EskinLab Home Page

ZarLab

Mailing Address:

Eleazar Eskin
Mail Code: 1596
Computer Science Department
University of California, Los Angeles
3532-J Boelter Hall
Los Angeles, CA 90095-1596

Location:	Math Sciences 2915 Map
Lab Phone:	(310) 206-6069
Email:	eeskin at cs dot ucla dot edu
URL:	http://zarlab.cs.ucla.edu

About our group...

Our research interests are in the relationship between human variation and human disease. We attempt 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.

Projects and Software:

EMMA Efficient Mixed-Model Association
POWERDESIGN Webserver for generating genetic association study designs which maximize statistical power.
MPAD Mouse Phenome Association Database. Genome browser displaying associations between common inbred strains and JAX Labs Mouse Pheome Database phenotypes.
WHAP Weighted HAPlotype association server which increases power of association studies by leveraging linkage disequilibrium patterns estimated from the HapMap.
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.

Available Projects:

The lab has plenty of projects in Bioinformatics and Machine Learning for interested students.
List of Available Projects

People:

Eleazar Eskin. Assistant Professor of Computer Science and Human Genetics. Web Page.

Jamal Benhami. Undergraduate Student in Computer Science: Bioinformatics.

Erik Corona. Undergraduate Student in Computer Science: Bioinformatics.

Buhm Han. PhD Student in Computer Science and Engineering..

Hyun Min Kang. PhD Student in Computer Science and Engineering. Web Page.

Sean O'Rourke. PhD Student in Computer Science and Engineering.

Mike Sanders. PhD Student in Bioinformatics.

Chun (Jimmie) Ye. PhD Student in Bioinformatics.

Noah Zaitlen. PhD Student in Bioinformatics. Web Page.

Alumni:

Robin Friedman. B.S. Computer Science with specialization in Bioinformatics. 2005.
Currently Ph.D. student at M.I.T.

Yujing (Tiffany) Liang. Undergraduate Student in Computer Science: Bioinformatics.

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.
7.29.07 ``A sequence-based variation map of 8.27 million SNPs in inbred mouse strains'' published in Nature. 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:

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].
Noah Zaitlen, Hyun Min Kang, Eleazar Eskin, Eran Halperin. ``Leveraging the HapMap Correlation Structure in Association Studies.'' Americal Journal of Human Genetics. 80(4):683-91, 2007. [pubmed].
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].
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].
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.
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.
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.
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]
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].
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]
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].
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].
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].
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].
Martin Tompa, Nan Li1, 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]
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]
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]. (Longer version to appear in BMC Bioinformatics).
Eran Halperin, Eleazar Eskin. ``Haplotype Reconstruction from Genotype Data using Imperfect Phylogeny.'' Bioinformatics. 20(12):1842-9, 2004. [pubmed]
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. ``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]