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Mardinoglu Lab

The Mardinoglu lab is interested in development of genome-scale metabolic models (GEMs) for human cells/tissues and employing these comprehensive models in the analysis of omics data obtained from subjects with complex diseases. The lab also focuses on the generation of Integrated Networks (INs) by merging GEMs with other biological networks. Such networks can lead to discovery of novel drug targets and biomarkers and subsequent development of efficient treatment strategies.

Members

Abdulahad Bayraktar

Abdulahad Bayraktar

PhD Student

Stephen Doran

Stephen Doran

PhD Student

Simon Lam

Simon Lam

PhD Student

Adil Mardinoglu

Adil Mardinoglu

Professor of Systems Biology

HeartBanner

Whole body modelling of patients with Cardiovascular Disease

There is strong evidence that oral/gut microbiota plays an important role in the appearance and development of metabolic diseases including Cardiovascular Disease (CVD). However, due to the complexity of the metabolic disorders in question, further studies are necessary to pinpoint the causative link between the microbiome and pathogenesis of the disease. In this project, we will generate Integrated Networks for the heart by merging metabolic, regulatory, signalling and protein-protein interaction networks as well as metabolic models for the 10 most abundant bacteria in saliva and faecel samples. We will integrate these models and study the interactions between the host and microbiome accounting for the effect of whole-body metabolism. We will discover biomarkers for early detection of the disease as well as the drug targets that can be used in developing effective treatment strategies.

BrainBanner.fw

A high-resolution molecular network of the human brain

Neurodegenerative diseases such as Alzheimer’s and Huntingdon’s, as well as cancers of the brain, are complex diseases and a growing problem for today’s ageing population. However, the brain, being the most complex organ in the body, is still relatively poorly understood, with disparate gene findings being unable to explain disease as a whole. To this end, we develop a high-resolution molecular network of the human brain based on single-cell, region-specific, and bulk tissue proteomics and transcriptomics data. Integrating proteomics and transcriptomics in this way allows the exploration of expression patterns at the resolution of single cells. This information can be used for systems-level modelling of gene and protein expression in the human brain. The network will be publicly available for open access.

View all publications

Research Grants as PI and Co-PI

  • PI, 18 M SEK for starting an independent Research Group at SciLifeLab, KTH during 2015-2023.
  • PI, 5M SEK proof of concept grant for HCC treatment from Knut and Alice Wallenberg Foundation during 2019-2021.
  • PI, 5M SEK proof of concept grant for NAFLD treatment from Knut and Alice Wallenberg Foundation during 2018-2020.
  • Co-PI, 4M SEK proof of concept grant for NAFLD treatment from Knut and Alice Wallenberg

Foundation during 2018-2020.

  • Co-PI, 4 M SEK from Vinnova Grant during 2018-2022.
  • Co-PI, 120.000 USD from Chan Zuckerberg Initiative in 2018.
  • Co-PI, ~20 M SEK from Wallenberg Centre for Protein Research, Knut and Alice Wallenberg Foundation, total of 320 MSEK during 2016-2023.
  • Co-PI, 281.982 Euros from Polymers in the Liver: Metabolism and Regulation, Horizon 2020 - Research and Innovation Framework Programme during 2019-2021.

 

Other Grants

  • Nils Pihlblads stipendiefond to attend Keystone Symposia on Integrating Metabolism and Tumor Biology, January 13th -18th, Vancouver, Canada, 2015.
  • Assar Gabrielssons Fond to attend the 22nd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2014) in July 11-15, 2014.
  • Knut and Alice Wallenberg Foundation Award, to attend Keystone Symposia on Big Data in Biology, March 23rd -25th, San Francisco, USA, 2014.
  • Assar Gabrielssons Fond to attend the conference on Cancer Therapeutics 2013: From bench to bedside, November 4th – 6th, La Jolla, USA, 2013.
  • InnoCentive Challange winner, Propose a Biomarker that Could Predict Potential for Plexiform Neurofibroma Growth, 2013.
  • Knut and Alice Wallenberg Foundation Award, to attend Keystone Symposia on Human Genomics and Personalized Medicine, June 17th – 21st, Stockholm, Sweden, 2013.
  • Abcam Travel Scholarships to attend Programming Obesity meeting, April 14th – 16th, Cambridge, UK, 2013.
  • InnoCentive Challange winner, Advancing Research into Facial Fat Redistribution, 2012.
  • Adlerbertska forskningsstiftelsen fellowship, Gothenburg, Sweden, 2012.
  • EMBL Corporate Partnership fellowship to attend EMBO|EMBL Symposium Diabetes and Obesity, Leipzig, Germany, 2012.
  • Knut and Alice Wallenberg Foundation Award, Chalmers to attend ISMB 8th Student Council Symposium, California, USA, 2012.
  • Knut and Alice Wallenberg Foundation Award, Chalmers to attend Conference on Constraint-based Reconstruction and Analyses, June 24th-26th,Reykjavik, Iceland, 2011.
  • The Society for Biological Engineering Award to attend the 3rd International Conference on Biomolecular Engineering, January 16th-19th, San Francisco, USA, 2011.
  • Enterprise Ireland for three years support for PhD research project under the Applied Research Enhancement programme as part of the SEAM Research Centre at WIT.
  • Cancer Research Ireland (Irish Cancer Society) for an Oncology Scholars Award, 2009.
  • Travel award for the 7th International Scientific and Clinical Applications of Magnetic Carriers, Vancouver, Canada, 2008.
  • Travel award for the 6th International Scientific and Clinical Applications of Magnetic Carriers, Krems, Austria, 2006.
  • ERASMUS scholarship during the ERASMUS Socrates Program between 2004 and 2005.
  • Tekfen, Zorlu and Koc Foundations scholarships during the fellow's education in ITU.

 

Awards

  • Knut and Alice Wallenberg Foundation Award, to attend Keystone Symposia on Big Data in Biology, March 23rd -25th, San Francisco, USA, 2014.
  • Assar Gabrielssons Fond to attend the conference on Cancer Therapeutics 2013: From bench to bedside, November 4th – 6th, La Jolla, USA, 2013.
  • InnoCentive Challange winner, Propose a Biomarker that Could Predict Potential for Plexiform Neurofibroma Growth, 2013.
  • Abcam Travel Scholarships to attend Programming Obesity meeting, Cambridge, UK.
  • InnoCentive Challange winner, Advancing Research into Facial Fat Redistribution, 2012.
  • Adlerbertska forskningsstiftelsen fellowship, Gothenburg, Sweden, 2012.
  • EMBL Corporate Partnership fellowship to attend EMBO|EMBL Symposium Diabetes and Obesity, Leipzig, Germany, 2012.
  • Knut and Alice Wallenberg Foundation Award, Chalmers to attend ISMB 8th Student Council Symposium, California, USA, 2012.
  • Knut and Alice Wallenberg Foundation Award, Chalmers to attend Conference on Constraint-based Reconstruction and Analyses, Reykjavik, Iceland, 2011.
  • The Society for Biological Engineering (SBE) Award to attend the 3rd International Conference on Biomolecular Engineering, San Francisco, USA, 2011.
  • Knut and Alice Wallenberg Foundation Award, Chalmers to attend 3rd International Conference on Biomolecular Engineering, San Francisco, USA, 2011.
  • Enterprise Ireland support for PhD research project under the Applied Research Enhancement (ARE) programme as part of the SEAM Research Centre at WIT, 2006.
  • Cancer Research Ireland (Irish Cancer Society) for an Oncology Scholars Travel Award to attend the 6th International Scientific and Clinical Applications of Magnetic Carriers, Krems, Austria, 2006.
  • Travel award for the 7th International Scientific and Clinical Applications of Magnetic Carriers, Vancouver, Canada, 2008.
  • Travel award for the 6th International Scientific and Clinical Applications of Magnetic Carriers, Krems, Austria, 2006.
  • ERASMUS scholarship during the ERASMUS Socrates Program (1 year) 2005.
  • Tekfen, Zorlu and Koc foundations scholarships during the fellow's education in ITU (4 years).
icdm

Seminar: The use of systems biology for development of treatment for liver diseases

International Congress of Diabetes and Metabolism (ICDM 2019), Seoul, South Korea, October, 2019.

ICDM 2019 website

An Integrated Understanding of the Rapid Metabolic Benefits of a Carbohydrate-Restricted Diet on Hepatic Steatosis in Humans
A. Mardinoglu, Hao Wu, Elias Bjornson, Cheng Zhang, Antti Hakkarainen, Sari M. Rasanen, Sunjae lee, Rosellina M. Mancina, Matthias Bergentall, Kirsi H. Pietilainen, Sanni Soderlund, Niina Matikainen, Marcus Stahlman, Per-Olof Bergh, Martin Adiels, Brian D. Piening, Marit Graner, Nina Lundbom, Kevin J. Williams, Stefano Romeo, Jens Nielsen, Michael Snyder, Mathias Uhlen, Goran Bergstrom, Rosie Perkins, Hanns-Ulrich Marschall, Fredrik Backhed, Marja-Riitta Taskinen, Jan Boren
Cell Metabolism
Highlighted at SCIENCE TRANSLATIONAL MEDICINE
 
Metabolic network-based stratification of hepatocellular carcinoma reveals three distinct tumor subtypes
Gholamreza Bidkhori, Rui Benfeitas, Martina Klevstig, Cheng Zhang, Jens Nielsen, Mathias Uhlen, Jan Boren, Adil Mardinoglu
PNAS (Proceedings of the National Academy of Sciences)
 
A pathology atlas of the human cancer transcriptome
M. Uhlén, C. Zhang, S. Lee, E. Sjöstedt, L. Fagerberg, G. Bidkhori, R. Benfeitas, M. Arif, Z. Liu, F. Edfors, K. Sanli, K. von Feilitzen, P. Oksvold, E. Lundberg, S. Hober, P. Nilsson, J. Mattsson, J. M. Schwenk, H. Brunnström, B. Glimelius, T. Sjöblom, P. Edqvist, D. Djureinovic, P. Micke, C. Lindskog, A. Mardinoglu, F.Ponten
Science
Highlighted at NATURE
 
Network analyses identify liver-specific targets for treating liver diseases
S. Lee, C. Zhang, Z. Liu, M. Klevstig, B. Mukhopadhyay, M. Bergentall, R. Cinar, M. Ståhlman, N. Sikanic, J. K. Park, S. Deshmukh, A. M. Harzandi, T. Kuijpers, M. Grøtli, S. J. Elsässer, B. D. Piening, M. Snyder, U. Smith, J. Nielsen, F. Bäckhed, G. Kunos, M. Uhlen, J. Boren, A. Mardinoglu,
Molecular Systems Biology, 13:938
 
Plasma Mannose Levels Are Associated with Incident Type 2 Diabetes and Cardiovascular Disease
A Mardinoglu, A Stančáková, L A Lotta, J Kuusisto, J Boren, M Blüher, N J Wareham, E Ferrannini, …
Cell Metabolism 26 (2), 281-283
 
Personal model‐assisted identification of NAD+ and glutathione metabolism as intervention target in NAFLD
A Mardinoglu, E Bjornson, C Zhang, M Klevstig, S Söderlund, M Ståhlman, …
Molecular systems biology 13 (3), 916
Highlighted at SCIENCE TRANSLATIONAL MEDICINE
 
Integrated Network Analysis Reveals an Association between Plasma Mannose Levels and Insulin Resistance
S Lee, C Zhang, M Kilicarslan, BD Piening, E Björnson, BM Hallström, …
Cell Metabolism 24(1), 172-184
Highlighted at NATURE REVIEWS ENDOCRINOLOGY
 
The gut microbiota modulates host amino acid and glutathione metabolism in mice
A Mardinoglu, S Shoaie, M Bergentall, P Ghaffari, C Zhang, E Larsson, …
Molecular systems biology 11 (10), 834
 
Stratification of hepatocellular carcinoma patients based on acetate utilization
E Björnson, B Mukhopadhyay, A Asplund, N Pristovsek, R Cinar, …
Cell reports 13 (9), 2014-2026
 
Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease
A Mardinoglu, R Agren, C Kampf, A Asplund, M Uhlen, J Nielsen
Nature communications 5
Highlighted at NATURE REVIEWS GASTROENTEROLOGY & HEPATOLOGY
 
Identification of anticancer drugs for hepatocellular carcinoma through personalized genome‐scale metabolic modeling
R Agren, A Mardinoglu, A Asplund, C Kampf, M Uhlen, J Nielsen
Molecular systems biology 10 (3), 721
Highlighted at NATURE REVIEWS GASTROENTEROLOGY & HEPATOLOGY
 
Integration of clinical data with a genome‐scale metabolic model of the human adipocyte
A Mardinoglu, R Agren, C Kampf, A Asplund, I Nookaew, P Jacobson, …
Molecular systems biology 9 (1), 649

Our partners

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Science for Life Laboratory, Sweden

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KTH Royal Institute of Technology

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University of Gothenburg

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Istanbul Medipol University

Contact us

Professor Adil Mardinglu
Professor of Systems Biology

Guy's Tower Wing
Guy's Hospital