Laura L Elnitski

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Genomic features defining exonic variants that modulate splicing
    Adam Woolfe
    Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland 20892, USA
    Genome Biol 11:R20. 2010
  2. pmc Word-based characterization of promoters involved in human DNA repair pathways
    Jens Lichtenberg
    Bioinformatics Laboratory, School of Electrical Engineering and Computer Science, Ohio University, Athens, Ohio, USA
    BMC Genomics 10:S18. 2009
  3. pmc Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and identification of species-specific transcripts
    Helen Piontkivska
    2Department of BiologicalSciences, Kent State University, Kent, Ohio 44242, USA
    BMC Genomics 10:189. 2009
  4. pmc WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures
    Jens Lichtenberg
    Bioinformatics Laboratory, School of EECS, Ohio University, Athens, Ohio 45701, USA
    BMC Bioinformatics 11:S6. 2010
  5. pmc Comparative analyses of bidirectional promoters in vertebrates
    Mary Qu Yang
    Genome Technology Branch, NHGRI, NIH, MD, USA
    BMC Bioinformatics 9:S9. 2008
  6. ncbi request reprint Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques
    Laura Elnitski
    Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland 20878, USA
    Genome Res 16:1455-64. 2006
  7. pmc Tissue-specific and ubiquitous expression patterns from alternative promoters of human genes
    Edwin Jacox
    National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland, United States of America
    PLoS ONE 5:e12274. 2010
  8. pmc Prediction-based approaches to characterize bidirectional promoters in the mammalian genome
    Mary Qu Yang
    National Human Genome Research Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD 20892, USA
    BMC Genomics 9:S2. 2008
  9. pmc Diversity of core promoter elements comprising human bidirectional promoters
    Mary Qu Yang
    National Human Genome Research Institute, National Institutes Health, Rockville, MD 20852, USA
    BMC Genomics 9:S3. 2008
  10. pmc The ENCODEdb portal: simplified access to ENCODE Consortium data
    Laura L Elnitski
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 17:954-9. 2007

Collaborators

Detail Information

Publications15

  1. pmc Genomic features defining exonic variants that modulate splicing
    Adam Woolfe
    Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland 20892, USA
    Genome Biol 11:R20. 2010
    ..In addition, little is known about which computational prediction approaches, such as those involving exonic splicing enhancers and exonic splicing silencers, are most informative...
  2. pmc Word-based characterization of promoters involved in human DNA repair pathways
    Jens Lichtenberg
    Bioinformatics Laboratory, School of Electrical Engineering and Computer Science, Ohio University, Athens, Ohio, USA
    BMC Genomics 10:S18. 2009
    ....
  3. pmc Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and identification of species-specific transcripts
    Helen Piontkivska
    2Department of BiologicalSciences, Kent State University, Kent, Ohio 44242, USA
    BMC Genomics 10:189. 2009
    ....
  4. pmc WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures
    Jens Lichtenberg
    Bioinformatics Laboratory, School of EECS, Ohio University, Athens, Ohio 45701, USA
    BMC Bioinformatics 11:S6. 2010
    ..Although a number of methods have been developed for motif discovery, most of them lack the scalability needed to analyze large genomic data sets...
  5. pmc Comparative analyses of bidirectional promoters in vertebrates
    Mary Qu Yang
    Genome Technology Branch, NHGRI, NIH, MD, USA
    BMC Bioinformatics 9:S9. 2008
    ..In this report we utilize orthology assignments for pairs of genes co-regulated by bidirectional promoters to map the ancestral history of the promoter regions...
  6. ncbi request reprint Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques
    Laura Elnitski
    Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland 20878, USA
    Genome Res 16:1455-64. 2006
    ..A variety of techniques useful for localized- and high-throughput analyses are discussed here, with emphasis on aspects of data generation and verification...
  7. pmc Tissue-specific and ubiquitous expression patterns from alternative promoters of human genes
    Edwin Jacox
    National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland, United States of America
    PLoS ONE 5:e12274. 2010
    ..We show that annotation of alternative promoters regulating expression of transcripts with distinct first exons enables a novel methodology to quantify expression levels and tissue specificity of mRNA isoforms...
  8. pmc Prediction-based approaches to characterize bidirectional promoters in the mammalian genome
    Mary Qu Yang
    National Human Genome Research Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD 20892, USA
    BMC Genomics 9:S2. 2008
    ..We proposed that knowledge gleaned from those methods could be further refined using a multiple class predictor to separate classes of promoter elements from enhancers or nonfunctional DNA...
  9. pmc Diversity of core promoter elements comprising human bidirectional promoters
    Mary Qu Yang
    National Human Genome Research Institute, National Institutes Health, Rockville, MD 20852, USA
    BMC Genomics 9:S3. 2008
    ..To define the core promoter elements of bidirectional promoters in human, we mapped motifs for TATA, INR, BRE, DPE, INR, as well as CpG-islands...
  10. pmc The ENCODEdb portal: simplified access to ENCODE Consortium data
    Laura L Elnitski
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 17:954-9. 2007
    ..The ENCODEdb portal is freely accessible at http://research.nhgri.nih.gov/ENCODEdb...
  11. pmc Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes
    Mary Q Yang
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland, United States of America
    PLoS Comput Biol 3:e72. 2007
    ..Interpreting the regulation of genes involved in co-expression networks, especially those involved in cancer, will be an important step toward defining molecular events that may contribute to disease...
  12. ncbi request reprint Computational prediction of cis-regulatory modules from multispecies alignments using Galaxy, Table Browser, and GALA
    Laura Elnitski
    Genome Technology Branch, National Institutes of Health, Rockville, MD, USA
    Methods Mol Biol 338:91-103. 2006
    ..Links to these servers can be accessed at http://www.bx.psu.edu/ and http://genome.ucsc.edu/...
  13. pmc Functional analysis of a novel cis-acting regulatory region within the human ankyrin gene (ANK-1) promoter
    Karina Laflamme
    National Institutes of Health, National Human Genome Research Institute, Genetics and Molecular Biology Branch, Bethesda, Maryland 20892, USA
    Mol Cell Biol 30:3493-502. 2010
    ..One sequence increased ANK-1 promoter function 5-fold, while randomly chosen sequences decreased ANK-1 promoter function. Our results demonstrate a novel functional motif in the ANK-1 promoter...
  14. pmc Detection and characterization of silencers and enhancer-blockers in the greater CFTR locus
    Hanna M Petrykowska
    Genome Technology Branch, National Human Genome Research Institute, NIH, Rockville, MD 20852, USA
    Genome Res 18:1238-46. 2008
    ..Overall, we identified 15 novel NREs, which contribute new insights into the prevalence and composition of sequences that negatively regulate gene expression...
  15. pmc Generation and comparative analysis of approximately 3.3 Mb of mouse genomic sequence orthologous to the region of human chromosome 7q11.23 implicated in Williams syndrome
    Udaya DeSilva
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 12:3-15. 2002
    ....