List of works - Nicola Zamboni

(13)C-based metabolic flux analysis.

scientific article published on 21 May 2009

13C metabolic flux analysis in complex systems ⬇️

scientific article published on September 15, 2010

2-Deoxy-D-glucose Restore Glucocorticoid Sensitivity in Acute Lymphoblastic Leukemia via Modification of N-Linked Glycosylation in an Oxygen Tension-Independent Manner.

scientific article published on 26 July 2017

6-Phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 is essential for p53-null cancer cells.

scientific article published on 16 January 2017

A Fatty Acid Oxidation-Dependent Metabolic Shift Regulates Adult Neural Stem Cell Activity

scientific article published on August 2017

A Fatty Acid Oxidation-dependent Metabolic Shift Regulates the Adaptation of BRAF-mutated Melanoma to MAPK Inhibitors

scientific article published on 02 August 2019

A Genome-Scale Database and Reconstruction of Caenorhabditis elegans Metabolism

scientific article published on 19 May 2016

A functional analysis of 180 cancer cell lines reveals conserved intrinsic metabolic programs

scientific article published in November 2022

A genetically encoded Förster resonance energy transfer sensor for monitoring in vivo trehalose-6-phosphate dynamics.

scientific article

A high-throughput metabolomics method to predict high concentration cytotoxicity of drugs from low concentration profiles

scientific article published in 2011

A roadmap for interpreting (13)C metabolite labeling patterns from cells

scientific article

A system suitability testing platform for untargeted, high-resolution mass spectrometry

scientific article published on 11 October 2022

ADAMTS18+ villus tip telocytes maintain a polarized VEGFA signaling domain and fenestrations in nutrient-absorbing intestinal blood vessels

scientific article published in 2022

Acute Activation of Oxidative Pentose Phosphate Pathway as First-Line Response to Oxidative Stress in Human Skin Cells

scientific article

An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments

scientific article

An integrative metabolomics and transcriptomics study to identify metabolic alterations in aged skin of humans in vivo

scientific article

Ancestral allele of DNA polymerase gamma modifies antiviral tolerance

scientific article published in 2024

Astrocyte glutathione maintains endothelial barrier stability

scientific article published on 19 May 2020

Bacterial response to acetate challenge: a comparison of tolerance among species

scientific article published on 01 August 2000

Bifunctional Malic/Malolactic Enzyme Provides a Novel Mechanism for NADPH-Balancing in Bacillus subtilis

scientific article published in 2021

Biological insights through nontargeted metabolomics.

scientific article

Bradyrhizobium diazoefficiens Requires Chemical Chaperones To Cope with Osmotic Stress during Soybean Infection

scientific article published in 2021

Branched-chain amino acid catabolism is a conserved regulator of physiological ageing

scientific article

CBMT-41. GLIOBLASTOMA CLONES DERIVED FROM TUMOR CORE AND EDGE DISPLAY SPATIAL METABOLIC HETEROGENEITY

scientific article published on 5 November 2018

Collisional fragmentation of central carbon metabolites in LC-MS/MS increases precision of ¹³C metabolic flux analysis

scientific article

Commensal Clostridiales strains mediate effective anti-cancer immune response against solid tumors

scientific article published in 2021

Computational Metabolomics: From Cheminformatics to Machine Learning (Dagstuhl Seminar 20051) ⬇️

proceedings

Computational Metabolomics: From Spectra to Knowledge (Dagstuhl Seminar 22181) ⬇️

proceedings

Cross-platform comparison of methods for quantitative metabolomics of primary metabolism

scientific article published on 01 March 2009

D-Glucosamine supplementation extends life span of nematodes and of ageing mice

scientific article published on 08 April 2014

Deficiency in glutamine but not glucose induces MYC-dependent apoptosis in human cells.

scientific article

Defining the metabolome: size, flux, and regulation

scientific article

Dietary excess regulates absorption and surface of gut epithelium through intestinal PPARα

scientific article published in 2021

Differential glucose repression in common yeast strains in response to HXK2 deletion

scientific article published on 22 January 2010

Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ

scientific article published on 22 December 2020

Dynamic exometabolome analysis reveals active metabolic pathways in non-replicating mycobacteria.

scientific article published on 16 September 2015

Dynamic flux responses in riboflavin overproducing Bacillus subtilis to increasing glucose limitation in fed-batch culture

scientific article published in March 2010

Dynamic tracing of sugar metabolism reveals the mechanisms of action of synthetic sugar analogs

scientific article published on 25 October 2021

Editorial overview: analytical biotechnology.

scientific article

Embryonic Lethality of Mitochondrial Pyruvate Carrier 1 Deficient Mouse Can Be Rescued by a Ketogenic Diet

scientific article

Engineering genetically encoded nanosensors for real-time in vivo measurements of citrate concentrations

scientific article (publication date: 2011)

FOXC2 controls adult lymphatic endothelial specialization, function, and gut lymphatic barrier preventing multiorgan failure

scientific article published in 2021

FiatFlux--a software for metabolic flux analysis from 13C-glucose experiments

scientific article

Fluxome Profiling in Microbes

scientific article

From biomarkers to integrated network responses

scientific article published on 01 October 2008

Frontiers of high-throughput metabolomics

scientific article published on 5 January 2017

Functional metabolic screen identifies 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 as an important regulator of prostate cancer cell survival.

scientific article

Functional screening identifies MCT4 as a key regulator of breast cancer cell metabolism and survival

scientific article published on 12 May 2015

Genetics. Getting closer to the whole picture.

scientific article

Genome engineering reveals large dispensable regions in Bacillus subtilis.

scientific article published on 29 August 2003

Genome-Scale CRISPR Screening in Human Intestinal Organoids Identifies Drivers of TGF-β Resistance

scientific article published on 01 March 2020

Genome-wide RNAi Screening Identifies Protein Modules Required for 40S Subunit Synthesis in Human Cells

scientific article published on 17 December 2015

Genome-wide RNAi screen identifies novel players in human 60S subunit biogenesis including key enzymes of polyamine metabolism

scientific article published on 01 March 2022

Genomewide landscape of gene-metabolome associations in Escherichia coli

scientific article published on 16 January 2017

Glucose-derived glutamate drives neuronal terminal differentiation in vitro

scholarly article published on 19 January 2024

Gut Microbiota Orchestrates Energy Homeostasis during Cold.

scientific article published in December 2015

HIF-driven SF3B1 induces KHK-C to enforce fructolysis and heart disease.

scientific article published on 17 June 2015

High-throughput discovery metabolomics

scientific article published on 03 September 2014

High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived 13C constraints.

scientific article published in February 2004

High-throughput quantitative metabolomics: workflow for cultivation, quenching, and analysis of yeast in a multiwell format

scientific article published in May 2009

High-throughput, accurate mass metabolome profiling of cellular extracts by flow injection-time-of-flight mass spectrometry.

scientific article

Hippocampal neural stem cells rapidly change their metabolic profile during neuronal differentiation in cell culture

scientific article published in 2016

Identification and functional expression of the mitochondrial pyruvate carrier

scientific article

Identification of HIF-dependent alternative splicing in gastrointestinal cancers and characterization of a long, coding isoform of SLC35A3

scientific article published on 05 January 2021

Inhibition of Mevalonate Pathway Prevents Adipocyte Browning in Mice and Men by Affecting Protein Prenylation

Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains

scientific article published in Nature Communications

Integration of Metabolomics and Transcriptomics Reveals a Complex Diet of Mycobacterium tuberculosis during Early Macrophage Infection

scientific article published on July 2017

Involvement of circulating factors in the transmission of paternal experiences through the germline

scientific article published on 09 October 2020

Knockout of the high-coupling cytochrome aa3 oxidase reduces TCA cycle fluxes in Bacillus subtilis.

scientific article published in September 2003

L-Arginine Modulates T Cell Metabolism and Enhances Survival and Anti-tumor Activity

scientific article published on 13 October 2016

LRH-1-dependent programming of mitochondrial glutamine processing drives liver cancer.

scientific article published on June 2016

Lipid signalling drives proteolytic rewiring of mitochondria by YME1L

scientific article published on 06 November 2019

Liposome-supported peritoneal dialysis in the treatment of severe hyperammonemia: An investigation on potential interactions

scholarly article by Giovanna Giacalone et al published May 2018 in Journal of Controlled Release

MSNovelist: de novo structure generation from mass spectra

scientific article published in 2022

Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices

scientific article published in 2021

Metabolic control of adult neural stem cell activity by Fasn-dependent lipogenesis

scientific article published on 2 December 2012

Metabolic landscape of the male mouse gut identifies different niches determined by microbial activities

scientific article published in 2023

Metabolic network segmentation: A probabilistic graphical modeling approach to identify the sites and sequential order of metabolic regulation from non-targeted metabolomics data.

scientific article

Metabolite Identification through Machine Learning- Tackling CASMI Challenge Using FingerID

scientific article published on 6 June 2013

Metabolite identification and molecular fingerprint prediction through machine learning.

scientific article

Metabolomic Profiling of Bradyrhizobium diazoefficiens-Induced Root Nodules Reveals Both Host Plant-Specific and Developmental Signatures

scientific article published on 27 May 2016

Metabolomics Identifies a Biomarker Revealing In Vivo Loss of Functional β-Cell Mass Before Diabetes Onset

scientific article published on 19 September 2019

Metabolomics and Dual RNA-Sequencing on Root Nodules Revealed New Cellular Functions Controlled by Paraburkholderia phymatum NifA

scientific article published in 2021

Metabolomics and Transcriptomics Identify Multiple Downstream Targets of Paraburkholderia phymatum σ54 During Symbiosis with Phaseolus vulgaris. ⬇️

scientific article

Metabolomics reveals tepotinib-related mitochondrial dysfunction in MET-activating mutations-driven models

scientific article published on 11 May 2019

Metabotypes of breast cancer cell lines revealed by non-targeted metabolomics

scientific article published on 27 December 2016

Mitochondrial spongiotic brain disease: astrocytic stress and harmful rapamycin and ketosis effect

scientific article published on 31 July 2020

Mitochondrial–cell cycle cross-talk drives endoreplication in heart disease

scientific article published in 2021

Model-independent fluxome profiling from 2H and 13C experiments for metabolic variant discrimination

scientific article

Modulation of Myelopoiesis Progenitors Is an Integral Component of Trained Immunity

scientific article published in January 2018

Molecular pathways behind acquired obesity: Adipose tissue and skeletal muscle multiomics in monozygotic twin pairs discordant for BMI

scientific article

Monitoring Mitochondrial Pyruvate Carrier Activity in Real Time Using a BRET-Based Biosensor: Investigation of the Warburg Effect

scientific article published on August 2015

Multi-omics analysis identifies ATF4 as a key regulator of the mitochondrial stress response in mammals

scientific article published on 31 May 2017

Multidimensional optimality of microbial metabolism

scientific article published in May 2012

Multilayered genetic and omics dissection of mitochondrial activity in a mouse reference population

scientific article

Multiomic profiling of the liver across diets and age in a diverse mouse population

scientific article published in 2022

Non-stationary (13)C-metabolic flux ratio analysis.

scientific article published on 12 August 2013

Non-targeted LC-MS based metabolomics analysis of the urinary steroidal profile

scientific article published on 31 January 2017

Nontargeted in vitro metabolomics for high-throughput identification of novel enzymes in Escherichia coli.

scientific article

Nontargeted profiling of coenzyme A thioesters in biological samples by tandem mass spectrometry

scientific article published on 14 August 2013

Novel biological insights through metabolomics and 13C-flux analysis.

scientific article published on 08 September 2009

Nrf2 Activation Promotes Keratinocyte Survival during Early Skin Carcinogenesis via Metabolic Alterations.

scientific article published on 3 November 2015

Paraburkholderia phymatum Homocitrate Synthase NifV Plays a Key Role for Nitrogenase Activity during Symbiosis with Papilionoids and in Free-Living Growth Conditions

scientific article published in 2021

Peroxisome Proliferator Activated Receptor Gamma Controls Mature Brown Adipocyte Inducibility through Glycerol Kinase

scientific article published in January 2018

Quantification and mass isotopomer profiling of α-keto acids in central carbon metabolism

scientific article published on 24 February 2014

Quantification of Cellular Folate Species by LC-MS after Stabilization by Derivatization.

scientific article published on 5 June 2018

Rapid, randomized development of genetically encoded FRET sensors for small molecules.

scientific article published on June 2015

Real-time metabolome profiling of the metabolic switch between starvation and growth

scientific article published on 14 September 2015

Recent advances in mass spectrometry-based computational metabolomics

Reducing maintenance metabolism by metabolic engineering of respiration improves riboflavin production by Bacillus subtilis.

scientific article published in January 2003

SLAW: A Scalable and Self-Optimizing Processing Workflow for Untargeted LC-MS

scientific article published in 2021

SPHN/PHRT: Forming a Swiss-Wide Infrastructure for Data-Driven Sepsis Research

scientific article published on 01 June 2020

SUMOFLUX: A Generalized Method for Targeted 13C Metabolic Flux Ratio Analysis

scientific article

Screening of Bacillus subtilis transposon mutants with altered riboflavin production.

scientific article published on 5 June 2008

Systems proteomics of liver mitochondria function

scientific article

Targeting glioma-initiating cells via the tyrosine metabolic pathway

scientific article published on 14 February 2020

Targeting lactate dehydrogenase B-dependent mitochondrial metabolism affects tumor initiating cells and inhibits tumorigenesis of non-small cell lung cancer by inducing mtDNA damage

scientific article published in 2022

Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast

scientific article published on January 2013

The Bacillus subtilis yqjI gene encodes the NADP+-dependent 6-P-gluconate dehydrogenase in the pentose phosphate pathway

scientific article published on July 2004

The RNA-Binding Protein PUM2 Impairs Mitochondrial Dynamics and Mitophagy During Aging

scientific article published on 11 January 2019

The Yeast Cyclin-Dependent Kinase Routes Carbon Fluxes to Fuel Cell Cycle Progression

scientific article

The alternative analog plasticizer BPS displays similar phenotypic and metabolomic responses to BPA in HepG2 and INS-1E cells

scientific article published in 2022

The coenzyme thiamine diphosphate displays a daily rhythm in the Arabidopsis nucleus

scientific article published on 05 May 2020

The integrated response of primary metabolites to gene deletions and the environment

scientific article published on 23 January 2013

The oxygen sensor PHD3 limits glycolysis under hypoxia via direct binding to pyruvate kinase.

scientific article published on 12 April 2011

The phosphoenolpyruvate carboxykinase also catalyzes C3 carboxylation at the interface of glycolysis and the TCA cycle of Bacillus subtilis

scientific article

The thioredoxin-1 system is essential for fueling DNA synthesis during T-cell metabolic reprogramming and proliferation.

scientific article

Tradeoff between enzyme and metabolite efficiency maintains metabolic homeostasis upon perturbations in enzyme capacity.

scientific article published on April 2010

Transient expression and flux changes during a shift from high to low riboflavin production in continuous cultures of Bacillus subtilis.

scientific article published in January 2005

Ultrahigh performance liquid chromatography-tandem mass spectrometry method for fast and robust quantification of anionic and aromatic metabolites

scientific article published in June 2010

Vegan diet in young children remodels metabolism and challenges the statuses of essential nutrients

scientific article published in 2021

Yin Yang 1 Orchestrates a Metabolic Program Required for Both Neural Crest Development and Melanoma Formation

scientific article published on 01 April 2019

Yin Yang 1 sustains biosynthetic demands during brain development in a stage-specific manner

article

YtsJ has the major physiological role of the four paralogous malic enzyme isoforms in Bacillus subtilis.

scientific article published on July 2006

anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data

scientific article

List of works by Nicola Zamboni

(13)C-based metabolic flux analysis.

13C metabolic flux analysis in complex systems ⬇️

2-Deoxy-D-glucose Restore Glucocorticoid Sensitivity in Acute Lymphoblastic Leukemia via Modification of N-Linked Glycosylation in an Oxygen Tension-Independent Manner.

6-Phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 is essential for p53-null cancer cells.

A Fatty Acid Oxidation-Dependent Metabolic Shift Regulates Adult Neural Stem Cell Activity

A Fatty Acid Oxidation-dependent Metabolic Shift Regulates the Adaptation of BRAF-mutated Melanoma to MAPK Inhibitors

A Genome-Scale Database and Reconstruction of Caenorhabditis elegans Metabolism

A functional analysis of 180 cancer cell lines reveals conserved intrinsic metabolic programs

A genetically encoded Förster resonance energy transfer sensor for monitoring in vivo trehalose-6-phosphate dynamics.

A high-throughput metabolomics method to predict high concentration cytotoxicity of drugs from low concentration profiles

A roadmap for interpreting (13)C metabolite labeling patterns from cells

A system suitability testing platform for untargeted, high-resolution mass spectrometry

ADAMTS18+ villus tip telocytes maintain a polarized VEGFA signaling domain and fenestrations in nutrient-absorbing intestinal blood vessels

Acute Activation of Oxidative Pentose Phosphate Pathway as First-Line Response to Oxidative Stress in Human Skin Cells

An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments

An integrative metabolomics and transcriptomics study to identify metabolic alterations in aged skin of humans in vivo

Ancestral allele of DNA polymerase gamma modifies antiviral tolerance

Astrocyte glutathione maintains endothelial barrier stability

Bacterial response to acetate challenge: a comparison of tolerance among species

Bifunctional Malic/Malolactic Enzyme Provides a Novel Mechanism for NADPH-Balancing in Bacillus subtilis

Biological insights through nontargeted metabolomics.

Bradyrhizobium diazoefficiens Requires Chemical Chaperones To Cope with Osmotic Stress during Soybean Infection

Branched-chain amino acid catabolism is a conserved regulator of physiological ageing

CBMT-41. GLIOBLASTOMA CLONES DERIVED FROM TUMOR CORE AND EDGE DISPLAY SPATIAL METABOLIC HETEROGENEITY

Collisional fragmentation of central carbon metabolites in LC-MS/MS increases precision of ¹³C metabolic flux analysis

Commensal Clostridiales strains mediate effective anti-cancer immune response against solid tumors

Computational Metabolomics: From Cheminformatics to Machine Learning (Dagstuhl Seminar 20051) ⬇️

Computational Metabolomics: From Spectra to Knowledge (Dagstuhl Seminar 22181) ⬇️

Cross-platform comparison of methods for quantitative metabolomics of primary metabolism

D-Glucosamine supplementation extends life span of nematodes and of ageing mice

Deficiency in glutamine but not glucose induces MYC-dependent apoptosis in human cells.

Defining the metabolome: size, flux, and regulation

Dietary excess regulates absorption and surface of gut epithelium through intestinal PPARα

Differential glucose repression in common yeast strains in response to HXK2 deletion

Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ

Dynamic exometabolome analysis reveals active metabolic pathways in non-replicating mycobacteria.

Dynamic flux responses in riboflavin overproducing Bacillus subtilis to increasing glucose limitation in fed-batch culture

Dynamic tracing of sugar metabolism reveals the mechanisms of action of synthetic sugar analogs

Editorial overview: analytical biotechnology.

Embryonic Lethality of Mitochondrial Pyruvate Carrier 1 Deficient Mouse Can Be Rescued by a Ketogenic Diet

Engineering genetically encoded nanosensors for real-time in vivo measurements of citrate concentrations

FOXC2 controls adult lymphatic endothelial specialization, function, and gut lymphatic barrier preventing multiorgan failure

FiatFlux--a software for metabolic flux analysis from 13C-glucose experiments

Fluxome Profiling in Microbes

From biomarkers to integrated network responses

Frontiers of high-throughput metabolomics

Functional metabolic screen identifies 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 as an important regulator of prostate cancer cell survival.

Functional screening identifies MCT4 as a key regulator of breast cancer cell metabolism and survival

Genetics. Getting closer to the whole picture.

Genome engineering reveals large dispensable regions in Bacillus subtilis.

Genome-Scale CRISPR Screening in Human Intestinal Organoids Identifies Drivers of TGF-β Resistance

Genome-wide RNAi Screening Identifies Protein Modules Required for 40S Subunit Synthesis in Human Cells

Genome-wide RNAi screen identifies novel players in human 60S subunit biogenesis including key enzymes of polyamine metabolism

Genomewide landscape of gene-metabolome associations in Escherichia coli

Glucose-derived glutamate drives neuronal terminal differentiation in vitro

Gut Microbiota Orchestrates Energy Homeostasis during Cold.

HIF-driven SF3B1 induces KHK-C to enforce fructolysis and heart disease.

High-throughput discovery metabolomics

High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived 13C constraints.

High-throughput quantitative metabolomics: workflow for cultivation, quenching, and analysis of yeast in a multiwell format

High-throughput, accurate mass metabolome profiling of cellular extracts by flow injection-time-of-flight mass spectrometry.

Hippocampal neural stem cells rapidly change their metabolic profile during neuronal differentiation in cell culture

Identification and functional expression of the mitochondrial pyruvate carrier

Identification of HIF-dependent alternative splicing in gastrointestinal cancers and characterization of a long, coding isoform of SLC35A3

Inhibition of Mevalonate Pathway Prevents Adipocyte Browning in Mice and Men by Affecting Protein Prenylation

Inhibition of Mevalonate Pathway Prevents Adipocyte Browning in Mice and Men by Affecting Protein Prenylation

Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains

Integration of Metabolomics and Transcriptomics Reveals a Complex Diet of Mycobacterium tuberculosis during Early Macrophage Infection

Involvement of circulating factors in the transmission of paternal experiences through the germline

Knockout of the high-coupling cytochrome aa3 oxidase reduces TCA cycle fluxes in Bacillus subtilis.

L-Arginine Modulates T Cell Metabolism and Enhances Survival and Anti-tumor Activity

LRH-1-dependent programming of mitochondrial glutamine processing drives liver cancer.

Lipid signalling drives proteolytic rewiring of mitochondria by YME1L

Liposome-supported peritoneal dialysis in the treatment of severe hyperammonemia: An investigation on potential interactions

MSNovelist: de novo structure generation from mass spectra

Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices

Metabolic control of adult neural stem cell activity by Fasn-dependent lipogenesis

Metabolic landscape of the male mouse gut identifies different niches determined by microbial activities

Metabolic network segmentation: A probabilistic graphical modeling approach to identify the sites and sequential order of metabolic regulation from non-targeted metabolomics data.