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Qingxiang Guo

Publications and source records attributed to Qingxiang Guo.

11 recordsLinked to original sources
PubMed2025

OctopuSV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis.

MOTIVATION: Structural variants (SVs) influence gene regulation, disease progression, and diagnostics, yet integrating SV calls across platforms remains difficult due to inconsistent annotations, limited merging flexibility, and fragmented workflows. Ambiguous breakend (BND) annotations, which comprise many variant calls, are often discarded or misclassified, hindering variant characterization. Existing tools lack advanced merging operations essential for precise identification of disease-specific or somatic variants across samples or patient groups. Additionally, current SV analysis pipelines require extensive manual intervention and complex parameter tuning, compromising reproducibility and scalability. Addressing these gaps is crucial for improving the accuracy, interpretability, and clinical utility of SV analyses. RESULTS: We developed OctopuSV and TentacleSV to address these long-standing challenges in SV analysis. OctopuSV features a specialized BND correction module that converts ambiguous BND annotations into canonical SV types, recovering important variants that are often overlooked by existing tools. Additionally, it provides advanced set operations (difference, complement, custom-defined) that enable sophisticated variant filtering without programming expertise, critical for identifying tumor-specific SVs or variants unique to specific sample groups. TentacleSV completes our solution by automating the entire SV analysis process from raw sequencing data to high-confidence callsets, ensuring consistency and reproducibility across projects. Benchmarking across short-read and long-read platforms showed superior F1 score, complete SV type consistency compared to existing tools. Our framework enables experimental biologists and clinical researchers to perform sophisticated analyses ranging from cancer subtype-specific SV identification to multi-sample comparative studies without requiring specialized programming skills. AVAILABILITY AND IMPLEMENTATION: All codes are available at https://github.com/ylab-hi/OctopuSV; https://github.com/ylab-hi/TentacleSV.

Software↗
PubMed2006

Studies on photoinduced H-atom and electron transfer reactions of o-naphthoquinones by laser flash photolysis.

The quenching of the triplets of 1,2-naphthoquinone (NQ) and 1,2-naphthoquinone-4-sulfonic acid sodium salt (NQS) by various electron and H-atom donors was investigated by laser flash photolysis measurement in acetonitrile and benzene. The results showed that the reactivities and configurations of 3NQ* (3NQS*) are governed by solvent polarity. All the quenching rate constants (kq) measured in benzene are larger than those in acetonitrile. The SO3Na substituent at the C-4 position of NQS makes 3NQS* more reactive than 3NQ* in electron/H-atom transfer reactions. Large differences of kq values were discovered in H-atom transfer reactions for alcohols and phenols, which can be explained by different H-abstraction mechanisms. Detection of radical cations of amines/anilines in time-resolved transient absorption spectra confirms an electron transfer mechanism. Triplets are identified as precursors of formed radical anions of NQ and NQS in photoinduced reactions. The dependence of electron transfer rate constants on the free energy changes (DeltaG) was treated by using the Rehm-Weller equation. For the four anilines with different substituents on the para or meta position of amidocyanogen, good correlation between log kq values with Hammett sigma constants testifies the correctness of empirical Hammett equation. Charge density distributions, adiabatic ionization/affinity potentials and redox potentials of NQ (NQS) and some quenchers were studied by quantum chemistry calculation.

Electrons↗
PubMed2006

Development of a liquid chromatography/tandem mass spectrometry assay for the quantification of lisinopril in human plasma.

A simple and sensitive liquid chromatography/tandem mass spectrometry method employing electrospray ionization, to quantify lisinopril in human plasma using pseudoephedrine hydrochloride as the internal standard (IS), has been developed and validated. A mixture of methanol and 0.1% formic acid in water (50:50, v/v) was used as the isocratic mobile phase. A simple liquid-liquid extraction procedure was used as sample preparation method. The method validation demonstrated the specificity, lower limit of quantification, accuracy, and precision of measurements. Selected reaction monitoring was specific for lisinopril and pseudoephedrine hydrochloride; no endogenous materials from blank plasma interfered with the analysis of lisinopril or the IS. The assay was linear over the concentration range 0.78-100 ng/mL. The correlation coefficients for the calibration curves ranged from 0.9984-0.9998. The intra- and inter-day precision, determined for quality control samples, were less than 4.18%. The method was employed in a pharmacokinetic study after oral administration of 10 mg lisinopril to 20 healthy volunteers.

Administration, Oral↗
PubMed2006

Liquid chromatography/tandem mass spectrometry assay for the quantification of troxerutin in human plasma.

A simple, rapid, sensitive and specific liquid chromatography/tandem mass spectrometry method was developed and validated to quantify troxerutin in human plasma. The analyte and rutin, used as the internal standard, were analyzed on a Phenomenex Synergi Fusion RP column interfaced with a triple-quadrupole tandem mass spectrometer using positive electrospray ionization. Acetonitrile/water (20:80 v/v) was used as the isocratic mobile phase, with 0.1% formic acid in water. A simple sample preparation method of protein precipitation with perchloric acid was employed. The assay was linear over the concentration range 31.25-4000 pg/mL. Correlation coefficients generated by linear regression with a 1/x(2) weighting factor ranged from 0.9991 to 0.9996. The intra- and inter-day precision over the entire concentration range were less than 12.28%. The method was successfully applied to a pharmacokinetic study after oral administration of a 300 mg troxerutin drop pill to 18 healthy volunteers.

Adult↗
PubMed2005

An efficient approach for theoretical study on the low-energy isomers of large fullerenes C90-C140.

An approach that consists of a molecular mechanics method based on the second generation reactive empirical bond order (REBO) potential and the more accurate semiempirical method PM3 (Parametric Method No. 3) was proposed to predict the energetically favored isomers of the fullerenes from C90 to C140 at the semiempirical level. All the 578,701 isolated-pentagon-rule isomers of fullerenes from C90 to C140 were enumerated from topological structures and systematically searched using an energy minimization method to select the best 100 low-energy isomers based on the REBO potential for each fullerene. Then these candidate isomers were further optimized by PM3 and ranked again to determine the top low-energy isomers. This approach was applied to calculate the energetically favored isomers of C90-C140. The results of C90-C120 are in good agreement with the published results by quantum-chemical methods. Furthermore, the top five low-energy isomers of C90-C120, as well as C122-C140 which have scarcely been systematically studied before, are also predicted with the approach. The analysis of the structures showed that the hexagon-neighbor rule is an important factor to the stability of C90-C140. The time cost for the systematical search based on the REBO potential was also discussed. It indicates that the approach proposed is efficient for predicting the energetically favored isomers of large fullerenes at the semiempirical level.

Journal Article↗
PubMed2005

Development of a liquid chromatography/tandem mass spectrometry assay for the quantification of rabeprazole in human plasma.

A simple and sensitive liquid chromatography/tandem mass spectrometry method, employing electrospray ionization, has been developed and validated to quantify rabeprazole in human plasma using omeprazole as the internal standard. The method was validated to demonstrate the specificity, lower limit of quantification, accuracy, and precision of measurements. Selected reaction monitoring was specific for rabeprazole and omeprazole (the internal standard, IS); no endogenous materials interfered with the analysis of rabeprazole and IS from blank plasma. The assay was linear over the concentration range 0.2-200 ng/mL using a 2 microL aliquot of plasma. The correlation coefficients for the calibration curves ranged from 0.9988-0.9994. The intra- and inter-day precision, calculated from quality control samples, were less than 6.65%. A mixture of methanol and water (50:50) was used as the isocratic mobile phase, with 0.1% of formic acid in water, that did not affect the stability of rabeprazole or IS. A simple sample preparation method of protein precipitation with methanol was chosen. The method was employed in a pharmacokinetic study after oral administration of 20 mg rabeprazole to 24 healthy volunteers.

2-Pyridinylmethylsulfinylbenzimidazoles↗
PubMed2004

Electron ionization mass spectrometric study of 1,4-dihydro-4-substituted 2,6-dimethyl-3,5-bis(alkoxycarbonyl)pyridines.

Using the accurate masses obtained from a time-of-flight instrument and the tandem mass spectrometric (MS/MS) data from an ion trap instrument, electron ionization mass spectra of a series of 1,4-dihydro-4-substituted 2,6-dimethyl-3,5-bis(alkoxycarbonyl)pyridines are reported and rationalized. Two sets of fragmentation pathways are proposed. One involves the formation of fragment ions containing the 1,4-dihydropyridine structure, and the other of ions containing a pyridine ring.

Molecular Structure↗
PubMed2004

Study of the inclusion processes of styrene and alpha-methyl-styrene in beta-cyclodextrin.

The inclusion complexes of styrene and alpha-methyl-styrene with beta-cyclodextrin (beta-CD) were investigated by using [1H] NMR titration in solution and X-ray diffraction (XRD) analysis, thermo-gravimetric analysis (TGA), elemental analysis (EA) in the solid state. The inclusion process has been studied by using PM3 quantum-mechanical semi-empirical method. The calculated results are in agreed with the experimental data. All results show that alpha-methyl-styrene has stronger interaction with beta-cyclodextrin than styrene does, so the complex of beta-CD-alpha-methyl-styrene is more stable.

Cyclodextrins↗
PubMed2003

Model studies of the (6-4) photoproduct photoreactivation: synthesis and photosensitized splitting of uracil oxetane adducts.

Uracil oxetane adducts, which are model compounds for the oxetane intermediates generated during the formation of (6-4) photoproducts or in their photoenzymatic repair, have been synthesized using 1,3-dimethyluracil with carbonyl compounds. On the basis of fluorescence measurements and photolysis experiments, it is demonstrated that the oxetane adducts can be split into the nucleotide base and carbonyl compounds via an electron transfer reaction from photosensitizer. The reaction is more efficient for a stronger electron donor.

DNA Adducts↗
PubMed2002

Addition of organozinc species to cyclic 1,3-diene monoepoxide.

[reaction: see text] The reaction of organozinc reagents (ZnEt(2), ZnPh(2)) with cyclic 1,3-diene monoepoxides in the presence of CF(3)COOH gave the cis-addition products. Lewis acids such as (CF(3)CO(2))(2)Zn and ZnCl(2) mediated the nucleophilic addition of ZnEt(2) to cyclooctadiene monoepoxide with high stereoselectivity.

Journal Article↗