UCLA UCLA Engineering UCLA Medical School ZarLab

Publications


Mouse Genetics:


  • Anatole Ghazalpour, Sudheer Doss, Hyun Kang, Charles Farber, Ping-Zi Wen, Alec Brozell, Ruth Castellanos, Eleazar Eskin, Desmond J. Smith, Thomas A. Drake, Aldons J. Lusis. ``High Resolution Mapping of Gene Expression Using Association in an Outbred Mouse Stock.'' PLoS Genetics, 4(8):e1000149, 2008. [pubmed].

  • Hyun Min Kang, Noah A. Zaitlen, Claire M. Wade, Andrew Kirby, David Heckerman, Mark J. Daly, and Eleazar Eskin. ``Efficient Control of Population Structure in Model Organism Association Mapping.'' Genetics. 178(3):1709-23, 2008. [pubmed].

  • Kelly A. Frazer, Eleazar Eskin, Hyun Min Kang, Molly A. Bogue, David A. Hinds, Erica J. Beilharz, Robert V. Gupta, Julie Montgomery, Matt M. Morenzoni, Geoffrey B. Nilsen, Charit L. Pethiyagoda, Laura L. Stuve, Frank M. Johnson, Mark J. Daly, Claire M. Wade & David R. Cox. ``A sequence-based variation map of 8.27 million SNPs in inbred mouse strains.'' Nature 448(7157):1050-3. 2007. [pubmed].

    Genetics of Expression:

  • Chun Ye, Eleazar Eskin. ``Discovering Tightly Regulated and Differentially Expressed Gene Sets in Whole Genome Expression Data.'' In Proceedings of the 5th European Conference on Computaional Biology (ECCB-2006). Eilat, Israel: January 21st-24th, 2007.

  • Chun Ye, Matthew A. Zapala, Hyun Min Kang, Jennifer Wessel, Eleazar Eskin, Nicholas Schork. ``High-Density QTL Mapping to Identify Phenotypes and Loci Influencing Gene Expression Patterns in Entire Biochemical Pathways.'' In Proceedings of the Second RECOMB Satellite Workshop of Systems Biology. San Diego, CA: December 1st-2nd, 2006.

    Haplotype Analysis and Genetic Variation:


  • Buhm Han, Hyun Min Kang, Myeong Seong Seo, Noah Zaitlen, Eleazar Eskin. ``Efficient Association Study Design via Power-Optimized Tag SNP Selection.'' Annals of Human Genetics, (In Press), 2008. [pubmed].

  • Eleazar Eskin. ``Increasing Power in Association Studies by using Linkage Disequilibrium Structure and Molecular Function as Prior Information.'' Genome Research. 18(4):653-60 Special Issue Proceedings of the 12th Annual Conference on Research in Computational Biology (RECOMB-2008), 2008. [pubmed].

  • Adam B Olshen , Bert Gold , Kirk E Lohmueller , Jeffrey P Struewing , Jaya Satagopan , Stefan A Stefanov , Eleazar Eskin , Tomas Kirchhoff , James A Lautenberger , Robert J Klein , Eitan Friedman , Larry Norton , Nathan A Ellis , Agnes Viale , Catherine S Lee , Patrick I Borgen , Andrew G Clark , Kenneth Offit and Jeff Boyd. ``Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping.'' BMC Genetics. 9:14, 2008. [pubmed].

  • Noah Zaitlen, Hyun Min Kang, Eleazar Eskin, Eran Halperin. ``Leveraging the HapMap Correlation Structure in Association Studies.'' American Journal of Human Genetics. 80(4):683-91, 2007. [pubmed].

  • Erik Corona, Benjamin Raphael, Eleazar Eskin. ``Identification of Deletion Polymorphisms from Haplotypes.'' In Proceedings of the Eleventh Annual Conference on Research in Computational Biology (RECOMB-2007). Oakland, CA: April 21st-25th, 2007. [ SpringerLink PDF].

  • Noah Zaitlen, Hyun Min Kang, Michael Feolo, Stephen Sherry, Eran Halperin, Eleazar Eskin. ``Inference and Analysis of Haplotypes from Combined Genotyping Studies Deposited in dbSNP.'' Genome Research. 15(11):1594-600. 2005. [pubmed].

  • David A. Hinds, Laura L. Stuve, Geoffrey B. Nilsen, Eran Halperin, Eleazar Eskin, Dennis G. Ballinger, Kelly A. Frazer, David R. Cox. ``Whole-Genome Patterns of Common DNA Variation in Three Human Populations'' Science 18 February 2005: 307(5712):1072-1079. [Science Website].

  • Jonathan Marchini, David Cutler, Nick Patterson, Matthew Stephens, Eleazar Eskin, Eran Halperin, Shin Lin, Steve Qin, Goncalo Abecassis, Heather Munro, Peter Donnelly. ``A comparison of phasing algorithms for trios and unrelated individuals.'' American Journal of Human Genetics. 78(3):437-50. 2006. [pubmed].

  • Eleazar Eskin, Eran Halperin, Roded Sharan. ``A Note on Optimally Phasing Long Genomic Regions using Local Haplotype Predictions.'' Journal of Bioinformatics and Computational Biology. 4(3):639-47. 2006. [pubmed].

  • Eran Halperin, Eleazar Eskin. ``Haplotype Reconstruction from Genotype Data using Imperfect Phylogeny.'' Bioinformatics. 20(12):1842-9, 2004. [full paper, PDF]

  • Eleazar Eskin, Eran Halperin, Richard Karp. ``Large Scale Reconstruction of Haplotypes from Genotype Data.'' In Proceedings of the Seventh Annual International Conference on Research in Computational Molecular Biology (RECOMB-2003). San Diego, CA: March 27-31, 2004. [full paper, PDF]

  • Eleazar Eskin, Eran Halperin, Roded Sharan. ``Optimally Phasing Long Genomic Regions using Local Haplotype Predictions.'' In Proceedings of the Second RECOMB Satellite Workshop on Computational Methods for SNPs and Haplotypes. Pittsburg, PA: Feburary 20-21, 2004.[full paper, PDF]

  • Eleazar Eskin, Eran Halperin, Richard Karp. ``Efficient Reconstruction of Haplotype Structure via Perfect Phylogeny.'' Journal of Bioinformatics and Computational Biology. 1:1,1-20, 2003.[full paper, PDF]



    Genomics:


  • Sean O'Rourke, Noah Zaitlen, Nebojsa Jojic, Eleazar Eskin. ``Reconstructing the Phylogeny of Mobile Elements.'' In Proceedings of the Eleventh Annual Conference on Research in Computational Biology (RECOMB-2007). Oakland, CA: April 21st-25th, 2007. [ SpringerLink PDF]

  • Sean O'Rourke, Noah Zaitlen, Nebojsa Jojic, Eleazar Eskin. ``Reconstructing the Phylogeny of Mobile Elements.'' In Proceedings of the NIPS 2006 Workshop on New Problems and Methods in Computational Biology. Whistler, CA: December 8th-9th, 2006.

  • Sean O'Rourke, Gal Chechik, Eleazar Eskin. ``Separation of overlapping subpopulations by mutual information.'' In Proceedings of the NIPS 2005 Workshop on Computational Biology and the Analysis of Heterogeneous Data. Whistler, CA: December 9th-10th, 2005. [PDF]

  • Shaojie Zhang, Brian Haas, Eleazar Eskin, Vineet Bafna. ``Searching genomes for non-coding RNA using FastR.'' IEEE IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2(4):366-379. 2005. [Journal website].

  • Alkes L. Price, Eleazar Eskin, Pavel A. Pevzner. ``Whole-genome analysis of Alu repeat elements reveals complex evolutionary history.'' Genome Research. 2004 Nov;14(11):2245-52. [pubmed]

    Disease Genetics:


  • Thomas B. Barrett, John E. Emberton, Caroline M. Nievergelt, Sherri G. Liang, Richard L. Hauger, Eleazar Eskin, Nicholas J. Schork, John R. Kelsoe. ``Further evidence for association of GRK3 to bipolar disorder suggests a second disease mutation.'' Psychiatric Genetics. 17(6):315-22., 2007. [pubmed].

  • Fangwen Rao, Gen Wen, Jiaur R. Gayen, Madhusudan Das, Sucheta M. Vaingankar, Brinda K. Rana, Manjula Mahata, Brian P. Kennedy, Rany M. Salem, Mats Stridsberg, Kenneth Abel, Douglas W. Smith, Eleazar Eskin, Nicholas J. Schork, Bruce A. Hamilton, Michael G. Ziegler, Sushil K. Mahata, Daniel T. O'Connor. ``Catecholamine Release Inhibitory Peptide Catestatin (Chromogranin A352-372). Naturally Occurring Amino Acid Variant Gly364Ser Causes Profound Changes in Human Autonomic Activity and Alters Risk for Hypertension.'' Circulation. 115(17):2271-81. 2007. [pubmed].

  • Tiffany A. Greenwood, Nicholas J. Schork, Eleazar Eskin, and John R. Kelsoe. ``Identification of Additional Variants within the Human Dopamine Transporter Gene Provides Further Evidence for an Association with Bipolar Disorder.'' Mol Psychiatry. 11(2):115. 2006. [pubmed].

  • Evan L. Riddle, Kenton K. Murthy, Eleazar Eskin, Daniel T. O'Connor, Brinda K. Rana, Paul A. Insel. ``Single Nucleotide Polymorphisms and Ethnic-specific Haplotypes of the Regulator of G-Protein Signaling-2 (RGS2) Gene in Hypertensive and Normotensive Subjects.'' Hypertension 47(3):415-20. 2006. [pubmed]

    Motif Finding and Regulation:


  • Martin Tompa, Nan Li, Timothy L. Bailey, George M. Church, Bart De Moor, Eleazar Eskin, Alexander V. Favorov, Martin C. Frith, Yutao Fu, W. James Kent, Vsevolod J. Makeev, Andrei A. Mironov, William Stafford Noble, Giulio Pavesi, Graziano Pesole, Mireille Regnier, Nicolas Simonis, Saurabh Sinha, Gert Thijs, Jacques van Helden, Mathias Vandenbogaert, Zhiping Weng, Christopher Workman, Chun Ye, Zhou Zhu. ``An Assessment of Computational Tools for the Discovery of Transcription Factor Binding Sites.'' Nature Biotechnology. 23(1):137-44. 2005. [pubmed]

  • Eleazar Eskin. ``From Profiles to Patterns and Back Again: A Branch and Bound Algorithm for Finding Near Optimal Motif Profiles.'' In Proceedings of the Eight Annual International Conference on Research in Computational Molecular Biology (RECOMB-2004). [full paper, PDF]

  • Chaya Ben-Zaken Zilberstein, Eleazar Eskin, Zohar Yakhini. ``Sequence Motifs in Ranked Expression Data.'' In Proceedings of the First RECOMB Satellite Workshop on Regulatory Genomics. San Diego, CA: March 26-27, 2004. [full paper, PDF]

  • Eleazar Eskin, Uri Keich, Mikhail S. Gelfand, Pavel A. Pevzner. ``Genome-Wide Analysis of Bacterial Promoter Regions.'' In Proceedings of the Pacific Symposium on Biocomputing (PSB-2003). Kaua'i, Hawaii: January 3-7, 2003. [full paper, PDF]

  • Eleazar Eskin, Pavel A. Pevzner. ``Finding Composite Regulatory Patterns in DNA Sequences.'' In Proceedings of the Tenth International Conference on Intelligent Systems for Molecular Biology (ISMB-2002). Edmonton, Canada: August 3-7, 2002. [full paper, PDF, power point slides]

    Protein Analysis:


  • Eleazar Eskin, Sagi Snir. ``Incorporating Homologues into Sequence Embeddings for Protein Analysis.'' Journal of Bioinformatics and Computational Biology. 5(3):717-38. 2007.

  • Sean O'Rourke, Gal Chechik, Robin Friedman, and Eleazar Eskin. ``Discrete profile alignment via constrained information bottleneck.'' In Proceedings of Advances in Neural Information Processing Systems 17 (NIPS-2004). Vancouver, Canada: December 13-18, 2004. [ PDF ]. (Full version BMC Bioinformatics. 2006 Mar 20;7 Suppl 1:S8. [Journal Website].

  • Eleazar Eskin, Sagi Snir. ``The Homology Kernel: A Biologically Motivated Sequence Embedding into Euclidean Space.'' In Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB-2005). La Jolla, CA: November 14th-15th, 2005.[ PDF]

  • Christina Leslie, Eleazar Eskin, Adiel Cohen, Jason Weston and William Stafford Noble. ``Mismatch String Kernels for Discriminative Protein Classification.'' Bioinformatics. 20:4, 467-476. 2004. [ full paper, PDF]

  • Eleazar Eskin, Eugene Agichtein. ``Combining Text Mining and Sequence Analysis to Discover Protein Functional Regions.'' In Proceedings of the Pacific Symposium on Biocomputing (PSB-2004). 288-299. Big Island of, Hawaii: January 6-10, 2004. [full paper, PDF]

  • Christina Leslie, Eleazar Eskin, Jason Weston and William Stafford Noble. ``Mismatch String Kernels for SVM Protein Classification.'' In Proceedings of Advances in Neural Information Processing Systems 15 (NIPS-2002). Vancouver, Canada: December 9-14, 2002. [ full paper, PDF]

  • Eleazar Eskin, William Noble Grundy and Yoram Singer. `` Using substitution matrices to estimate probability distributions for biological sequences.'' Journal of Computational Biology. 2:6, 775-792, 2002. [full paper, PDF]

  • Christina Leslie, Eleazar Eskin and William Stafford Noble. ``The Spectrum Kernel: A String Kernel for SVM protein Classification'' In Proceedings of the Pacific Symposium on Biocomputing (PSB-2002). Kaua'i, Hawaii: January 2-7, 2002. [full paper, PDF]

  • Eleazar Eskin, William Noble Grundy and Yoram Singer. ``Using mixtures of common ancestors for estimating the probabilities of discrete events in biological sequences.'' Long Version of Paper that Appears in Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology (ISMB-2001). Copenhagen, Denmark: July 21-25, 2001. [long version, long version PDF]

  • Eleazar Eskin, William Noble Grundy, and Yoram Singer. ``Protein Family Classification using Sparse Markov Transducers'' Long Version of Paper that Appeared in Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology (ISMB-2000). San Diego, CA: August 20-23, 2000. [full paper, PDF]

    Machine Learning:


  • Alex Smola, S. V. Vishwanathan, Eleazar Eskin. ``Laplace Propagation.'' In Proceedings of Advances in Neural Information Processing Systems 16 (NIPS-2003). Vancouver, Canada: December 8-13, 2003. [full paper, PDF]

  • Bernhard Scholkopf, Jason Weston, Eleazar Eskin, Christina Leslie and William Stafford Noble. ``A Kernel Approach for Learning from Almost Orthogonal Patterns.'' In Proceedings of the 13th European Conference on Machine Learning (ECML'2002) and Proceedings of the 6th European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD'2002). Helsinki, Finland: August 19th-23rd, 2002. Long version published in Principles of Data Mining and Knowledge Discovery, Springer LNCS 243. [full paper, PDF, long version, long version PDF]

    Complete List of Published Papers

    Ph. D. Thesis:

  • Sparse Sequence Modeling with Applications to Computational Biology and Intrusion Detection. [PS, PDF]

    •       Eleazar Eskin • Department of Computer Science and Department of Human Genetics • University of California, Los Angeles