Gabriela Loots

Summary

Affiliation: Lawrence Livermore National Laboratory
Country: USA

Publications

  1. pmc Effect of age and cytoskeletal elements on the indentation-dependent mechanical properties of chondrocytes
    Nadeen O Chahine
    The Feinstein Institute for Medical Research, Hofstra North Shore LIJ School of Medicine, Manhasset, New York, United States of America
    PLoS ONE 8:e61651. 2013
  2. pmc Global gene expression analysis of murine limb development
    Leila Taher
    Computational Biology Branch, National Center for Biotechnology Information, Bethesda, Maryland, United States of America
    PLoS ONE 6:e28358. 2011
  3. pmc Interrogating transcriptional regulatory sequences in Tol2-mediated Xenopus transgenics
    Gabriela G Loots
    Biology and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California, United States of America
    PLoS ONE 8:e68548. 2013
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

Research Grants

  1. Deciphering Principles of Regulatory Genomics
    Gabriela G Loots; Fiscal Year: 2010
  2. Deciphering Principles of Regulatory Genomics
    Gabriela Loots; Fiscal Year: 2009
  3. Deciphering Principles of Regulatory Genomics
    Gabriela Loots; Fiscal Year: 2007
  4. MECHANISMS OF INHIBITING BONE FORMATION THROUGH ANTAGONISM
    Gabriela Loots; Fiscal Year: 2009
  5. MECHANISMS OF INHIBITING BONE FORMATION THROUGH ANTAGONISM
    Gabriela G Loots; Fiscal Year: 2010

Collaborators

Detail Information

Publications22

  1. pmc Effect of age and cytoskeletal elements on the indentation-dependent mechanical properties of chondrocytes
    Nadeen O Chahine
    The Feinstein Institute for Medical Research, Hofstra North Shore LIJ School of Medicine, Manhasset, New York, United States of America
    PLoS ONE 8:e61651. 2013
    ..This study improves our understanding of the mechanical properties of articular cartilage at the single cell level...
  2. pmc Global gene expression analysis of murine limb development
    Leila Taher
    Computational Biology Branch, National Center for Biotechnology Information, Bethesda, Maryland, United States of America
    PLoS ONE 6:e28358. 2011
    ..Here, we provide for the first time a comprehensive analysis of developmentally regulated genes during murine limb development, and provide some novel insights into the expression dynamics governing limb morphogenesis...
  3. pmc Interrogating transcriptional regulatory sequences in Tol2-mediated Xenopus transgenics
    Gabriela G Loots
    Biology and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California, United States of America
    PLoS ONE 8:e68548. 2013
    ....
  4. 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...
  5. 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...
  6. 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
    ....
  7. 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...
  8. 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
    ....
  9. 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...
  10. 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
    ....
  11. pmc Control of the SOST bone enhancer by PTH using MEF2 transcription factors
    Olivier Leupin
    Bone and Cartilage Unit, Musculoskeletal Disease Area, Novartis Institutes for BioMedical Research, Basel, Switzerland
    J Bone Miner Res 22:1957-67. 2007
    ..Expression of the osteocyte-derived bone formation inhibitor sclerostin in adult bone requires a distant enhancer. We show that MEF2 transcription factors control this enhancer and mediate inhibition of sclerostin expression by PTH...
  12. pmc Evolution and functional classification of vertebrate gene deserts
    Ivan Ovcharenko
    Energy, Environment, Biology, and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
    Genome Res 15:137-45. 2005
    ..Stable gene deserts resist chromosomal rearrangements and appear to harbor multiple distant regulatory elements physically linked to their neighboring genes, with the linearity of conservation invariant throughout vertebrate evolution...
  13. 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
  14. 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...
  15. 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...
  16. 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/...
  17. 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...
  18. 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...
  19. 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...
  20. 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/...
  21. ncbi request reprint Modifying yeast artificial chromosomes to generate Cre/LoxP and FLP/FRT site-specific deletions and inversions
    Gabriela G Loots
    Genome Biology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
    Methods Mol Biol 349:75-84. 2006
    ....
  22. 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...

Research Grants6

  1. Deciphering Principles of Regulatory Genomics
    Gabriela G Loots; Fiscal Year: 2010
    ..Finally, we will create a publicly available resource for sharing the generated computational methods and tools along with experimental data with the broad research community. ..
  2. Deciphering Principles of Regulatory Genomics
    Gabriela Loots; Fiscal Year: 2009
    ..Finally, we will create a publicly available resource for sharing the generated computational methods and tools along with experimental data with the broad research community. ..
  3. Deciphering Principles of Regulatory Genomics
    Gabriela Loots; Fiscal Year: 2007
    ..Finally, we will create a publicly available resource for sharing the generated computational methods and tools along with experimental data with the broad research community. ..
  4. MECHANISMS OF INHIBITING BONE FORMATION THROUGH ANTAGONISM
    Gabriela Loots; Fiscal Year: 2009
    ....
  5. MECHANISMS OF INHIBITING BONE FORMATION THROUGH ANTAGONISM
    Gabriela G Loots; Fiscal Year: 2010
    ....