Nils Homer

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Local alignment of two-base encoded DNA sequence
    Nils Homer
    Department of Computer Science, University of California Los Angeles, Los Angeles, California 90095, USA
    BMC Bioinformatics 10:175. 2009
  2. pmc Local alignment of generalized k-base encoded DNA sequence
    Nils Homer
    Department of Computer Science, University of California Los Angeles, Los Angeles, California 90095, USA
    BMC Bioinformatics 11:347. 2010
  3. pmc Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA
    Nils Homer
    Department of Computer Science, University of California, Los Angeles, Boelter Hall, Los Angeles, CA 90095, USA
    Genome Biol 11:R99. 2010
  4. pmc Improving the efficiency of genomic loci capture using oligonucleotide arrays for high throughput resequencing
    Hane Lee
    Department of Human Genetics, University of California, Los Angeles, California, USA
    BMC Genomics 10:646. 2009
  5. pmc BFAST: an alignment tool for large scale genome resequencing
    Nils Homer
    Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA
    PLoS ONE 4:e7767. 2009
  6. pmc U87MG decoded: the genomic sequence of a cytogenetically aberrant human cancer cell line
    Michael James Clark
    Department of Human Genetics, University of California Los Angeles, Los Angeles, California, United States of America
    PLoS Genet 6:e1000832. 2010

Collaborators

Detail Information

Publications6

  1. pmc Local alignment of two-base encoded DNA sequence
    Nils Homer
    Department of Computer Science, University of California Los Angeles, Los Angeles, California 90095, USA
    BMC Bioinformatics 10:175. 2009
    ..The decoding is deterministic, but the possibility of measurement errors requires searching among all possible error modes and resulting alignments to achieve an optimal balance of fewer errors versus greater sequence similarity...
  2. pmc Local alignment of generalized k-base encoded DNA sequence
    Nils Homer
    Department of Computer Science, University of California Los Angeles, Los Angeles, California 90095, USA
    BMC Bioinformatics 11:347. 2010
    ..The encoded DNA sequence may contain technical errors, and therefore encoded sequencing errors must be incorporated when comparing an encoded DNA sequence to a reference DNA sequence...
  3. pmc Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA
    Nils Homer
    Department of Computer Science, University of California, Los Angeles, Boelter Hall, Los Angeles, CA 90095, USA
    Genome Biol 11:R99. 2010
    ..A novel short-read micro realigner, SRMA, that leverages this correlation to better resolve a consensus of the underlying DNA sequence of the targeted genome is described here...
  4. pmc Improving the efficiency of genomic loci capture using oligonucleotide arrays for high throughput resequencing
    Hane Lee
    Department of Human Genetics, University of California, Los Angeles, California, USA
    BMC Genomics 10:646. 2009
    ..This approach is being used by our group and others routinely and we are continuing to improve its performance...
  5. pmc BFAST: an alignment tool for large scale genome resequencing
    Nils Homer
    Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA
    PLoS ONE 4:e7767. 2009
    ..Speed is obviously of great importance, but equally important is maintaining alignment accuracy of short reads, in the 25-100 base range, in the presence of errors and true biological variation...
  6. pmc U87MG decoded: the genomic sequence of a cytogenetically aberrant human cancer cell line
    Michael James Clark
    Department of Human Genetics, University of California Los Angeles, Los Angeles, California, United States of America
    PLoS Genet 6:e1000832. 2010
    ..The sequence analysis of U87MG provides an unparalleled level of mutational resolution compared to any cell line to date...