Publication

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

Related publications (30)

Catalytic enantioselective Pictet-Spengler reaction of carbonyl compounds: Development and application to the asymmetric total synthesis of indole alkaloids

This thesis consists in an extensive study about the enantioselective Pictet-Spengler reaction (EPSR) and its application to the total synthesis of monoterpene indole alkaloids (MIAs). The general introduction presents the literature background about this ...

EPFL2022

Dynamic partitioning of branched-chain amino acids-derived nitrogen supports renal cancer progression

Ming Yang, Vassily Hatzimanikatis, Maria Masid Barcon

Metabolic reprogramming is critical for tumor initiation and progression. However, the exact impact of specific metabolic changes on cancer progression is poorly understood. Here, we integrate multimodal analyses of primary and metastatic clonally-related ...

Nature Portfolio2022

Multidisciplinary Investigation of the Gut-Brain Ecosystem in a Model of Alzheimer's Disease

Arielle Louise Planchette

The search for an understanding of the causal elements that lead to neurodegenerative diseases has motivated researchers for decades. Today, Alzheimer's disease is the most prevalent form of dementia and affects approximately fifty million people worldwide ...

EPFL2022

NICEpath: Finding metabolic pathways in large networks through atom-conserving substrate-product pairs

Vassily Hatzimanikatis, Jasmin Maria Hafner

Motivation: Finding biosynthetic pathways is essential for metabolic engineering of organisms to produce chemicals, biodegradation prediction of pollutants and drugs, and for the elucidation of bioproduction pathways of secondary metabolites. A key step in ...

OXFORD UNIV PRESS2021

Constraint-based metabolic control analysis for rational strain engineering

Ljubisa Miskovic, Vassily Hatzimanikatis, Meriç Ataman, Tuure Eelis Hameri, Sofia Tsouka

The advancements in genome editing techniques over the past years have rekindled interest in rational metabolic engineering strategies. While Metabolic Control Analysis (MCA) is a well-established method for quantifying the effects of metabolic engineering ...

2021

Radical-free hyperpolarized MRI using endogenously occurring pyruvate analogues and UV-induced nonpersistent radicals

Rolf Gruetter, Josefina Adriana Maria Bastiaansen, Lionel Pierre Arn, Andrea Capozzi, Hikari Ananda Infinity Yoshihara, Claudia Christina Zanella, Alice Radaelli

It was recently demonstrated that nonpersistent radicals can be generated in frozen solutions of metabolites such as pyruvate by irradiation with UV light, enabling radical-free dissolution dynamic nuclear polarization. Although pyruvate is endogenous, the ...

WILEY2021

Late post‐natal neurometabolic development in healthy male rats using 1 H and 31 P Magnetic Resonance Spectroscopy

Rolf Gruetter, Cristina Ramona Cudalbu, Guillaume Donati, Veronika Rackayová, Dunja Simicic

Brain metabolism evolves rapidly during early post‐natal development in the rat. While changes in amino acids, energy metabolites, antioxidants or metabolites involved in phospholipid metabolism have been reported in the early stages, neurometabolic change ...

2021

Emergence of diauxie as an optimal growth strategy under resource allocation constraints in cellular metabolism

Vassily Hatzimanikatis, Pierre Guy Rémy Salvy

Diauxie, or the sequential consumption of carbohydrates in bacteria such as Escherichia coli, has been hypothesized to be an evolutionary strategy which allows the organism to maximize its instantaneous specific growth-giving the bacterium a competitive ad ...

National Academy of Sciences2021

Chiral Alkyl Amine Synthesis via Catalytic Enantioselective Hydroalkylation of Enecarbamates

Xile Hu, Deyun Qian, Srikrishna Bera

Chiral alkyl amines are omnipresent as bioactive molecules and synthetic intermediates. The catalytic and enantioselective synthesis of alkyl amines from readily accessible precursors is challenging. Here we develop a nickel-catalyzed hydroalkylation metho ...

AMER CHEMICAL SOC2021

Natural Product Synthesis Enabled by Domino Processes Incorporating a 1,2-Rearrangement Step

Qian Wang, Jieping Zhu, Bastien Delayre

The art of natural product total synthesis is closely associated with two major determinants: the development/application of novel chemical reactions and the innovation in strategic use of classic organic reactions. While purposely seeking/applying a new s ...

2021