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  • Springer  (242)
  • Oxford University Press  (36)
  • 2015-2019  (192)
  • 2005-2009  (25)
  • 1995-1999  (61)
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  • 1
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    Accurate disulfide-bonding network predictions improve ab initio structure prediction of cysteine-rich proteins (2015)
    Oxford University Press
    Details
    Publication Date: 2015-11-21
    Description: Motivation: Cysteine-rich proteins cover many important families in nature but there are currently no methods specifically designed for modeling the structure of these proteins. The accuracy of disulfide connectivity pattern prediction, particularly for the proteins of higher-order connections, e.g. 〉3 bonds, is too low to effectively assist structure assembly simulations. Results: We propose a new hierarchical order reduction protocol called Cyscon for disulfide-bonding prediction. The most confident disulfide bonds are first identified and bonding prediction is then focused on the remaining cysteine residues based on SVR training. Compared with purely machine learning-based approaches, Cyscon improved the average accuracy of connectivity pattern prediction by 21.9%. For proteins with more than 5 disulfide bonds, Cyscon improved the accuracy by 585% on the benchmark set of PDBCYS. When applied to 158 non-redundant cysteine-rich proteins, Cyscon predictions helped increase (or decrease) the TM-score (or RMSD) of the ab initio QUARK modeling by 12.1% (or 14.4%). This result demonstrates a new avenue to improve the ab initio structure modeling for cysteine-rich proteins. Availability and implementation: http://www.csbio.sjtu.edu.cn/bioinf/Cyscon/ Contact: zhng@umich.edu or hbshen@sjtu.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 2
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    Global intron retention mediated gene regulation during CD4+ T cell activation (2016)
    Oxford University Press
    Details
    Publication Date: 2016-08-20
    Description: T cell activation is a well-established model for studying cellular responses to exogenous stimulation. Using strand-specific RNA-seq, we observed that intron retention is prevalent in polyadenylated transcripts in resting CD4 + T cells and is significantly reduced upon T cell activation. Several lines of evidence suggest that intron-retained transcripts are less stable than fully spliced transcripts. Strikingly, the decrease in intron retention (IR) levels correlate with the increase in steady-state mRNA levels. Further, the majority of the genes upregulated in activated T cells are accompanied by a significant reduction in IR. Of these 1583 genes, 185 genes are predominantly regulated at the IR level, and highly enriched in the proteasome pathway, which is essential for proper T cell proliferation and cytokine release. These observations were corroborated in both human and mouse CD4 + T cells. Our study revealed a novel post-transcriptional regulatory mechanism that may potentially contribute to coordinated and/or quick cellular responses to extracellular stimuli such as an acute infection.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality using next generation sequencing data (2016)
    Oxford University Press
    Details
    Publication Date: 2016-03-01
    Description: Tumors are characterized by properties of genetic instability, heterogeneity, and significant oligoclonality. Elucidating this intratumoral heterogeneity is challenging but important. In this study, we propose a framework, BubbleTree, to characterize the tumor clonality using next generation sequencing (NGS) data. BubbleTree simultaneously elucidates the complexity of a tumor biopsy, estimating cancerous cell purity, tumor ploidy, allele-specific copy number, and clonality and represents this in an intuitive graph. We further developed a three-step heuristic method to automate the interpretation of the BubbleTree graph, using a divide-and-conquer strategy. In this study, we demonstrated the performance of BubbleTree with comparisons to similar commonly used tools such as THetA2, ABSOLUTE, AbsCN-seq and ASCAT, using both simulated and patient-derived data. BubbleTree outperformed these tools, particularly in identifying tumor subclonal populations and polyploidy. We further demonstrated BubbleTree's utility in tracking clonality changes from patients’ primary to metastatic tumor and dating somatic single nucleotide and copy number variants along the tumor clonal evolution. Overall, the BubbleTree graph and corresponding model is a powerful approach to provide a comprehensive spectrum of the heterogeneous tumor karyotype in human tumors. BubbleTree is R-based and freely available to the research community ( https://www.bioconductor.org/packages/release/bioc/html/BubbleTree.html ).
    Keywords: Computational Methods, Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Fine mapping the MHC region identified four independent variants modifying susceptibility to chronic hepatitis B in Han Chinese (2016)
    Oxford University Press
    Details
    Publication Date: 2016-02-24
    Description: Several genome-wide association studies (GWAS) have demonstrated the association between genetic variants in the major histocompatibility complex (MHC) region and chronic hepatitis B (CHB) virus infection, but it is still unknown about the disease-causing loci and potential mechanisms owing to the complicated linkage disequilibrium for this region. To systematically characterize the MHC variations in relation to the CHB infection, we fine mapped the MHC region on our existing GWAS data with SNP2HLA taken the Pan-Asian panel as reference and finally identified four independent associations. The HLA-DPβ1 amino acid positions 84–87, which drove the effect of reported single nucleotide polymorphisms rs9277535 and rs3077, showed the most significant association (OR = 0.65, P = 2.03 x 10 –8 ). The Leu-15 of HLA-C, conferring the effect of rs3130542, increased the risk of CHB infection independently (OR = 1.61, P = 3.42 x 10 –7 ). The HLA-DRβ1*13 , in perfect LD with glutamic at site 71, and rs400488, an expression quantitative trait locus for HLA-J , were newly identified to be associated with CHB infection independently (OR = 1.84, P = 3.84 x 10 –9 ; OR = 0.28, P = 6.27 x 10 –7 , respectively). HLA-DPβ1 positions 84–87 and HLA-DRβ1 position 71 implicated the P1 and P4 in the antigen-binding groove, whereas HLA-C position 15 affected the signal peptide. These four independent loci together can explain ~6% of the phenotypic variance for CHB infection, accounting for 72.94% of that explained by known genetic variations. We fine mapped the MHC region and identified four loci that independently drove the chronic HBV infection. The results provided a deeper understanding of the GWAS signals and identified additional susceptibility loci which were missed in previous association studies.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 5
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    Inversion of Rayleigh Wave Dispersion Curves via Adaptive GA and Nested DLS (2019)
    Oxford University Press
    Details
    Publication Date: 2019
    Description: 〈span〉〈div〉Summary〈/div〉Dispersion curve inversion is one of the core components of Rayleigh wave surveys, which mainly include linear and nonlinear inversion theoretical systems. Damped least squares (DLS) is the most mature and commonly used method of linear optimization, but it relies heavily on more accurate initial models, otherwise it can easily fall into a local minimum or can even result in an incorrect inversion. As a representative method of nonlinear optimization, genetic algorithm (GA) may be more feasible to obtain a global optimal solution for the geophysical inversion in theory. However, the GA algorithm is less stable, as well as less efficient in the later period of the inversion. In the past, the above two systems have been used independently to perform inversion processing. Faced with complex seismic geological conditions, they often display poor adaptability and lack balance between speed and accuracy. For this reason, we made a reasonable and effective improvement to the generation of the initial population and the coding of the classic GA to overcome the time-consuming and memory-intensive computational issues. We redefined the selection and crossover function to prevent the ‘premature convergence’ phenomenon in genetic iterations. Simultaneously, the DLS and the steepest descent method (SD) are embedded in the GA inversion process to linearly optimize the dominant individuals in the population (i.e. local extrema) in the local space to guide the population to move quickly and stably advance towards the global optimal direction. Next, a robust DLS inversion is used to obtain the final S-wave velocity model using the adaptive GA inversion results as the input velocity model. The model and actual dataset processing results show that our proposed nested joint inversion can combine the advantages of linear and nonlinear inversion that can effectively suppress the multi-solution problem of the dispersion curve inversion and significantly improve the inversion efficiency and accuracy.〈/span〉
    Print ISSN: 2051-1965
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 6
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    Bioimaging-based detection of mislocalized proteins in human cancers by semi-supervised learning (2015)
    Oxford University Press
    Details
    Publication Date: 2015-04-03
    Description: Motivation: There is a long-term interest in the challenging task of finding translocated and mislocated cancer biomarker proteins. Bioimages of subcellular protein distribution are new data sources which have attracted much attention in recent years because of their intuitive and detailed descriptions of protein distribution. However, automated methods in large-scale biomarker screening suffer significantly from the lack of subcellular location annotations for bioimages from cancer tissues. The transfer prediction idea of applying models trained on normal tissue proteins to predict the subcellular locations of cancerous ones is arbitrary because the protein distribution patterns may differ in normal and cancerous states. Results: We developed a new semi-supervised protocol that can use unlabeled cancer protein data in model construction by an iterative and incremental training strategy. Our approach enables us to selectively use the low-quality images in normal states to expand the training sample space and provides a general way for dealing with the small size of annotated images used together with large unannotated ones. Experiments demonstrate that the new semi-supervised protocol can result in improved accuracy and sensitivity of subcellular location difference detection. Availability and implementation: The data and code are available at: www.csbio.sjtu.edu.cn/bioinf/SemiBiomarker/ . Contact: hbshen@sjtu.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 7
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    Inversion of Rayleigh wave dispersion curves via adaptive GA and nested DLS (2019)
    Oxford University Press
    Details
    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉Dispersion curve inversion is one of the core components of Rayleigh wave surveys, which mainly include linear and non-linear inversion theoretical systems. Damped least squares (DLS) is the most mature and commonly used method of linear optimization, but it relies heavily on more accurate initial models, otherwise it can easily fall into a local minimum or can even result in an incorrect inversion. As a representative method of non-linear optimization, genetic algorithm (GA) may be more feasible to obtain a global optimal solution for the geophysical inversion in theory. However, the GA algorithm is less stable, as well as less efficient in the later period of the inversion. In the past, the above two systems have been used independently to perform inversion processing. Faced with complex seismic geological conditions, they often display poor adaptability and lack balance between speed and accuracy. For this reason, we made a reasonable and effective improvement to the generation of the initial population and the coding of the classic GA to overcome the time-consuming and memory-intensive computational issues. We redefined the selection and crossover function to prevent the ‘premature convergence’ phenomenon in genetic iterations. Simultaneously, the DLS and the steepest descent method are embedded in the GA inversion process to linearly optimize the dominant individuals in the population (i.e. local extrema) in the local space to guide the population to move quickly and stably advance towards the global optimal direction. Next, a robust DLS inversion is used to obtain the final 〈span〉S〈/span〉-wave velocity model using the adaptive GA inversion results as the input velocity model. The model and actual data set processing results show that our proposed nested joint inversion can combine the advantages of linear and nonlinear inversion that can effectively suppress the multisolution problem of the dispersion curve inversion and significantly improve the inversion efficiency and accuracy.〈/span〉
    Print ISSN: 2051-1965
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 8
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    Fault geometry and slip distribution of the 2008 Mw 7.9 Wenchuan, China earthquake, inferred from GPS and InSAR measurements (2016)
    Oxford University Press
    Details
    Publication Date: 2016-12-21
    Description: We revisit the problem of coseismic rupture of the 2008 M w 7.9 Wenchuan earthquake. Precise determination of the fault structure and slip distribution provides critical information about the mechanical behaviour of the fault system and earthquake rupture. We use all the geodetic data available, craft a more realistic Earth structure and fault model compared to previous studies, and employ a nonlinear inversion scheme to optimally solve for the fault geometry and slip distribution. Compared to a homogeneous elastic half-space model and laterally uniform layered models, adopting separate layered elastic structure models on both sides of the Beichuan fault significantly improved data fitting. Our results reveal that: (1) The Beichuan fault is listric in shape, with near surface fault dip angles increasing from ~36° at the southwest end to ~83° at the northeast end of the rupture. (2) The fault rupture style changes from predominantly thrust at the southwest end to dextral at the northeast end of the fault rupture. (3) Fault slip peaks near the surface for most parts of the fault, with ~8.4 m thrust and ~5 m dextral slip near Hongkou and ~6 m thrust and ~8.4 m dextral slip near Beichuan, respectively. (4) The peak slips are located around fault geometric complexities, suggesting that earthquake style and rupture propagation were determined by fault zone geometric barriers. Such barriers exist primarily along restraining left stepping discontinuities of the dextral-compressional fault system. (5) The seismic moment released on the fault above 20 km depth is 8.2 x 10 21  N m, corresponding to an M w 7.9 event. The seismic moments released on the local slip concentrations are equivalent to events of M w 7.5 at Yingxiu-Hongkou, M w 7.3 at Beichuan-Pingtong, M w 7.2 near Qingping, M w 7.1 near Qingchuan, and M w 6.7 near Nanba, respectively. (6) The fault geometry and kinematics are consistent with a model in which crustal deformation at the eastern margin of the Tibetan plateau is decoupled by differential motion across a decollement in the mid crust, above which deformation is dominated by brittle reverse faulting and below which deformation occurs by viscous horizontal shortening and vertical thickening.
    Keywords: Seismology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 9
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    Crustal layering in northeastern Tibet: a case study based on joint inversion of receiver functions and surface wave dispersion (2015)
    Oxford University Press
    Details
    Publication Date: 2015-09-06
    Description: Recently constructed models of crustal structure across Tibet based on surface wave data display a prominent mid-crustal low velocity zone (LVZ) but are vertically smooth in the crust. Using six months of broad-band seismic data recorded at 22 stations arrayed approximately linearly over a 440 km observation profile across northeastern Tibet (from the Songpan–Ganzi block, through the Qaidam block, into the Qilian block), we perform a Bayesian Monte Carlo joint inversion of receiver function data with surface wave dispersion to address whether crustal layering is needed to fit both data sets simultaneously. On some intervals a vertically smooth crust is consistent with both data sets, but across most of the observation profile two types of layering are required: a discrete LVZ or high velocity zone (HVZ) formed by two discontinuities in the middle crust and a doublet Moho formed by two discontinuities from 45–50 km to 60–65 km depth connected by a linear velocity gradient in the lowermost crust. The final model possesses (1) a mid-crustal LVZ that extends from the Songpan–Ganzi block through the Kunlun suture into the Qaidam block consistent with partial melt and ductile flow and (2) a mid-crustal HVZ bracketing the south Qilian suture coincident with ultrahigh pressure metamorphic rocks at the surface. (3) Additionally, the model possesses a doublet Moho extending from the Qaidam to the Qilian blocks which probably reflects increased mafic content with depth in the lowermost crust perhaps caused by a vertical gradient of ecologitization. (4) Crustal thickness is consistent with a step-Moho that jumps discontinuously by 6 km from 63.8 km (±1.8 km) south of 35° to 57.8 km (±1.4 km) north of this point coincident with the northern terminus of the mid-crustal LVZ. These results are presented as a guide to future joint inversions across a much larger region of Tibet.
    Keywords: Seismology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 10
    Electronic Resource
    Electronic Resource
    The first measurement of an absolute surface concentration of reaction intermediates in ethylene hydrogenation (1996)
    Springer
    Catalysis letters 40 (1996), S. 143-145 
    Details
    ISSN: 1572-879X
    Keywords: absolute surface intermediate concentration ; ethylene hydrogenation ; reaction intermediates in catalysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The first measurement of a turnover rate with respect to surface intermediate concentration in a high pressure heterogeneous catalytic reaction is reported. By using infrared-visible sum frequency generation to study the hydrogenation of ethylene on Pt(111), it was found that the surface concentration of π-bonded ethylene, the key reaction intermediate, represented approximately 4% of a monolayer. Thus the absolute turnover rate per surface adsorbed ethylene molecule is 25 times faster than the rate measured per platinum atom. To explain these results, we propose a model of weakly adsorbed ethylene intermediates reacting on atop sites.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00815274
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