Publications by authors named "Haoxing Du"
Article Synopsis
- The study identifies the unique nonnegative quasiprobability representation of the stabilizer subtheory in odd dimensions, which is Gross's discrete Wigner function, tying it to Spekkens' epistemically restricted model for a noncontextual ontological perspective.
- The principle of noncontextuality effectively highlights a specific classical realist interpretation, revealing that negativity in Gross's representation signals generalized contextuality, which is crucial for universal quantum computation.
- Conversely, in even dimensions, the research demonstrates that no nonnegative quasiprobability representation exists for the stabilizer subtheory, indicating an inherent contextual nature in these cases.
Multiple Optimal Reconciliations Under the Duplication-Loss-Coalescence Model.
IEEE/ACM Trans Comput Biol Bioinform
January 2022
Gene trees can differ from species trees due to a variety of biological phenomena, the most prevalent being gene duplication, horizontal gene transfer, gene loss, and coalescence. To explain topological incongruence between the two trees, researchers apply reconciliation methods, often relying on a maximum parsimony framework. However, while several studies have investigated the space of maximum parsimony reconciliations (MPRs) under the duplication-loss and duplication-transfer-loss models, the space of MPRs under the duplication-loss-coalescence (DLC) model remains poorly understood.
View Article and Find Full Text PDFPerfect matching of an assembled physical sequence to a specified designed sequence is crucial to verify design principles in genome synthesis. We designed and de novo synthesized 536,024-base pair chromosome synV in the "Build-A-Genome China" course. We corrected an initial isolate of synV to perfectly match the designed sequence using integrative cotransformation and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated editing in 22 steps; synV strains exhibit high fitness under a variety of culture conditions, compared with that of wild-type V strains.
View Article and Find Full Text PDFMultigene pathway engineering usually needs amounts of part libraries on transcriptional and translational regulation as well as mutant enzymes to achieve the optimal part combinations of the target pathways. We report a new strategy for multigene pathway engineering with regulatory linkers (M-PERL) focusing on tuning the transcriptional start site (TSS) of yeast promoters. The regulatory linkers are composed of two homologous ends of two adjacent gene parts for assembly and a central regulatory region between them.
View Article and Find Full Text PDFCampesterol is an important precursor for many sterol drugs, e.g. progesterone and hydrocortisone.
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