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Lisitsyna A, Moritz F, Liu Y, Al Sadat L, Hauner H, Claussnitzer M, Schmitt-Kopplin P, Forcisi S. Feature Selection Pipelines with Classification for Non-targeted Metabolomics Combining the Neural Network and Genetic Algorithm. Anal Chem 2022; 94:5474-5482. [PMID: 35344349 DOI: 10.1021/acs.analchem.1c03237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Non-targeted metabolomics via high-resolution mass spectrometry methods, such as direct infusion Fourier transform-ion cyclotron resonance mass spectrometry (DI-FT-ICR MS), produces data sets with thousands of features. By contrast, the number of samples is in general substantially lower. This disparity presents challenges when analyzing non-targeted metabolomics data sets and often requires custom methods to uncover information not always accessible via classical statistical techniques. In this work, we present a pipeline that combines a convolutional neural network with traditional statistical approaches and an adaptation of a genetic algorithm. The developed method was applied to a lifestyle intervention cohort data set, where subjects at risk of type 2 diabetes underwent an oral glucose tolerance test. Feature selection is the final result of the pipeline, achieved through classification of the data set via a neural network, with a precision-recall score of over 0.9 on the test set. The features most relevant for the described classification were then chosen via a genetic algorithm. The output of the developed pipeline encompasses approximately 200 features with high predictive scores, providing a fingerprint of the metabolic changes in the prediabetic class on the data set. Our framework presents a new approach which allows to apply complex modeling based on convolutional neural networks for the analysis of high-resolution mass spectrometric data.
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Affiliation(s)
- Anna Lisitsyna
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg 85764, Germany.,German Center for Diabetes Research (DZD), Neuherberg 85764, Germany
| | - Franco Moritz
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Youzhong Liu
- Analytical Development, Small Molecule Development, Janssen Pharmaceutical Companies of Johnson and Johnson, Beerse 2340, Belgium
| | - Loubna Al Sadat
- Institute for Nutritional Medicine, School of Medicine, Technical University of Munich, Munich 80686, Germany
| | - Hans Hauner
- Institute for Nutritional Medicine, School of Medicine, Technical University of Munich, Munich 80686, Germany.,Else Kröner-Fresenius-Centre for Nutritional Medicine, School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Melina Claussnitzer
- Broad Institute of MIT and Harvard, Cambridge 02141-2023 Massachusetts, United States.,Division of Gerontology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02108, United States.,Harvard Medical School, Harvard University, Boston, Massachusetts 02108, United States
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg 85764, Germany.,Chair of Analytical Food Chemistry, TUM School of Life Sciences, Technical University Munich, Munich 80686, Germany
| | - Sara Forcisi
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg 85764, Germany.,German Center for Diabetes Research (DZD), Neuherberg 85764, Germany
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Dong S, Qian L, Cheng Z, Chen C, Wang K, Hu S, Zhang X, Wu T. Lactate and Myocadiac Energy Metabolism. Front Physiol 2021; 12:715081. [PMID: 34483967 PMCID: PMC8415870 DOI: 10.3389/fphys.2021.715081] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/29/2021] [Indexed: 12/05/2022] Open
Abstract
The myocardium is capable of utilizing different energy substrates, which is referred to as “metabolic flexibility.” This process assures ATP production from fatty acids, glucose, lactate, amino acids, and ketones, in the face of varying metabolic contexts. In the normal physiological state, the oxidation of fatty acids contributes to approximately 60% of energy required, and the oxidation of other substrates provides the rest. The accumulation of lactate in ischemic and hypoxic tissues has traditionally be considered as a by-product, and of little utility. However, recent evidence suggests that lactate may represent an important fuel for the myocardium during exercise or myocadiac stress. This new paradigm drives increasing interest in understanding its role in cardiac metabolism under both physiological and pathological conditions. In recent years, blood lactate has been regarded as a signal of stress in cardiac disease, linking to prognosis in patients with myocardial ischemia or heart failure. In this review, we discuss the importance of lactate as an energy source and its relevance to the progression and management of heart diseases.
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Affiliation(s)
- Shuohui Dong
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Linhui Qian
- Department of Colorectal and Anal Surgery, Feicheng Hospital Affiliated to Shandong First Medical University, Feicheng, China
| | - Zhiqiang Cheng
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Chang Chen
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Kexin Wang
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Sanyuan Hu
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Xiang Zhang
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Tongzhi Wu
- Adelaide Medical School and Centre of Research Excellence in Translating Nutritional Science to Good Health, The University of Adelaide, Adelaide, SA, Australia.,Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, SA, Australia
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Stakišaitis D, Juknevičienė M, Damanskienė E, Valančiūtė A, Balnytė I, Alonso MM. The Importance of Gender-Related Anticancer Research on Mitochondrial Regulator Sodium Dichloroacetate in Preclinical Studies In Vivo. Cancers (Basel) 2019; 11:cancers11081210. [PMID: 31434295 PMCID: PMC6721567 DOI: 10.3390/cancers11081210] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/16/2019] [Accepted: 08/16/2019] [Indexed: 12/28/2022] Open
Abstract
Sodium dichloroacetate (DCA) is an investigational medicinal product which has a potential anticancer preparation as a metabolic regulator in cancer cells’ mitochondria. Inhibition of pyruvate dehydrogenase kinases by DCA keeps the pyruvate dehydrogenase complex in the active form, resulting in decreased lactic acid in the tumor microenvironment. This literature review displays the preclinical research data on DCA’s effects on the cell pyruvate dehydrogenase deficiency, pyruvate mitochondrial oxidative phosphorylation, reactive oxygen species generation, and the Na+–K+–2Cl− cotransporter expression regulation in relation to gender. It presents DCA pharmacokinetics and the hepatocarcinogenic effect, and the safety data covers the DCA monotherapy efficacy for various human cancer xenografts in vivo in male and female animals. Preclinical cancer researchers report the synergistic effects of DCA combined with different drugs on cancer by reversing resistance to chemotherapy and promoting cell apoptosis. Researchers note that female and male animals differ in the mechanisms of cancerogenesis but often ignore studying DCA’s effects in relation to gender. Preclinical gender-related differences in DCA pharmacology, pharmacological mechanisms, and the elucidation of treatment efficacy in gonad hormone dependency could be relevant for individualized therapy approaches so that gender-related differences in treatment response and safety can be proposed.
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Affiliation(s)
- Donatas Stakišaitis
- Laboratory of Molecular Oncology, National Cancer Institute, 08660 Vilnius, Lithuania.
- Department of Histology and Embryology, Medical Academy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania.
| | - Milda Juknevičienė
- Department of Histology and Embryology, Medical Academy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Eligija Damanskienė
- Department of Histology and Embryology, Medical Academy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Angelija Valančiūtė
- Department of Histology and Embryology, Medical Academy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Ingrida Balnytė
- Department of Histology and Embryology, Medical Academy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Marta Maria Alonso
- Department of Pediatrics, Clínica Universidad de Navarra, University of Navarra, 55 Pamplona, Spain.
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Abstract
Metformin has been associated with lactic acidosis. Lactate levels are not commonly tested in clinical practice, and it is unclear to what extent metformin would typically increase lactate levels with chronic use. The aim of this review was to determine whether regular monitoring of the plasma lactate level would be beneficial in avoiding lactate accumulation and, ultimately, minimising the incidence of lactic acidosis in metformin-treated patients.A comprehensive search of PubMed, Embase, Web of Science, Cochrane and International Pharmaceutical Abstracts databases covering the period up to 30 May 2017 was performed. Search terms included combinations of terms and keywords, including "metformin", "lactate", "lactic acid" and "lactic acidosis". Cases series of lactic acidosis or metformin-associated lactic acidosis were excluded.Of 1539 potentially relevant articles, a total of 52 reported lactate levels from routine/regular pathological tests in metformin users. The studies were subdivided into four themes, regarding metformin usage and the reported lactate levels in patients who: (1) did not have contraindications to the use of metformin; (2) had contraindications, or renal impairment but without other contraindications; (3) exercised; or (4) also received any nucleoside reverse transcriptase inhibitor. Studies have reported that metformin treatment could increase lactate level of users. However, most results showed that the lactate level remained in the normal range.No definitive conclusions on the benefits of regular lactate monitoring in patients taking metformin can be made. Future research on larger populations focusing on the measurement of lactate levels with continuous metformin use is warranted.
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Effect of Ethanolic Extract from Seeds or Pods of Xylopia Aethiopica (Dunal) A. Rich (Annonaceae) on the Testicular Function of Adult Male Rats. Indian J Clin Biochem 2016; 32:420-428. [PMID: 29062173 DOI: 10.1007/s12291-016-0622-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 10/07/2016] [Indexed: 10/20/2022]
Abstract
Xylopia aethiopica (Annonaceae) is used in some folk medicines and widely consumed as a spice in some parts of Nigeria. Its efficacy as an anti-androgenic substance has warranted the attention of African scholars. This study evaluated the enzymatic activity of lactate dehydrogenase (LDH), γ-glutamyl transferase (γ-GT), sperm quality (motility, count, morphology), testosterone level and histo-pathological changes of the testis of rats chronically treated with ethanolic extract of the pods (without seeds), seeds, and fruits (pods + seeds) of Xylopia aethiopica. Male Wistar (224-246 g) rats were treated with the extract of the pods, seeds, and fruits of Xylopia aethiopica at the dose of 0, 50, 100, and 200 mg/kg body wt. for 60 days. Serum biochemistry, sperm quality and histo-pathological examination of the testis were assessed for any treatment-related adverse effects. After treatment with Xylopia aethiopica, testosterone level was decreased dose-dependently in the animals treated with the seed extract compared to all other groups. The enzymatic activities of LDH and γ-GT were higher in rats treated with the seed and fruit extracts compared with those treated with the pods. The numbers of motile sperm, and counts were decreased while the numbers of sperm with morphological defects were higher in rats treated with the seed and fruit extracts compared to the control. Histopathological changes of the testis were also more severe in rats treated with the highest dose of the seed extract. We conclude that the compounds related to the anti-infertility effects of Xylopia aethiopica are present in the seeds.
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He R, Ai L, Zhang D, Wan L, Zheng T, Yin J, Lu H, Lu J, Lu F, Liu F, Jia W. Different effect of testosterone and oestrogen on urinary excretion of metformin via regulating OCTs and MATEs expression in the kidney of mice. J Cell Mol Med 2016; 20:2309-2317. [PMID: 27469532 PMCID: PMC5134372 DOI: 10.1111/jcmm.12922] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 06/09/2016] [Indexed: 12/03/2022] Open
Abstract
The aim of this study was to investigate the effect of testosterone and oestrogen on regulating organic cation transporters (Octs) and multidrug and toxin extrusions (Mates) expression in the kidney of mice and urinary excretion of metformin. 8 week‐old male db/db mice were treated with estradiol (5 mg/kg), testosterone (50 mg/kg) or olive oil with same volume. Metformin (150 mg/kg) was injected in daily for successive 7 days. Plasma, urine and tissue concentrations of metformin were determined by liquid chromatography‐tandem mass spectrometry (LCMS) assay. Western blotting and Real‐time PCR analysis were successively used to evaluate the renal protein and mRNA expression of Octs and MATEs. After treatment, the protein expression of Mate1 and Oct2 in testosterone group was significantly increased than those in control group (both P < 0.05). The protein expression of Mate1 and Oct2 in estradiol group was significantly reduced by 29.4% and 43.3%, respectively, compared to those in control group (all P < 0.05). These data showed a good agreement with the change in mRNA level (all P < 0.05). The plasma metformin concentration (ng/ml) in mice treated with estradiol was significantly higher than control and testosterone group (677.56 ± 72.49 versus 293.92 ± 83.27 and 261.46 ± 79.45; P < 0.01). Moreover, testosterone increased the metformin urine excretion of mice while estradiol decreasing (both P < 0.01). Spearman correlation analysis showed that gonadal hormone was closely associated with Mate1 and Oct2 expression and metformin urine excretion in db/db mice (all P < 0.05). Testosterone and oestrogen exerted reverse effect on metformin urinary excretion via regulating Octs and Mates expression in the kidney of mice.
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Affiliation(s)
- Rui He
- Shanghai Key Laboratory of Diabetes, Shanghai Institute for Diabetes, Shanghai Clinical Medical Centre of Diabetes, Shanghai Key Clinical Centre of Metabolic Diseases, Department of Endocrinology and Metabolism, Shanghai Jiao-Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Ligen Ai
- Shanghai Key Laboratory of Diabetes, Shanghai Institute for Diabetes, Shanghai Clinical Medical Centre of Diabetes, Shanghai Key Clinical Centre of Metabolic Diseases, Department of Endocrinology and Metabolism, Shanghai Jiao-Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Dandan Zhang
- Shanghai Key Laboratory of Diabetes, Shanghai Institute for Diabetes, Shanghai Clinical Medical Centre of Diabetes, Shanghai Key Clinical Centre of Metabolic Diseases, Department of Endocrinology and Metabolism, Shanghai Jiao-Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Lili Wan
- Department of Pharmacy, Shanghai Jiao-Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Taishan Zheng
- Shanghai Key Laboratory of Diabetes, Shanghai Institute for Diabetes, Shanghai Clinical Medical Centre of Diabetes, Shanghai Key Clinical Centre of Metabolic Diseases, Department of Endocrinology and Metabolism, Shanghai Jiao-Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Jun Yin
- Shanghai Key Laboratory of Diabetes, Shanghai Institute for Diabetes, Shanghai Clinical Medical Centre of Diabetes, Shanghai Key Clinical Centre of Metabolic Diseases, Department of Endocrinology and Metabolism, Shanghai Jiao-Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Huijuan Lu
- Shanghai Key Laboratory of Diabetes, Shanghai Institute for Diabetes, Shanghai Clinical Medical Centre of Diabetes, Shanghai Key Clinical Centre of Metabolic Diseases, Department of Endocrinology and Metabolism, Shanghai Jiao-Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Junxi Lu
- Shanghai Key Laboratory of Diabetes, Shanghai Institute for Diabetes, Shanghai Clinical Medical Centre of Diabetes, Shanghai Key Clinical Centre of Metabolic Diseases, Department of Endocrinology and Metabolism, Shanghai Jiao-Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Fengdi Lu
- Shanghai Key Laboratory of Diabetes, Shanghai Institute for Diabetes, Shanghai Clinical Medical Centre of Diabetes, Shanghai Key Clinical Centre of Metabolic Diseases, Department of Endocrinology and Metabolism, Shanghai Jiao-Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Fang Liu
- Shanghai Key Laboratory of Diabetes, Shanghai Institute for Diabetes, Shanghai Clinical Medical Centre of Diabetes, Shanghai Key Clinical Centre of Metabolic Diseases, Department of Endocrinology and Metabolism, Shanghai Jiao-Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Weiping Jia
- Shanghai Key Laboratory of Diabetes, Shanghai Institute for Diabetes, Shanghai Clinical Medical Centre of Diabetes, Shanghai Key Clinical Centre of Metabolic Diseases, Department of Endocrinology and Metabolism, Shanghai Jiao-Tong University Affiliated Sixth People's Hospital, Shanghai, China
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Krumsiek J, Mittelstrass K, Do KT, Stückler F, Ried J, Adamski J, Peters A, Illig T, Kronenberg F, Friedrich N, Nauck M, Pietzner M, Mook-Kanamori DO, Suhre K, Gieger C, Grallert H, Theis FJ, Kastenmüller G. Gender-specific pathway differences in the human serum metabolome. Metabolomics 2015; 11:1815-1833. [PMID: 26491425 PMCID: PMC4605991 DOI: 10.1007/s11306-015-0829-0] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 07/08/2015] [Indexed: 02/07/2023]
Abstract
The susceptibility for various diseases as well as the response to treatments differ considerably between men and women. As a basis for a gender-specific personalized healthcare, an extensive characterization of the molecular differences between the two genders is required. In the present study, we conducted a large-scale metabolomics analysis of 507 metabolic markers measured in serum of 1756 participants from the German KORA F4 study (903 females and 853 males). One-third of the metabolites show significant differences between males and females. A pathway analysis revealed strong differences in steroid metabolism, fatty acids and further lipids, a large fraction of amino acids, oxidative phosphorylation, purine metabolism and gamma-glutamyl dipeptides. We then extended this analysis by a network-based clustering approach. Metabolite interactions were estimated using Gaussian graphical models to get an unbiased, fully data-driven metabolic network representation. This approach is not limited to possibly arbitrary pathway boundaries and can even include poorly or uncharacterized metabolites. The network analysis revealed several strongly gender-regulated submodules across different pathways. Finally, a gender-stratified genome-wide association study was performed to determine whether the observed gender differences are caused by dimorphisms in the effects of genetic polymorphisms on the metabolome. With only a single genome-wide significant hit, our results suggest that this scenario is not the case. In summary, we report an extensive characterization and interpretation of gender-specific differences of the human serum metabolome, providing a broad basis for future analyses.
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Affiliation(s)
- Jan Krumsiek
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Kirstin Mittelstrass
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany
| | - Kieu Trinh Do
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Ferdinand Stückler
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Janina Ried
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jerzy Adamski
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Institute of Experimental Genetics, Genome Analysis Center, Helmholtz Zentrum München, Neuherberg, Germany
- Lehrstuhl für Experimentelle Genetik, Technische Universität München, Freising-Weihenstephan, Germany
| | - Annette Peters
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Cardiovascular Disease Research (DZHK e.V.), Munich, Germany
| | - Thomas Illig
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
| | - Nele Friedrich
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), Greifswald, Greifswald, Germany
| | - Matthias Nauck
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), Greifswald, Greifswald, Germany
| | - Maik Pietzner
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), Greifswald, Greifswald, Germany
| | - Dennis O. Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, Netherlands
- Department of Endocrinology, Leiden University Medical Center, Leiden, Netherlands
- Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Qatar Foundation, Doha, Qatar
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Qatar Foundation, Doha, Qatar
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany
| | - Fabian J. Theis
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Mathematics, Technische Universität München, Garching, Germany
| | - Gabi Kastenmüller
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
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