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Articles by X. Xie
Total Records ( 5 ) for X. Xie
  M Garber , M Guttman , M Clamp , M. C Zody , N Friedman and X. Xie

Motivation: Comparing the genomes from closely related species provides a powerful tool to identify functional elements in a reference genome. Many methods have been developed to identify conserved sequences across species; however, existing methods only model conservation as a decrease in the rate of mutation and have ignored selection acting on the pattern of mutations.

Results: We present a new approach that takes advantage of deeply sequenced clades to identify evolutionary selection by uncovering not only signatures of rate-based conservation but also substitution patterns characteristic of sequence undergoing natural selection. We describe a new statistical method for modeling biased nucleotide substitutions, a learning algorithm for inferring site-specific substitution biases directly from sequence alignments and a hidden Markov model for detecting constrained elements characterized by biased substitutions. We show that the new approach can identify significantly more degenerate constrained sequences than rate-based methods. Applying it to the ENCODE regions, we identify as much as 10.2% of these regions are under selection.

Availability: The algorithms are implemented in a Java software package, called SiPhy, freely available at


Supplementary information: Supplementary data are available at Bioinformatics online.

  F. Bragg , L. Li , M. Smith , Y. Guo , Y. Chen , I. Millwood , Z. Bian , R. Walters , J. Chen , L. Yang , R. Collins , R. Peto , Y. Lu , B. Yu , X. Xie , Y. Lei , G. Luo and Z. Chen


To examine the relationship of self-reported diabetes, and of random blood glucose levels among individuals without known diabetes, with the prevalence of cardiovascular disease in Chinese adults.


We examined cross-sectional data from the China Kadoorie Biobank of 0.5 million people aged 30-79 years recruited from 10 diverse regions of China in the period 2004-2008. Logistic regression was used to estimate the odds ratios of prevalent cardiovascular disease associated with self-reported diabetes, and with measured random blood glucose levels among participants with no history of diabetes, adjusting simultaneously for age, sex, area, education, smoking, alcohol, blood pressure and physical activity.


A total of 3.2% of participants had self-reported diabetes (men 2.9%; women 3.3%) and 2.8% had screen-detected diabetes (men 2.6%; women 2.8%), i.e. they had no self-reported history of diabetes but a blood glucose level suggestive of a diagnosis of diabetes. Compared with individuals without a history of diabetes, the odds ratios associated with self-reported diabetes were 2.18 (95% CI 2.06-2.30) and 1.88 (95% CI 1.75-2.01) for prevalent ischaemic heart disease and stroke/transient ischaemic attack, respectively. Among participants without self-reported diabetes there was a positive association between random blood glucose and ischaemic heart disease and stroke/transient ischaemic attack prevalence (P for trend <0.0001). Below the diabetic threshold (<11.1 mmol/l) each additional 1 mmol/l of random blood glucose was associated with 4% (95% CI 2-5%) and 5% (95% CI 3-7%) higher odds of prevalent ischaemic heart disease and stroke/transient ischaemic attack, respectively.


In this adult Chinese population, self-reported diabetes was associated with a doubling of the odds of prevalent cardiovascular disease. Below the threshold for diabetes there was still a modest, positive association between random blood glucose and prevalent cardiovascular disease.

  J. Chen , Y. Lu and X. Xie
  This study proposes a testing approach of component security based on dynamic fault tree and then specifies some related definitions of fault tree, fault injection model and attack pattern. A testing algorithm of component security based on dynamic fault tree and test-case generating approach are also proposed. The proposed testing approach generates fault injection cases which can trigger component vulnerabilities in maximum probability based on fault tree. At the same time, the fault tree can be improved according to the testing results after injecting faults. The proposed approach was implemented based on research projects CSTS (Component Security Testing System). The experimental results show that the approach is effective and can trigger lots of component exceptions by using fewer test-cases.
  G. Lan , L. Peng , X. Xie , F. Peng , Y. Wang and S. Yu
  Bone loss is a common complication among renal transplant patients. Some studies have shown that alendronate may be effective to treat bone loss in these patients. In this study, we have reported our experience with administration of alendronate to treat bone loss in renal transplanted patients.

Methods: The 46 kidney transplant recipients with bone loss were randomly divided into 2 groups: group I was treated with calcium and calcitriol, and group II with calcium, calcitriol, and alendronate. We examined bone mineral density (BMD) and biochemical indicators of both groups. All patients received cyclosporine and prednisone treatment.

Results: There was no significant difference in age, body mass index, gender, immunosuppression, time since transplantation, 25(OH)D3, or intact parathyroid hormone levels at study commencement. The BMD of the femoral neck was significantly increased (P < .05), and the serum type I collagen-cross-linked N telopeptide (NTx) dramatically (P < .05) decreased in posttransplantation group II recipients treated with calcium, calcitriol, and alendronate. There were also significant differences in BMD and serum NTx between recipients treated with versus without alendronate (P < .05).

Conclusion: At least in the short term, alendronate is a effective inhibitor for the treatment of bone loss in renal transplantation patients.
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