Eleazar Eskin

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping
    Adam B Olshen
    Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
    BMC Genet 9:14. 2008
  2. ncbi request reprint A note on phasing long genomic regions using local haplotype predictions
    Eleazar Eskin
    Computer Science and Engineering, University of California, San Diego, USA
    J Bioinform Comput Biol 4:639-47. 2006
  3. pmc Genome-wide association mapping of blood cell traits in mice
    Richard C Davis
    Department of Medicine Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
    Mamm Genome 24:105-18. 2013
  4. pmc Effectively identifying eQTLs from multiple tissues by combining mixed model and meta-analytic approaches
    Jae Hoon Sul
    Computer Science Department, University of California, Los Angeles, California, USA
    PLoS Genet 9:e1003491. 2013
  5. pmc Genotyping common and rare variation using overlapping pool sequencing
    Dan He
    Department of Computer Science, University of California, Los Angeles, CA 90095, USA
    BMC Bioinformatics 12:S2. 2011
  6. pmc Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data
    Wen Yun Yang
    Department of Computer Science and Inter Departmental Program in Bioinformatics, University of California, Los Angeles, CA 90095, USA
    Bioinformatics 29:2245-52. 2013
  7. pmc Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice
    Brian W Parks
    Department of Medicine Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
    Cell Metab 17:141-52. 2013
  8. pmc Genome-wide association mapping with longitudinal data
    Nicholas A Furlotte
    Department of Computer Science, University of California, Los Angeles, California 90095 1596, USA
    Genet Epidemiol 36:463-71. 2012
  9. pmc Increasing power of groupwise association test with likelihood ratio test
    Jae Hoon Sul
    Department of Computer Science, University of California, Los Angeles, California, USA
    J Comput Biol 18:1611-24. 2011
  10. pmc Gene networks associated with conditional fear in mice identified using a systems genetics approach
    Christopher C Park
    Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
    BMC Syst Biol 5:43. 2011

Detail Information

Publications57

  1. pmc Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping
    Adam B Olshen
    Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
    BMC Genet 9:14. 2008
    ..435,632 SNPs overlapped and met annotation criteria in the two groups...
  2. ncbi request reprint A note on phasing long genomic regions using local haplotype predictions
    Eleazar Eskin
    Computer Science and Engineering, University of California, San Diego, USA
    J Bioinform Comput Biol 4:639-47. 2006
    ..in press; Marchini et al., in preparation). Our method is publicly available via a webserver at http://research.calit2.net/hap/...
  3. pmc Genome-wide association mapping of blood cell traits in mice
    Richard C Davis
    Department of Medicine Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
    Mamm Genome 24:105-18. 2013
    ..These results provide intermediate phenotypes and candidate loci for genetic studies of atherosclerosis and cancer as well as inflammatory and immune disorders in mice...
  4. pmc Effectively identifying eQTLs from multiple tissues by combining mixed model and meta-analytic approaches
    Jae Hoon Sul
    Computer Science Department, University of California, Los Angeles, California, USA
    PLoS Genet 9:e1003491. 2013
    ..Additionally, our method provides an interpretation framework that accurately predicts whether an eQTL has an effect in a particular tissue...
  5. pmc Genotyping common and rare variation using overlapping pool sequencing
    Dan He
    Department of Computer Science, University of California, Los Angeles, CA 90095, USA
    BMC Bioinformatics 12:S2. 2011
    ..These methods, however, are limited to the detection of rare variants...
  6. pmc Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data
    Wen Yun Yang
    Department of Computer Science and Inter Departmental Program in Bioinformatics, University of California, Los Angeles, CA 90095, USA
    Bioinformatics 29:2245-52. 2013
    ..However, this information is generally ignored in existing approaches for haplotype phasing and genotype-calling from short read data...
  7. pmc Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice
    Brian W Parks
    Department of Medicine Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
    Cell Metab 17:141-52. 2013
    ..We also show strong relationships between genotype and gut microbiota plasticity during HF/HS feeding and identify gut microbial phylotypes associated with obesity...
  8. pmc Genome-wide association mapping with longitudinal data
    Nicholas A Furlotte
    Department of Computer Science, University of California, Los Angeles, California 90095 1596, USA
    Genet Epidemiol 36:463-71. 2012
    ..The software implementing this method may be found at http://genetics.cs.ucla.edu/longGWAS/...
  9. pmc Increasing power of groupwise association test with likelihood ratio test
    Jae Hoon Sul
    Department of Computer Science, University of California, Los Angeles, California, USA
    J Comput Biol 18:1611-24. 2011
    ..With this optimization, we can efficiently compute an LRT statistic and its significance at a genome-wide level. The software for our method is publicly available at http://genetics.cs.ucla.edu/rarevariants ...
  10. pmc Gene networks associated with conditional fear in mice identified using a systems genetics approach
    Christopher C Park
    Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
    BMC Syst Biol 5:43. 2011
    ..To explore the genetic networks governing the biology of conditional fear, we used a systems genetics approach to analyze a hybrid mouse diversity panel (HMDP) with high mapping resolution...
  11. ncbi request reprint Incorporating homologues into sequence embeddings for protein analysis
    Eleazar Eskin
    Department of Computer Science, Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
    J Bioinform Comput Biol 5:717-38. 2007
    ..Finally, we show how the homology kernel can be used to incorporate information from homologous sequences in local sequence alignment...
  12. pmc Colocalization of GWAS and eQTL Signals Detects Target Genes
    Farhad Hormozdiari
    Department of Computer Science, University of California, Los Angeles, Los Angeles, CA 90095, USA
    Am J Hum Genet 99:1245-1260. 2016
    ..Using publicly available eQTL data on 45 different tissues, we demonstrate that eCAVIAR can prioritize likely relevant tissues and target genes for a set of glucose- and insulin-related trait loci...
  13. pmc Fast pairwise IBD association testing in genome-wide association studies
    Buhm Han
    Division of Genetics, Brigham and Women s Hospital and Division of Rheumatology, Brigham and Women s Hospital, Harvard Medical School, Boston, MA 02115, USA, Partners Center for Personalized Genetic Medicine, Boston, MA 02115, USA, Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA, Computer Science Department, University of California, Los Angeles, CA 90095, USA, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands, Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands and Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
    Bioinformatics 30:206-13. 2014
    ....
  14. pmc Improving the accuracy and efficiency of partitioning heritability into the contributions of genomic regions
    Emrah Kostem
    Department of Computer Science, University of California, Los Angeles, Los Angeles, CA 90095, USA
    Am J Hum Genet 92:558-64. 2013
    ..Using a data set from a genome-wide association study on human height, we demonstrate the utility of our method by estimating the heritability contributions of chromosomes and subchromosomal regions...
  15. pmc Increasing association mapping power and resolution in mouse genetic studies through the use of meta-analysis for structured populations
    Nicholas A Furlotte
    Department of Computer Science, Immunology and Molecular Genetic, University of California, Los Angeles, CA 90095, USA
    Genetics 191:959-67. 2012
    ..We also map HDL cholesterol and show a dramatic increase in the significance of a previously identified result...
  16. pmc Accurate discovery of expression quantitative trait loci under confounding from spurious and genuine regulatory hotspots
    Hyun Min Kang
    Department of Human Genetics, University of California, Los Angeles, California 90095, USA
    Genetics 180:1909-25. 2008
    ..The concordances of cis and trans associations have consistently increased between different replicates, tissues, and populations, demonstrating the higher accuracy of our method to identify real genetic effects...
  17. pmc A high-resolution association mapping panel for the dissection of complex traits in mice
    Brian J Bennett
    Department of Medicine Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
    Genome Res 20:281-90. 2010
    ..This resource, termed the Hybrid Mouse Diversity Panel, makes possible the integration of multiple data sets and should prove useful for systems-based approaches to complex traits and studies of gene-by-environment interactions...
  18. pmc Efficient control of population structure in model organism association mapping
    Hyun Min Kang
    Department of Computer Science, University of California, Los Angeles, California 90095 1596, USA
    Genetics 178:1709-23. 2008
    ..An R package implementation and webserver of our EMMA method are publicly available...
  19. pmc Imputing Phenotypes for Genome-wide Association Studies
    Farhad Hormozdiari
    Department of Computer Science, University of California, Los Angeles, Los Angeles, CA 90095, USA
    Am J Hum Genet 99:89-103. 2016
    ..We illustrate our approach by analyzing associated loci to triglycerides (TGs), body mass index (BMI), and systolic blood pressure (SBP) in the Northern Finland Birth Cohort dataset. ..
  20. pmc Genetic and environmental control of host-gut microbiota interactions
    Elin Org
    Department of Medicine Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
    Genome Res 25:1558-69. 2015
    ..In an effort to further understand host-microbiota interactions, we mapped loci controlling microbiota composition and prioritized candidate genes. Our publicly available data provide a resource for future studies. ..
  21. pmc Privacy preserving protocol for detecting genetic relatives using rare variants
    Farhad Hormozdiari
    Department of Computer Science, Bioinformatics IDP, Department of Mathematics and Department of Human Genetics, University of California, LA 90095, USA
    Bioinformatics 30:i204-11. 2014
    ..The main drawback of this approach is the requirement of sharing your genetic data with a trusted third party to perform the relatedness test...
  22. pmc Incorporating prior information into association studies
    Gregory Darnell
    Department of Computer Science, University of California, Los Angeles, CA 90095, USA
    Bioinformatics 28:i147-53. 2012
    ....
  23. pmc A model-based approach for analysis of spatial structure in genetic data
    Wen Yun Yang
    Interdepartmental Program in Bioinformatics, University of California, Los Angeles, California, USA
    Nat Genet 44:725-31. 2012
    ..These regions include SNPs in the well-characterized LCT region, as well as at loci including FOXP2, OCA2 and LRP1B...
  24. pmc Detecting the presence and absence of causal relationships between expression of yeast genes with very few samples
    Eun Yong Kang
    Department of Computer Science, University of California, Los Angeles, Los Angeles, California 90095, USA
    J Comput Biol 17:533-46. 2010
    ..In addition, our method can detect the absence of causal relationships and can distinguish between direct and indirect effects of variation on a gene expression level...
  25. pmc Increasing power of genome-wide association studies by collecting additional single-nucleotide polymorphisms
    Emrah Kostem
    Department of Computer Science, University of California, Los Angeles, California 90095 1596, USA
    Genetics 188:449-60. 2011
    ..Our method is publicly available at http://genetics.cs.ucla.edu/followupSNPs...
  26. pmc Inference and analysis of haplotypes from combined genotyping studies deposited in dbSNP
    Noah A Zaitlen
    Bioinformatics Program, University of California, San Diego, La Jolla, California 92093, USA
    Genome Res 15:1594-600. 2005
    ..Although HAP is slightly less accurate than PHASE, HAP is over 1000 times faster than PHASE, making it suitable for application to the entire set of genotypes in dbSNP...
  27. pmc Whole-genome analysis of Alu repeat elements reveals complex evolutionary history
    Alkes L Price
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093 0114, USA
    Genome Res 14:2245-52. 2004
    ..We apply a novel method to identify and statistically validate 213 Alu subfamilies. We build an evolutionary tree of these subfamilies and conclude that the history of Alu evolution is more complex than previous studies had indicated...
  28. ncbi request reprint Discovering tightly regulated and differentially expressed gene sets in whole genome expression data
    Chun Ye
    Bioinformatics Program, University of California San Diego, La Jolla, CA 92093 0404, USA
    Bioinformatics 23:e84-90. 2007
    ..We present a new method based on notions of tight regulation and differential expression to look for sets of genes which appear to be significantly affected by genetic variation...
  29. pmc Using network component analysis to dissect regulatory networks mediated by transcription factors in yeast
    Chun Ye
    Bioinformatics Program, University of California San Diego, La Jolla, California, United States of America
    PLoS Comput Biol 5:e1000311. 2009
    ..The software package implementing the algorithms discussed in this work is available as a MATLAB package upon request...
  30. pmc Multiple testing correction in linear mixed models
    Jong Wha J Joo
    Bioinformatics IDP, University of California, Los Angeles, CA, USA
    Genome Biol 17:62. 2016
    ..Recently, the linear mixed model (LMM) has become the standard practice in GWAS, addressing issues of population structure and insufficient power. However, none of the current multiple testing approaches are applicable to LMM...
  31. pmc Identification of causal genes for complex traits
    Farhad Hormozdiari
    Department of Computer Science, Inter Departmental Program in Bioinformatics, Department of Human Genetics and Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA 90095, USA
    Bioinformatics 31:i206-13. 2015
    ..Furthermore, these model organisms are highly structured and require correction for population structure to remove potential spurious associations...
  32. pmc Allele-specific expression and eQTL analysis in mouse adipose tissue
    Yehudit Hasin-Brumshtein
    Department of Medicine Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
    BMC Genomics 15:471. 2014
    ..Yet, due to technical limitations of expression microarrays, the vast majority of eQTL studies performed in the last decade used a genomic distance based definition as a surrogate for cis, therefore exploring local rather than cis-eQTLs...
  33. pmc Identifying genetic relatives without compromising privacy
    Dan He
    Department of Computer Science, University of California, Los Angeles, Los Angeles, California 90095, USA
    Genome Res 24:664-72. 2014
    ....
  34. pmc Hybrid mouse diversity panel: a panel of inbred mouse strains suitable for analysis of complex genetic traits
    Anatole Ghazalpour
    Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
    Mamm Genome 23:680-92. 2012
    ..In this essay, we review our experience with the HMDP, describe various ongoing projects, and discuss how the HMDP may fit into the larger picture of common diseases and different approaches...
  35. pmc Discrete profile comparison using information bottleneck
    Sean O'Rourke
    Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr, San Diego, CA 92093, USA
    BMC Bioinformatics 7:S8. 2006
    ..Discrete IB encoding can therefore expand the range of sequence problems to which profile information can be applied to include batch queries over large databases like SwissProt, which were previously computationally infeasible...
  36. pmc Increasing power in association studies by using linkage disequilibrium structure and molecular function as prior information
    Eleazar Eskin
    Department of Computer Science and Human Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
    Genome Res 18:653-60. 2008
    ....
  37. pmc Linkage effects and analysis of finite sample errors in the HapMap
    Noah Zaitlen
    Bioinformatics Program, University of California, San Diego, Calif, USA
    Hum Hered 68:73-86. 2009
    ..We show that a reasonable increase in the number of individuals, such as that proposed by the 1000 genomes project, greatly reduces the errors due to finite sample size for a large proportion of SNPs...
  38. pmc Mixed-model coexpression: calculating gene coexpression while accounting for expression heterogeneity
    Nicholas A Furlotte
    Department of Computer Science, University of California, Los Angeles, CA 90024, USA
    Bioinformatics 27:i288-94. 2011
    ..Therefore, a method that specifically aims to calculate gene coexpression between gene expression arrays, while accounting for confounding effects, is desirable...
  39. pmc Imputation aware meta-analysis of genome-wide association studies
    Noah Zaitlen
    Bioinformatics Program, University of California, San Diego, California, USA
    Genet Epidemiol 34:537-42. 2010
    ..Through simulation experiments, we show that our imputation aware meta-analysis approach outperforms or matches standard meta-analysis approaches...
  40. ncbi request reprint Searching genomes for noncoding RNA using FastR
    Shaojie Zhang
    Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0114, USA
    IEEE/ACM Trans Comput Biol Bioinform 2:366-79. 2005
    ..Our results point to a number of novel candidates for each of these subfamilies and include genomes that were not known to contain riboswitches...
  41. ncbi request reprint Further evidence for association of GRK3 to bipolar disorder suggests a second disease mutation
    Thomas B Barrett
    Department of Psychiatry, University of California at San Diego, San Diego VA Healthcare System, San Diego, California 92093 0603, USA
    Psychiatr Genet 17:315-22. 2007
    ..This SNP, however, was too rare (allele frequency 0.007) to explain the evidence for linkage...
  42. pmc An optimal weighted aggregated association test for identification of rare variants involved in common diseases
    Jae Hoon Sul
    Computer Science Department, University of California, Los Angeles, CA 90095, USA
    Genetics 188:181-8. 2011
    ..Our method is publicly available at http://genetics.cs.ucla.edu/rarevariants...
  43. doi request reprint Postassociation cleaning using linkage disequilibrium information
    Buhm Han
    Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA
    Genet Epidemiol 35:1-10. 2011
    ..This locus turns out to be in a region recently identified as significant by a meta-analysis performed after the WTCCC study was published...
  44. ncbi request reprint Catecholamine release-inhibitory peptide catestatin (chromogranin A(352-372)): naturally occurring amino acid variant Gly364Ser causes profound changes in human autonomic activity and alters risk for hypertension
    Fangwen Rao
    Department of Medicine, University of California at San Diego, USA
    Circulation 115:2271-81. 2007
    ..We identified a natural nonsynonymous variant of catestatin, Gly364Ser, that alters human autonomic function and blood pressure...
  45. ncbi request reprint Haplotype reconstruction from genotype data using Imperfect Phylogeny
    Eran Halperin
    CS Division, University of California Berkeley, Berkeley, CA 92093 0114, USA
    Bioinformatics 20:1842-9. 2004
    ..Our method is extremely efficient compared with previous methods such as PHASE and HAPLOTYPER. Its efficiency allows us to find the block partition of the haplotypes, to cope with missing data and to work with large datasets...
  46. ncbi request reprint Mismatch string kernels for discriminative protein classification
    Christina S Leslie
    Department of Computer Science, Columbia University, 1214 Amsterdam Avenue, Mail Code 0401, New York, NY 10027, USA
    Bioinformatics 20:467-76. 2004
    ..Discriminative supervised machine learning approaches provide good performance, but simplicity and computational efficiency of training and prediction are also important concerns...
  47. ncbi request reprint Efficient reconstruction of haplotype structure via perfect phylogeny
    Eleazar Eskin
    Computer Science Department, Columbia University, USA
    J Bioinform Comput Biol 1:1-20. 2003
    ..Our webserver (http://www.cs.columbia.edu/compbio/hap/) is publicly available for predicting haplotypes from genotype data and partitioning genotype data into blocks...
  48. ncbi request reprint Assessing computational tools for the discovery of transcription factor binding sites
    Martin Tompa
    Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, Washington 98195 2350, USA
    Nat Biotechnol 23:137-44. 2005
    ..The purpose of the current assessment is twofold: to provide some guidance to users regarding the accuracy of currently available tools in various settings, and to provide a benchmark of data sets for assessing future tools...
  49. ncbi request reprint Whole-genome patterns of common DNA variation in three human populations
    David A Hinds
    Perlegen Sciences Inc, 2021 Stierlin Court, Mountain View, CA 94043, USA
    Science 307:1072-9. 2005
    ..Our data provide a tool for exploring many questions that remain regarding the causal role of common human DNA variation in complex human traits and for investigating the nature of genetic variation within and between human populations...
  50. ncbi request reprint Polymorphisms and haplotypes of the regulator of G protein signaling-2 gene in normotensives and hypertensives
    Evan L Riddle
    Department of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA
    Hypertension 47:415-20. 2006
    ..Moreover, certain RGS2 variants that occur at greater frequency in hypertensive blacks may serve as ethnicity-specific genetic variants for this disease...
  51. pmc A comparison of phasing algorithms for trios and unrelated individuals
    Jonathan Marchini
    Department of Statistics, University of Oxford, Oxford OX1 3TG, United Kingdom
    Am J Hum Genet 78:437-50. 2006
    ..Finally, we evaluated methods of estimating the value of r(2) between a pair of SNPs and concluded that all methods estimated r(2) well when the estimated value was >or=0.8...
  52. pmc High-resolution mapping of gene expression using association in an outbred mouse stock
    Anatole Ghazalpour
    Department of Human Genetics, University of California Los Angeles, Los Angeles, California, United States of America
    PLoS Genet 4:e1000149. 2008
    ..Our results also highlight the importance of correcting for population structure in whole-genome association studies in the outbred stock...
  53. ncbi request reprint A sequence-based variation map of 8.27 million SNPs in inbred mouse strains
    Kelly A Frazer
    Perlegen Sciences, 2021 Stierlin Court, Mountain View, California 94043, USA
    Nature 448:1050-3. 2007
    ..The considerable regional redundancy of the SNP data will facilitate imputation of the majority of these genotypes in less-densely typed classical inbred strains to provide a complete view of variation in additional strains...
  54. pmc Leveraging the HapMap correlation structure in association studies
    Noah Zaitlen
    Bioinformatics Program, University of California San Diego, La Jolla, CA, USA
    Am J Hum Genet 80:683-91. 2007
    ..Our results are supported by empirical evaluation across the HapMap reference panel data sets, and a software implementation for the Affymetrix 500k and Illumina HumanHap 550 chips is available for download...
  55. ncbi request reprint Finding composite regulatory patterns in DNA sequences
    Eleazar Eskin
    Department of Computer Science, Columbia University, New York, 10027 NY, USA
    Bioinformatics 18:S354-63. 2002
    ..We demonstrate that MITRA performs well for both monad and composite patterns by presenting experiments over biological and synthetic data...
  56. ncbi request reprint Protein family classification using sparse markov transducers
    Eleazar Eskin
    Department of Computer Science, Columbia University, New York, NY 10027, USA
    J Comput Biol 10:187-213. 2003
    ..SMTs outperform previous probabilistic suffix tree methods and under certain conditions perform comparably to state-of-the-art protein homology methods...
  57. ncbi request reprint Using substitution matrices to estimate probability distributions for biological sequences
    Eleazar Eskin
    Department of Computer Science, Columbia University, NY 10027, USA
    J Comput Biol 9:775-91. 2002
    ..The method is also applied to estimate probability distributions over protein families and improves protein classification accuracy...