Eleazar Eskin Assistant Professor Computer Science Human Genetics University of California, Los Angeles Mail Code: 1596 3532-J Boelter Hall Los Angeles, CA 90095-1596 Office: Math Sciences (MS) 2915 Office Phone: (310) 594-5112 Lab Phone: (310) 206-4490 Department Fax: (310) 825-2273 Email: eeskin at cs dot ucla dot edu URL: http://www.cs.ucla.edu/~eeskin/ Group URL: http://zarlab.cs.ucla.edu/

Teaching:

I am currently teaching CM124/224 Computational Genetics. website

In Winter 2008, I taught CS279 Current Topics in Bioinformatics
website

Available Projects/Positions:

I currently have plenty of available projects in Bioinformatics, Computational Biology, Genetics and Machine Learning for interested students at all levels (Undergraduate, Masters, PhD)
List of Available Projects

Research Interests:

My current research interests are in the relationship between human variation and human disease. My group's research attempts to understand the genetic basis of disease by analyzing human variation data and attempting to discover functional variants which contribute to disease. Our research is in the intersection of genetics and genomics. We use techniques from genetics to identify genetic variants which are associated to disease related phenotypes. Then we apply techniques from genomics to attempt to understand the function of these variants. While our goals are focused toward human disease, we take advantage of the model organism systems, such as inbred mouse strains and are currently working on developing genetic, genomic and computational resources which allow the use of such model systems to gain insights into human disease related penotypes.

Our group is split between the Computer Science and the Human Genetics departments and our research focuses on developing techniques for solving the challenging computational problems that arise in attempting to understand the genetic basis of human disease.

Projects and Software:

• EMMA Efficient Mixed-Model Association
• WHAP Weighted HAPlotype association webserver for performing associations at ungenotyped SNPs.
• MPAD Mouse Phenotype Association Database genome browser for performing whole genome association in inbred mouse strains.
• HAP Haplotype Resolution using Imperfect Phylogeny to recover haplotypes from genotype data. Resolve genotypes using our webserver.
• MITRA MIsmatch TRee Aproach to discovering regulatory elements in DNA sequences. Find Motifs using MITRA on our webserver.
• Sparse Markov Transducers Homepage of Sparse Markov Transducers (SMTs). Sequence Modeling Software implementing SMT algorithm available under GPL.

Group URL: http://zarlab.cs.ucla.edu.

About me:

I am an Assistant Professor in the Computer Science and Human Genetics departments at the University of California Los Angeles. I am also affiliated with Cal-IT2.

Previously, I was an Assistant Professor in Residence in Computer Science Engineering at the University of California, San Diego. Prior ot that, I was a post doc at Hebrew University in the Computer Science Department under the supervision of Yoram Singer and Nir Friedman. I completed my Ph. D. in the Computer Science Department of Columbia University in New York City. My thesis advisor was Sal Stolfo. Previously, I did research in Intrusion Detection and Data Mining. At Columbia, I was previously a member of the Data Mining Lab, the Computational Biology and the Natural Language Processing group.

News:

• 7.29.07 ``A sequence-based variation map of 8.27 million SNPs in inbred mouse strains'' published in Nature. Full Article. Nature Editor's Summary. Nature Editorial. Nature Genetics Editorial. NIH Press Release. Wired News. Nature Podcast.
• 7.9.07 Noah Zaitlen's poster on "Leveraging the HapMap correlation structure in association studies" wins best post award at Genomics of Common Disease meeting in Cambridge, UK.
• 07.01.06 Our group moved to UCLA. Article
• 1.13.06 Noah Zaitlen is awarded a Microsoft Research Fellowship. Article.
• 10.26.05 Results of our collaboration with National Library of Medicine on phasing the entire NCBI's dbSNP is published in a special issue of Genome Research on Human Variation. UCSD Article.
• 6.17.05 Dafna Bitton, my student, participates in research project in Australia through PRIME program. UCSD Article.
• 2.22.05 Research Training in Bioinformatics course profiled in article about undergraduate research. UCSD Article.
• 2.17.05 "Whole-Genome Patterns of Common DNA Variation in Three Human Populations" is published on the cover of Science. UCSD Article. AAAS Release. USA Today . LA Times. NPR. MSNBC.
• 2.03.05 Robin Friedman, my student, wins Cal-IT2 Undergraduate Scholar Award. Article.
• 1.08.05 HAP project recieves von Liebig funding. Article.

Recent Papers:

Mouse Genetics:

• 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 (in Press) 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:

• 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:

• 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. (In Press), 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]