Publications

Our group publishes papers presenting new methodologies, describing the results of studies that use our software, and reviewing current topics in the field of Bioinformatics. Scroll down or click here for a complete list of papers produced by our lab. Since 2013, we write blog posts summarizing new research papers and review articles:

GWAS

Mouse Genetics

Population Structure

Review Articles

Publications

186 entries « 4 of 4 »

2006

O'Rourke, Sean; Chechik, Gal ; Friedman, Robin ; Eskin, Eleazar

Discrete profile comparison using information bottleneck. Journal Article

BMC Bioinformatics, 7 Suppl 1 , pp. S8, 2006, ISSN: 1471-2105.

Abstract | Links | BibTeX | Tags:

Greenwood, T A; Schork, N J; Eskin, E; Kelsoe, J R

Identification of additional variants within the human dopamine transporter gene provides further evidence for an association with bipolar disorder in two independent samples. Journal Article

Mol Psychiatry, 11 (2), pp. 125-33, 115, 2006, ISSN: 1359-4184.

Abstract | Links | BibTeX | Tags:

Riddle, Evan L; Rana, Brinda K; Murthy, Kenton K; Rao, Fangwen ; Eskin, Eleazar ; O'Connor, Daniel T; Insel, Paul A

Polymorphisms and haplotypes of the regulator of G protein signaling-2 gene in normotensives and hypertensives. Journal Article

Hypertension, 47 (3), pp. 415-20, 2006, ISSN: 1524-4563.

Abstract | Links | BibTeX | Tags:

2005

Tompa, Martin; Li, Nan ; Bailey, Timothy L; Church, George M; Moor, Bart De ; Eskin, Eleazar ; Favorov, Alexander V; Frith, Martin C; Fu, Yutao ; Kent, James W; Makeev, Vsevolod J; Mironov, Andrei A; Noble, William Stafford ; Pavesi, Giulio ; Pesole, Graziano ; Régnier, Mireille ; Simonis, Nicolas ; Sinha, Saurabh ; Thijs, Gert ; van Helden, Jacques ; Vandenbogaert, Mathias ; Weng, Zhiping ; Workman, Christopher ; Ye, Chun ; Zh, Zhou

Assessing computational tools for the discovery of transcription factor binding sites. Journal Article

Nat Biotechnol, 23 (1), pp. 137-44, 2005, ISSN: 1087-0156.

Abstract | Links | BibTeX | Tags: Motif Finding

Zaitlen, Noah A; Kang, Hyun Min ; Feolo, Michael L; Sherry, Stephen T; Halperin, Eran ; Eskin, Eleazar

Inference and analysis of haplotypes from combined genotyping studies deposited in dbSNP. Journal Article

Genome Res, 15 (11), pp. 1594-600, 2005, ISSN: 1088-9051.

Abstract | Links | BibTeX | Tags: Haplotype Phasing

Zhang, Shaojie; Haas, Brian ; Eskin, Eleazar ; Bafna, Vineet

Searching genomes for noncoding RNA using FastR. Journal Article

IEEE/ACM Trans Comput Biol Bioinform, 2 (4), pp. 366-79, 2005, ISSN: 1545-5963.

Abstract | Links | BibTeX | Tags:

Eskin, E; Snir, S

The Homology Kernel: A Biologically Motivated Sequence Embedding into Euclidean Space Conference

Computational Intelligence in Bioinformatics and Computational Biology, 2005 CIBCB '05 Proceedings of the 2005 IEEE Symposium on, 2005.

Abstract | BibTeX | Tags:

Yakhini, Zohar; Zilberstein, Chaya Ben-Zaken ; Eskin, Eleazar

Using Expression Data to Discover RNA and DNA Regulatory Sequence Motifs Conference

Lecture Notes in Computer Science, 3318/2005 , Lecture Notes in Computer Science Springer Berlin / Heidelberg, 2005, ISSN: 0302-9743 (Print) 1611-3349 (Online).

Abstract | Links | BibTeX | Tags: Motif Finding

Hinds, David A; Stuve, Laura L; Nilsen, Geoffrey B; Halperin, Eran ; Eskin, Eleazar ; Ballinger, Dennis G; Frazer, Kelly A; Cox, David R

Whole-genome patterns of common DNA variation in three human populations. Journal Article

Science, 307 (5712), pp. 1072-9, 2005, ISSN: 1095-9203.

Abstract | Links | BibTeX | Tags: Association Study Methods, Population Genetics

2004

Eskin, Eleazar; Agichtein, Eugene

Combining text mining and sequence analysis to discover protein functional regions. Journal Article

Pac Symp Biocomput, pp. 288-99, 2004, ISSN: 1793-5091.

Abstract | Links | BibTeX | Tags:

Eskin, ; Eleazar, Eleazar

From profiles to patterns and back again: a branch and bound algorithm for finding near optimal motif profiles Conference

RECOMB '04: Proceedings of the eighth annual international conference on Resaerch in computational molecular biology, ACM, New York, NY, USA, 2004, ISBN: 1-58113-755-9.

Abstract | Links | BibTeX | Tags: Motif Finding

Halperin, Eran; Eskin, Eleazar

Haplotype reconstruction from genotype data using Imperfect Phylogeny. Journal Article

Bioinformatics, 20 (12), pp. 1842-9, 2004, ISSN: 1367-4803.

Abstract | Links | BibTeX | Tags: Haplotype Phasing

Leslie, Christina S; Eskin, Eleazar ; Cohen, Adiel ; Weston, Jason ; Noble, William Stafford

Mismatch string kernels for discriminative protein classification. Journal Article

Bioinformatics, 20 (4), pp. 467-76, 2004, ISSN: 1367-4803.

Abstract | Links | BibTeX | Tags:

Price, Alkes L; Eskin, Eleazar ; Pevzner, Pavel A

Whole-genome analysis of Alu repeat elements reveals complex evolutionary history. Journal Article

Genome Res, 14 (11), pp. 2245-52, 2004, ISSN: 1088-9051.

Abstract | Links | BibTeX | Tags:

2003

Noble, William Stafford; Weston, Jason ; Schölkopf, Bernhard ; Eskin, Eleazar ; Leslie, Christina

Dealing with large diagonals in kernel matrices Journal Article

Annals of the Institute of Statistical Mathematics, pp. 391-408, 2003, ISSN: 0020-3157 (Print) 1572-9052 (Online).

Abstract | Links | BibTeX | Tags:

Eskin, Eleazar; Halperin, Eran; Karp, Richard M

Efficient reconstruction of haplotype structure via perfect phylogeny. Journal Article

J Bioinform Comput Biol, 1 (1), pp. 1-20, 2003, ISSN: 0219-7200.

Abstract | Links | BibTeX | Tags: Haplotype Phasing

Eskin, Eleazar; Keich, Uri; Gelfand, Mikhail S; Pevzner, Pavel A

Genome-wide analysis of bacterial promoter regions. Journal Article

Pac Symp Biocomput, pp. 29-40, 2003, ISSN: 1793-5091.

Abstract | Links | BibTeX | Tags: Motif Finding

Eskin, Eleazar; Halperin, Eran; Karp, Richard

Large scale reconstruction of haplotypes from genotype data Conference

RECOMB '03: Proceedings of the seventh annual international conference on Research in computational molecular biology, ACM, New York, NY, USA, 2003, ISBN: 1-58113-635-8.

Abstract | Links | BibTeX | Tags: Haplotype Phasing

Eskin, Eleazar; Noble, William Stafford ; Singer, Yoram

Protein family classification using sparse markov transducers. Journal Article

J Comput Biol, 10 (2), pp. 187-213, 2003, ISSN: 1066-5277.

Abstract | Links | BibTeX | Tags:

2002

Noble, William Stafford; Schölkopf, Bernhard ; Weston, Jason ; Eskin, Eleazar ; Leslie, Christina

A Kernel Approach for Learning from almost Orthogonal Patterns Conference

Lecture Notes in Computer Science, 2430/2002 , Lecture Notes in Computer Science Springer Berlin / Heidelberg, 2002, ISSN: 0302-9743 (Print) 1611-3349 (Online).

Abstract | Links | BibTeX | Tags:

Noble, William Stafford; Schölkopf, Bernhard ; Weston, Jason ; Eskin, Eleazar ; Leslie, Christina

A Kernel Approach for Learning from Almost Orthogonal Patterns Conference

Lecture Notes in Computer Science, 2431/2002 , Lecture Notes in Computer Science Springer Berlin / Heidelberg, 2002, ISSN: 0302-9743 (Print) 1611-3349 (Online).

Abstract | Links | BibTeX | Tags:

Apap, Frank; Honig, Andrew ; Hershkop, Shlomo ; Eskin, Eleazar ; Stolfo, Sal

Detecting Malicious Software by Monitoring Anomalous Windows Registry Accesses Conference

Lecture Notes in Computer Science, 2516/2002 , Lecture Notes in Computer Science Springer Berlin / Heidelberg, 2002, ISSN: 0302-9743 (Print) 1611-3349 (Online).

Abstract | Links | BibTeX | Tags:

Eskin, Eleazar; Pevzner, Pavel A

Finding composite regulatory patterns in DNA sequences. Journal Article

Bioinformatics, 18 Suppl 1 , pp. S354-63, 2002, ISSN: 1367-4803.

Abstract | Links | BibTeX | Tags: Motif Finding

Bhattacharyya, Manasi; Hershkop, Shlomo; Eskin, Eleazar

MET: an experimental system for Malicious Email Tracking Conference

NSPW '02: Proceedings of the 2002 workshop on New security paradigms, ACM, New York, NY, USA, 2002, ISBN: 1-58113-598-X.

Abstract | Links | BibTeX | Tags:

Eskin, Eleazar

Sparse sequence modeling with applications to computational biology and intrusion detection PhD Thesis

2002.

BibTeX | Tags:

Leslie, Christina; Eskin, Eleazar; Noble, William Stafford

The spectrum kernel: a string kernel for SVM protein classification. Journal Article

Pac Symp Biocomput, pp. 564-75, 2002, ISSN: 1793-5091.

Abstract | Links | BibTeX | Tags:

Eskin, Eleazar; Noble, William Stafford ; Singer, Yoram

Using substitution matrices to estimate probability distributions for biological sequences. Journal Article

J Comput Biol, 9 (6), pp. 775-91, 2002, ISSN: 1066-5277.

Abstract | Links | BibTeX | Tags:

2001

Schultz, M G; Eskin, E; Zadok, F; Stolfo, S J

Data mining methods for detection of new malicious executables Conference

Security and Privacy, 2001 S&P 2001 Proceedings 2001 IEEE Symposium on, 2001.

Abstract | Links | BibTeX | Tags:

Stolfo, Salvatore; Lee, Wenke; Chan, Philip; Fan, Wei; Eskin, Eleazar

Data mining-based intrusion detectors: an overview of the columbia IDS project Journal Article

SIGMOD Rec., 30 (4), pp. 5-14, 2001, ISSN: 0163-5808.

Abstract | Links | BibTeX | Tags:

Eskin, E; Lee, Wenke ; Stolfo, S J

Modeling system calls for intrusion detection with dynamic window sizes Conference

DARPA Information Survivability Conference & Exposition II, 2001 DISCEX '01 Proceedings, 1 , 2001.

Abstract | Links | BibTeX | Tags:

Lee, Wenke; Stolfo, S J; Chan, P K; Eskin, E; Fan, Wei ; Miller, M; Hershkop, S; Zhang, Junxin

Real time data mining-based intrusion detection Conference

DARPA Information Survivability Conference & Exposition II, 2001 DISCEX '01 Proceedings, 1 , 2001.

Abstract | Links | BibTeX | Tags:

Eskin, Eleazar; Grundy, William N; Singer, Yoram

Using mixtures of common ancestors for estimating the probabilities of discrete events in biological sequences. Journal Article

Bioinformatics, 17 Suppl 1 , pp. S65-73, 2001, ISSN: 1367-4803.

Abstract | Links | BibTeX | Tags:

2000

Eskin, Eleazar

Detecting errors within a corpus using anomaly detection Conference

Proceedings of the 1st North American chapter of the Association for Computational Linguistics conference, Morgan Kaufmann Publishers Inc., San Francisco, CA, USA, 2000.

Abstract | BibTeX | Tags: anomaly detection

Eskin, Eleazar; Grundy, William N; Singer, Yoram

Protein family classification using sparse Markov transducers. Journal Article

Proc Int Conf Intell Syst Mol Biol, 8 , pp. 134-45, 2000, ISSN: 1553-0833.

Abstract | Links | BibTeX | Tags: classification, proteins, sparse Markov transducers

1999

McKeown, Kathleen R; Klavans, Judith L; Hatzivassiloglou, Vasileios; Barzilay, Regina; Eskin, Eleazar

Towards multidocument summarization by reformulation: progress and prospects Conference

AAAI '99/IAAI '99: Proceedings of the sixteenth national conference on Artificial intelligence and the eleventh Innovative applications of artificial intelligence conference innovative applications , American Association for Artificial Intelligence, Menlo Park, CA, USA, 1999, ISBN: 0-262-51106-1.

BibTeX | Tags: artificial intelligence

Eskin, Eleazar; Siegel, Eric

Genetic programming applied to Othello: introducing students to machine learning research Conference

SIGCSE '99: The proceedings of the thirtieth SIGCSE technical symposium on Computer science education, ACM, New York, NY, USA, 1999, ISBN: 1-58113-085-6.

Links | BibTeX | Tags: instruction

186 entries « 4 of 4 »