Xiaodong Wang

Summary

Affiliation: Columbia University
Country: USA

Publications

  1. pmc Inference of gene regulatory networks from genome-wide knockout fitness data
    Liming Wang
    Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
    Bioinformatics 29:338-46. 2013
  2. pmc Maximum parsimony xor haplotyping by sparse dictionary selection
    Abdulkadir Elmas
    Department of Electrical Engineering, Columbia University, 500 W 120th St, New York, 10027 NY, USA
    BMC Genomics 14:645. 2013
  3. pmc Maximum-parsimony haplotype frequencies inference based on a joint constrained sparse representation of pooled DNA
    Guido H Jajamovich
    Electrical Engineering Department, Columbia University, New York NY 10027, USA
    BMC Bioinformatics 14:270. 2013
  4. pmc Hierarchical Dirichlet process model for gene expression clustering
    Liming Wang
    Department of Electrical Engineering, Columbia University, New York, NY, 10027, USA
    EURASIP J Bioinform Syst Biol 2013:5. 2013
  5. ncbi request reprint A profile-based deterministic sequential Monte Carlo algorithm for motif discovery
    Kuo Ching Liang
    Columbia University, Department of Electrical Engineering, New York, NY 10025, USA
    Bioinformatics 24:46-55. 2008
  6. pmc A haplotype inference algorithm for trios based on deterministic sampling
    Alexandros Iliadis
    Department of Electrical Engineering, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA
    BMC Genet 11:78. 2010
  7. pmc Fast and accurate haplotype frequency estimation for large haplotype vectors from pooled DNA data
    Alexandros Iliadis
    Center for Computational Biology and Bioinformatics and Department of Electrical Engineering, Columbia University, New York, NY, USA
    BMC Genet 13:94. 2012
  8. doi request reprint A unified framework for haplotype inference in nuclear families
    Alexandros Iliadis
    Department of Electrical Engineering, Columbia University, New York, NY, USA
    Ann Hum Genet 76:312-25. 2012
  9. pmc Bayesian multiple-instance motif discovery with BAMBI: inference of recombinase and transcription factor binding sites
    Guido H Jajamovich
    Electrical Engineering Department, Columbia University, New York, NY 10027, USA
    Nucleic Acids Res 39:e146. 2011
  10. doi request reprint Designing DNA barcodes orthogonal in melting temperature by simulated annealing optimization
    Abdulkadir Elmas
    Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
    Nucleic Acid Ther 23:140-51. 2013

Collaborators

Detail Information

Publications13

  1. pmc Inference of gene regulatory networks from genome-wide knockout fitness data
    Liming Wang
    Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
    Bioinformatics 29:338-46. 2013
    ..Yet, to date, few algorithms have been proposed for systematically using genome-wide mutant fitness data for gene regulatory network inference...
  2. pmc Maximum parsimony xor haplotyping by sparse dictionary selection
    Abdulkadir Elmas
    Department of Electrical Engineering, Columbia University, 500 W 120th St, New York, 10027 NY, USA
    BMC Genomics 14:645. 2013
    ..Given the xor-genotypes of a group of unrelated individuals, it is possible to infer the haplotype pairs for each individual with the aid of a small number of regular genotypes...
  3. pmc Maximum-parsimony haplotype frequencies inference based on a joint constrained sparse representation of pooled DNA
    Guido H Jajamovich
    Electrical Engineering Department, Columbia University, New York NY 10027, USA
    BMC Bioinformatics 14:270. 2013
    ..The identification of haplotype frequencies from pooled data in addition to single locus analysis is of separate interest within these studies as haplotypes could increase statistical power and provide additional insight...
  4. pmc Hierarchical Dirichlet process model for gene expression clustering
    Liming Wang
    Department of Electrical Engineering, Columbia University, New York, NY, 10027, USA
    EURASIP J Bioinform Syst Biol 2013:5. 2013
    ..For the yeast cell cycle data, we compare the HDP result to the standard result and show that the HDP algorithm provides more information and reduces the unnecessary clustering fragments...
  5. ncbi request reprint A profile-based deterministic sequential Monte Carlo algorithm for motif discovery
    Kuo Ching Liang
    Columbia University, Department of Electrical Engineering, New York, NY 10025, USA
    Bioinformatics 24:46-55. 2008
    ..With the increasing number of sequenced genomic data, faster and more accurate tools are needed to automate the process of motif discovery...
  6. pmc A haplotype inference algorithm for trios based on deterministic sampling
    Alexandros Iliadis
    Department of Electrical Engineering, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA
    BMC Genet 11:78. 2010
    ..Several phasing algorithms have been developed for data from unrelated individuals, based on different models, some of which have been extended to father-mother-child "trio" data...
  7. pmc Fast and accurate haplotype frequency estimation for large haplotype vectors from pooled DNA data
    Alexandros Iliadis
    Center for Computational Biology and Bioinformatics and Department of Electrical Engineering, Columbia University, New York, NY, USA
    BMC Genet 13:94. 2012
    ..Knowledge of haplotype structure can provide additional information to single locus analyses. Several methods have been proposed for estimating haplotype frequencies in a population from pooled DNA data...
  8. doi request reprint A unified framework for haplotype inference in nuclear families
    Alexandros Iliadis
    Department of Electrical Engineering, Columbia University, New York, NY, USA
    Ann Hum Genet 76:312-25. 2012
    ..We believe that our proposed framework could be the method of choice for haplotype inference in studies that include nuclear families with multiple children. Our software (tds2.0) is downloadable from www.ee.columbia.edu/∼anastas/tds...
  9. pmc Bayesian multiple-instance motif discovery with BAMBI: inference of recombinase and transcription factor binding sites
    Guido H Jajamovich
    Electrical Engineering Department, Columbia University, New York, NY 10027, USA
    Nucleic Acids Res 39:e146. 2011
    ..C++ and Matlab code is available at http://www.ee.columbia.edu/~guido/BAMBI or http://genomics.lbl.gov/BAMBI/...
  10. doi request reprint Designing DNA barcodes orthogonal in melting temperature by simulated annealing optimization
    Abdulkadir Elmas
    Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
    Nucleic Acid Ther 23:140-51. 2013
    ..An application of this approach is demonstrated using 2 different DNA probe sets...
  11. pmc Robust discovery of periodically expressed genes using the laplace periodogram
    Kuo Ching Liang
    Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
    BMC Bioinformatics 10:15. 2009
    ..The detection of genes that are periodically expressed is an important step which allows us to study the regulatory mechanisms associated with the cell cycle...
  12. pmc Identification of gene interactions associated with disease from gene expression data using synergy networks
    John Watkinson
    Center for Computational Biology and Bioinformatics and Department of Electrical Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, USA
    BMC Syst Biol 2:10. 2008
    ..If, however, the aim is the discovery of disease-related biological mechanisms, then the criterion for defining such interactions must be specifically linked to disease...
  13. ncbi request reprint Bayesian basecalling for DNA sequence analysis using hidden Markov models
    Kuo Ching Liang
    Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
    IEEE/ACM Trans Comput Biol Bioinform 4:430-40. 2007
    ....