An atlas of human metabolism
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An open-source, genome-scale human metabolic model and a web portal to explore the model are generated.
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The DLKcat-based pipeline improves the number of reactions with enzymatic constraints in comparison with original-ecGEMs that have previously been constructed.
“it even improves the number of reactions with enzymatic constraints in comparison with original-ecGEMs that have previously been constr ucted 2,8-12,50 .”
From Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction (2022) · cites this paper as [12]
Currently, ~87% of the proteome is targeted by >1 HPA antibody, detected through an encyclopaedia of >10 M annotated high-resolution digital images.
“Currently, ~87% of the proteome is targeted by >1 HPA Ab, detected though an encyclopaedia of >10 M annotated high-resolution digital images, partitioned into a number of sub-atlases that are interconnected44–48.”
From A high-stringency blueprint of the human proteome (2020) · cites this paper as [48]
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Role of Glutathione in Cancer: From Mechanisms to Therapies
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Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction
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“…applicability, and it even improves the number of reactions with enzymatic constraints in comparison with original-ecGEMs that have previously been constr ucted 2,8–12,50 Even though the DLKcat-based pipeline yields ecGEMs with superior performance over original-ecGEMs, various challenges remain.”
BackgroundSelf-citationA high-stringency blueprint of the human proteome
Adhikari, S., Nice, E. C., Deutsch, E. W., Lane, L., Omenn, G. S., Pennington, S. R., Paik, Y.-K., Overall, C. M., Corrales, F. J., Cristea, I. M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19045-9 · Cited by 210 · see citing works
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- Authors
- Robinson, J. L., Kocabaş, P., Wang, H., Cholley, P.-E., Cook, D., Nilsson, A., Anton, M., Ferreira, R., Domenzain, I., Billa, V., Limeta, A., Hedin, A., Gustafsson, J., Kerkhoven, E. J., Svensson, L. T., Palsson, B. O., Mardinoglu, A., Hansson, L., Uhlén, M., & Nielsen, J.
- Affiliations
- Chalmers University of Technology (SE)
- Science for Life Laboratory (SE)
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-41258 Gothenburg, Sweden.
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
- Department of Protein Science, Science for Life Laboratory, KTH–Royal Institute of Technology, SE-10044 Stockholm, Sweden.
- Novo Nordisk Foundation (DK)
- Corresponding author
- Robinson, Jonathan L.
- Kocabaş, Pınar
- Wang, Hao
- Cholley, Pierre-Etienne
- Nielsen, Jens
- ORCID
- Venue
- Science Signaling
- Published
- 2020-03-24
- Volume
- 13
- Issue
- 624
- ISSN
- 1937-9145 (ISSN-L)
- 1945-0877
- PMC
- PMC7331181
- OpenAlex
- W3013554928
- Cited by
- 442
- References
- 68
- Citations by year
- 2026: 67 · 2025: 86 · 2024: 85 · 2023: 62 · 2022: 57 · 2021: 56 · 2020: 29
- FWCI
- 16.53
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science Signaling (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Research Portal (King's College London) (submittedVersion)
- Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion, other-oa)
- Chalmers Research (Chalmers University of Technology) (submittedVersion)
- Funders
- National Institutes of Health (F32CA220848)
- Knut och Alice Wallenbergs Stiftelse
- Horizon 2020 (720824)
- Novo Nordisk Fonden (NNF10CC1016517)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- human metabolism, genome-scale metabolic models, metabolic kinetics
- MeSH terms
- Humans, Software, Computational Biology, Metabolome
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