Affiliation: University of California
- HapCUT: an efficient and accurate algorithm for the haplotype assembly problemVikas 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...
- Evidence for large inversion polymorphisms in the human genome from HapMap dataVikas 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...
- An MCMC algorithm for haplotype assembly from whole-genome sequence dataVikas 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/)...
- Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite levelOlivier Harismendy
Moores UCSD Cancer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
Genome Biol 11:R118. 2010....
- A covering method for detecting genetic associations between rare variants and common phenotypesGaurav 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...
- Genetic structure of community acquired methicillin-resistant Staphylococcus aureus USA300Ryan Tewhey
Scripps Genomic Medicine, Scripps Translational Science Institute, La Jolla, CA, USA
BMC Genomics 13:508. 2012..The broad range of disease severity may be influenced by bacterial genetic variation...
- Strobe sequence design for haplotype assemblyChristine 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...
- A decomposition theory for phylogenetic networks and incompatible charactersDan 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...
- Accurate detection and genotyping of SNPs utilizing population sequencing dataVikas 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...
- The importance of phase information for human genomicsRyan 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...
- The number of recombination events in a sample history: conflict graph and lower boundsVineet 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...
- Inference about recombination from haplotype data: lower bounds and recombination hotspotsVineet 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/...
- Statistical analysis strategies for association studies involving rare variantsVikas 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...
- Designing deep sequencing experiments: detecting structural variation and estimating transcript abundanceAli 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...
- A statistical method for the detection of variants from next-generation resequencing of DNA poolsVikas 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...
- Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencingSiddarth Selvaraj
1 Ludwig Institute for Cancer Research, La Jolla, California, USA 2 Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, California, USA 3
Nat Biotechnol 31:1111-8. 2013..Whereas methods based on proximity ligation were originally designed to investigate spatial organization of genomes, our results lend support for their use as a general tool for haplotyping. ..
- A probabilistic method for the detection and genotyping of small indels from population-scale sequence dataVikas Bansal
Scripps Genomic Medicine, Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA
Bioinformatics 27:2047-53. 2011....
- The diploid genome sequence of an individual humanSamuel 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...