Chiara Sabatti

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc An evaluation of tyramide signal amplification and archived fixed and frozen tissue in microarray gene expression analysis
    Stanislav L Karsten
    Department of Neurology, Program in Neurogenetics, UCLA School of Medicine, 710 Westwood Plaza, Los Angeles, CA 90095 1769, USA
    Nucleic Acids Res 30:E4. 2002
  2. pmc Volume measures for linkage disequilibrium
    Yuguo Chen
    Department of Statistics, University of Illinois at Urbana Champaign, Champaign IL 61820, USA
    BMC Genet 7:54. 2006
  3. ncbi request reprint Vocabulon: a dictionary model approach for reconstruction and localization of transcription factor binding sites
    Chiara Sabatti
    Department of Human Genetics, UCLA Los Angeles, CA 90095 7088, USA
    Bioinformatics 21:922-31. 2005
  4. ncbi request reprint Thresholding rules for recovering a sparse signal from microarray experiments
    Chiara Sabatti
    Department of Human Genetics, UCLA, 695 Charles Young Dr South, Los Angeles, CA 90095 7088, USA
    Math Biosci 176:17-34. 2002
  5. pmc Homozygosity and linkage disequilibrium
    Chiara Sabatti
    Department of Human Genetics and Statistics, University of California, Los Angeles, California 90095 7088, USA
    Genetics 160:1707-19. 2002
  6. ncbi request reprint Bayesian sparse hidden components analysis for transcription regulation networks
    Chiara Sabatti
    Department of Human Genetics, UCLA, Los Angeles, CA 90095 7088, USA
    Bioinformatics 22:739-46. 2006
  7. pmc False discovery rate in linkage and association genome screens for complex disorders
    Chiara Sabatti
    Department of Human Genetics and Statistics, University of California, Los Angeles 90095 7088, USA
    Genetics 164:829-33. 2003
  8. ncbi request reprint Linkage disequilibrium and haplotype homozygosity in population samples genotyped at a high marker density
    Hui Wang
    Department of Statistics, UCLA, Los Angeles, CA 90095, USA
    Hum Hered 62:175-89. 2006
  9. ncbi request reprint A generalized framework for network component analysis
    Riccardo Boscolo
    Electrical Engineering Department, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
    IEEE/ACM Trans Comput Biol Bioinform 2:289-301. 2005
  10. ncbi request reprint Results of a SNP genome screen in a large Costa Rican pedigree segregating for severe bipolar disorder
    Susan Service
    Center for Neurobehavioral Genetics, University of California, Los Angeles, 90095 1761, USA
    Am J Med Genet B Neuropsychiatr Genet 141:367-73. 2006

Detail Information

Publications33

  1. pmc An evaluation of tyramide signal amplification and archived fixed and frozen tissue in microarray gene expression analysis
    Stanislav L Karsten
    Department of Neurology, Program in Neurogenetics, UCLA School of Medicine, 710 Westwood Plaza, Los Angeles, CA 90095 1769, USA
    Nucleic Acids Res 30:E4. 2002
    ..Consistent results are more easily obtainable using ethanol-fixed tissues, whereas formalin-fixed tissue does not typically provide a useful substrate for cDNA synthesis and labeling...
  2. pmc Volume measures for linkage disequilibrium
    Yuguo Chen
    Department of Statistics, University of Illinois at Urbana Champaign, Champaign IL 61820, USA
    BMC Genet 7:54. 2006
    ..The potential of volume measures in this context has been noted before, but their use has been hampered by computational challenges...
  3. ncbi request reprint Vocabulon: a dictionary model approach for reconstruction and localization of transcription factor binding sites
    Chiara Sabatti
    Department of Human Genetics, UCLA Los Angeles, CA 90095 7088, USA
    Bioinformatics 21:922-31. 2005
    ..We illustrate these properties with examples in E.coli. The results of gene expression arrays are used both to guide the search and corroborate it...
  4. ncbi request reprint Thresholding rules for recovering a sparse signal from microarray experiments
    Chiara Sabatti
    Department of Human Genetics, UCLA, 695 Charles Young Dr South, Los Angeles, CA 90095 7088, USA
    Math Biosci 176:17-34. 2002
    ..Given the amount of information actually available, the thresholding rule described provides a reasonable estimator for the change in expression of any gene in two compared cell lines...
  5. pmc Homozygosity and linkage disequilibrium
    Chiara Sabatti
    Department of Human Genetics and Statistics, University of California, Los Angeles, California 90095 7088, USA
    Genetics 160:1707-19. 2002
    ..They are particularly advantageous to measure linkage disequilibrium between highly polymorphic markers...
  6. ncbi request reprint Bayesian sparse hidden components analysis for transcription regulation networks
    Chiara Sabatti
    Department of Human Genetics, UCLA, Los Angeles, CA 90095 7088, USA
    Bioinformatics 22:739-46. 2006
    ..However, this goal can only be achieved if all information sources are used in concert...
  7. pmc False discovery rate in linkage and association genome screens for complex disorders
    Chiara Sabatti
    Department of Human Genetics and Statistics, University of California, Los Angeles 90095 7088, USA
    Genetics 164:829-33. 2003
    ..This adaptive multiple comparison procedure may offer an important tool for mapping susceptibility genes for complex diseases...
  8. ncbi request reprint Linkage disequilibrium and haplotype homozygosity in population samples genotyped at a high marker density
    Hui Wang
    Department of Statistics, UCLA, Los Angeles, CA 90095, USA
    Hum Hered 62:175-89. 2006
    ..Analyze the information contained in homozygous haplotypes detected with high density genotyping...
  9. ncbi request reprint A generalized framework for network component analysis
    Riccardo Boscolo
    Electrical Engineering Department, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
    IEEE/ACM Trans Comput Biol Bioinform 2:289-301. 2005
    ....
  10. ncbi request reprint Results of a SNP genome screen in a large Costa Rican pedigree segregating for severe bipolar disorder
    Susan Service
    Center for Neurobehavioral Genetics, University of California, Los Angeles, 90095 1761, USA
    Am J Med Genet B Neuropsychiatr Genet 141:367-73. 2006
    ..The difficulties of analyzing genome wide SNP data for complex disorders in large, potentially informative, kindreds are discussed...
  11. ncbi request reprint Tag SNPs chosen from HapMap perform well in several population isolates
    Susan Service
    Center for Neurobehavioral Genetics, University of California, Los Angeles, California 90095 1761, USA
    Genet Epidemiol 31:189-94. 2007
    ....
  12. ncbi request reprint A genome-wide linkage scan of familial benign recurrent vertigo: linkage to 22q12 with evidence of heterogeneity
    Hane Lee
    Department of Human Genetics, University of California, Los Angeles, 90095, USA
    Hum Mol Genet 15:251-8. 2006
    ..Additional family and population-based linkage and association studies will be needed to determine the causative alleles...
  13. pmc Reconstructing DNA copy number by joint segmentation of multiple sequences
    Zhongyang Zhang
    Department of Statistics, University of California, Los Angeles, CA, USA
    BMC Bioinformatics 13:205. 2012
    ..This problem encompasses the cases of copy number polymorphisms, related samples, technical replicates, and cancerous sub-populations from the same individual...
  14. ncbi request reprint A dictionary model for haplotyping, genotype calling, and association testing
    Kristin L Ayers
    Department of Biomathematics, UCLA School of Medicine, Los Angeles, CA 90095 1766, USA
    Genet Epidemiol 31:672-83. 2007
    ..These imputed counts can serve as genetic predictors in association studies, as we illustrate by examples on cystic fibrosis, Friedreich's ataxia, and angiotensin-I converting enzyme levels...
  15. ncbi request reprint Global analysis of gene expression in neural progenitors reveals specific cell-cycle, signaling, and metabolic networks
    Stanislav L Karsten
    Department of Neurology, UCLA School of Medicine, 710 Westwood Plaza, Los Angeles, CA 90095 1769, USA
    Dev Biol 261:165-82. 2003
    ..We propose a putative network of gene expression linking cell cycle control to cell fate pathways, providing a framework for further investigations of neural stem cell proliferation and differentiation...
  16. pmc Co-expression pattern from DNA microarray experiments as a tool for operon prediction
    Chiara Sabatti
    Department of Human Genetics and Statistics and Department of Chemical Engineering, University of California, Los Angeles, CA 90095, USA
    Nucleic Acids Res 30:2886-93. 2002
    ..These results provide a rationale for conducting expression studies comparing conditions that cause global changes in gene expression...
  17. pmc Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis
    Katy C Kao
    Department of Chemical Engineering, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 101:641-6. 2004
    ..We used Escherichia coli carbon source transition from glucose to acetate as a model system. Key results from this analysis were either consistent with physiology or verified by using independent measurements...
  18. ncbi request reprint Avoiding false discoveries in association studies
    Chiara Sabatti
    Department of Human Genetics, UCLA School of Medicine, Los Angeles, CA, USA
    Methods Mol Biol 376:195-211. 2007
    ..We then examine the underlying similarities and differences between linkage and association studies and document some of the most recent methodological developments for association mapping...
  19. ncbi request reprint Reconstructing ancestral haplotypes with a dictionary model
    Kristin L Ayers
    Department of Biomathematics, University of California, Los Angeles, CA 90095 1766, USA
    J Comput Biol 13:767-85. 2006
    ..Application of the model to simulated data gives encouraging results. In a real dataset, we are able to reconstruct a parsimonious dictionary that captures patterns of linkage disequilibrium well...
  20. pmc Network component analysis: reconstruction of regulatory signals in biological systems
    James C Liao
    Departments of Chemical Engineering, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 100:15522-7. 2003
    ....
  21. pmc Genome-wide association analysis of metabolic traits in a birth cohort from a founder population
    Chiara Sabatti
    Department of Human Genetics and Los Angeles, Los Angeles, California 90095, USA
    Nat Genet 41:35-46. 2009
    ..The association observed between low-density lipoprotein and an infrequent variant in AR suggests the potential of such a cohort for identifying associations with both common, low-impact and rarer, high-impact quantitative trait loci...
  22. ncbi request reprint Overrepresentation of rare variants in a specific ethnic group may confuse interpretation of association analyses
    Dianne Keen-Kim
    Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
    Hum Mol Genet 15:3324-8. 2006
    ....
  23. ncbi request reprint The use of pedigree, sib-pair and association studies of common diseases for genetic mapping and epidemiology
    Nelson Freimer
    Center for Neurobehavioral Genetics, Neuropsychiatric Institute, Los Angeles, CA 90095, USA
    Nat Genet 36:1045-51. 2004
    ..Recent studies suggest that the technology and statistical methodology will soon be available to make well-powered studies feasible using any of these approaches...
  24. ncbi request reprint A novel mutation in KCNA1 causes episodic ataxia without myokymia
    Hane Lee
    Department of Human Genetics, University of California, Los Angeles, California, USA
    Hum Mutat 24:536. 2004
    ..This mutation leads to a distinct clinical phenotype without myokymia broadening the scope of clinical characteristics of EA1 and highlighting the heterogeneity of phenotypic effects from distinct missense mutations...
  25. pmc Clinical features and associated syndromes of mal de debarquement
    Yoon Hee Cha
    Dept of Neurology, University of California, 710 Westwood Plaza, 951769, Los Angeles, CA 90095, USA
    J Neurol 255:1038-44. 2008
    ..To investigate the clinical features and natural history of mal de debarquement (MdD)...
  26. ncbi request reprint Magnitude and distribution of linkage disequilibrium in population isolates and implications for genome-wide association studies
    Susan Service
    Center for Neurobehavioral Genetics, University of California, Los Angeles, California 90095, USA
    Nat Genet 38:556-60. 2006
    ..Young isolates known to have had relatively few founders show particularly extensive LD with very few holes; these populations offer substantial advantages for genome-wide association mapping...
  27. pmc Inferring protein domain interactions from databases of interacting proteins
    Robert Riley
    Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, CA 90095, USA
    Genome Biol 6:R89. 2005
    ..DPEA may prove useful in guiding experiment-based discovery of previously unrecognized domain interactions...
  28. ncbi request reprint Guidelines for association studies in Human Molecular Genetics
    Nelson B Freimer
    Department of Psychiatry, UCLA Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Los Angeles, CA 90095 1761, USA
    Hum Mol Genet 14:2481-3. 2005
  29. ncbi request reprint The human phenome project
    Nelson Freimer
    Center for Neurobehavioral Genetics, Neuropsychiatric Institute, Gonda Building Room 3506, 695 Charles E Young Drive South, Los Angeles, California 90095, USA
    Nat Genet 34:15-21. 2003
  30. ncbi request reprint Human genetics: variants in common diseases
    Nelson B Freimer
    Nature 445:828-30. 2007
  31. pmc Large recurrent microdeletions associated with schizophrenia
    Hreinn Stefansson
    CNS Division, deCODE Genetics, Sturlugata 8, IS 101 Reykjavik, Iceland
    Nature 455:232-6. 2008
    ..CNV analysis may also point the way to the identification of additional and more prevalent risk variants in genes and pathways involved in schizophrenia...
  32. pmc Recurrent CNVs disrupt three candidate genes in schizophrenia patients
    Terry Vrijenhoek
    Department of Human Genetics, Radboud University Nijmegen Medical Centre, 6500 HB Nijmegen, The Netherlands
    Am J Hum Genet 83:504-10. 2008
    ..Our study supports a role for rare CNVs in schizophrenia susceptibility and identifies at least three candidate genes for this complex disorder...
  33. ncbi request reprint Convergent linkage evidence from two Latin-American population isolates supports the presence of a susceptibility locus for bipolar disorder in 5q31-34
    Ibi Herzberg
    Galton Laboratory, Department of Biology, University College London, Wolfson House, 4 Stephenson Way, London NW1 2HE, UK
    Hum Mol Genet 15:3146-53. 2006
    ..00004). Interestingly, this region has been implicated in several previous genetic studies of schizophrenia and psychosis, including disease association with variants of the enthoprotin and gamma-aminobutyric acid receptor genes...