Xiaohui Xie

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Low-rank regularization for learning gene expression programs
    Guibo Ye
    Department of Computer Science, University of California Irvine, Irvine, California, United States of America Department of Mathematics, University of California Irvine, Irvine, California, United States of America
    PLoS ONE 8:e82146. 2013
  2. pmc Identifying novel constrained elements by exploiting biased substitution patterns
    Manuel Garber
    Department of Biology, Broad Institute of MIT and Harvard, 7 Cambridge Center, MIT, Cambridge, MA 02142, USA
    Bioinformatics 25:i54-62. 2009
  3. pmc A gradient boosting algorithm for survival analysis via direct optimization of concordance index
    Yifei Chen
    Department of Computer Science, University of California Irvine, Irvine, CA 92697, USA
    Comput Math Methods Med 2013:873595. 2013
  4. pmc Improving read mapping using additional prefix grams
    Jongik Kim
    Department of Computer Science, University of California, Irvine, USA
    BMC Bioinformatics 15:42. 2014
  5. pmc MotifMap: a human genome-wide map of candidate regulatory motif sites
    Xiaohui Xie
    Department of Computer Sciences, University of California, Irvine, CA 92697, USA
    Bioinformatics 25:167-74. 2009
  6. doi request reprint The site-frequency spectrum of linked sites
    Xiaohui Xie
    Department of Computer Science, Center for Complex Biological Systems, Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92697, USA
    Bull Math Biol 73:459-94. 2011
  7. pmc Genome-wide analysis of hepatic LRH-1 reveals a promoter binding preference and suggests a role in regulating genes of lipid metabolism in concert with FXR
    Hansook Kim Chong
    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
    BMC Genomics 13:51. 2012
  8. pmc Distinguishing protein-coding and noncoding genes in the human genome
    Michele Clamp
    Broad Institute of Massachusetts Institute of Technology and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 104:19428-33. 2007
  9. pmc Genome-wide interrogation of hepatic FXR reveals an asymmetric IR-1 motif and synergy with LRH-1
    Hansook Kim Chong
    Department of Molecular Biology and Biochemistry, Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92697, USA
    Nucleic Acids Res 38:6007-17. 2010
  10. pmc Systematic discovery of regulatory motifs in Fusarium graminearum by comparing four Fusarium genomes
    Lokesh Kumar
    Broad Institute, Cambridge, MA, USA
    BMC Genomics 11:208. 2010

Detail Information

Publications39

  1. pmc Low-rank regularization for learning gene expression programs
    Guibo Ye
    Department of Computer Science, University of California Irvine, Irvine, California, United States of America Department of Mathematics, University of California Irvine, Irvine, California, United States of America
    PLoS ONE 8:e82146. 2013
    ..Finally, we test the algorithms on three gene expression datasets, and show that the low-rank regularization improves the accuracy of gene expression prediction in these three datasets. ..
  2. pmc Identifying novel constrained elements by exploiting biased substitution patterns
    Manuel Garber
    Department of Biology, Broad Institute of MIT and Harvard, 7 Cambridge Center, MIT, Cambridge, MA 02142, USA
    Bioinformatics 25:i54-62. 2009
    ..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...
  3. pmc A gradient boosting algorithm for survival analysis via direct optimization of concordance index
    Yifei Chen
    Department of Computer Science, University of California Irvine, Irvine, CA 92697, USA
    Comput Math Methods Med 2013:873595. 2013
    ..Our experiment shows that GBMCI consistently outperforms other methods based on a number of covariate settings. GBMCI is implemented in R and is freely available online. ..
  4. pmc Improving read mapping using additional prefix grams
    Jongik Kim
    Department of Computer Science, University of California, Irvine, USA
    BMC Bioinformatics 15:42. 2014
    ....
  5. pmc MotifMap: a human genome-wide map of candidate regulatory motif sites
    Xiaohui Xie
    Department of Computer Sciences, University of California, Irvine, CA 92697, USA
    Bioinformatics 25:167-74. 2009
    ..Such efforts, however, have been significantly hindered by the overwhelming size of non-coding DNA regions and the statistical variability and complex spatial organizations of mammalian regulatory elements...
  6. doi request reprint The site-frequency spectrum of linked sites
    Xiaohui Xie
    Department of Computer Science, Center for Complex Biological Systems, Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92697, USA
    Bull Math Biol 73:459-94. 2011
    ..More generally, the Green's function construction should be able to aid in studying the genetic drift of multiple alleles in other cases...
  7. pmc Genome-wide analysis of hepatic LRH-1 reveals a promoter binding preference and suggests a role in regulating genes of lipid metabolism in concert with FXR
    Hansook Kim Chong
    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
    BMC Genomics 13:51. 2012
    ....
  8. pmc Distinguishing protein-coding and noncoding genes in the human genome
    Michele Clamp
    Broad Institute of Massachusetts Institute of Technology and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 104:19428-33. 2007
    ..It also provides a principled methodology for evaluating future proposed additions to the human gene catalog. Finally, the results indicate that there has been relatively little true innovation in mammalian protein-coding genes...
  9. pmc Genome-wide interrogation of hepatic FXR reveals an asymmetric IR-1 motif and synergy with LRH-1
    Hansook Kim Chong
    Department of Molecular Biology and Biochemistry, Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92697, USA
    Nucleic Acids Res 38:6007-17. 2010
    ..Other broad gene clusters related to metabolism, transport, signaling and glycolysis were also significantly enriched. Thus, FXR may have a much wider role in cellular metabolism than previously appreciated...
  10. pmc Systematic discovery of regulatory motifs in Fusarium graminearum by comparing four Fusarium genomes
    Lokesh Kumar
    Broad Institute, Cambridge, MA, USA
    BMC Genomics 11:208. 2010
    ..The generation of whole genome sequence assemblies for Fg and three closely related Fusarium species provides a unique opportunity for such a study...
  11. ncbi request reprint Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
    Tarjei S Mikkelsen
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 447:167-77. 2007
    ..A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation...
  12. pmc Genome-wide localization of SREBP-2 in hepatic chromatin predicts a role in autophagy
    Young Kyo Seo
    Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
    Cell Metab 13:367-75. 2011
    ..Thus, the lipid droplet could be viewed as a third source of cellular cholesterol, which along with sterol synthesis and uptake, is also regulated by SREBP-2...
  13. pmc AREM: aligning short reads from ChIP-sequencing by expectation maximization
    Daniel Newkirk
    Department of Biological Chemistry, University of California, Irvine, California 92697, USA
    J Comput Biol 18:1495-505. 2011
    ..6%) Rad21 peaks and 227 (13%) Srebp-1 peaks that were missed using only uniquely mapped reads. The open source implementation of our algorithm is available at http://sourceforge.net/projects/arem...
  14. pmc Discovering and mapping chromatin states using a tree hidden Markov model
    Jacob Biesinger
    Department of Computer Science, University of California Irvine, CA, USA
    BMC Bioinformatics 14:S4. 2013
    ..The source code for our model is available at http:// http://github.com/uci-cbcl/tree-hmm...
  15. pmc A high-resolution map of human evolutionary constraint using 29 mammals
    Kerstin Lindblad-Toh
    Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 478:476-82. 2011
    ..Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease...
  16. doi request reprint Common polymorphic transcript variation in human disease
    Hunter B Fraser
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Genome Res 19:567-75. 2009
    ..A catalog of PTV will be a valuable resource for interpreting results from future disease-association studies and understanding the spectrum of phenotypic differences among humans...
  17. pmc Data structures and compression algorithms for high-throughput sequencing technologies
    Kenny Daily
    Department of Computer Science, University of California Irvine, Irvine, CA 92697 USA
    BMC Bioinformatics 11:514. 2010
    ..As experiments scale up, HTS technologies create new bioinformatics challenges for the storage and sharing of HTS data...
  18. pmc Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium
    Li Jun Ma
    The Broad Institute, Cambridge, Massachusetts 02141, USA
    Nature 464:367-73. 2010
    ..oxysporum. These findings put the evolution of fungal pathogenicity into a new perspective...
  19. ncbi request reprint Genome sequence, comparative analysis and haplotype structure of the domestic dog
    Kerstin Lindblad-Toh
    Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 438:803-19. 2005
    ..The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health...
  20. pmc MotifMap: integrative genome-wide maps of regulatory motif sites for model species
    Kenneth Daily
    Department of Computer Science, University of California Irvine, Irvine, CA 92697, USA
    BMC Bioinformatics 12:495. 2011
    ..Genome-wide catalogs of regulatory elements for all model species simply do not yet exist...
  21. pmc A large family of ancient repeat elements in the human genome is under strong selection
    Michael Kamal
    Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 103:2740-5. 2006
    ..Although the precise function of these elements remains unknown, the evidence suggests that this unusual family may play a cis-regulatory or structural role in mammalian genomes...
  22. pmc A family of conserved noncoding elements derived from an ancient transposable element
    Xiaohui Xie
    Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 103:11659-64. 2006
    ..In addition, we identify 95 additional CNE families that likely predate the mammalian radiation. The results highlight both the creative role of transposons and the importance of CNE families...
  23. pmc Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites
    Xiaohui Xie
    Broad Institute of MIT and Harvard, Massachusetts Institute of Technology and Harvard Medical School, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 104:7145-50. 2007
    ..These sites may thus partition the human genome into domains of expression...
  24. pmc Genome-wide detection and characterization of positive selection in human populations
    Pardis C Sabeti
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
    Nature 449:913-8. 2007
    ....
  25. doi request reprint Human genomes as email attachments
    Scott Christley
    Department of Computer Science, University of California Irvine, Irvine, CA 92697, USA
    Bioinformatics 25:274-5. 2009
    ..We apply a series of techniques to James Watson's genome that in combination reduce it to a mere 4MB, small enough to be sent as an email attachment...
  26. pmc Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns
    Zhenzhen Zheng
    Department of Mathematics, University of California, Irvine, CA 92697, USA
    BMC Syst Biol 8:3. 2014
    ....
  27. pmc Hobbes: optimized gram-based methods for efficient read alignment
    Athena Ahmadi
    Department of Computer Science, University of California, Irvine, CA 92697, USA
    Nucleic Acids Res 40:e41. 2012
    ..Hobbes supports the SAM output format and is publicly available at http://hobbes.ics.uci.edu...
  28. pmc Identifying gene regulatory networks in schizophrenia
    Steven G Potkin
    Department of Psychiatry and Human Behavior, 5251 California Avenue, Suite 240, University of California, Irvine, CA 92617, USA
    Neuroimage 53:839-47. 2010
    ..The model demonstrates epistatic interactions between FGF and glypican on brain development and may be a useful model of negative symptom schizophrenia...
  29. pmc Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
    Tarjei S Mikkelsen
    Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
    Nature 448:553-60. 2007
    ..This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations...
  30. pmc Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent
    Yuanfeng Wang
    Department of Physics and Astronomy, University of California, Irvine, 92617, USA
    BMC Syst Biol 4:99. 2010
    ..In this article we focus on the parameter inference problem for stochastic kinetic models of biochemical reactions given discrete time-course observations of either some or all of the molecular species...
  31. pmc Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation
    Chengguo Yao
    Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697, USA
    Proc Natl Acad Sci U S A 109:18773-8. 2012
    ..Taken together, our findings provide insight into the mechanisms of PAS recognition and identify CstF64 as an important global regulator of APA...
  32. pmc A mixture model for expression deconvolution from RNA-seq in heterogeneous tissues
    Yi Li
    Department of Computer Science, University of California Irvine, CA, USA
    BMC Bioinformatics 14:S11. 2013
    ....
  33. ncbi request reprint Disease gene discovery through integrative genomics
    Cosmas Giallourakis
    Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02139, USA
    Annu Rev Genomics Hum Genet 6:381-406. 2005
    ..Finally, we discuss future prospects and challenges for using integrative genomics to systematically discover not only single genes but also entire gene networks that underlie and modify human disease...
  34. pmc Genome-wide analysis of SREBP-1 binding in mouse liver chromatin reveals a preference for promoter proximal binding to a new motif
    Young Kyo Seo
    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
    Proc Natl Acad Sci U S A 106:13765-9. 2009
    ..SREBP-1 bound not only to many well-characterized SREBP-1 target genes but to several other previously unknown targets in lipid and carbohydrate metabolism as well as many putative target genes in other diverse biological pathways...
  35. ncbi request reprint Systematic identification of human mitochondrial disease genes through integrative genomics
    Sarah Calvo
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nat Genet 38:576-82. 2006
    ..The integrative approach promises to better define the role of mitochondria in both rare and common human diseases...
  36. pmc Incorporating existing network information into gene network inference
    Scott Christley
    Department of Mathematics, University of California Irvine, Irvine, CA, USA
    PLoS ONE 4:e6799. 2009
    ..We show that including the prior network information constructs a more closely representative regulatory network versus when no information is provided...
  37. pmc Integrative ChIP-seq/microarray analysis identifies a CTNNB1 target signature enriched in intestinal stem cells and colon cancer
    Kazuhide Watanabe
    Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, United States of America
    PLoS ONE 9:e92317. 2014
    ....
  38. pmc Biallelic genome modification in F(0) Xenopus tropicalis embryos using the CRISPR/Cas system
    Ira L Blitz
    Department of Developmental and Cell Biology, University of California, Irvine, California
    Genesis 51:827-34. 2013
    ..We also find that off-target mutagenesis seems to be negligible, and therefore, CRISPR/Cas may be a useful system for creating genome modifications in this important model organism...
  39. pmc SNP-based pathway enrichment analysis for genome-wide association studies
    Lingjie Weng
    Department of Computer Science, University of California, Irvine, USA
    BMC Bioinformatics 12:99. 2011
    ..Most current methods choose the most significant SNP from each gene as a representative, ignoring the joint action of multiple SNPs within a gene. This approach leads to preferential identification of genes with a greater number of SNPs...