Scale Separation
, 2014
3. The EGFR demonstrates linear signal transmission.
Integrative biology , 8 , 2014

2013

1. Control of protein concentrations in heterogeneous cell populations
In Proceeding of the European Control Conference , 2013
2. Stochastic simulation of enzymatic reactions under transcriptional feedback regulation
In Proceeding of the European Control Conference , 2013
3. Cumulative Signal Transmission in Nonlinear Reaction-Diffusion Networks
PLoS ONE , 8 , 2013
4. Synthetic gene circuits for metabolic control: design trade-offs and constraints.
Journal of the Royal Society, Interface / the Royal Society , 10 , 2013

2012

1. Analytic computation of the integrated response in nonlinear reaction-diffusion systems
In 51st IEEE Conference on Decision and Control , 2012
2. Design constraints in an operon circuit for engineered control of metabolic networks
In 51st Conference on Decision and Control , 2012
3. Design tradeoffs in a synthetic gene control circuit for metabolic networks
In Proceedings of the American Control Conference , 2012
4. Predicting the F(ab)-mediated effect of monoclonal antibodies in vivo by combining cell-level kinetic and pharmacokinetic modelling.
Journal of pharmacokinetics and pharmacodynamics , 39 , 2012
5. Multistability and oscillations in genetic control of metabolism
Journal of theoretical biology , 295 , 2012

2011

1. Optimal control of metabolic networks with saturable enzyme kinetics.
IET systems biology , 5 , 2011
2. Optimal adaptation of metabolic networks in dynamic equilibrium
In Proceedings of the American Control Conference , 2011
3. Global gene regulation in metabolic networks
In Proceedings of the 18th IFAC World Congress , 2011

2010

1. Control structure and limitations of biochemical networks
In Proceedings of the American Control Conference , 2010

2009

1. Sequential activation of metabolic pathways: a dynamic optimization approach.
Bulletin of mathematical biology , 71 , 2009
2. Ligand accumulation counteracts therapeutic inhibition of receptor systems
In Foundations of Systems Biology and Engineering , 2009
3. An analytic characterization of all stabilizing feedbacks for LTI plants
In Proceeding of the European Control Conference , 2009

2008

1. Optimal metabolic pathway activation
In Proceedings of the IFAC World Congress , 2008
2. Cascaded Multilevel Inverter With Regeneration Capability and Reduced Number of Switches
IEEE Transactions on Industrial Electronics , 55 , 2008

2007

1. H\textlessinf\textgreater2\textless/inf\textgreater optimal ripple-free deadbeat controller design
Automatica , 43 , 2007
2. Optimal metabolic regulation by temporal variation of enzyme activities: a control theoretic approach
In Foundations of Systems Biology and Engineering , 2007
3. Effect of downstream feedback on the achievable performance of feedback control loops for serial processes
In Proceeding of the European Control Conference , 2007
4. Optimal triangular approximation for linear stable multivariable systems
In Proceedings of the American Control Conference , 2007
5. On structurally constrained H2 performance bounds for stable MIMO plant models
IET Control Theory & Applications , 1 , 2007
6. H2 Optimal ripple-free deadbeat controller design
Automatica , 43 , 2007
7. Double objective optimal multivariable ripple-free deadbeat control
International Journal of Control , 80 , 2007

2006

1. Suboptimal triangular controller design methodology for full MIMO stable systems
In Proceedings of the UKACC Conference , 2006
2. Basic integrated modelling: a case study
International Journal of Electrical Engineering Education , 43 , 2006

2005

1. MIMO interactions in sampled data systems
In Proceedings of the 16th IFAC World Congress , 2005
2. Novel cell based on reduced single-phase active front end for multicell converters
In 31st Annual Conference of IEEE Industrial Electronics Society, 2005. IECON 2005. , 2005

–>