Gill Bejerano

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi Algorithms for variable length Markov chain modeling
    Gill Bejerano
    Center for Biomolecular Science and Engineering, School of Engineering, University of California, Santa Cruz, CA 95064, USA
    Bioinformatics 20:788-9. 2004
  2. ncbi A distal enhancer and an ultraconserved exon are derived from a novel retroposon
    Gill Bejerano
    Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA
    Nature 441:87-90. 2006
  3. ncbi Computational screening of conserved genomic DNA in search of functional noncoding elements
    Gill Bejerano
    Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA
    Nat Methods 2:535-45. 2005
  4. ncbi Efficient exact p-value computation for small sample, sparse, and surprising categorical data
    Gill Bejerano
    Center for Biomolecular Science and Engineering, School of Engineering, University of California, Santa Cruz, CA 95064, USA
    J Comput Biol 11:867-86. 2004
  5. ncbi Into the heart of darkness: large-scale clustering of human non-coding DNA
    Gill Bejerano
    Center for Biomolecular Science and Engineering, Baskin School of Engineering University of California in Santa Cruz, Santa Cruz, CA 95064, USA
    Bioinformatics 20:i40-8. 2004
  6. ncbi Ultraconserved elements in the human genome
    Gill Bejerano
    Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Science 304:1321-5. 2004
  7. pmc Identification and classification of conserved RNA secondary structures in the human genome
    Jakob Skou Pedersen
    Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California, USA
    PLoS Comput Biol 2:e33. 2006
  8. pmc Forces shaping the fastest evolving regions in the human genome
    Katherine S Pollard
    Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
    PLoS Genet 2:e168. 2006
  9. pmc Endangered species hold clues to human evolution
    Craig B Lowe
    Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA
    J Hered 101:437-47. 2010
  10. pmc Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish
    Michael Hiller
    Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA, Department of Computer Science, Stanford University, Stanford, CA 94305, USA and Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
    Nucleic Acids Res 41:e151. 2013

Detail Information

Publications17

  1. ncbi Algorithms for variable length Markov chain modeling
    Gill Bejerano
    Center for Biomolecular Science and Engineering, School of Engineering, University of California, Santa Cruz, CA 95064, USA
    Bioinformatics 20:788-9. 2004
    ..As both theoretical and experimental results show, these models are capable of capturing rich signals from a modest amount of training data, without the use of hidden states...
  2. ncbi A distal enhancer and an ultraconserved exon are derived from a novel retroposon
    Gill Bejerano
    Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA
    Nature 441:87-90. 2006
    ....
  3. ncbi Computational screening of conserved genomic DNA in search of functional noncoding elements
    Gill Bejerano
    Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA
    Nat Methods 2:535-45. 2005
  4. ncbi Efficient exact p-value computation for small sample, sparse, and surprising categorical data
    Gill Bejerano
    Center for Biomolecular Science and Engineering, School of Engineering, University of California, Santa Cruz, CA 95064, USA
    J Comput Biol 11:867-86. 2004
    ..Our computational framework could be applied in these, and similar cases, to improve performance...
  5. ncbi Into the heart of darkness: large-scale clustering of human non-coding DNA
    Gill Bejerano
    Center for Biomolecular Science and Engineering, Baskin School of Engineering University of California in Santa Cruz, Santa Cruz, CA 95064, USA
    Bioinformatics 20:i40-8. 2004
    ..It is currently believed that the human genome contains about twice as much non-coding functional regions as it does protein-coding genes, yet our understanding of these regions is very limited...
  6. ncbi Ultraconserved elements in the human genome
    Gill Bejerano
    Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Science 304:1321-5. 2004
    ....
  7. pmc Identification and classification of conserved RNA secondary structures in the human genome
    Jakob Skou Pedersen
    Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California, USA
    PLoS Comput Biol 2:e33. 2006
    ....
  8. pmc Forces shaping the fastest evolving regions in the human genome
    Katherine S Pollard
    Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
    PLoS Genet 2:e168. 2006
    ..A combination of evolutionary forces has contributed to accelerated evolution of the fastest evolving elements in the human genome...
  9. pmc Endangered species hold clues to human evolution
    Craig B Lowe
    Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA
    J Hered 101:437-47. 2010
    ....
  10. pmc Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish
    Michael Hiller
    Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA, Department of Computer Science, Stanford University, Stanford, CA 94305, USA and Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
    Nucleic Acids Res 41:e151. 2013
    ..stanford.edu) are highly enriched in known enhancers and extend existing experimental (ChIP-Seq) sets. The same framework can now be applied to the isolated genomes of frog, amphioxus, Caenorhabditis elegans and many others. ..
  11. ncbi Human genome ultraconserved elements are ultraselected
    Sol Katzman
    Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA
    Science 317:915. 2007
    ..However, analysis of the derived allele frequency spectrum shows that these regions are in fact under negative selection that is much stronger than that in protein coding genes...
  12. ncbi Comparative genomic analysis using the UCSC genome browser
    Donna Karolchik
    UCSC Genome Bioinformatics Group, Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA, USA
    Methods Mol Biol 395:17-34. 2007
    ..Here, we describe a procedure for examining a genomic region of interest in the Genome Browser, analyzing characteristics of the region, filtering the data, and downloading data sets for further study...
  13. ncbi Branch and bound computation of exact p-values
    Gill Bejerano
    Center for Biomolecular Science and Engineering, School of Engineering, 1156 High Street, University of California, Santa Cruz, CA 95064, USA
    Bioinformatics 22:2158-9. 2006
    ..This code base can also be adapted to compute exact p-values of other statistics in diverse sampling scenarios. AVAILABILITY: Freely available at http://www.soe.ucsc.edu/~jill/src/...
  14. pmc Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    Adam Siepel
    Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, California 95064, USA
    Genome Res 15:1034-50. 2005
    ..Noncoding HCEs also show strong statistical evidence of an enrichment for RNA secondary structure...
  15. pmc Thousands of human mobile element fragments undergo strong purifying selection near developmental genes
    Craig B Lowe
    Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA
    Proc Natl Acad Sci U S A 104:8005-10. 2007
    ..5% of all constrained nonexonic elements unique to mammals, suggesting that mobile elements may have played a larger role than previously recognized in shaping and specializing the landscape of gene regulation during mammalian evolution...
  16. pmc Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing
    Evgeny A Glazov
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
    Genome Res 15:800-8. 2005
    ....