Publications related to Modeling, analysis, and design of complex biological networks

EXPLORING CHEMODIVERSITY IN METABOLISM TOWARDS THE SUPERVISED INTEGRATION OF CHEMISTRY INTO BIOLOGY

Vassily Hatzimanikatis, Jasmin Maria Hafner, Homa Mohammadi Peyhani, Noushin Hadadi

The availability of different levels of omics data helps us to observe cells with higher resolution and from different perspectives. However, complete understanding of metabolism lags behind in explaining the chemodiversity observed in living organisms – t ...

2017

Unlocking the full potential of kinetic metabolic models through characterization and reduction of uncertainty

Vassily Hatzimanikatis, Ljubisa Miskovic

Kinetic models are the most promising tool for comprehending the complex dynamic behavior of living cells. The primary goal of kinetic models is to capture the properties of the metabolic networks as a whole, and we need large-scale models for dependable i ...

2017

Reconstruction of biological pathways and metabolic networks from in silico labeled metabolites

Vassily Hatzimanikatis, Jasmin Maria Hafner, Noushin Hadadi, Keng Cher Soh

Reaction atom mappings track the positional changes of all of the atoms between the substrates and the products as they undergo the biochemical transformation. However, information on atom transitions in the context of metabolic pathways is not widely avai ...

Wiley-V C H Verlag Gmbh2017

lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites

Vassily Hatzimanikatis, Meriç Ataman

In the post-genomic era, Genome-scale metabolic networks (GEMs) have emerged as invaluable tools to understand metabolic capabilities of organisms. Different parts of these metabolic networks are defined as subsystems/pathways, which are sets of functional ...

2017

Transforming Growth Factor beta/Activin signaling in neurons increases susceptibility to starvation

Bruno Lemaitre, Wen Bin Chng, Xiaoxue Li

Animals rely on complex signaling network to mobilize its energy stores during starvation. We have previously shown that the sugar-responsive TGF beta/Activin pathway, activated through the TGF beta ligand Dawdle, plays a central role in shaping the post-p ...

2017

Discovery and Evaluation of Novel Pathways for Production of the Second Generation of Biofuels

Vassily Hatzimanikatis, Ljubisa Miskovic, Meriç Ataman, Noushin Hadadi, Milenko Tokic

In an effort of overcoming the limited availability of fossil energy resources the focus of the research and development in the area of biofuels has moved towards developing the second generation of fuels that should be produced via microbial fermentation. ...

2016

ATLAS of Biochemistry: A Repository of All Possible Biochemical Reactions for Synthetic Biology and Metabolic Engineering Studies

Vassily Hatzimanikatis, Jasmin Maria Hafner, Adrian Shajkofci, Noushin Hadadi, Aikaterini Zisaki

Because the complexity of metabolism cannot be intuitively understood or analyzed, computational methods are indispensable for studying biochemistry and deepening our understanding of cellular metabolism to promote new discoveries. We used the computationa ...

Amer Chemical Soc2016

“ATLAS of Biochemistry”: A repository of all possible biochemical reactions for synthetic biology, metabolic engineering and metabolomics studies

Vassily Hatzimanikatis, Jasmin Maria Hafner, Adrian Shajkofci, Noushin Hadadi, Aikaterini Zisaki

Recent technical and analytical progress in the field of metabolomics has lead to the identification of vast amounts of new compounds in living organisms. However, the integration of these compounds into the context of known metabolism remains difficult. T ...

2016

Exploring enhancement of 1,4-butanediol production in recombinant E. coli using Large-scale kinetic models

Vassily Hatzimanikatis, Ljubisa Miskovic, Anirikh Chakrabarti, Stefano Andreozzi

Rational metabolic engineering methods are increasingly employed in designing the commercially viable processes for the production of chemicals relevant to pharmaceutical, biotechnology, and food and beverage industries. With the growing availability of om ...

2016

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Modeling, analysis, and design of complex biological networks

EXPLORING CHEMODIVERSITY IN METABOLISM TOWARDS THE SUPERVISED INTEGRATION OF CHEMISTRY INTO BIOLOGY

Unlocking the full potential of kinetic metabolic models through characterization and reduction of uncertainty

Reconstruction of biological pathways and metabolic networks from in silico labeled metabolites

lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites

Transforming Growth Factor beta/Activin signaling in neurons increases susceptibility to starvation

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

Discovery and Evaluation of Novel Pathways for Production of the Second Generation of Biofuels

ATLAS of Biochemistry: A Repository of All Possible Biochemical Reactions for Synthetic Biology and Metabolic Engineering Studies

“ATLAS of Biochemistry”: A repository of all possible biochemical reactions for synthetic biology, metabolic engineering and metabolomics studies

Exploring enhancement of 1,4-butanediol production in recombinant E. coli using Large-scale kinetic models

Graph Chatbot

Chat with Graph Search

Unlocking the full potential of kinetic metabolic models through characterization and reduction of uncertainty

EXPLORING CHEMODIVERSITY IN METABOLISM TOWARDS THE SUPERVISED INTEGRATION OF CHEMISTRY INTO BIOLOGY

lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites

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

Reconstruction of biological pathways and metabolic networks from in silico labeled metabolites

Transforming Growth Factor beta/Activin signaling in neurons increases susceptibility to starvation

ATLAS of Biochemistry: A Repository of All Possible Biochemical Reactions for Synthetic Biology and Metabolic Engineering Studies

“ATLAS of Biochemistry”: A repository of all possible biochemical reactions for synthetic biology, metabolic engineering and metabolomics studies

Discovery and Evaluation of Novel Pathways for Production of the Second Generation of Biofuels

Exploring enhancement of 1,4-butanediol production in recombinant E. coli using Large-scale kinetic models