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].
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.
Eleazar Eskin, Sagi Snir. ``Incorporating Homologues into Sequence
Embeddings for Protein Analysis.'' Journal of Bioinformatics and
Computational Biology. (In Press), 2007.
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.
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.
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.
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].
Sean O'Rourke, Gal Chechik, Robin Friedman, and Eleazar Eskin.
``Discrete profile alignment via constrained information
bottleneck.'' BMC Bioinformatics. 2006 Mar
20;7 Suppl 1:S8. [Journal
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].
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]
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].
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, 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]
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].
Salvatore J. Stolfo, Frank Apap, Eleazar Eskin, Katherine Heller,
Shlomo Hershkop,
Andrew Honig, and Krysta Svore. ``A Comparative Evaluation of Two
Algorithms
forWindows Registry Anomaly Detection.'' Journal of Computer
Security. 13(4):659-
693. 2005.
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].
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. ``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). 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]
Eran Halperin, Eleazar Eskin. ``Haplotype Reconstruction
from Genotype Data using Imperfect Phylogeny.''
Bioinformatics. 20(12):1842-9, 2004. [full paper, PDF]
Christina Leslie, Eleazar Eskin, Adiel Cohen,
Jason Weston and William Stafford Noble.
``Mismatch String Kernels for Discriminative Protein Classification.''
Bioinformatics. 20(4):467-76. 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]
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]
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]
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).
[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]
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]
Manasi Bhattacharyya, Matthew G. Schultz, Eleazar Eskin, Shlomo
Hershkop, and Salvatore J. Stolfo.
``MET: An Experimental System for Malicious Email Tracking.''
In Proceedings of the 2002 New Security Paradigms Workshop (NSPW-2002).
Virginia Beach, VA: September 23rd - 26th, 2002.
[full paper,
PDF]
Frank Apap, Andrew Honig, Shlomo Hershkop, Eleazar Eskin,
Salvatore J. Stolfo. ``Detecting Malicious Software by Monitoring
Anomalous Windows Registry Accesses.''
In Proceedings of the Fifth International Symposium on
Recent Advances in Intrusion Detection (RAID-2002). Zurich,
Switzerland: October 16-18, 2002.
[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]
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]
Eleazar Eskin, Andrew Arnold, Michael Prerau, Leonid Portnoy and
Salvatore Stolfo. ``A Geometric Framework for Unsupervised Anomaly
Detection: Detecting Intrusions in Unlabeled Data.''
To Appear in Data Mining for Security Applications. Kluwer 2002.
[full paper,
PDF]
Andrew Honig, Andrew Howard, Eleazar Eskin, and Salvatore Stolfo.
``Adaptive Model Generation: An Architecture for the Deployment of
Data Minig-based Intrusion Detection Systems.''
To Appear in Data Mining for Security Applications. Kluwer 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]
Leonid Portnoy, Eleazar Eskin and Salvatore J. Stolfo.
``Intrusion Detection with Unlabeled Data using Clustering''
To Appear in Proceedings of ACM CSS Workshop on Data Mining Applied to
Security (DMSA-2001). Philadelphia, PA: November 5-8, 2001.
[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.'' In Proceedings of the
Ninth International Conference on Intelligent Systems for Molecular
Biology (ISMB-2001). Copenhagen, Denmark: July 21-25, 2001.
[
full paper, PDF],
Eleazar Eskin, Wenke Lee and Salvatore J. Stolfo.
``Modeling System Calls for Intrusion Detection with Dynamic Window Sizes.''
In Proceedings of DARPA Information Survivabilty Conference and
Exposition II (DISCEX II). Anaheim, CA: June 12-14 2001.
[ full paper, PDF]
Wenke Lee, Salvatore J. Stolfo, Philip K. Chan, Eleazar Eskin,
Wei Fan, Matthew Miller, Shlomo Hershkop and Junxin Zhang.
``Real Time Data Mining-based Intrusion Detection.''
In Proceedings of DARPA Information Survivabilty Conference and
Exposition II (DISCEX II). Anaheim, CA: June 12-14 2001.
[ full paper, PDF]
Matthew G. Schultz, Eleazar Eskin, Erez Zadok, Manasi
Bhattacharyya, and Salvatore J. Stolfo.
``Malicious Email Filter - A UNIX Mail Filter that Detects Malicious
Windows Executables.''
In Proceedings of USENIX Annual Technical Conference -
FREENIX Track. Boston, MA: June 2001. (Best
Student Paper Award)
[ full paper, PDF]
Matthew G. Schultz, Eleazar Eskin, Erez Zadok, and Salvatore J. Stolfo.
``Data Mining Methods for Detection of New Malicious Executables''
In Proceedings of IEEE Symposium on Security and
Privacy (IEEE S&P-2001). Oakland, CA: May 14-17, 2001.
[ full paper, PDF]
Eleazar Eskin, Matthew Miller, Zhi-Da Zhong, George Yi, Wei-Ang Lee,
and Sal Stolfo.
``Adaptive Model Generation for Intrusion Detection''
In Proceedings of the 2000 ACM CCS Workshop on
Intrusion Detection and Prevention (WIDS-2000).
Athens, Greece: November 1, 2000.
[
full paper]
Eleazar Eskin, William Noble Grundy, and Yoram Singer.
``Protein Family Classification using Sparse Markov Transducers''
In Proceedings of the Eighth International Conference on
Intelligent Systems for Molecular Biology (ISMB-2000). San Diego, CA: August
20-23, 2000.
[abstract,
full paper, PDF]
Eleazar Eskin. ``Anomaly Detection over Noisy Data using
Learned Probability Distributions'' In Proceedings of the 2000
International Conference on Machine Learning (ICML-2000), Palo Alto, CA: July, 2000.
[abstract,
full paper]
Eugene Agichtein, Eleazar Eskin and Luis Gravano. ``Combining
Strategies for Extracting Relations from Text Collections.'' In
Proceedings of 2000 ACM SIGMOD Workshop on Research Issues in Data
Mining and Knowledge Discovery (DMKD-2000).
Dallas, TX: May 14, 2000.
[abstract, full paper, PDF, ]
Eleazar Eskin. ``Detecting Errors within a Corpus using Anomaly
Detection'' In Proceedings of 2000 North American Chapter of the
Association of Computational Linguistics (NAACL-2000). Seatle, WA:
April 29-May 4, 2000.
[abstract,
full paper]
Vasileios Hatzivassiloglou, Judith Klavans, and Eleazar
``Detecting Text Similarity over Short Passages: Exploring Linguistic Feature
Combinations via Machine Learning.'' In Proceedings of
the Joint SIGDAT Conference on Empirical Methods in Natural Language
Processing and Very Large Corpora (EMNLP/VLC-1999).
College Park, MD: June 21-22, 1999.
[abstract,
full paper]
Kathy McKeown, Judith Klavans, Vasileios Hatzivassiloglou, Regina
Barzilay, and Eleazar Eskin.
``Towards Multidocument Summarization by Reformulation: Progress and
Prospects.'' In Proceedings of the Sixteenth National Conference
on Artificial Intelligence (AAAI-1999), Orlando, FL: July 18-22, 1999.
[abstract,
full paper]
Eleazar Eskin and Eric Siegel.
``Genetic Programming Applied to Othello: Introducing Students to
Machine Learning Research.''
In Proceedings of the 30th Technical Symposium of the ACM Special
Interest Group in Computer Science Education.
New Orleans, LA: March 24-28th, 1999.
[abstract,
full paper]
Eleazar Eskin and Matthew Bogosian.
``Classifying Text Documents using Modular Categories and
Linguistically Motivated Indicators''.
In Proceedings of the AAAI-1998 Workshop on Machine Learning for
Text Classification (MLTC-98), Madison, WI: July 26-30, 1998.
[abstract,
full paper]