Affiliation: University of California
- An evaluation of tyramide signal amplification and archived fixed and frozen tissue in microarray gene expression analysisStanislav 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...
- Volume measures for linkage disequilibriumYuguo 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...
- Bayesian sparse hidden components analysis for transcription regulation networksChiara 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...
- Vocabulon: a dictionary model approach for reconstruction and localization of transcription factor binding sitesChiara 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...
- False discovery rate in linkage and association genome screens for complex disordersChiara 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...
- Homozygosity and linkage disequilibriumChiara 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...
- Thresholding rules for recovering a sparse signal from microarray experimentsChiara 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...
- A generalized framework for network component analysisRiccardo 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....
- Linkage disequilibrium and haplotype homozygosity in population samples genotyped at a high marker densityHui Wang
Department of Statistics, UCLA, Los Angeles, CA 90095, USA
Hum Hered 62:175-89. 2006..CONCLUSIONS: It is crucial to take into account LD patterns when interpreting long stretches of homozygous markers...
- Results of a SNP genome screen in a large Costa Rican pedigree segregating for severe bipolar disorderSusan 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...
- Tag SNPs chosen from HapMap perform well in several population isolatesSusan Service
Center for Neurobehavioral Genetics, University of California, Los Angeles, California 90095 1761, USA
Genet Epidemiol 31:189-94. 2007....
- A genome-wide linkage scan of familial benign recurrent vertigo: linkage to 22q12 with evidence of heterogeneityHane 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...
- A dictionary model for haplotyping, genotype calling, and association testingKristin 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...
- Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysisKaty 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...
- Global analysis of gene expression in neural progenitors reveals specific cell-cycle, signaling, and metabolic networksStanislav 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...
- Co-expression pattern from DNA microarray experiments as a tool for operon predictionChiara 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...
- Reconstructing ancestral haplotypes with a dictionary modelKristin 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...
- Avoiding false discoveries in association studiesChiara 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...
- Genome-wide association analysis of metabolic traits in a birth cohort from a founder populationChiara 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...
- Network component analysis: reconstruction of regulatory signals in biological systemsJames 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....
- Overrepresentation of rare variants in a specific ethnic group may confuse interpretation of association analysesDianne 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....
- A novel mutation in KCNA1 causes episodic ataxia without myokymiaHane 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...
- The use of pedigree, sib-pair and association studies of common diseases for genetic mapping and epidemiologyNelson 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...
- Clinical features and associated syndromes of mal de debarquementYoon 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)...
- Magnitude and distribution of linkage disequilibrium in population isolates and implications for genome-wide association studiesSusan 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...
- Reconstructing DNA copy number by joint segmentation of multiple sequencesZhongyang 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...
- Inferring protein domain interactions from databases of interacting proteinsRobert 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...
- Guidelines for association studies in Human Molecular GeneticsNelson 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
- The human phenome projectNelson 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
- Human genetics: variants in common diseasesNelson B Freimer
Nature 445:828-30. 2007
- Convergent linkage evidence from two Latin-American population isolates supports the presence of a susceptibility locus for bipolar disorder in 5q31-34Ibi 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...
- Large recurrent microdeletions associated with schizophreniaHreinn 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...
- Recurrent CNVs disrupt three candidate genes in schizophrenia patientsTerry 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...