Xiaohui Xie

Summary

Affiliation: University of California
Country: USA

Publications

  1. doi request reprint Improving read mapping using additional prefix grams
    Jongik Kim
    Department of Computer Science, University of California, Irvine, USA
    BMC Bioinformatics 15:42. 2014
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

Collaborators

Detail Information

Publications21

  1. doi request reprint Improving read mapping using additional prefix grams
    Jongik Kim
    Department of Computer Science, University of California, Irvine, USA
    BMC Bioinformatics 15:42. 2014
    ....
  2. 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...
  3. 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...
  4. 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...
  5. 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
    ....
  6. 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...
  7. 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...
  8. 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...
  9. 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...
  10. 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...
  11. 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...
  12. 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...
  13. 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...
  14. doi request reprint 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
    ....
  15. 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...
  16. 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...
  17. 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...
  18. 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
    ....
  19. doi request reprint 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...
  20. 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...
  21. 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...