Vikas Bansal

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi An MCMC algorithm for haplotype assembly from whole-genome sequence data
    Vikas Bansal
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
    Genome Res 18:1336-46. 2008
  2. ncbi Evidence for large inversion polymorphisms in the human genome from HapMap data
    Vikas Bansal
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093 0004, USA
    Genome Res 17:219-30. 2007
  3. ncbi HapCUT: an efficient and accurate algorithm for the haplotype assembly problem
    Vikas Bansal
    Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0404, USA
    Bioinformatics 24:i153-9. 2008
  4. ncbi Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level
    Olivier Harismendy
    Moores UCSD Cancer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Genome Biol 11:R118. 2010
  5. ncbi A covering method for detecting genetic associations between rare variants and common phenotypes
    Gaurav Bhatia
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
    PLoS Comput Biol 6:e1000954. 2010
  6. ncbi Strobe sequence design for haplotype assembly
    Christine Lo
    Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
    BMC Bioinformatics 12:S24. 2011
  7. ncbi A decomposition theory for phylogenetic networks and incompatible characters
    Dan Gusfield
    Department of Computer Science, University of California, Davis, CA 95616, USA
    J Comput Biol 14:1247-72. 2007
  8. ncbi Accurate detection and genotyping of SNPs utilizing population sequencing data
    Vikas Bansal
    Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA
    Genome Res 20:537-45. 2010
  9. ncbi The importance of phase information for human genomics
    Ryan Tewhey
    The Scripps Translational Science Institute, 3344 North Torrey Pines Road, Suite 300, La Jolla, California 92037, USA
    Nat Rev Genet 12:215-23. 2011
  10. ncbi The number of recombination events in a sample history: conflict graph and lower bounds
    Vineet Bafna
    Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093 0114, USA
    IEEE/ACM Trans Comput Biol Bioinform 1:78-90. 2004

Collaborators

Detail Information

Publications16

  1. ncbi An MCMC algorithm for haplotype assembly from whole-genome sequence data
    Vikas Bansal
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
    Genome Res 18:1336-46. 2008
    ..The code implementing the methods and the phased individual haplotypes can be downloaded from (http://www.cse.ucsd.edu/users/vibansal/HASH/)...
  2. ncbi Evidence for large inversion polymorphisms in the human genome from HapMap data
    Vikas Bansal
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093 0004, USA
    Genome Res 17:219-30. 2007
    ..Although the power of our method to detect inversions is restricted because of inherently noisy LD patterns in population data, inversions predicted by our method represent strong candidates for experimental validation and analysis...
  3. ncbi HapCUT: an efficient and accurate algorithm for the haplotype assembly problem
    Vikas Bansal
    Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0404, USA
    Bioinformatics 24:i153-9. 2008
    ..In this article, we consider the haplotype assembly problem in the most general setting, i.e. fragments of any length and with an arbitrary number of gaps...
  4. ncbi Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level
    Olivier Harismendy
    Moores UCSD Cancer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Genome Biol 11:R118. 2010
    ....
  5. ncbi A covering method for detecting genetic associations between rare variants and common phenotypes
    Gaurav Bhatia
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
    PLoS Comput Biol 6:e1000954. 2010
    ..The data suggests that the RVs help disrupt the expression of the two genes, leading to lowered metabolism of the corresponding cannabinoids. Overall, our results point to the power of including RVs in measuring genetic associations...
  6. ncbi Strobe sequence design for haplotype assembly
    Christine Lo
    Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
    BMC Bioinformatics 12:S24. 2011
    ..Here, we describe the different design parameters that can be adjusted with next generation and upcoming sequencing technologies, and study the impact of design choice on the length of the haplotype...
  7. ncbi A decomposition theory for phylogenetic networks and incompatible characters
    Dan Gusfield
    Department of Computer Science, University of California, Davis, CA 95616, USA
    J Comput Biol 14:1247-72. 2007
    ..We also show that counterexamples to the conjecture are rare (for the case of single-crossover recombination) in simulated data...
  8. ncbi Accurate detection and genotyping of SNPs utilizing population sequencing data
    Vikas Bansal
    Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA
    Genome Res 20:537-45. 2010
    ..Collectively, these results suggest that analysis of population sequencing data is a powerful approach for the accurate detection of SNPs and the assignment of genotypes to individual samples...
  9. ncbi The importance of phase information for human genomics
    Ryan Tewhey
    The Scripps Translational Science Institute, 3344 North Torrey Pines Road, Suite 300, La Jolla, California 92037, USA
    Nat Rev Genet 12:215-23. 2011
    ..Thus, the existing technological impediments to obtaining phase information must be overcome if human genomics is to reach its full potential...
  10. ncbi The number of recombination events in a sample history: conflict graph and lower bounds
    Vineet Bafna
    Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093 0114, USA
    IEEE/ACM Trans Comput Biol Bioinform 1:78-90. 2004
    ..Our results also offer some insight into the structural properties of this graph and are of interest for the general Ancestral Recombination Graph reconstruction problem...
  11. ncbi Inference about recombination from haplotype data: lower bounds and recombination hotspots
    Vineet Bafna
    Department of Computer Science and Engineering, University of California at San Diego, La Jolla, 92093, USA
    J Comput Biol 13:501-21. 2006
    ..The programs implementing the methods in this paper are available at www.cs.ucsd.edu/users/vibansal/RecBounds/...
  12. ncbi Statistical analysis strategies for association studies involving rare variants
    Vikas Bansal
    The Scripps Translational Science Institute, 3344 North Torrey Pines Court, Suite 300, La Jolla, California 92037, USA
    Nat Rev Genet 11:773-85. 2010
    ..Ultimately, although a wide variety of analytical approaches exist, more work is needed to refine them and determine their properties and power in different contexts...
  13. ncbi Designing deep sequencing experiments: detecting structural variation and estimating transcript abundance
    Ali Bashir
    Dept, of Computer Science and Engineering, UC San Diego, La Jolla, CA, USA
    BMC Genomics 11:385. 2010
    ..Here we describe a number of analytical and empirical results to address design questions for two applications: detection of structural variations from paired-end sequencing and estimating mRNA transcript abundance...
  14. ncbi A statistical method for the detection of variants from next-generation resequencing of DNA pools
    Vikas Bansal
    Scripps Genomic Medicine, Scripps Translational Science Institute, La Jolla, CA 92037, USA
    Bioinformatics 26:i318-24. 2010
    ..Detection of rare variants from pooled sequencing represents a different challenge than detection of variants from individual sequencing...
  15. ncbi A probabilistic method for the detection and genotyping of small indels from population-scale sequence data
    Vikas Bansal
    Scripps Genomic Medicine, Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA
    Bioinformatics 27:2047-53. 2011
    ....
  16. ncbi The diploid genome sequence of an individual human
    Samuel Levy
    J Craig Venter Institute, Rockville, Maryland, USA
    PLoS Biol 5:e254. 2007
    ..These data depict a definitive molecular portrait of a diploid human genome that provides a starting point for future genome comparisons and enables an era of individualized genomic information...