Thesis

2024

Optimality principles for the analysis of biological processes across scales: From enzyme kinetics to microbiome dynamics

A. Sahin / Director(s) : V. Hatzimanikatis 

Lausanne: EPFL

2024

p. 237.

DOI : 10.5075/epfl-thesis-10518

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Reconstruction and analysis of genome-scale metabolic networks in single organisms and microbial communities

E. Vagena / Director(s) : V. Hatzimanikatis 

Lausanne: EPFL

2024

p. 240.

DOI : 10.5075/epfl-thesis-10501

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Neuroprotection in the Retina: From Preventing Inflammatory Cell Death to Promoting Vascular Stability in the Central Nervous System

B. Kim / Director(s) : V. Hatzimanikatis; P. D. Westenskow 

Lausanne: EPFL

2024

p. 186.

DOI : 10.5075/epfl-thesis-10432

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2023

Expanding computational biochemistry towards complex and non-natural compounds

A. Sveshnikova / Director(s) : V. Hatzimanikatis 

Lausanne: EPFL

2023

p. 180.

DOI : 10.5075/epfl-thesis-10200

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Modeling, analysis, and design of complex biological networks

M. O. Oftadeh / Director(s) : V. Hatzimanikatis 

Lausanne: EPFL

2023

p. 214.

DOI : 10.5075/epfl-thesis-10210

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2022

An optimized high throughput platform, from genetic transformation to fermentation, to screen for secreted laccases in Aspergillus niger

L. M. C. Leynaud-Kieffer Curran / Director(s) : V. Hatzimanikatis; B. Simmons 

Lausanne: EPFL

2022

p. 193.

DOI : 10.5075/epfl-thesis-10804

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2021

Modelling the Intracellular Environment under Uncertainty, from Post-translational Modification to Metabolic Networks

R. A. Denhardt-Eriksson / Director(s) : V. Hatzimanikatis 

Lausanne: EPFL

2021

p. 220.

DOI : 10.5075/epfl-thesis-8764

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New and improved methods for integrated models of metabolism and gene expression

P. G. R. Salvy / Director(s) : V. Hatzimanikatis 

Lausanne: EPFL

2021

p. 285.

DOI : 10.5075/epfl-thesis-8489

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2020

Algorithms and flowchart for the design of synthetic biochemical networks

H. Mohammadi Peyhani / Director(s) : V. Hatzimanikatis 

Lausanne: EPFL

2020

p. 225.

DOI : 10.5075/epfl-thesis-8382

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Optimization methods and objective functions for analysis of metabolic network models

Z. Hosseini / Director(s) : V. Hatzimanikatis 

Lausanne: EPFL

2020

p. 163.

DOI : 10.5075/epfl-thesis-8005

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Modeling biochemical reaction networks in complex intracellular environments

D. R. Weilandt / Director(s) : V. Hatzimanikatis; B. Fierz 

Lausanne: EPFL

2020

p. 158.

DOI : 10.5075/epfl-thesis-7900

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Modeling metabolic and signaling pathways in cancer cells

M. Masid Barcon / Director(s) : V. Hatzimanikatis 

Lausanne: EPFL

2020

p. 190.

DOI : 10.5075/epfl-thesis-7725

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Modeling, predicting and mining metabolism at atom-level resolution

J. M. Hafner / Director(s) : V. Hatzimanikatis 

Lausanne: EPFL

2020

p. 169.

DOI : 10.5075/epfl-thesis-7415

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Mapping and Analysis of the Complexity of Lipid Metabolism for Applications in Health and Sustainability

S. Tsouka / Director(s) : V. Hatzimanikatis 

Lausanne: EPFL

2020

p. 155.

DOI : 10.5075/epfl-thesis-7697

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2019

Towards comprehensive and consistent kinetic models of metabolism under uncertainty

T. E. Hameri / Director(s) : V. Hatzimanikatis 

Lausanne: EPFL

2019

p. 156.

DOI : 10.5075/epfl-thesis-9194

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Computational studies of industrial hosts for improved production of the 2nd generation of biofuels

M. Tokic / Director(s) : V. Hatzimanikatis; L. Miskovic 

Lausanne: EPFL

2019

p. 167.

DOI : 10.5075/epfl-thesis-9068

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2018

Analysis of cellular and drug action mechanisms in the malaria parasites using systems biology approaches

A. Chiappino-Pepe / Director(s) : V. Hatzimanikatis 

Lausanne: EPFL

2018

p. 435.

DOI : 10.5075/epfl-thesis-8602

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Modeling and analysis of parts and devices of genetic regulation

Y. Berset / Director(s) : V. Hatzimanikatis; J. R. van der Meer 

Lausanne: EPFL

2018

p. 103.

DOI : 10.5075/epfl-thesis-8081

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2017

Computational methods and modeling of cellular function for the optimization of protein production and the study of cellular disease states

J. R. Pinto Vieira / Director(s) : V. Hatzimanikatis 

Lausanne: EPFL

2017

p. 260.

DOI : 10.5075/epfl-thesis-7865

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Novel systems biology approaches for design and analysis of palmitoylation networks reveal its regulatory effects on protein stability, activity and localization

T. Dallavilla / Director(s) : V. Hatzimanikatis; F. G. van der Goot Grunberg 

Lausanne: EPFL

2017

p. 218.

DOI : 10.5075/epfl-thesis-7383

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2016

Navigating and Managing the Complexity of Genome Scale Metabolic Networks for Studies in Cellular Physiology and Industrial Biotechnology

M. Ataman / Director(s) : V. Hatzimanikatis 

Lausanne: EPFL

2016

p. 178.

DOI : 10.5075/epfl-thesis-7102

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Enhancing the photo-Fenton treatment of contaminated water by use of ultrasound and iron-complexing agents

S. Papoutsakis / Director(s) : C. Pulgarin; S. Malato Rodriguez 

Lausanne: EPFL

2016

p. 125.

DOI : 10.5075/epfl-thesis-6830

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2015

Computational Studies on Cellular Metabolism

N. Hadadi / Director(s) : V. Hatzimanikatis 

Lausanne: EPFL

2015

p. 180.

DOI : 10.5075/epfl-thesis-6667

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Reconstruction and systems analysis of metabolism in apicomplexan parasites Toxoplasma gondii and Plasmodium falciparum

S. Tymoshenko / Director(s) : V. Hatzimanikatis; D. Soldati-Favre 

Lausanne: EPFL

2015

p. 168.

DOI : 10.5075/epfl-thesis-6692

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Computational studies on Escherichia coli metabolism

S. Andreozzi / Director(s) : V. Hatzimanikatis; L. Miskovic 

Lausanne: EPFL

2015

DOI : 10.5075/epfl-thesis-6558

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2014

Mathematical models and computational methods for the analysis of genome-scale protein synthesis

J. Racle / Director(s) : V. Hatzimanikatis 

Lausanne: EPFL

2014

DOI : 10.5075/epfl-thesis-6235

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2013

Metabolic modeling and experimental studies on carbon and energy metabolism of Mycobacterium tuberculosis

M. E. Özdemir / Director(s) : J. McKinney; V. Hatzimanikatis 

Lausanne: EPFL

2013

DOI : 10.5075/epfl-thesis-5970

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Computational Studies on Cellular Bioenergetics

K. C. Soh / Director(s) : V. Hatzimanikatis 

Lausanne: EPFL

2013

DOI : 10.5075/epfl-thesis-5560

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