Xiaoming Liu

Summary

Affiliation: Texas Medical Center
Country: USA

Publications

  1. pmc dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions
    Xiaoming Liu
    Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
    Hum Mutat 32:894-9. 2011
  2. doi request reprint dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations
    Xiaoming Liu
    Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
    Hum Mutat 34:E2393-402. 2013
  3. pmc Translational signatures and mRNA levels are highly correlated in human stably expressed genes
    Sergio R P Line
    Piracicaba Dental School, University of Campinas, PO Box 52, Piracicaba, SP, 13414 903, Brazil
    BMC Genomics 14:268. 2013
  4. pmc Age-of-onset of hypertension vs. a single measurement of systolic blood pressure in a combined linkage and segregation analysis
    E Warwick Daw
    Department of Epidemiology, University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, USA
    BMC Genet 4:S80. 2003
  5. pmc Estimating population genetic parameters and comparing model goodness-of-fit using DNA sequences with error
    Xiaoming Liu
    Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
    Genome Res 20:101-9. 2010
  6. pmc Algorithms to estimate the lower bounds of recombination with or without recurrent mutations
    Xiaoming Liu
    Human Genetics Center, School of Public Health, University of Texas at Houston, Houston, Texas 77030, USA
    BMC Genomics 9:S24. 2008
  7. pmc Significantly fewer protein functional changing variants for lipid metabolism in Africans than in Europeans
    Cheng Xue
    Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
    J Transl Med 11:67. 2013
  8. pmc Inferring population mutation rate and sequencing error rate using the SNP frequency spectrum in a sample of DNA sequences
    Xiaoming Liu
    Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, TX, USA
    Mol Biol Evol 26:1479-90. 2009
  9. pmc Simulating sequences of the human genome with rare variants
    Bo Peng
    Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
    Hum Hered 70:287-91. 2010
  10. pmc Smaller genetic risk in catabolic process explains lower energy expenditure, more athletic capability and higher prevalence of obesity in Africans
    Cheng Xue
    Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
    PLoS ONE 6:e26027. 2011

Collaborators

Detail Information

Publications24

  1. pmc dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions
    Xiaoming Liu
    Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
    Hum Mutat 32:894-9. 2011
    ..It is the first integrated database of functional predictions from multiple algorithms for the comprehensive collection of human NSs. dbNSFP is freely available for download at http://sites.google.com/site/jpopgen/dbNSFP...
  2. doi request reprint dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations
    Xiaoming Liu
    Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
    Hum Mutat 34:E2393-402. 2013
    ..dbNSFP v2.0 is freely available for download at http://sites.google.com/site/jpopgen/dbNSFP...
  3. pmc Translational signatures and mRNA levels are highly correlated in human stably expressed genes
    Sergio R P Line
    Piracicaba Dental School, University of Campinas, PO Box 52, Piracicaba, SP, 13414 903, Brazil
    BMC Genomics 14:268. 2013
    ....
  4. pmc Age-of-onset of hypertension vs. a single measurement of systolic blood pressure in a combined linkage and segregation analysis
    E Warwick Daw
    Department of Epidemiology, University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, USA
    BMC Genet 4:S80. 2003
    ..The measures selected were age-of-onset of hypertension and systolic blood pressure at first visit...
  5. pmc Estimating population genetic parameters and comparing model goodness-of-fit using DNA sequences with error
    Xiaoming Liu
    Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
    Genome Res 20:101-9. 2010
    ..The MCLE method is applied to sequence data on the ANGPTL4 gene in 1832 African American and 1045 European American individuals...
  6. pmc Algorithms to estimate the lower bounds of recombination with or without recurrent mutations
    Xiaoming Liu
    Human Genetics Center, School of Public Health, University of Texas at Houston, Houston, Texas 77030, USA
    BMC Genomics 9:S24. 2008
    ..However, recurrent mutations are relatively common in genes with high mutation rates or mutation hot-spots, such as those in the genomes of bacteria or viruses...
  7. pmc Significantly fewer protein functional changing variants for lipid metabolism in Africans than in Europeans
    Cheng Xue
    Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
    J Transl Med 11:67. 2013
    ..In this study, we explored the genetic risk differences among human populations in metabolism (catabolism and biosynthesis) of energy substances, including lipids, carbohydrates and amino acids...
  8. pmc Inferring population mutation rate and sequencing error rate using the SNP frequency spectrum in a sample of DNA sequences
    Xiaoming Liu
    Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, TX, USA
    Mol Biol Evol 26:1479-90. 2009
    ..We demonstrate the application of the estimators with 10-kb noncoding region sequence sampled from a human population and provide suggestions for choosing theta estimators with error...
  9. pmc Simulating sequences of the human genome with rare variants
    Bo Peng
    Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
    Hum Hered 70:287-91. 2010
    ....
  10. pmc Smaller genetic risk in catabolic process explains lower energy expenditure, more athletic capability and higher prevalence of obesity in Africans
    Cheng Xue
    Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
    PLoS ONE 6:e26027. 2011
    ..Therefore, the smaller genetic risk in the catabolic process might be at the core of understanding lower EE, more athletic capability and higher prevalence of obesity in Africans...
  11. pmc Summary statistics of neutral mutations in longitudinal DNA samples
    Xiaoming Liu
    Human Genetics Center, School of Public Health, University of Texas at Houston, 1200 Herman Pressler, Houston, TX 77030, USA
    Theor Popul Biol 74:56-67. 2008
    ..We derived the formulas for calculating statistical properties, e.g. expectations, variances and covariances, of these new summary statistics under the two models. Potential applications of these results were discussed...
  12. pmc Test of genetical isochronism for longitudinal samples of DNA sequences
    Xiaoming Liu
    Human Genetics Center, School of Public Health, University of Texas, Houston, Texas 77030, USA
    Genetics 176:327-42. 2007
    ..The possible choices and usages of these test statistics are discussed...
  13. pmc Evidence for recombination in Mycobacterium tuberculosis
    Xiaoming Liu
    Human Genetics Center, University of Texas at Houston, P O Box 20186, Houston, TX 77225, USA
    J Bacteriol 188:8169-77. 2006
    ..tuberculosis and possibly a major contributor to the diversity observed ahead of the MT0105 locus...
  14. doi request reprint Whole-genome sequence-based analysis of high-density lipoprotein cholesterol
    Alanna C Morrison
    Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, USA
    Nat Genet 45:899-901. 2013
    ..Whole-genome sequencing analyses highlight the value of regulatory and non-protein-coding regions of the genome in addition to protein-coding regions. ..
  15. pmc Incorporating predicted functions of nonsynonymous variants into gene-based analysis of exome sequencing data: a comparative study
    Peng Wei
    Division of Biostatistics, University of Texas School of Public Health, 1200 Herman Presser Drive, Houston, TX 77030, USA
    BMC Proc 5:S20. 2011
    ..We also propose a simple mixture model that can effectively combine test results based on different functional prediction algorithms...
  16. pmc Identification of common prognostic gene expression signatures with biological meanings from microarray gene expression datasets
    Jun Yao
    Department of Neuro Oncology, The University of Texas M D Anderson Cancer Center, Houston, TX, USA
    PLoS ONE 7:e45894. 2012
    ..These results demonstrate the power of SCoR to identify common and biologically meaningful prognostic gene expression signatures...
  17. pmc Biological Differences in rAAV Transduction of Airway Epithelia in Humans and in Old World Non-human Primates
    Xiaoming Liu
    Department of Anatomy and Cell Biology, College of Medicine, The University of Iowa, Iowa City, Iowa 52242, USA
    Mol Ther 15:2114-23. 2007
    ..These findings suggest that the IndianRhesusmonkey may not be the best model for preclinical testing of rAAV-mediated gene therapy to the airway in humans...
  18. pmc IkappaBalpha and IkappaBbeta possess injury context-specific functions that uniquely influence hepatic NF-kappaB induction and inflammation
    Chenguang Fan
    Molecular Biology Program, College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
    J Clin Invest 113:746-55. 2004
    ....
  19. pmc Targeted correction of single-base-pair mutations with adeno-associated virus vectors under nonselective conditions
    Xiaoming Liu
    Department of Anatomy and Cell Biology and the Center for Gene Therapy of Cystic Fibrosis and Other Genetic Diseases, University of Iowa College of Medicine, Iowa City, Iowa 52242, USA
    J Virol 78:4165-75. 2004
    ..However, the failure of direct cytoplasm- or nucleus-injected rAAV DNA to facilitate gene repair suggests that some aspect of intracellular viral processing may be required to prime recombinant viral genomes for gene repair events...
  20. ncbi request reprint Molecular phylogeny and taxonomy of wood mice (genus Apodemus Kaup, 1829) based on complete mtDNA cytochrome b sequences, with emphasis on Chinese species
    Xiaoming Liu
    Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China
    Mol Phylogenet Evol 33:1-15. 2004
    ..17-9.95 Mya. Four species of the Sylvaemus group were estimated to diverge at about 2.92-5.21 Mya. The Hengduan Mountains Region was hypothesized to have played important roles in Apodemus evolutionary histories since the Pleistocene...
  21. ncbi request reprint PITX2, beta-catenin and LEF-1 interact to synergistically regulate the LEF-1 promoter
    Usha Vadlamudi
    Department of Biological Science, The University of Tulsa, 600 S College Ave, Tulsa, OK 74104 3189, USA
    J Cell Sci 118:1129-37. 2005
    ..LEF-1 and beta-catenin interactions with PITX2 provide new mechanisms for the regulation of PITX2 transcriptional activity...
  22. ncbi request reprint Bending effect on fiber acousto-optic mode coupling
    Jianhui Zhao
    Department of Electronic Engineering, Tsinghua University, Beijing 100084, China
    Appl Opt 44:5101-4. 2005
    ..The strength of new peaks increases as the fiber-bending curvature increases with a redshift or blueshift in wavelength, strongly depending on the orientation of fiber bending with respect to the acoustic-wave vibration direction...
  23. pmc Species-specific differences in mouse and human airway epithelial biology of recombinant adeno-associated virus transduction
    Xiaoming Liu
    Department of Anatomy and Cell Biology, University of Iowa College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA
    Am J Respir Cell Mol Biol 34:56-64. 2006
    ..These studies emphasize species-specific differences in airway biology between mice and humans that significantly influence the use of mice as surrogate models for rAAV transduction and gene therapy for CF...
  24. ncbi request reprint Partial correction of endogenous DeltaF508 CFTR in human cystic fibrosis airway epithelia by spliceosome-mediated RNA trans-splicing
    Xiaoming Liu
    Department of Anatomy and Cell Biology, College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
    Nat Biotechnol 20:47-52. 2002
    ..These results provide functional evidence for SMaRT-mediated repair of mutant endogenous CFTR mRNA in intact polarized CF airway epithelial models...