Nature Search

Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease

Alterations in hepatocyte metabolism can lead to disorders such as non-alcoholic steatohepatitis (NASH). Here the authors create a comprehensive model of hepatocyte metabolism and use it to identify metabolic pathways altered in disease, revealing that serine levels are reduced in patients with NASH.

Adil Mardinoglu
Rasmus Agren
Jens Nielsen
Research14 Jan 2014
Nature Communications

Volume: 5, P: 1-11
Microbial collagenase activity is linked to oral–gut translocation in advanced chronic liver disease

While oral bacteria rarely colonize the healthy gut, they dominate the gut microbiome of patients with chronic liver disease. Here a bacterial gene encoded by microbial translocators is linked to gut barrier disruption and fibrosis.

Shen Jin
Aurelie Cenier
Melanie Schirmer
ResearchOpen Access29 Dec 2025
Nature Microbiology

Volume: 11, P: 211-227
Author Correction: Spatiotemporal dissection of the cell cycle with single-cell proteogenomics

Diana Mahdessian
Anthony J. Cesnik
Emma Lundberg
Amendments and Corrections05 Aug 2022
Nature

Volume: 608, P: E32
Revisiting the role of serine metabolism in hepatic lipogenesis

Hong Yang
Cheng Zhang
Adil Mardinoglu
Research11 May 2023
Nature Metabolism

Volume: 5, P: 760-761
Genome-scale models in human metabologenomics

Metabologenomics integrates multi-omics data into genome-scale metabolic models (GEMs) to analyse complex metabolic networks. Mardinoglu and Palsson review advancements in GEMs at the global, cell- and tissue-specific, microbiome and whole-body levels, with insights into their applications towards improving health care.

Adil Mardinoglu
Bernhard Ø. Palsson
Reviews19 Sept 2024
Nature Reviews Genetics

Volume: 26, P: 123-140
Subjective cognitive decline in major depressive patients is associated with altered entropy and connectivity changes of temporal and insular region

Burak Yulug
Ali Yalcinkaya
Adil Mardinoglu
ResearchOpen Access01 Sept 2025
Translational Psychiatry

Volume: 15, P: 1-10
Phenotypic and genetic variance: a systems approach to the liver

Elucidating the entire complexity of biological functions in the liver is vital to understand its key role in the progression of complex diseases. A new mouse study integrates complementary '–omics' data across various environmental states using the liver as a platform for multiomics analysis and identifies new mechanisms in hepatic mitochondrial function.

Adil Mardinoglu
Mathias Uhlén
News & Views22 Jun 2016
Nature Reviews Gastroenterology & Hepatology

Volume: 13, P: 439-440
Systematic transcriptional analysis of human cell lines for gene expression landscape and tumor representation

During preclinical drug development, the ability of cancer cell lines to faithfully model human disease is important for identifying potential therapeutic strategies. Here, using transcriptomic datasets of over 1000 cell lines, the authors evaluate how representative each line is of its cancer type and present their cell line selection tool.

Han Jin
Cheng Zhang
Adil Mardinoglu
ResearchOpen Access05 Sept 2023
Nature Communications

Volume: 14, P: 1-15
Depression is an independent risk factor for stroke reccurence and cognitive impairment in stroke patients

Seyda Cankaya
Shair Shah Safa
Burak Yulug
ResearchOpen Access21 Nov 2025
Translational Psychiatry

Volume: 15, P: 1-8
Next generation pan-cancer blood proteome profiling using proximity extension assay

Comprehensive and scalable proteomic profiling of plasma samples can improve the screening and diagnosis of cancer patients. Here, the authors use the Olink Proximity Extension Assay technology to characterise the plasma proteomes of 1477 patients across twelve cancer types, and use machine learning to obtain a protein panel for cancer classification.

María Bueno Álvez
Fredrik Edfors
Mathias Uhlén
ResearchOpen Access18 Jul 2023
Nature Communications

Volume: 14, P: 1-13
Spatiotemporal dissection of the cell cycle with single-cell proteogenomics

Spatial and temporal variations among individual human cell proteomes are comprehensively mapped across the cell cycle using proteomic imaging and transcriptomics.

Diana Mahdessian
Anthony J. Cesnik
Emma Lundberg
Research24 Feb 2021
Nature

Volume: 590, P: 649-654
Extensive weight loss reveals distinct gene expression changes in human subcutaneous and visceral adipose tissue

Adil Mardinoglu
John T. Heiker
Matthias Blüher
ResearchOpen Access05 Oct 2015
Scientific Reports

Volume: 5, P: 1-11
BMP4 and Gremlin 1 regulate hepatic cell senescence during clinical progression of NAFLD/NASH

Baboota et al. investigate senescence as a driver of human NAFLD/NASH and show the roles of BMP4 and its antagonist Gremlin 1 as anti-senescent and pro-senescent molecules, respectively.

Ritesh K. Baboota
Aidin Rawshani
Ulf Smith
ResearchOpen Access22 Aug 2022
Nature Metabolism

Volume: 4, P: 1007-1021
Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

Christian Lieven
Moritz E. Beber
Cheng Zhang
Amendments and CorrectionsOpen Access19 Mar 2020
Nature Biotechnology

Volume: 38, P: 504
Integration of molecular profiles in a longitudinal wellness profiling cohort

An important aspect of precision medicine is to probe the stability in molecular profiles among healthy individuals over time. Here, the authors sample a longitudinal wellness cohort and analyse blood molecular profiles as well as gut microbiota composition.

Abdellah Tebani
Anders Gummesson
Linn Fagerberg
ResearchOpen Access08 Sept 2020
Nature Communications

Volume: 11, P: 1-14
Extensively acquired antimicrobial-resistant bacteria restructure the individual microbial community in post-antibiotic conditions

Jae Woo Baek
Songwon Lim
Sunjae Lee
ResearchOpen Access14 May 2025
npj Biofilms and Microbiomes

Volume: 11, P: 1-13
Transient colonizing microbes promote gut dysbiosis and functional impairment

Sunjae Lee
Victoria Meslier
Saeed Shoaie
ResearchOpen Access08 Sept 2024
npj Biofilms and Microbiomes

Volume: 10, P: 1-11
Drug repositioning for immunotherapy in breast cancer using single-cell analysis

Elyas Mohammadi
Samira Dashti
Mohammad Hadi Sekhavati
ResearchOpen Access08 Apr 2024
npj Systems Biology and Applications

Volume: 10, P: 1-11
MEMOTE for standardized genome-scale metabolic model testing

Christian Lieven
Moritz E. Beber
Cheng Zhang
Correspondence02 Mar 2020
Nature Biotechnology

Volume: 38, P: 272-276
Systems biology in hepatology: approaches and applications

Biological network models can provide a scaffold for studying the biological pathways operating in connection with disease development. Here, the authors review how biological network models can integrate multiomics data to advance our understanding of complex liver diseases, which might lead to improved treatment strategies.

Adil Mardinoglu
Jan Boren
Jens Nielsen
Reviews23 Apr 2018
Nature Reviews Gastroenterology & Hepatology

Volume: 15, P: 365-377
Adipose tissue morphology, imaging and metabolomics predicting cardiometabolic risk and family history of type 2 diabetes in non-obese men

Aidin Rawshani
Björn Eliasson
Ulf Smith
ResearchOpen Access19 Jun 2020
Scientific Reports

Volume: 10, P: 1-13
Vimentin deficiency in macrophages induces increased oxidative stress and vascular inflammation but attenuates atherosclerosis in mice

Liliana Håversen
Jeanna Perman Sundelin
Jan Borén
ResearchOpen Access19 Nov 2018
Scientific Reports

Volume: 8, P: 1-13
Characterization of different fat depots in NAFLD using inflammation-associated proteome, lipidome and metabolome

Alen Lovric
Marit Granér
Jan Boren
ResearchOpen Access21 Sept 2018
Scientific Reports

Volume: 8, P: 1-14
Predicting growth of the healthy infant using a genome scale metabolic model

Avlant Nilsson
Adil Mardinoglu
Jens Nielsen
ResearchOpen Access31 Jan 2017
npj Systems Biology and Applications

Volume: 3, P: 1-9
Understanding the interactions between bacteria in the human gut through metabolic modeling

Saeed Shoaie
Fredrik Karlsson
Jens Nielsen
ResearchOpen Access28 Aug 2013
Scientific Reports

Volume: 3, P: 1-10
The effect of the TM6SF2 E167K variant on liver steatosis and fibrosis in patients with chronic hepatitis C: a meta-analysis

Zhengtao Liu
Shuping Que
Luca Valenti
ResearchOpen Access24 Aug 2017
Scientific Reports

Volume: 7, P: 1-11
Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling

Pouyan Ghaffari
Adil Mardinoglu
Jens Nielsen
ResearchOpen Access02 Feb 2015
Scientific Reports

Volume: 5, P: 1-10

Search

Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease

Microbial collagenase activity is linked to oral–gut translocation in advanced chronic liver disease

Author Correction: Spatiotemporal dissection of the cell cycle with single-cell proteogenomics

Revisiting the role of serine metabolism in hepatic lipogenesis

Genome-scale models in human metabologenomics

Subjective cognitive decline in major depressive patients is associated with altered entropy and connectivity changes of temporal and insular region

Phenotypic and genetic variance: a systems approach to the liver

Systematic transcriptional analysis of human cell lines for gene expression landscape and tumor representation

Depression is an independent risk factor for stroke reccurence and cognitive impairment in stroke patients

Next generation pan-cancer blood proteome profiling using proximity extension assay

Spatiotemporal dissection of the cell cycle with single-cell proteogenomics

Extensive weight loss reveals distinct gene expression changes in human subcutaneous and visceral adipose tissue

BMP4 and Gremlin 1 regulate hepatic cell senescence during clinical progression of NAFLD/NASH

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

Integration of molecular profiles in a longitudinal wellness profiling cohort

Extensively acquired antimicrobial-resistant bacteria restructure the individual microbial community in post-antibiotic conditions

Transient colonizing microbes promote gut dysbiosis and functional impairment

Drug repositioning for immunotherapy in breast cancer using single-cell analysis

MEMOTE for standardized genome-scale metabolic model testing

Systems biology in hepatology: approaches and applications

Adipose tissue morphology, imaging and metabolomics predicting cardiometabolic risk and family history of type 2 diabetes in non-obese men

Vimentin deficiency in macrophages induces increased oxidative stress and vascular inflammation but attenuates atherosclerosis in mice

Characterization of different fat depots in NAFLD using inflammation-associated proteome, lipidome and metabolome

Predicting growth of the healthy infant using a genome scale metabolic model

Understanding the interactions between bacteria in the human gut through metabolic modeling

The effect of the TM6SF2 E167K variant on liver steatosis and fibrosis in patients with chronic hepatitis C: a meta-analysis

Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling

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