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2023
A NON-CD25-BINDING IL-2 VARIANT FOR THE EXPANSION OR ENGINEERING OF T CELLS THAT CONFER SUPERIOR TUMOR CONTROL
Human Gene Therapy
2023-11-01
Asian Transplantation Week (ATW)/ Annual congress of the Korean-Society-for-Transplantation (KST), Seoul, SOUTH KOREA, NOV 17-19, 2022.p. A21-A22
SYSTEMS BIOLOGY APPROACHES ALLOW INVESTIGATING THE SIGNALING AND METABOLIC REPROGRAMMING OF T CELLS
Human Gene Therapy
2023-11-01
Asian Transplantation Week (ATW)/ Annual congress of the Korean-Society-for-Transplantation (KST), Seoul, SOUTH KOREA, NOV 17-19, 2022.p. A20-A20
2018
ETFL: A Formulation of ME-Models Accounting for Expression and Thermodynamics in Constraint-Based Models
5th Conference on Constraint-Based Reconstruction and Analysis (COBRA 2018), Seattle, WA, USA, October 14-16th 2018.
Predicted responses of a large-scale Pseudomonas putida KT2440 kinetic metabolic model to several single-gene knockouts are consistent with experimental observations
5th Conference on Constraint-Based Reconstruction and Analysis, Seattle, USA, October 14-16, 2018.
Exploring Biosynthetic Pathways for the Production of Five Methyl Ethyl Ketone Precursors
5th Conference on Constraint-Based Reconstruction and Analysis, Seattle, USA, October 14-16, 2018.
Machine Learning for Uncertainty Reduction in Biochemical Kinetic Models
5th Conference on Constraint-Based Reconstruction and Analysis, Seattle, USA, October 14-16, 2018.
Modeling CLiMP-63 spatio-temporal distribution and its interplay with Post-translational modification
5th Conference on Constraint-Based Reconstruction and Analysis, Seattle, United States of America, October 14-16, 2018.
Systematic reduction of genome-scale models for the study of metabolic phenotypes of human cells
Constraint-Based Reconstruction and Analysis (COBRA) 2018, Seattle, USA, 14-16 October 2018.
Studying cancer cells phenotypes integrating omics data in human reduced genome-scale metabolic models.
European Conference on Computational Biology (ECCB) 2018, Athens, 8-12 September 2018.
Identification of the enzymes responsible for diverse phenotypic states of yeast lipid metabolism using comprehensive mechanistic models
Conference on Constraint-Based Reconstruction and Analysis (COBRA 2018), Seattle, USA, 14-16/10/2018.
Mapping the diverse phenotypic states of yeast lipid metabolism to enzymes using mechanistic kinetic models
International Conference on the Bioscience of Lipids (ICBL 2018), Helsinki, Finland, 4-7/09/2018.
In silico tracing of the fate of single carbon atoms in different physiological states of E. coli
Metabolic Engineering 12, Munich, Germany, June 24-28, 2018.
Computational analysis of Pseudomonas Putida metabolism Using Large-scale Kinetic Models
Metabolic Engineering 12, Munich, Germany, June 24-28, 2018.
Evaluating the similarity of biochemical reactions and its uses for mapping novel and orphan reactions to protein sequences
Metabolic Engineering 12, Munich, Germany, June 24-28, 2018.
2017
Toward the identification of cellular mechanisms behind the lethal phenotypes in malaria parasites blood stages with PlasmoGEM and metabolic modeling
Biochemical and Molecular Engineering XX, Newport Beach, CA, USA, July 16-20, 2017.
Identifying and targeting key cellular mechanisms for proliferation in Plasmodium parasites: a combined experimental and computational strategy
3rd International SystemsX.ch Conference on Systems Biology, ETH Zurich, Zurich, Switzerland, September 4-7, 2017.
Facing The Unknown: Suggesting Alternative Novel Biochemistry in Escherichia coli and Saccharomyces cerevisiae
253rd ACS National Meeting & Exposition, San Francisco, CA, USA, April 2-6, 2017.
Toward the identification of cellular mechanisms behind the lethal phenotypes in Plasmodium berghei blood stages with PlasmoGEM and metabolic modeling
BioMalPar XIII: Biology and Pathology of the Malaria Parasite, EMBL conference center, Heidelberg, Germany, May 29-31, 2017.
Toward fully characterized knowledge gaps in metabolic networks: discovery of missing biochemistry in Escherichia coli
Biochemical and Molecular Engineering XX, Newport Beach, CA, USA, July 16-20, 2017.
Identifying and targeting key cellular mechanisms for proliferation in Plasmodium parasites: a combined experimental and computational strategy
Gordon Research Conference: Malaria, Les Diableretes, Switzerland, July 2-7, 2017.
EXPLORING CHEMODIVERSITY IN METABOLISM TOWARDS THE SUPERVISED INTEGRATION OF CHEMISTRY INTO BIOLOGY
3rd International SystemsX.ch Conference on system biology, Zurich,Switzerland, September 4-7, 2017.
Evaluating the similarity of biochemical reactions and its uses for mapping novel reactions to protein sequences
3rd International SystemsX.ch Conference on system biology, Zurich, Switzerland, September 4-7, 2017.
Fusing Individual-based Models with Genome-scale Metabolic Networks – a Novel Approach for Quantifying Emergent Microbial Community Spatiotemporal Dynamics
253rd ACS National Meeting & Exposition, San Francisco, CA, USA, April 2-6, 2017.
Toward the identification of new cancer therapy targets using metabolic modeling in a human genome scale
Biochemical and Molecular Engineering XX, Newport Beach, California, USA, July 16-20, 2017.
Generation and Analysis of Large-Scale Dynamic Non-Linear Models of Metabolism
Biochemical and Molecular Engineering XX, Newport Beach, CA, USA, July 16-20, 2017.
Exploring chemodiversity in metabolism towards the selective integration of chemistry into biology
Biochemical and Molecular Engineering XX, Newport Beach, California, USA, July 16-20, 2017.
Design of novel enzyme-catalyzed reactions linked to protein sequences for finding enzyme engineering targets
Enzyme Engineering XXIV, Toulouse, France, September 24-28, 2017.
Discovery, evaluation, and analysis of novel pathways for production of five methyl ethyl ketone precursors
3rd International SystemsX.ch Conference, Zurich, Switzerland, September 4-7, 2017.
Optimization of the production of methyl ethyl ketone in recombinant Pseudomonas putida using large-scale kinetic models
Biochemical and Molecular Engineering XX, Newport Beach, CA, USA, July 16-20, 2017.
Discovery and evaluation of novel pathways for production of methyl ethyl ketone
Biochemical and Molecular Engineering XX, Newport Beach, CA, USA, July 16-20, 2017.
Identification of the enzymes that determine the robustness of lipid profiles in yeast
58th International Conference on the Bioscience of Lipids, Zurich, Switzerland, September 10-14, 2017.
A kinetic model of the lipid network in yeast
3rd International SystemsX.ch Conference on Systems Biology, Zurich, Switzerland, September 4-7, 2017.
Unlocking the full potential of kinetic metabolic models through characterization and reduction of uncertainty
3rd International SystemsX.ch Conference on Systems Biology, Zurich, Switzerland, September 4-7, 2017.
Deciphering ambiguous control over fluxes through characterization and reduction of uncertainty
Biochemical & Molecular Engineering XX, Newport Beach, California, USA, July 16-20, 2017.
Understanding reprogramming of cancer cell metabolism using metabolic modeling
7th LIMNA Symposium, CHUV, Lausanne, Switzerland, April 4, 2017.
2016
Analysis and Design of Metabolic Engineering and Synthetic Biology Strategies using Large Scale Dynamic Models of Metabolism
Metabolic Engineering 11, Awaji Island, Japan, June 26-30, 2016.
“ATLAS of Biochemistry”: A repository of all possible biochemical reactions for synthetic biology, metabolic engineering and metabolomics studies
Metabolic Engineering 11, Awaji Island, Japan, June 26-30, 2016.
Large Scale Dynamic Models of Metabolism as a Tool for Analysis and Design of Metabolic Engineering and Synthetic Biology Strategies
251st American Chemical Society National Meeting, San Diego, California, USA, March 13-17, 2016.
iSCHRUNK – In Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks
251st American Chemical Society National Meeting, San Diego, California, USA, March 13-17, 2016.
Exploring enhancement of 1,4-butanediol production in recombinant E. coli using Large-scale kinetic models
251st American Chemical Society National Meeting, San Diego, California, USA, March 13-17, 2016.
Discovery and Evaluation of Novel Pathways for Production of the Second Generation of Biofuels
Metabolic Engineering XI, Awaji island, Japan, June 24-30, 2016.
Analysis and Design of Metabolic Engineering and Synthetic Biology Strategies using Large Scale Dynamic Models of Metabolism
Metabolic Engineering XI, Awaji island, Japan, June 24-30, 2016.
How uncertainty in kinetic parameters affects metabolic control analysis of optimally grown E.coli
Metabolic Engineering XI, Awaji island, Japan, June 24-30, 2016.
Identifying patterns in kinetic parameters that determine the impact of rate-limiting enzymes
Metabolic Engineering XI, Awaji island, Japan, June 24-30, 2016.
2015
Data Repository for Automated Metabolomics Administration (DRAMA)
Bioengineering Day 2015, SwissTech Convention Center, Lausanne, Switzerland, November 4, 2015.
Study on how underlying uncertainty in the flux values affects metabolic control analysis of optimally grown E. coli
4th Conference on Constraint-Based Reconstruction and Analysis (COBRA 2015), Heidelberg, Germany, September 16-18, 2015.
Developing a Reconciled Genome-Scale Model of the Malaria Parasite Plasmodium falciparum and its Thermodynamics-based Flux Balance Analysis
4th Conference on Constraint-Based Reconstruction and Analysis, Heidelberg, Germany, September 16-18, 2015.
Systematic Reduction of Genome Scale Metabolic Reconstructions – redGEM
4th Conference on Constraint-Based Reconstruction and Analysis (COBRA 2015), Crowne Plaza Heidelberg, Germany, September 16-18, 2015.
Integrating Transcriptomic Data with Thermodynamically Consistent Metabolic Models
4th Conference on Constraint-Based Reconstruction and Analysis (COBRA 2015), Heidelberg, Germany, September 16-18, 2015.
A Study of Dynamic Responses of E. coli Metabolism Upon Large Perturbations Using Large-Scale Kinetic Models
4th Conference on Constraint-Based Reconstruction and Analysis (COBRA 2015), Heidelberg, Germany, September 16-18, 2015.
Characterization of intracellular metabolic states in the origin of the metabolic reprogramming of cancer cells
Biochemical and Molecular Engineering XIX, Puerto Vallarta, Mexico, July 12-16, 2015.
In Silico Atom Labeling for the Reconstruction of Atom-mapped Metabolic Networks
Biochemical and Biomolecular Engineering, Puerto Vallarta, Mexico, July 12-16, 2015.
Automated reconstruction of E-coli metabolic network from labeled metabolites
Cell Factories and Biosustainability, Copenhagen, Denmark, May 17 – 21, 2015.
Systematic Reduction of Genome Scale Metabolic Reconstructions – redGEM
Biomolecular Engineering 2015 Conference, Puerto Vallarta, Mexico, July 12-16 2015.
iSCHRUNK – in Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks
Biochemical and Molecular Engineering XIX, Puerto Vallarta, Mexico, July 12-16, 2015.
Exploring enhancement of 1,4-butanediol production in recombinant E. coli using large-scale kinetic models
NovoNordisk Conference: Cell Factories and Biosustainability, Hillerød, Denmark, May, 17-21, 2015.
2014
Characterization of intracellular metabolic states in cells presenting the Warburg phenotype
Metabolic Engineering X Conference, Vancouver, BC, Canada, June 15-19, 20144.
Characterisation of intracellular metabolic states in cells presenting the Warburg phenotype
COBRA 2014 – 3rd Conference on Constraint-Based Reconstruction and Analysis, Wintergreen Resort, Charlottesville, VA, USA, May 20-23, 2014.
The design of “Super E. coli” through automated reaction network generation and genome scale models
Metabolic Engineering X Conference, Vancouver, Canada, June14-19, 2014.
Protein synthesis – computational modeling and experimental integration
LS2 Annual Meeting 2014, Lausanne, Switzerland, February 4-5, 2014.
Deciphering thermodynamics in metabolic networks: A priority list of candidates for metabolomics
Metabolic Engineering X, Vancouver, BC, Canada, June 15-19, 2014.
Towards a kinetic model of the phospholipids biosynthesis of the yeast Saccharomyces cerevisiae
LS2 Annual Meeting 2014, Lausanne, Vaud, Switzerland, February 4-5, 2014.
Kinetic reconstruction and analysis of sphingolipid metabolism
2nd International SystemsX Conference, Lausanne, Vaud, Switzerland, October 20-23, 2014.
Kinetic reconstruction and analysis of sphingolipid metabolism
Metabolic Engineering X Conference, Vancouver, British Columbia, Canada, June 15-19, 2014.
A Novel Approach to Design of Metabolic Engineering Strategiesa
Metabolic Engineering X, Vancouver, Canada, June 15-19, 2014.
Implications of the Assumptions on Intracellular Metabolic Operational States in Metabolic Control Analysis
Metabolic Engineering X, Vancouver, Canada, June 15-19, 2014.
Unraveling the inhibitory effects of acetate on ethanol production in CEN.PK
Metabolic Engineering X, Vancouver, Canada, June 15-19, 2014.
Engineering improved productivity of 1,4-butanediol in E. coli – a kinetic modeling approach
Metabolic Engineering X, Vancouver, Canada, June 15-19, 2014.
2013
Computational analysis of the interplay between tRNA competitive behavior and decoding type on the modulation of translation elongation rate
ICSB 2013 – 14th International Conference on Systems Biology, Copenhagen, Denmark, August 30th – September 3rd, 2013.
Analysis of the dynamics and competition for resources in the system of protein translation using stochastic simulations
9th European Biophysics Congress, Lisbon. Portugal, July 13-17, 2013.
Thermodynamics-Based Significance Ranking of Candidates for Metabolomics
2013 AIChE Annual Meeting, San Francisco, CA, USA, November 3-8, 2013.
Unlocking Yeast Metabolism: Identification of optimal flux directionalities
2013 AIChE Annual Meeting, San Francisco, CA, USA, November 3-8, 2013.
Thermodynamics-based Significance Ranking of Candidates for Metabolomics
Biochemical and Molecular Engineering XVIII – Frontiers in Biological Design, Synthetic Biology and Processing: East Meets West, Beijing, June 16-20,2013.
A comprehensive reconstruction of the fatty acid biosynthesis in Saccharomyces cerevisiae
All SystemsX.ch Day 2013, Bern, Switzerland, May 13, 2013.
Integrating omics data into metabolic models of lipids: a platform for the identification of gene mutations from lipidomics data
2013 AIChE Annual Meeting, San Fransisco, California, USA, November 3-8, 2013.
In silico analysis of the interplay between P/O ratio and physiological states of the optimally grown Escherichia coli
ICSB 2013, Copenhagen, Denmark, 29 August – 4 September 2013.
The interplay between tRNA competition and decoding on mRNA translation elongation rate modulation
European Biophysics Journal With Biophysics Letters
2013
9th European-Biophysical-Societies-Association Congress.p. S75-S75
Identification of Feasible Metabolic Fluxes and Metabolite Concentrations using Large-scale Kinetic Models
Biochemical and Molecular Engineering XVIII, Beijing, China, June 16-20, 2013.
Data, Parameters & Nonlinearities: Development and Applications of Large-scale Dynamic Models of Metabolism
Biochemical and Molecular Engineering XVIII, Beijing, China, June 16-20, 2013.
Investigation of network flexibility and identification of reaction essentiality of human host cells infected by S. flexneri
Systems Biology of Infection, Monte Verità, Switzerland, June 23 – 27, 2013.
2012
Kinetic modeling of the yeast sphingolipid metabolism identifies prevalent mutant strains through integration of lipidomic data profiles
Foundations of Systems Biology in Engineering 2012, Tsuruoka, Japan, October 21-25, 2012.
A novel approach to find the missing links in genome-scale metabolic models: The BridgeIt mrthod
FOSBE 2012, Tsuruoka, Japan, October 21-25 2012.
Large-scale dynamic models of metabolic networks
FOSBE 2012 conference, Tsuruoka, Japan, October 21-25, 2012.
Systematic Metabolic Engineering of Recombinant Xylose-Utilizing S. cerevisiae: Strategies for Improving Xylose Uptake Rate
FOSBE 2012 conference, Tsuruoka, Japan, October 21-25, 2012.
Systematic characterization of flux and network thermodynamic states for identification of metabolic engineering targets
Metabolic Engineering IX, Biarritz, France, June 03-07, 2012.
Metabolic control analysis of the central carbon pathway in optimally grown E. coli
Metabolic Engineering IX, Biarritz, France, June 03-07, 2012.
2011
Stochastic noise in translation
12th International Conference on Systems Biology, Heidelberg/Mannheim, Germany, August 28-September1, 2011.
Stochastic noise in translation
Gordon Research Conference on Stochastic Physics in Biology, Ventura, USA, January 23-28, 2011.
2010
Deciphering Translation – a Genome-Wide Analysis of Translation Limitations and Competitions in Saccharomyces cerevisiae
2010 AIChE Annual Meeting, Salt Lake City, Utah, USA, November 7-12, 2010.
Deciphering translation – a genome-wide analysis of translation in Escherichia coli
11th International Conference on Systems Biology, Edinburgh, UK, October 10-16, 2010.
Improving Ethanol Production of Xylose-Utilizing Saccharomyces cerevisiae
2010 AIChE Annual Meeting, Salt Lake City, UT, November 7-12, 2010.
Kinetic modeling of the central carbon metabolism of Escherichia Coli
2010 AIChE Annual Meeting, Salt Lake City, UT, November 7-12, 2010.
Exploration of Signaling Cycles using Dynamic Optimization
AIChE Annual Meeting, Salt Lake City, UT, USA, November 7-12, 2010.
Exploration of signaling cycles using dynamic optimization
11th International Conference on Systems Biology, Edinburgh, Scotland, UK., October 11-14, 2010.
Computational Analysis of Xylose-Utilizing Saccharomyces cerevisiae
Metabolic Engineering VIII: Metabolic Engineering for Green Growth, Jeju Island, South Korea, June 13-17, 2010.
Quantitative Analysis of Metabolic Networks Through the Explicit Consideration of Kinetic Mechanisms
Metabolic Engineering VIII: Metabolic Engineering for Green Growth, Jeju Island, South Korea, June 13-17, 2010.
2009
Network-based optimization of protein production
Abstracts Of Papers Of The American Chemical Society
2009
p. 57-BIOT
Analysis of genome-scale metabolic model of mycobacterium tuberculosis for new combat strategies
Abstracts Of Papers Of The American Chemical Society
2009
p. 329-BIOT
BIOT 428-Optimization of ethanol production from xylose in Saccharomyces cerevisiae
Abstracts Of Papers Of The American Chemical Society
2009
Analysis and synthesis of novel metabolic pathways
Abstracts Of Papers Of The American Chemical Society
2009
p. 375-BIOT
Quantification of uncertainty in metabolic networks through the sampling of kinetic data space
Proceedings of FOSBE 2009 Conference
2009
Fosbe2009, Denver, Colorado, August 9-12, 2009.2008
Enzyme States Allow Identification of Rate-Limiting Steps
Metabolic Engineering VII: Health and Sustainability, Puerto Vallarta, Mexico, September 14-19, 2008.
Study of Tricyclic Cascade Networks using Dynamic Optimization
AIChE Annual Meeting, Philadelphia, PA, November 16-21 2008.
Identification of the Design Principles of Signaling Pathways for Metabolic Engineering
Metabolic Engineering VII: Health and Sustainability, Puerto Vallarta, Mexico, September 14-19, 2008.
2007
Understanding the Optimal Response Properties of Tricyclic Cascade Networks through Dynamic Optimization
AIChE Annual Meeting, Salt Lake City, UT, November 4-9, 2007.
2005
Analysis of yeast metabolism using metabolic control analysis under uncertainty
Abstracts of Papers, 229th ACS National Meeting, San Diego, CA, United States, March 13-17, 2005
2005
p. BIOT-287
Bistability of protein aggregation as a function of molecular chaperone concentration
Abstracts of Papers, 229th ACS National Meeting, San Diego, CA, United States, March 13-17, 2005
2005
p. BIOT-326
From single module to signaling cascade networks: Network performance of ultrasensitive modules
Abstracts of Papers, 229th ACS National Meeting, San Diego, CA, United States, March 13-17, 2005
2005
p. BIOT-419
Systems-wide mathematical and computational framework for translation: Insights into regulation of protein expression in S. cerevisiae
Abstracts of Papers, 229th ACS National Meeting, San Diego, CA, United States, March 13-17, 2005
2005
p. BIOT-420
Analysis of free energy change and thermodynamic feasibility in a genome scale metabolic model
Abstracts of Papers, 229th ACS National Meeting, San Diego, CA, United States, March 13-17, 2005
2005
p. BIOT-095
Exploring the diversity of metabolism
Abstracts of Papers, 229th ACS National Meeting, San Diego, CA, United States, March 13-17, 2005
2005
p. BTEC-019
2003
A computational framework for the discovery of novel biotransformations
Abstracts of Papers, 225th ACS National Meeting, New Orleans, LA, United States, March 23-27, 2003
2003
p. BIOT-111
Quantification and characterization of uncertainty in metabolic engineering
Abstracts of Papers, 225th ACS National Meeting, New Orleans, LA, United States, March 23-27, 2003
2003
p. BIOT-169
2000
Mathematical framework for correlating mRNA and protein expression profiles
Book of Abstracts, 219th ACS National Meeting, San Francisco, CA, March 26-30, 2000
2000
p. BIOT-296
1997
Metabolic fluxes in central carbon metabolism of Bacillus subtilis
Book of Abstracts, 213th ACS National Meeting, San Francisco, April 13-17
1997
p. BIOC-051