Gabriela G Loots

Summary

Affiliation: Lawrence Berkeley National Laboratory
Country: USA

Publications

  1. pmc rVista for comparative sequence-based discovery of functional transcription factor binding sites
    Gabriela G Loots
    Genome Sciences Department, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Genome Res 12:832-9. 2002
  2. pmc CREME: Cis-Regulatory Module Explorer for the human genome
    Roded Sharan
    International Computer Science Institute, 1947 Center Street, Berkeley, CA 94704, USA
    Nucleic Acids Res 32:W253-6. 2004
  3. ncbi request reprint SNPs in putative regulatory regions identified by human mouse comparative sequencing and transcription factor binding site data
    Poulabi Banerjee
    Genome Sciences Department, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Mamm Genome 13:554-7. 2002
  4. pmc Mulan: multiple-sequence alignment to predict functional elements in genomic sequences
    Gabriela G Loots
    Lawrence Berkeley National Laboratory, USA
    Methods Mol Biol 395:237-54. 2007
  5. pmc Predicting tissue-specific enhancers in the human genome
    Len A Pennacchio
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Genome Res 17:201-11. 2007
  6. ncbi request reprint Strategies for characterising cis-regulatory elements in Xenopus
    Mustafa K Khokha
    Department of Molecular and Cell Biology at the University of California, Berkeley, USA
    Brief Funct Genomic Proteomic 4:58-68. 2005
  7. pmc Genomic deletion of a long-range bone enhancer misregulates sclerostin in Van Buchem disease
    Gabriela G Loots
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Genome Res 15:928-35. 2005
  8. pmc Dcode.org anthology of comparative genomic tools
    Gabriela G Loots
    Genome Biology Division, Lawrence Livermore National Laboratory, 7000 East Avenue, L 441 Livermore, CA 94550, USA
    Nucleic Acids Res 33:W56-64. 2005
  9. pmc Mulan: multiple-sequence local alignment and visualization for studying function and evolution
    Ivan Ovcharenko
    Energy, Environment, Biology and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
    Genome Res 15:184-94. 2005
  10. pmc ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes
    Ivan Ovcharenko
    Genome Biology Division and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
    Nucleic Acids Res 32:W280-6. 2004

Collaborators

Detail Information

Publications16

  1. pmc rVista for comparative sequence-based discovery of functional transcription factor binding sites
    Gabriela G Loots
    Genome Sciences Department, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Genome Res 12:832-9. 2002
    ....
  2. pmc CREME: Cis-Regulatory Module Explorer for the human genome
    Roded Sharan
    International Computer Science Institute, 1947 Center Street, Berkeley, CA 94704, USA
    Nucleic Acids Res 32:W253-6. 2004
    ..The identified cis-regulatory modules are statistically scored and significant combinations are reported and graphically visualized. Our web server is available at http://creme.dcode.org...
  3. ncbi request reprint SNPs in putative regulatory regions identified by human mouse comparative sequencing and transcription factor binding site data
    Poulabi Banerjee
    Genome Sciences Department, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Mamm Genome 13:554-7. 2002
  4. pmc Mulan: multiple-sequence alignment to predict functional elements in genomic sequences
    Gabriela G Loots
    Lawrence Berkeley National Laboratory, USA
    Methods Mol Biol 395:237-54. 2007
    ....
  5. pmc Predicting tissue-specific enhancers in the human genome
    Len A Pennacchio
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Genome Res 17:201-11. 2007
    ..These results indicate the power of combining complementary genomic data sets as an initial computational foray into a global view of tissue-specific gene regulation in vertebrates...
  6. ncbi request reprint Strategies for characterising cis-regulatory elements in Xenopus
    Mustafa K Khokha
    Department of Molecular and Cell Biology at the University of California, Berkeley, USA
    Brief Funct Genomic Proteomic 4:58-68. 2005
    ..In particular, Xenopus tropicalis may become particularly powerful for elucidating regulatory networks, chiefly because it is amenable to genetic manipulations, and its genome is being sequenced...
  7. pmc Genomic deletion of a long-range bone enhancer misregulates sclerostin in Van Buchem disease
    Gabriela G Loots
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Genome Res 15:928-35. 2005
    ..5 (E14.5) mouse embryo, and discovered a novel function for sclerostin during limb development. Our approach represents a framework for characterizing distant regulatory elements associated with abnormal human phenotypes...
  8. pmc Dcode.org anthology of comparative genomic tools
    Gabriela G Loots
    Genome Biology Division, Lawrence Livermore National Laboratory, 7000 East Avenue, L 441 Livermore, CA 94550, USA
    Nucleic Acids Res 33:W56-64. 2005
    ..Here, we briefly describe each one of these tools and provide specific examples on their practical applications. All the tools are publicly available at the http://www.dcode.org/ website...
  9. pmc Mulan: multiple-sequence local alignment and visualization for studying function and evolution
    Ivan Ovcharenko
    Energy, Environment, Biology and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
    Genome Res 15:184-94. 2005
    ..Source code for the aligners and the aligner-evaluation software can be freely downloaded from http://www.bx.psu.edu/miller_lab/...
  10. pmc ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes
    Ivan Ovcharenko
    Genome Biology Division and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
    Nucleic Acids Res 32:W280-6. 2004
    ..The interconnection of the ECR Browser with other DNA sequence analysis tools creates a unique portal for studying and exploring vertebrate genomes...
  11. pmc rVISTA 2.0: evolutionary analysis of transcription factor binding sites
    Gabriela G Loots
    Genome Biology Division and EEBI Computing Division, Lawrence Livermore National Laboratory, 7000 East Avenue, L 441, Livermore, CA 94550, USA
    Nucleic Acids Res 32:W217-21. 2004
    ..The rVISTA tool is publicly available at http://rvista.dcode.org/...
  12. ncbi request reprint Interpreting mammalian evolution using Fugu genome comparisons
    Ivan Ovcharenko
    Genome Biology Division, Lawrence Livermore National Laboratory, 7000 East Avenue, L 441, Livermore, CA 94550, USA
    Genomics 84:890-5. 2004
    ..This newly defined threshold identifies 90% of all human/Fugu noncoding ECRs without the assistance of human-Fugu genome alignments and provides a very efficient filter for identifying functional human/mouse ECRs...
  13. pmc Array2BIO: from microarray expression data to functional annotation of co-regulated genes
    Gabriela G Loots
    Lawrence Livermore National Laboratory, Livermore, California 94550, USA
    BMC Bioinformatics 7:307. 2006
    ..To provide an integrative, easy-to-use and automated toolkit for the analysis of Affymetrix microarray expression data we have developed Array2BIO, an application that couples several analytical methods into a single web based utility...
  14. pmc eShadow: a tool for comparing closely related sequences
    Ivan Ovcharenko
    Energy, Environment, Biology and Institutional Computing EEBI, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
    Genome Res 14:1191-8. 2004
    ..Here, we describe the eShadow comparative tool and its potential uses for analyzing both multiple nucleotide and protein alignments to predict putative functional elements...
  15. pmc zPicture: dynamic alignment and visualization tool for analyzing conservation profiles
    Ivan Ovcharenko
    Energy, Environment, Biology and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
    Genome Res 14:472-7. 2004
    ..Finally, we describe how this tool can be efficiently applied to the analysis of nonvertebrate genomes, including those of microbial organisms...
  16. pmc Genomic identification of regulatory elements by evolutionary sequence comparison and functional analysis
    Gabriela G Loots
    Biosciences and Biotechnology Division, Chemistry, Materials and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
    Adv Genet 61:269-93. 2008
    ....