Affiliation: Texas Medical Center
- Weighted pedigree-based statistics for testing the association of rare variantsYin Yao Shugart
Unit of Statistical Genomics, Division of Intramural Division Program, National Institute of Mental Health, National Institute of Health, Bethesda, MD, USA
BMC Genomics 13:667. 2012..Note that while the proposed statistic can be applied with and without statistical weighting, our simulations show that its power increases when weighting (WSS and VT) are applied...
- Quantitative trait locus analysis for next-generation sequencing with the functional linear modelsLi Luo
Division of Epidemiology, Biostatistics and Preventive Medicine, University of New Mexico, Albuquerque, NM, USA
J Med Genet 49:513-24. 2012..Analysis from low dimensional data to high dimensional genomic data demands changes in statistical methods from multivariate data analysis to functional data analysis...
- Implication of next-generation sequencing on association studiesHoicheong Siu
MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200433, China
BMC Genomics 12:322. 2011..In this report, we explore different strategies and study designs for the near future GWAS in the post-era, based on both low coverage pilot data and exon pilot data in 1000 Genomes Project...
- Common variants of four bilirubin metabolism genes and their association with serum bilirubin and coronary artery disease in Chinese Han populationRong Lin
State Key Laboratory of Genetic Engineering, School of Life Sciences, Institute of Biomedical Sciences, Fudan University, and Ruijin Hospital, Shanghai, China
Pharmacogenet Genomics 19:310-8. 2009....
- Association of polymorphisms in four bilirubin metabolism genes with serum bilirubin in three Asian populationsRong Lin
Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
Hum Mutat 30:609-15. 2009..Finally, we observed that significant differences of TBIL levels existed among the three populations; however, this could not be completely explained by the differences at the (TA)n repeat polymorphism and SNP rs4148323:G>A...
- Investigation gene and microRNA expression in glioblastomaHua Dong
State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
BMC Genomics 11:S16. 2010..Glioblastoma is the most common primary brain tumor in adults. Though a lot of research has been focused on this disease, the causes and pathogenesis of glioblastoma have not been indentified clearly...
- Gene co-expression network and functional module analysis of ovarian cancerShengjun Hong
MOE Key Laboratory of Contemporary Anthropology and State Key, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
Int J Comput Biol Drug Des 4:147-64. 2011..In addition, we detected two ovarian cancer susceptibility genes: CCEN2 and BRIC5...
- Integrated analysis of mutations, miRNA and mRNA expression in glioblastomaHua Dong
State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
BMC Syst Biol 4:163. 2010....
- Accelerating haplotype-based genome-wide association study using perfect phylogeny and phase-known reference dataYungang He
Department of Computational Genomics, CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
PLoS ONE 6:e22097. 2011..With only a medium-size reference panel, phasing error in our method is comparable to the genotyping error afforded by commercial genotyping solutions...
- Mutual information for testing gene-environment interactionXuesen Wu
School of Life Science, Theoretic Systems Biology Laboratory and Center for Evolutionary Biology, Fudan University, Shanghai, China
PLoS ONE 4:e4578. 2009..Our results showed that P-values for the mutual information-based statistics were much smaller than that obtained by other approaches including logistic regression models...
- Generalized T2 test for genome association studiesMomiao Xiong
Human Genetics Center, University of Texas Houston, 77225, USA
Am J Hum Genet 70:1257-68. 2002..Finally, examples are given to evaluate the performance of the proposed T2 statistic for association studies using simulated and real data...
- Network-based regulatory pathways analysisMomiao Xiong
Human Genetic Center, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
Bioinformatics 20:2056-66. 2004..It is important to extend the concept of network-based metabolic pathways to genetic networks and develop mathematical procedures for network-based regulatory pathway analysis...
- Haplotype block linkage disequilibrium mappingMomiao Xiong
Human Genetics Center, University of Texas Houston Health Science Center, Houston, Texas 77225, USA
Front Biosci 8:a85-93. 2003..Our preliminary results of theoretic analysis further demonstrate that the haplotype block LD analysis is a breakthrough in LD mapping and is a promising tool for genome-wide association studies...
- Identification of genetic networksMomiao Xiong
Human Genetics Center, University of Texas, Houston Health Science Center, TX 77030, USA
Genetics 166:1037-52. 2004..To illustrate the concepts and methods for reconstruction of genetic networks and identification of association of genetic networks with function, we applied the proposed models and algorithms to three data sets...
- cDNA microarrays reveal distinct gene expression clusters in idiopathic inflammatory myopathiesXiaodong Zhou
Division of Rheumatology and Clinical Immunogenetics, Department of Internal Medicine, The University of Texas Medical School at Houston, Houston, TX 77030, USA
Med Sci Monit 10:BR191-7. 2004..This study was to use gene microarray analysis of muscle biopsies from PM and DM patients to obtain a comprehensive view of molecules participating in disease pathogenesis...
- Gene and pathway-based second-wave analysis of genome-wide association studiesGang Peng
School of Life Science, Fudan University, Shanghai, China
Eur J Hum Genet 18:111-7. 2010..The results also showed that the new paradigm for GWAS was able to identify biologically meaningful pathways associated with the diseases, which were confirmed by a gene-set-rich analysis using gene expression data...
- Composite measure of linkage disequilibrium for testing interaction between unlinked lociXuesen Wu
School of Life Science, Fudan University, Shanghai, China
Eur J Hum Genet 16:644-51. 2008..The preliminary results demonstrate that the composite LD-based statistic is a strong alternative to the logistic regressions and the intragametic LD-based statistic for the detection of interaction between two unlinked loci...
- A novel genome-information content-based statistic for genome-wide association analysis designed for next-generation sequencing dataLi Luo
Human Genetics Center, School of Public Health, University of Texas, Houston, TX, USA
J Comput Biol 19:731-44. 2012..We report that the genome-information content-based statistic has significantly improved type 1 error rates and higher power than the other six statistics in both simulated and empirical datasets...
- Dissecting linkage disequilibrium in African-American genomes: roles of markers and individualsShuhua Xu
MOE Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
Mol Biol Evol 24:2049-58. 2007....
- Manifold learning for human population structure studiesHoicheong Siu
MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
PLoS ONE 7:e29901. 2012..The preliminary results demonstrated that next generation sequencing offers a rich resources and LLE provide a powerful tool for population structure analysis...
- Association studies for next-generation sequencingLi Luo
Human Genetics Center, University of Texas School of Public Health, Houston, TX 77030, USA
Genome Res 21:1099-108. 2011..We report that FPCA-based statistics have a higher power to detect association of rare variants and a stronger ability to filter sequence errors than the other seven methods...
- Family-based association studies for next-generation sequencingYun Zhu
Human Genetics Center and Division of Biostatistics, The University of Texas School of Public Health, Houston, 77030, USA
Am J Hum Genet 90:1028-45. 2012..The proposed statistics are applied to two data sets with pedigree structures. The results show that the smoothed FPCA has a much smaller p value than other statistics...
- Genome-wide gene and pathway analysisLi Luo
Human Genetics Center, School of Public Health, The University of Texas, Houston, TX 77225, USA
Eur J Hum Genet 18:1045-53. 2010..Third, replication of association findings at the gene or pathway level is much easier than replication at the individual SNP level...
- Extended kalman filter for estimation of parameters in nonlinear state-space models of biochemical networksXiaodian Sun
Laboratory of Theoretical Systems Biology and Center for Evolutionary Biology, School of Life Science and Institute for Biomedical Sciences, Fudan University, Shanghai, China
PLoS ONE 3:e3758. 2008..The preliminary results show that EKF can accurately estimate the parameters and predict states in nonlinear state-space equations for modeling dynamic biochemical networks...
- Network Approach to GWA Studies of Rheumatoid Arthritis (RA), Ankylosing SpondyliMomiao Xiong; Fiscal Year: 2010..We believe that the proposed study is timely and we expect that the methodological developments and insights we gain will influence genetic studies of RA, AS, psoriasis and other complex diseases and continue beyond this project. ..