| 1. |
- Ding, Shaozhen, et al.
(författare)
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novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model
- 2020
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 48:W1, s. W477-W487
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Tidskriftsartikel (refereegranskat)abstract
- To increase the number of value-added chemicals that can be produced by metabolic engineering and synthetic biology, constructing metabolic space with novel reactions/pathways is crucial. However, with the large number of reactions that existed in the metabolic space and complicated metabolisms within hosts, identifying novel pathways linking two molecules or heterologous pathways when engineering a host to produce a target molecule is an arduous task. Hence, we built a user-friendly web server, novoPathFinder, which has several features: (i) enumerate novel pathways between two specified molecules without considering hosts; (ii) construct heterologous pathways with known or putative reactions for producing target molecule within Escherichia coli or yeast without giving precursor; (iii) estimate novel pathways with considering several categories, including enzyme promiscuity, Synthetic Complex Score (SCScore) and LD50 of intermediates, overall stoichiometric conversions, pathway length, theoretical yields and thermodynamic feasibility. According to the results, novoPathFinder is more capable to recover experimentally validated pathways when comparing other rule-based web server tools. Besides, more efficient pathways with novel reactions could also be retrieved for further experimental exploration. novoPathFinder is available at http://design.rxnfinder.org/novopathfinder/.
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| 2. |
- Han, Mengying, et al.
(författare)
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ChemHub: a knowledgebase of functional chemicals for synthetic biology studies
- 2021
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811 .- 1460-2059. ; 37:22, s. 4275-4276
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Tidskriftsartikel (refereegranskat)abstract
- The field of synthetic biology lacks a comprehensive knowledgebase for selecting synthetic target molecules according to their functions, economic applications and known biosynthetic pathways. We implemented ChemHub, a knowledgebase containing >90 000 chemicals and their functions, along with related biosynthesis information for these chemicals that was manually extracted from >600 000 published studies by more than 100 people over the past 10 years.
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| 3. |
- Wang, Nan, 1988, et al.
(författare)
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Tailoring the Thermal and Mechanical Properties of Graphene Film by Structural Engineering
- 2018
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Ingår i: Small. - : Wiley. - 1613-6810 .- 1613-6829. ; 14:29
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Tidskriftsartikel (refereegranskat)abstract
- Due to substantial phonon scattering induced by various structural defects, the in-plane thermal conductivity (K) of graphene films (GFs) is still inferior to the commercial pyrolytic graphite sheet (PGS). Here, the problem is solved by engineering the structures of GFs in the aspects of grain size, film alignment, and thickness, and interlayer binding energy. The maximum K of GFs reaches to 3200 W m−1K−1and outperforms PGS by 60%. The superior K of GFs is strongly related to its large and intact grains, which are over four times larger than the best PGS. The large smooth features about 11 µm and good layer alignment of GFs also benefit on reducing phonon scattering induced by wrinkles/defects. In addition, the presence of substantial turbostratic-stacking graphene is found up to 37% in thin GFs. The lacking of order in turbostratic-stacking graphene leads to very weak interlayer binding energy, which can significantly decrease the phonon interfacial scattering. The GFs also demonstrate excellent flexibility and high tensile strength, which is about three times higher than PGS. Therefore, GFs with optimized structures and properties show great potentials in thermal management of form-factor-driven electronics and other high-power-driven systems.
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| 4. |
- Zhang, Dachuan, et al.
(författare)
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FRCD: A comprehensive food risk component database with molecular scaffold, chemical diversity, toxicity, and biodegradability analysis
- 2020
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Ingår i: Food Chemistry. - : Elsevier BV. - 0308-8146 .- 1873-7072. ; 318
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Tidskriftsartikel (refereegranskat)abstract
- The presence of natural toxins, pesticide residues, and illegal additives in food products has been associated with a range of potential health hazards. However, no systematic database exists that comprehensively includes and integrates all research information on these compounds, and valuable information remains scattered across numerous databases and extensive literature reports. Thus, using natural language processing technology, we curated 12,018 food risk components from 152,737 literature reports, 12 authoritative databases, and numerous related regulatory documents. Data on molecular structures, physicochemical properties, chemical taxonomy, absorption, distribution, metabolism, excretion, toxicity properties, and physiological targets within the human body were integrated to afford the comprehensive food risk component database (FRCD, http://www.rxnfinder.org/frcd/). We also analyzed the molecular scaffold and chemical diversity, in addition to evaluating the toxicity and biodegradability of the food risk components. The FRCD could be considered a highly promising tool for future food safety studies.
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