A community-driven global reconstruction of human metabolism

Cited by (1,000)

Items 101–200 of 1,000

1. Systems biology in hepatology: approaches and applications
   Adil Mardinoğlu, Jan Borén, Ulf Smith, Mathias Uhlén, Jens Nielsen · 2018 · Nature Reviews Gastroenterology & Hepatology
2. Finding novel pharmaceuticals in the systems biology era using multiple effective drug targets, phenotypic screening and knowledge of transporters: where drug discovery went wrong and how to fix it
   Douglas Bruce Kell · 2013 · FEBS Journal
3. From directed evolution to computational enzyme engineering—A review
   Ratul Chowdhury, Costas D. Maranas · 2019 · AIChE Journal
4. An appeal to magic? The discovery of a non-enzymatic metabolism and its role in the origins of life
   Ralser, Markus · 2018 · Biochemical Journal
5. A systems approach to traditional oriental medicine
   Hyun Uk Kim, Jae Yong Ryu, Jong Ok Lee, Sang Yup Lee · 2015 · Nature Biotechnology
6. From next-generation sequencing to systematic modeling of the gut microbiome
   Boyang Ji, Jens Nielsen · 2015 · Frontiers in Genetics
7. Recent advances in the reconstruction of metabolic models and integration of omics data
   Rajib Saha, Anupam Chowdhury, Costas D. Maranas · 2014 · Current Opinion in Biotechnology
8. Combination therapeutics in complex diseases
   He, Bing, Lu, Cheng, Zheng, Guang, He, Xiaojuan, Wang, Maolin, Chen, Gao, Zhang, Ge, Lu, Aiping · 2016 · Journal of Cellular and Molecular Medicine
9. A metabolic core model elucidates how enhanced utilization of glucose and glutamine, with enhanced glutamine-dependent lactate production, promotes cancer cell growth: The WarburQ effect
   Chiara Damiani, Riccardo Colombo, Daniela Gaglio, Fabrizia Mastroianni, Dario Pescini, Hans Victor Westerhoff, Giancarlo Mauri, Marco Vanoni, Lilia Alberghina · 2017 · PLoS Computational Biology
10. Kinetic Modeling of Mammalian Cell Culture Bioprocessing: The Quest to Advance Biomanufacturing
    Sarantos Kyriakopoulos, Kok Siong Ang, Meiyappan Lakshmanan, Zhuangrong Huang, Seongkyu Yoon, Rudiyanto Gunawan, Dong‐Yup Lee · 2017 · Biotechnology Journal
11. Applications of genome-scale metabolic network model in metabolic engineering
    Byoung‐Jin Kim, Won Jun Kim, Dong In Kim, Sang Yup Lee · 2014 · Journal of Industrial Microbiology & Biotechnology
12. The Human Blood Metabolome-Transcriptome Interface
    Jörg Bartel, Jan Krumsiek, Katharina Schramm, Jerzy Adamski, Christian Gieger, Christian Herder, Maren Carstensen, Annette Peters, Wolfgang Rathmann, Michael Roden et al. · 2015 · PLoS Genetics
13. Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework
    Almut Heinken, Ines Thiele · 2015 · Gut Microbes
14. A ‘rule of 0.5’ for the metabolite-likeness of approved pharmaceutical drugs
    Steve O’Hagan, Neil Swainston, Julia Handl, Douglas Bruce Kell · 2014 · Metabolomics
15. Urea cycle activation triggered by host-microbiota maladaptation driving colorectal tumorigenesis
    Haoyan Chen, Tianying Tong, Shiyuan Lu, Linhua Ji, Baoqin Xuan, Gang Zhao, Yuqing Yan, Linhong Song, Licong Zhao, Yile Xie et al. · 2023 · Cell Metabolism
16. Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism
    Daniel Craig Zielinski, Neema Jamshidi, Austin J. Corbett, Aarash Bordbar, Alex Thomas, Bernhard Ørn Palsson · 2017 · Scientific Reports
17. Membrane transporters in a human genome-scale metabolic knowledgebase and their implications for disease
    Swagatika Sahoo, Maike Kathrin Aurich, Jón J. Jónsson, Ines Thiele · 2014 · Frontiers in Physiology
18. Gut microbiota dysbiosis is associated with malnutrition and reduced plasma amino acid levels: Lessons from genome-scale metabolic modeling
    Manish Kumar, Boyang Ji, Parizad Babaei, Promi Das, Dimitra Lappa, Girija Ramakrishnan, Todd E. Fox, Rashidul Haque, William A. Petri, Fredrik Bäckhed et al. · 2018 · Metabolic Engineering
19. Flux balance analysis predicts essential genes in clear cell renal cell carcinoma metabolism
    Francesco Gatto, Heike Miess, Almut Schulze, Jens Nielsen · 2015 · Scientific Reports
20. Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis
    Stepan Tymoshenko, Rebecca D. Oppenheim, Rasmus Ågren, Jens Nielsen, Dominique Soldati‐Favre, Vassily Hatzimanikatis A · 2015 · PLoS Computational Biology
21. Systems biology of host–microbe metabolomics
    Almut Heinken, Ines Thiele · 2015 · WIREs Systems Biology and Medicine
22. A Dormant Microbial Component in the Development of Preeclampsia
    Douglas Bruce Kell, Louise C. Kenny · 2016 · Frontiers in Medicine
23. From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes
    Clémence Frioux, Dipali Singh, Tamás Korcsmáros, Falk Hildebrand · 2020 · Computational and Structural Biotechnology Journal
24. Alterations in cancer cell metabolism: The Warburg effect and metabolic adaptation
    Yazdan Asgari, Zahra Zabihinpour, Ali Salehzadeh‐Yazdi, Falk Schreiber, Ali Masoudi‐Nejad · 2015 · Genomics
25. Collection and Preparation of Clinical Samples for Metabolomics
    Andrew J. Chetwynd, Warwick B. Dunn, Giovanny Rodriguez Blanco · 2017 · Advances in experimental medicine and biology
26. Computational Approaches for Integrative Analysis of the Metabolome and Microbiome
    Jasmine Chong, Jianguo Xia · 2017 · Metabolites
27. Model-based identification of drug targets that revert disrupted metabolism and its application to ageing
    Keren Yizhak, Orshay Gabay, Haim Yosef Cohen, Eytan Ruppin · 2013 · Nature Communications
28. CHO-omics review: the impact of current and emerging technologies on Chinese hamster ovary based bioproduction
    Stolfa, Gino, Smonskey, Matthew T., Boniface, Ryan, Hachmann, Anna‐Barbara, Gulde, Paul, Joshi, Atul D., Pierce, Anson P., Jacobia, Scott J., Campbell, Andrew · 2018 · Biotechnology Journal
29. Hepatic Dysfunction Caused by Consumption of a High-Fat Diet
    Anthony R. Soltis, Norman J. Kennedy, Xiaofeng Xin, Feng Zhou, Scott B. Ficarro, Yoon Sing Yap, Bryan J. Matthews, Douglas A. Lauffenburger, Forest M. White, Jarrod A. Marto et al. · 2017 · Cell Reports
30. Integrated In Vitro and In Silico Modeling Delineates the Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived Cells
    Kacy Greenhalgh, Javier Ramiro‐Garcia, Almut Heinken, Pit Ullmann, Tamara Bintener, Maria Pires Pacheco, Joanna Bagińska, Pranjul Shah, Audrey Frachet, Rashi Halder et al. · 2019 · Cell Reports
31. Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications
    Min‐Ying Su, Tao Pan, Qiu-Zhen Chen, Weiwei Zhou, Yi Gong, Gang Xu, Huan-Yu Yan, Si Li, Qiao-Zhen Shi, Ya Zhang et al. · 2022 · Military Medical Research
32. Assessing the Metabolic Impact of Nitrogen Availability Using a Compartmentalized Maize Leaf Genome-Scale Model
    Margaret Simons, Rajib Saha, Nardjis Amiour, Akhil Kumar, Lenaïg Guillard, Gilles Clément, Martine Miquel, Zhenni Li, Grégory Mouille, Peter John Lea et al. · 2014 · PLANT PHYSIOLOGY
33. Genetic variants in Alzheimer disease — molecular and brain network approaches
    Chris Gaiteri, Sara Mostafavi, Christopher John Honey, Philip L. De Jager, David Alan Bennett · 2016 · Nature Reviews Neurology
34. Network Medicine in Pathobiology
    Lee, Laurel Yong-Hwa, Loscalzo, Joseph · 2019 · The American Journal of Pathology
35. CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models
    Hulda S. Haraldsdóttir, Ben Cousins, Ines Thiele, Ronan M. T. Fleming, Santosh Vempala · 2017 · Bioinformatics
36. Elucidating the interactions between the human gut microbiota and its host through metabolic modeling
    Saeed Shoaie, Jens Nielsen · 2014 · Frontiers in Genetics
37. Circadian regulation in human white adipose tissue revealed by transcriptome and metabolic network analysis
    Skevoulla Christou, Sophie M. T. Wehrens, C Isherwood, Carla S. Möller‐Levet, Huihai Wu, Victoria Louise Revell, Giselda Bucca, Debra Jean Skene, Emma Laing, Simon N Archer et al. · 2019 · Scientific Reports
38. Systems biology in drug discovery and development
    Ellen Lakey Berg · 2013 · Drug Discovery Today
39. A Next Generation Multiscale View of Inborn Errors of Metabolism
    Carmen Argmann, Sander M. Houten, Jun Zhu, Eric E. Schadt · 2015 · Cell Metabolism
40. Understanding metabolism with flux analysis: From theory to application
    Ziwei Dai, Jason W. Locasale · 2016 · Metabolic Engineering
41. Uncoupling of mucosal gene regulation, mRNA splicing and adherent microbiota signatures in inflammatory bowel disease
    Robert Häsler, Raheleh Sheibani‐Tezerji, Anupam N. Sinha, Matthias Barann, Ateequr Rehman, Daniela Esser, Konrad Aden, Carolin Knecht, Berenice Brandt, Susanna Nikolaus et al. · 2016 · Gut
42. Human Systems Biology and Metabolic Modelling: A Review—From Disease Metabolism to Precision Medicine
    Claudio Angione · 2019 · BioMed Research International
43. Metabolic Network Prediction of Drug Side Effects
    Itay Shaked, Matthew Oberhardt, Nir Atias, Roded Sharan, Eytan Ruppin · 2016 · Cell Systems
44. Confronting the catalytic dark matter encoded by sequenced genomes
    Kenneth W. Ellens, Nils Christian, Charandeep Singh, Venkata Satagopam, Patrick May, Carole L. Linster · 2017 · Nucleic Acids Research
45. Nitrogen-use efficiency in maize (Zea mays L.): from ‘omics’ studies to metabolic modelling
    Simons, M., Saha, R., Guillard, L., Clement, G., Armengaud, P., Canas, R., Maranas, C. D., Lea, P. J., Hirel, B. · 2014 · Journal of Experimental Botany
46. The evolution of genome-scale models of cancer metabolism
    Lewis, Nathan E., Abdel-Haleem, Alyaa M. · 2013 · Frontiers in Physiology
47. The metabolic background is a global player in Saccharomyces gene expression epistasis
    Mohammad Tauqeer Alam, Aleksej Zelezniak, Michael Mülleder, Pavel V. Shliaha, Roland F. Schwarz, Floriana Capuano, Jakob Vowinckel, Elahe Radmaneshfar, Antje Krüger, Enrica Calvani et al. · 2016 · Nature Microbiology
48. From metagenomic data to personalized in silico microbiotas: predicting dietary supplements for Crohn’s disease
    Eugen Bauer, Ines Thiele · 2018 · npj Systems Biology and Applications
49. Community-driven roadmap for integrated disease maps
    Marek Ostaszewski, Stephan Gebel, Inna Kuperstein, Alexander Mazein, Andrei Y. Zinovyev, Uğur Doğrusöz, Jan Hasenauer, Ronan M. T. Fleming, Nicolas Gambardella Le Novère, Piotr Gawron et al. · 2018 · Briefings in Bioinformatics
50. Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview
    Partho Sen, Matej Orešič · 2019 · Metabolites
51. Human metabolic atlas: an online resource for human metabolism
    Natapol Pornputtapong, Intawat Nookaew, Jens Nielsen · 2015 · Database
52. Leigh map: A novel computational diagnostic resource for mitochondrial disease
    Joyeeta Rahman, Alberto Noronha, Ines Thiele, Shamima Rahman · 2016 · Annals of Neurology
53. Proteins behaving badly. Substoichiometric molecular control and amplification of the initiation and nature of amyloid fibril formation: lessons from and for blood clotting
    Douglas Bruce Kell, Etheresia Pretorius · 2016 · Progress in Biophysics and Molecular Biology
54. ROS networks: designs, aging, Parkinson’s disease and precision therapies
    Alexey N. Kolodkin, Raju Prasad Sharma, Anna Maria Colangelo, Andrew Ignatenko, Francesca Martorana, Danyel G. J. Jennen, Jacob J. Briedé, Nathan Ryan Brady, Matteo Barberis, Thierry D.G.A. Mondeel et al. · 2020 · npj Systems Biology and Applications
55. Tissue-Specific Molecular Biomarker Signatures of Type 2 Diabetes: An Integrative Analysis of Transcriptomics and Protein–Protein Interaction Data
    Beste Turanlı, Kübra Karagoz, Tuba Sevimoğlu, Elif Kılıç, Esra Göv, Kazım Yalçın Arğa · 2015 · OMICS A Journal of Integrative Biology
56. Metabolic remodeling in early development and cardiomyocyte maturation
    Rebecca E Kreipke, Yuliang Wang, Jason Wayne Miklas, Julie Mathieu, Hannele Ruohola‐Baker · 2016 · Seminars in Cell and Developmental Biology
57. How to deal with parameters for whole-cell modelling
    Ann C. Babtie, Michael P. H. Stumpf · 2017 · Journal of The Royal Society Interface
58. Activated Drp1-mediated mitochondrial ROS influence the gut microbiome and intestinal barrier after hemorrhagic shock
    Duan, Chenyang, Kuang, Lei, Xiang, Xinming, Zhang, Jie, Zhu, Yu, Wu, Yue, Yan, Qingguang, Liu, Liangming, Li, Tao · 2020 · Aging
59. Systems biology strategies to study lipidomes in health and disease
    Tuulia Hyötyläinen, Matej Orešič · 2014 · Progress in Lipid Research
60. New paradigms for metabolic modeling of human cells
    Adil Mardinoğlu, Jens Nielsen · 2015 · Current Opinion in Biotechnology
61. Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions
    Anne Richelle, Austin W.T. Chiang, Chih‐Chung Kuo, Nathan E. Lewis · 2019 · PLoS Computational Biology
62. A census of pathway maps in cancer systems biology
    Brent M. Kuenzi, Trey Ideker · 2020 · Nature reviews. Cancer
63. A new dawn beyond lysine ubiquitination
    Daniel R. Squair, Satpal Virdee · 2022 · Nature Chemical Biology
64. Accelerating the DC algorithm for smooth functions
    Francisco J. Aragón Artacho, Ronan M. T. Fleming, Phan Tu Vuong · 2017 · Mathematical Programming
65. Software platforms to facilitate reconstructing genome‐scale metabolic networks
    Joshua J. Hamilton, Jennifer L. Reed · 2013 · Environmental Microbiology
66. Spatial modeling of prostate cancer metabolic gene expression reveals extensive heterogeneity and selective vulnerabilities
    Yuliang Wang, Shuyi Ma, Walter L. Ruzzo · 2020 · Scientific Reports
67. Systems modeling approaches for microbial community studies: from metagenomics to inference of the community structure
    Mark Hanemaaijer, Wilfred F. M. Röling, Brett G. Olivier, Ruchir A. Khandelwal, Bas Teusink, Frank J. Bruggeman · 2015 · Frontiers in Microbiology
68. A novel untargeted metabolomics correlation-based network analysis incorporating human metabolic reconstructions
    Helen L. Kotze, Emily Grace Armitage, Kieran J. Sharkey, James William Allwood, Warwick B. Dunn, Kaye Janine Williams, Royston Goodacre · 2013 · BMC Systems Biology
69. Identifying and targeting cancer-specific metabolism with network-based drug target prediction
    Maria Pires Pacheco, Tamara Bintener, Dominik Ternes, Dagmar Kulms, Serge Haan, Elisabeth Letellier, Thomas Sauter · 2019 · EBioMedicine
70. Cancer Metabolism: A Modeling Perspective
    Pouyan Ghaffari, Adil Mardinoğlu, Jens Nielsen · 2015 · Frontiers in Physiology
71. Enzyme capacity-based genome scale modelling of CHO cells
    Yeo, Hock Chuan, Hong, Jongkwang, Lakshmanan, Meiyappan, Lee, Dong-Yup · 2020 · Metabolic Engineering
72. Event-based text mining for biology and functional genomics
    Sophia Ananiadou, P. Thompson, Raheel Nawaz, John McNaught, Douglas Bruce Kell · 2014 · Briefings in Functional Genomics
73. Integrating Omics Data in Genome-Scale Metabolic Modeling: A Methodological Perspective for Precision Medicine
    Partho Sen, Matej Orešič · 2023 · Metabolites
74. Computational methods to identify metabolic sub-networks based on metabolomic profiles
    Clément Frainay, Fabien Jourdan · 2016 · Briefings in Bioinformatics
75. Integrated transcriptomics and metabolomics reveal signatures of lipid metabolism dysregulation in HepaRG liver cells exposed to PCB 126
    Robin Mesnage, Martina Biserni, Sucharitha Balu, Clément Frainay, Nathalie Poupin, Fabien Jourdan, Eva L. Woźniak, Theodoros A. Xenakis, Charles A. Mein, Michael Nicolas Antoniou · 2018 · Archives of Toxicology
76. ReconMap: an interactive visualization of human metabolism
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77. Pathway Analysis for Targeted and Untargeted Metabolomics
    Alla Karnovsky, Shuzhao Li · 2020 · Methods in molecular biology
78. A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks
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79. Integrated analysis of motif activity and gene expression changes of transcription factors
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80. Reconstruction of a high‐quality metabolic model enables the identification of gene overexpression targets for enhanced antibiotic production in Streptomyces coelicolor A3(2)
    Minsuk Kim, Jeong Sang Yi, Joonwon Kim, Jinu Kim, Min Woo Kim, Byung‐Gee Kim · 2014 · Biotechnology Journal
81. MEBOCOST maps metabolite-mediated intercellular communications using single-cell RNA-seq
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82. iSCHRUNK – In Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks
    Stefano Andreozzi, Ljubiša Mišković, Vassily Hatzimanikatis A · 2015 · Metabolic Engineering
83. Integrating bioinformatics approaches for a comprehensive interpretation of metabolomics datasets
    Dinesh Kumar Barupal, Sili Fan, Oliver Fiehn · 2018 · Current Opinion in Biotechnology
84. Understanding the physiology of the ageing individual: computational modelling of changes in metabolism and endurance
    Hans van Beek, Thomas B. L. Kirkwood, James B. Bassingthwaighte · 2016 · Interface Focus
85. Mind the Gap: Mapping Mass Spectral Databases in Genome-Scale Metabolic Networks Reveals Poorly Covered Areas
    Clément Frainay, Emma Schymanski, Steffen Neumann, Benjamin Merlet, Reza M. Salek, Fabien Jourdan, Óscar Yanes · 2018 · Metabolites
86. Metabolomics of Endurance Capacity in World Tour Professional Cyclists
    Iñigo San-Millán, Davide Stefanoni, Janel L. Martinez, Kirk Charles Hansen, Angelo D’Alessandro, Travis G. Nemkov · 2020 · Frontiers in Physiology
87. Candidate genes linking maternal nutrient exposure to offspring health via DNA methylation: a review of existing evidence in humans with specific focus on one-carbon metabolism
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88. Systems Biology Approaches to Understand the Host–Microbiome Interactions in Neurodegenerative Diseases
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89. Assessing key decisions for transcriptomic data integration in biochemical networks
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90. Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering
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91. The Time Is Right to Focus on Model Organism Metabolomes
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92. More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes
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93. Computational Biology and Machine Learning Approaches to Understand Mechanistic Microbiome-Host Interactions
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94. Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling
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95. Large-scale non-targeted metabolomic profiling in three human population-based studies
    Andrea Ganna, Tove Fall, Samira Salihović, Woojoo Lee, Corey D. Broeckling, Jitender Kumar, Sara Hägg, Markus Stenemo, Patrik K. E. Magnusson, Jessica E. Prenni et al. · 2015 · Metabolomics
96. The apparent permeabilities of Caco-2 cells to marketed drugs: magnitude, and independence from both biophysical properties and endogenite similarities
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97. Prediction of intracellular metabolic states from extracellular metabolomic data
    Maike Kathrin Aurich, Giuseppe Paglia, Óttar Rolfsson, Sigrún Hrafnsdóttir, Manuela Magnúsdóttir, Magdalena M. Stefaniak‐Vidarsson, Bernhard Ørn Palsson, Ronan M. T. Fleming, Ines Thiele · 2014 · Metabolomics
98. An overview of graph databases and their applications in the biomedical domain
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99. Genome-scale metabolic network models: from first-generation to next-generation
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100. Metabolic interactions in cancer: cellular metabolism at the interface between the microenvironment, the cancer cell phenotype and the epigenetic landscape
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